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Spandole-Dinu S, Catrina AM, Voinea OC, Andone A, Radu S, Haidoiu C, Călborean O, Hertzog RG, Popescu DM. Evaluating the radioprotective effect of green barley juice on male rats. Int J Radiat Biol 2024; 100:281-288. [PMID: 37769021 DOI: 10.1080/09553002.2023.2264923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 09/23/2023] [Indexed: 09/30/2023]
Abstract
PURPOSE DNA damage accounts for most biological effects of ionizing radiation. Antioxidants are known for their protective effect by preventing DNA damage. This pilot study aimed to evaluate the potential radioprotective effect of Natural SOD®, a green barley juice rich in antioxidants, on DNA damage in the testes and lymphocytes of Wistar rats exposed to ionizing radiation. MATERIALS AND METHODS Male Wistar rats (n = 15) were selected and equally divided into three groups. Rats in one of the groups were pretreated orally with Natural SOD® for 14 days, while rats in another group were sham-pretreated with saline solution. Rats in both these groups were afterwards subjected to a single dose of 6 Gy X-ray whole-body irradiation. The control group did not receive any treatment and was not irradiated. Shortly after X-ray exposure, all rats were sacrificed and testes and blood were collected. Gamma-H2AX and histopathological assessment in the testes, along with comet assay of lymphocytes were performed. RESULTS Histopathological examination of the testes showed no significant architectural alterations. Immunofluorescent staining of γ-H2AX revealed more DNA double-strand break sites in testicular cells from sham animals compared to Natural SOD® pretreated rats. Alkaline comet assay results showed increased DNA damage in lymphocytes of irradiated rats compared to the control group with little differences between the pretreated groups. Animals pretreated with Natural SOD showed slightly reduced DNA damage compared to sham-pretreated rats. These findings suggest a potential protective effect of Natural SOD® against radiation-induced DNA damage. CONCLUSIONS Natural SOD® exhibited a potential prophylactic radioprotective effect in rats, particularly in testes. Further investigations to determine medium and long-term effects of X-ray in animals administered Natural SOD® are needed to better estimate the radioprotective effect.
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Affiliation(s)
- Sonia Spandole-Dinu
- Experimental Radiobiology Laboratory, Cantacuzino National Medical Military Institute for Research and Development, Bucharest, Romania
| | - Ana-Maria Catrina
- Neurobiology Laboratory, Cantacuzino National Medical Military Institute for Research and Development, Bucharest, Romania
| | - Oana Cristina Voinea
- Experimental Pharmacotoxicology Laboratory, Cantacuzino National Medical Military Institute for Research and Development, Bucharest, Romania
- Pathology Department, Faculty of Medicine, University of Medicine and Pharmacy Carol Davila, Bucharest, Romania
| | - Alina Andone
- Experimental Radiobiology Laboratory, Cantacuzino National Medical Military Institute for Research and Development, Bucharest, Romania
| | - Speranța Radu
- Experimental Radiobiology Laboratory, Cantacuzino National Medical Military Institute for Research and Development, Bucharest, Romania
| | - Cerasela Haidoiu
- Neurobiology Laboratory, Cantacuzino National Medical Military Institute for Research and Development, Bucharest, Romania
| | - Octavian Călborean
- Experimental Radiobiology Laboratory, Cantacuzino National Medical Military Institute for Research and Development, Bucharest, Romania
| | - Radu Gabriel Hertzog
- National Center for Expertise and Intervention in Public Health for CBRN agents, Cantacuzino National Medical Military Institute for Research and Development, Bucharest, Romania
| | - Diana Mihaela Popescu
- Regenerative Medicine Laboratory, Cantacuzino National Medical Military Institute for Research and Development, Bucharest, Romania
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2
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van Bueren MAE, Janssen A. The impact of chromatin on double-strand break repair: Imaging tools and discoveries. DNA Repair (Amst) 2024; 133:103592. [PMID: 37976899 DOI: 10.1016/j.dnarep.2023.103592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/16/2023] [Accepted: 11/07/2023] [Indexed: 11/19/2023]
Abstract
Eukaryotic nuclei are constantly being exposed to factors that break or chemically modify the DNA. Accurate repair of this DNA damage is crucial to prevent DNA mutations and maintain optimal cell function. To overcome the detrimental effects of DNA damage, a multitude of repair pathways has evolved. These pathways need to function properly within the different chromatin domains present in the nucleus. Each of these domains exhibit distinct molecular- and bio-physical characteristics that can influence the response to DNA damage. In particular, chromatin domains highly enriched for repetitive DNA sequences, such as nucleoli, centromeres and pericentromeric heterochromatin require tailored repair mechanisms to safeguard genome stability. Work from the past decades has led to the development of innovative imaging tools as well as inducible DNA damage techniques to gain new insights into the impact of these repetitive chromatin domains on the DNA repair process. Here we summarize these tools with a particular focus on Double-Strand Break (DSB) repair, and discuss the insights gained into our understanding of the influence of chromatin domains on DSB -dynamics and -repair pathway choice.
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Affiliation(s)
- Marit A E van Bueren
- Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Aniek Janssen
- Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands.
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3
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Gruntman AM, Xue W, Flotte TR. Approaches to Therapeutic Gene Editing in Alpha-1 Antitrypsin Deficiency. Methods Mol Biol 2024; 2750:11-17. [PMID: 38108963 DOI: 10.1007/978-1-0716-3605-3_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Five distinct gene therapy approaches have been developed for treating AATD. These approaches include knockout of the mutant (PiZ) allele by introduction of double-strand breaks (DSBs) and subsequent creation of insertions and deletions (indels) by DSB repair, homology-directed repair (HDR) targeted to the mutation site, base editing, prime editing, and alternatively targeted knock-in techniques. Each approach will be discussed and a brief summary of a standard CRISPR-Cas9 targeting method will be presented.
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Affiliation(s)
- Alisha M Gruntman
- Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Wen Xue
- Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Terence R Flotte
- Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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4
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Özdemir C, Muratoğlu B, Özel BN, Alpdündar-Bulut E, Tonyalı G, Ünal Ş, Uçkan-Çetinkaya D. Multiparametric analysis of etoposide exposed mesenchymal stem cells and Fanconi anemia cells: implications in development of secondary myeloid malignancy. Clin Exp Med 2023; 23:4511-4524. [PMID: 37179284 DOI: 10.1007/s10238-023-01087-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023]
Abstract
Secondary acute myeloid leukemia (sAML) may develop following a prior therapy or may evolve from an antecedent hematological disorder such as Fanconi Anemia (FA). Pathophysiology of leukemic evolution is not clear. Etoposide (Eto) is a chemotherapeutic agent implicated in development of sAML. FA is an inherited bone marrow (BM) failure disease characterized by genomic instability and xenobiotic susceptibility. Here, we hypothesized that alterations in the BM niche may play a critical/driver role in development of sAML in both conditions. Expression of selected genes involved in xenobiotic metabolism, DNA double-strand break response, endoplasmic reticulum (ER) stress, heat shock response and cell cycle regulation were determined in BM mesenchymal stem cells (MSCs) of healthy controls and FA patients at steady state and upon exposure to Eto at different concentrations and in recurrent doses. Expression of CYPA1, p53, CCNB1, Dicer1, CXCL12, FLT3L and TGF-Beta genes were significantly downregulated in FA-MSCs compared with healthy controls. Eto exposure induced significant alterations in healthy BM-MSCs with increased expression of CYP1A1, GAD34, ATF4, NUPR1, CXCL12, KLF4, CCNB1 and nuclear localization of Dicer1. Interestingly, FA-MSCs did not show significant alterations in these genes upon Eto exposure. As opposed to healthy MSCs DICER1 gene expression and intracellular localization was not altered on FA BM-MSCs after Eto treatment. These results showed that Eto is a highly potent molecule and has pleiotropic effects on BM-MSCs, FA cells show altered expression profile compared to healthy controls and Eto exposure on FA cells shows differential profile than healthy controls.
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Affiliation(s)
- Cansu Özdemir
- Center for Stem Cell Research and Development (PEDI-STEM), Hacettepe University, 06100 Gevher Nesibe Street, Sihhiye, Altındağ, Ankara, Turkey.
| | - Bihter Muratoğlu
- Center for Stem Cell Research and Development (PEDI-STEM), Hacettepe University, 06100 Gevher Nesibe Street, Sihhiye, Altındağ, Ankara, Turkey
- Department of Stem Cell Sciences, Hacettepe University Graduate School of Health Sciences, 06100 Gevher Nesibe Street, Sihhiye, Altındağ, Ankara, Turkey
| | - Buse Nurten Özel
- Center for Stem Cell Research and Development (PEDI-STEM), Hacettepe University, 06100 Gevher Nesibe Street, Sihhiye, Altındağ, Ankara, Turkey
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - Esin Alpdündar-Bulut
- Center for Stem Cell Research and Development (PEDI-STEM), Hacettepe University, 06100 Gevher Nesibe Street, Sihhiye, Altındağ, Ankara, Turkey
- Division of Hematology-Oncology, Faculty of Medicine, Department of Pediatrics, Hacettepe University, 06100 Gevher Nesibe Street, Sihhiye, Altındağ, Ankara, Turkey
| | - Gülsena Tonyalı
- Center for Stem Cell Research and Development (PEDI-STEM), Hacettepe University, 06100 Gevher Nesibe Street, Sihhiye, Altındağ, Ankara, Turkey
- Department of Stem Cell Sciences, Hacettepe University Graduate School of Health Sciences, 06100 Gevher Nesibe Street, Sihhiye, Altındağ, Ankara, Turkey
| | - Şule Ünal
- Division of Hematology-Oncology, Faculty of Medicine, Department of Pediatrics, Hacettepe University, 06100 Gevher Nesibe Street, Sihhiye, Altındağ, Ankara, Turkey
- Research Center for Fanconi Anemia and Other IBMFSs, Hacettepe University, 06100 Gevher Nesibe Street, Sihhiye, Altındağ, Ankara, Turkey
| | - Duygu Uçkan-Çetinkaya
- Center for Stem Cell Research and Development (PEDI-STEM), Hacettepe University, 06100 Gevher Nesibe Street, Sihhiye, Altındağ, Ankara, Turkey.
- Department of Stem Cell Sciences, Hacettepe University Graduate School of Health Sciences, 06100 Gevher Nesibe Street, Sihhiye, Altındağ, Ankara, Turkey.
- Division of Hematology-Oncology, Faculty of Medicine, Department of Pediatrics, Hacettepe University, 06100 Gevher Nesibe Street, Sihhiye, Altındağ, Ankara, Turkey.
- Research Center for Fanconi Anemia and Other IBMFSs, Hacettepe University, 06100 Gevher Nesibe Street, Sihhiye, Altındağ, Ankara, Turkey.
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5
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Kumari N, Antil H, Kumari S, Raghavan SC. Deficiency of ligase IV leads to reduced NHEJ, accumulation of DNA damage, and can sensitize cells to cancer therapeutics. Genomics 2023; 115:110731. [PMID: 37871849 DOI: 10.1016/j.ygeno.2023.110731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 09/14/2023] [Accepted: 10/19/2023] [Indexed: 10/25/2023]
Abstract
Ligase IV is a key enzyme involved during DNA double-strand breaks (DSBs) repair through nonhomologous end joining (NHEJ). However, in contrast to Ligase IV deficient mouse cells, which are embryonic lethal, Ligase IV deficient human cells, including pre-B cells, are viable. Using CRISPR-Cas9 mediated genome editing, we have generated six different LIG4 mutants in cervical cancer and normal kidney epithelial cell lines. While the LIG4 mutant cells showed a significant reduction in NHEJ, joining mediated through microhomology-mediated end joining (MMEJ) and homologous recombination (HR) were significantly high. The reduced NHEJ joining activity was restored by adding purified Ligase IV/XRCC4. Accumulation of DSBs and reduced cell viability were observed in LIG4 mutant cells. LIG4 mutant cells exhibited enhanced sensitivity towards DSB-inducing agents such as ionizing radiation (IR) and etoposide. More importantly, the LIG4 mutant of cervical cancer cells showed increased sensitivity towards FDA approved drugs such as Carboplatin, Cisplatin, Paclitaxel, Doxorubicin, and Bleomycin used for cervical cancer treatment. These drugs, in combination with IR showed enhanced cancer cell death in the background of LIG4 gene mutation. Thus, our study reveals that mutation in LIG4 results in compromised NHEJ, leading to sensitization of cervical cancer cells towards currently used cancer therapeutics.
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Affiliation(s)
- Nitu Kumari
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Himanshu Antil
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Susmita Kumari
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India.
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6
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Bai Y, Zhao H, Liu H, Wang W, Dong H, Zhao C. RNA methylation, homologous recombination repair and therapeutic resistance. Biomed Pharmacother 2023; 166:115409. [PMID: 37659205 DOI: 10.1016/j.biopha.2023.115409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/28/2023] [Accepted: 08/28/2023] [Indexed: 09/04/2023] Open
Abstract
Homologous recombination (HR) repair of DNA double-strand breaks (DSBs) is critical for maintaining genomic integrity and stability. Defects in HR increase the risk of tumorigenesis. However, many human tumors exhibit enhanced HR repair capabilities, consequently endowing tumor cells with resistance to DNA-damaging chemotherapy and radiotherapy. This review summarizes the role of RNA methylation in HR repair and therapeutic resistance in human tumors. We also analyzed the interactions between RNA methylation and other HR-modulating modifications including histone acetylation, histone deacetylation, ubiquitination, deubiquitination, protein arginine methylation, and gene transcription. This review proposes that targeting RNA methylation is a promising approach to overcoming HR-mediated therapeutic resistance.
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Affiliation(s)
- Yu Bai
- Department of Pathophysiology, College of Basic Medical Science, China Medical University, Shenyang, China; Department of Nephrology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Hanlin Zhao
- Department of Ion Channel Pharmacology, School of Pharmacy, China Medical University, Shenyang, China
| | - Haijun Liu
- Department of Thoracic Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Wei Wang
- Department of Pathophysiology, College of Basic Medical Science, China Medical University, Shenyang, China.
| | - Hongming Dong
- Department of Anatomy, College of Basic Medical Science, China Medical University, Shenyang, China.
| | - Chenghai Zhao
- Department of Pathophysiology, College of Basic Medical Science, China Medical University, Shenyang, China.
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7
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Koob L, Friskes A, van Bergen L, Feringa FM, van den Broek B, Koeleman ES, van Beek E, Schubert M, Blomen VA, Brummelkamp TR, Krenning L, Medema RH. MND1 enables homologous recombination in somatic cells primarily outside the context of replication. Mol Oncol 2023. [PMID: 37195379 DOI: 10.1002/1878-0261.13448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 03/28/2023] [Indexed: 05/18/2023] Open
Abstract
Faithful and timely repair of DNA double-strand breaks (DSBs) is fundamental for the maintenance of genomic integrity. Here, we demonstrate that the meiotic recombination co-factor MND1 facilitates the repair of DSBs in somatic cells. We show that MND1 localizes to DSBs, where it stimulates DNA repair through homologous recombination (HR). Importantly, MND1 is not involved in the response to replication-associated DSBs, implying that it is dispensable for HR-mediated repair of one-ended DSBs. Instead, we find that MND1 specifically plays a role in the response to two-ended DSBs that are induced by irradiation (IR) or various chemotherapeutic drugs. Surprisingly, we find that MND1 is specifically active in G2 phase, whereas it only marginally affects repair during S phase. MND1 localization to DSBs is dependent on resection of the DNA ends, and seemingly occurs through direct binding of MND1 to RAD51- coated ssDNA. Importantly, the lack of MND1-driven HR repair directly potentiates the toxicity of IR-induced damage, which could open new possibilities for therapeutic intervention, specifically in HR-proficient tumors.
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Affiliation(s)
- Lisa Koob
- Oncode Institute, Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - Anoek Friskes
- Oncode Institute, Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - Louise van Bergen
- Oncode Institute, Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - Femke M Feringa
- Oncode Institute, Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research (CNCR), VU University Amsterdam, 1081, Amsterdam, The Netherlands
| | - Bram van den Broek
- Bioimaging facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - Emma S Koeleman
- Oncode Institute, Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
- Chromatin Networks, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Ellis van Beek
- Oncode Institute, Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - Michael Schubert
- Oncode Institute, Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - Vincent A Blomen
- Oncode Institute, Division of Biochemistry, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
- Scenic Biotech, 1098 XG, Amsterdam, The Netherlands
| | - Thijn R Brummelkamp
- Oncode Institute, Division of Biochemistry, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - Lenno Krenning
- Oncode Institute, Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
- Crown Bioscience, 3584 CM, Utrecht, The Netherlands
| | - René H Medema
- Oncode Institute, Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
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Argyris PP, Saavedra F, Malz C, Stone IA, Wei Y, Boyle WS, Johnstone KF, Khammanivong A, Herzberg MC. Intracellular calprotectin (S100A8/A9) facilitates DNA damage responses and promotes apoptosis in head and neck squamous cell carcinoma. Oral Oncol 2023; 137:106304. [PMID: 36608459 PMCID: PMC9877195 DOI: 10.1016/j.oraloncology.2022.106304] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 12/01/2022] [Accepted: 12/28/2022] [Indexed: 01/06/2023]
Abstract
OBJECTIVES In head and neck squamous cell carcinoma (HNSCC), poor prognosis and low survival rates are associated with downregulated calprotectin. Calprotectin (S100A8/A9) inhibits cancer cell migration and invasion and facilitates G2/M cell cycle arrest. We investigated whether S100A8/A9 regulates DNA damage responses (DDR) and apoptosis in HNSCC after chemoradiation. MATERIALS AND METHODS Human HNSCC cases in TCGA were analyzed for relationships between S100A8/A9 and expression of apoptosis-related genes. Next, S100A8/A9-expressing and non-expressing carcinoma lines (two different lineages) were exposed to genotoxic agents and assessed for 53BP1 and γH2AX expression and percent of viable/dead cells. Finally, S100A8/A9-wild-type and S100A8/A9null C57BL/6j mice were treated with 4-NQO to induce oral dysplastic and carcinomatous lesions, which were compared for levels of 53BP1. RESULTS In S100A8/A9-high HNSCC tumors, apoptosis-related caspase family member genes were upregulated, whereas genes limiting apoptosis were significantly downregulated based on TCGA analyses. After X-irradiation or camptothecin treatment, S100A8/A9-expressing carcinoma cells (i.e., TR146 and KB-S100A8/A9) showed significantly higher 53BP1 and γH2AX expression, DNA fragmentation, proportions of dead cells, and greater sensitivity to cisplatin than wild-type KB or TR146-S100A8/A9-KD cells. Interestingly, KB-S100A8/A9Δ113-114 cells showed similar 53BP1 and γH2AX levels to S100A8/A9-negative KB and KB-EGFP cells. After 4-NQO treatment, 53BP1 expression in oral lesions was significantly greater in calprotectin+/+ than S100A8/A9null mice. CONCLUSIONS In HNSCC cells, intracellular calprotectin is strongly suggested to potentiate DDR and promote apoptosis in response to genotoxic agents. Hence, patients with S100A8/A9-high HNSCC may encounter more favorable outcomes because more tumor cells enter apoptosis with increased sensitivity to chemoradiation therapy.
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Affiliation(s)
- Prokopios P Argyris
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA; Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA; Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN, USA; Division of Oral and Maxillofacial Pathology, School of Dentistry, University of Minnesota, Minneapolis, MN, USA.
| | - Flávia Saavedra
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN, USA
| | - Chris Malz
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN, USA
| | - Ian A Stone
- Department of Immunology, Microbiology and Virology, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA
| | - Yuping Wei
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN, USA
| | - William S Boyle
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN, USA
| | - Karen F Johnstone
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN, USA
| | - Ali Khammanivong
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA; Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - Mark C Herzberg
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN, USA.
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Tamanoi F, Yoshikawa K. Overview of DNA damage and double-strand breaks. Enzymes 2022; 51:1-5. [PMID: 36336403 DOI: 10.1016/bs.enz.2022.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
DNA is under a variety of assaults. As a result, different damages accumulate on DNA. These include base changes, single-strand breaks and double-strand breaks. In this volume and also briefly in the following volume, we discuss DNA damage and double-strand breaks. In particular, we focus on double-strand breaks. We discuss types of double-strand breaks as well as methods to detect them. We also discuss how DNA breaks are formed.
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Affiliation(s)
- Fuyuhiko Tamanoi
- Institute for Integrated Cell-Material Sciences, Institute for Advanced Study, Kyoto University, Kyoto, Japan.
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, Japan
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10
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Stubbins RJ, Korotev S, Godley LA. Germline CHEK2 and ATM Variants in Myeloid and Other Hematopoietic Malignancies. Curr Hematol Malig Rep 2022; 17:94-104. [PMID: 35674998 DOI: 10.1007/s11899-022-00663-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/11/2022] [Indexed: 12/01/2022]
Abstract
PURPOSE OF REVIEW An intact DNA damage response is crucial to preventing cancer development, including in myeloid and lymphoid malignancies. Deficiencies in the homologous recombination (HR) pathway can lead to defective DNA damage responses, and this can occur through inherited germline mutations in HR pathway genes, such as CHEK2 and ATM. We now understand that germline mutations can be identified frequently (~ 5-10%) in patients with myeloid and lymphoid malignancies, and among the most common of these are CHEK2 and ATM. We review the role that deleterious germline CHEK2 and ATM variants play in the development of hematopoietic malignancies, and how this influences clinical practice, including cancer screening, hematopoietic stem cell transplantation, and therapy choice. RECENT FINDINGS In recent large cohorts of patients diagnosed with myeloid or lymphoid malignancies, deleterious germline loss of function variants in CHEK2 and ATM are among the most common identified. Germline CHEK2 variants predispose to a range of myeloid malignancies, most prominently myeloproliferative neoplasms and myelodysplastic syndromes (odds ratio range: 2.1-12.3), and chronic lymphocytic leukemia (odds ratio 14.83). Deleterious germline ATM variants have been shown to predispose to chronic lymphocytic leukemia (odds ratio range: 1.7-10.1), although additional studies are needed to demonstrate the risk they confer for myeloid malignancies. Early studies suggest there may also be associations between deleterious germline CHEK2 and ATM variants and development of clonal hematopoiesis. Identifying CHEK2 and ATM variants is crucial for the optimal management of patients and families affected by hematopoietic malignancies. OPENING CLINICAL CASE: "A 45 year-old woman presents to your clinic with a history of triple-negative breast cancer diagnosed five years ago, treated with surgery, radiation, and chemotherapy. About six months ago, she developed cervical lymphadenopathy, and a biopsy demonstrated small lymphocytic leukemia. Peripheral blood shows a small population of lymphocytes with a chronic lymphocytic leukemia immunophenotype, and FISH demonstrates a complex karyotype: gain of one to two copies of IGH and FGFR3; gain of two copies of CDKN2C at 1p32.3; gain of two copies of CKS1B at 1q21; tetrasomy for chromosome 3; trisomy and tetrasomy for chromosome 7; tetrasomy for chromosome 9; tetrasomy for chromosome 12; gain of one to two copies of ATM at 11q22.3; deletion of chromosome 13 deletion positive; gain of one to two copies of TP53 at 17p13.1). Given her history of two cancers, you arrange for germline genetic testing using DNA from cultured skin fibroblasts, which demonstrates pathogenic variants in ATM [c.1898 + 2 T > G] and CHEK2 [p.T367Metfs]. Her family history is significant for multiple cancers. (Fig. 1)." Fig. 1 Representative pedigree from a patient with germline pathogenic ATM and CHEK2 variants who was affected by early onset breast cancer and chronic lymphocytic leukemia. Arrow indicates proband. Colors indicate cancer type/disease: purple, breast cancer; blue, lymphoma; brown, melanoma; yellow, colon cancer; and green, autoimmune disease.
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Affiliation(s)
- Ryan J Stubbins
- Section of Hematology Oncology, Department of Medicine, The University of Chicago, 5841 S. Maryland Ave., MC 2115, Chicago, IL, 60637, USA.,Leukemia/BMT Program of BC, BC Cancer, Vancouver, BC, Canada
| | - Sophia Korotev
- Section of Hematology Oncology, Department of Medicine, The University of Chicago, 5841 S. Maryland Ave., MC 2115, Chicago, IL, 60637, USA
| | - Lucy A Godley
- Section of Hematology Oncology, Department of Medicine, The University of Chicago, 5841 S. Maryland Ave., MC 2115, Chicago, IL, 60637, USA.
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11
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Khan SR, Kuzminov A. Thymine-starvation-induced chromosomal fragmentation is not required for thymineless death in Escherichia coli. Mol Microbiol 2022; 117:1138-1155. [PMID: 35324030 DOI: 10.1111/mmi.14897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 11/29/2022]
Abstract
Thymine or thymidine starvation induces robust chromosomal fragmentation in E. coli thyA deoCABD mutants, and is proposed to be the cause of thymineless death (TLD). However, fragmentation kinetics challenges the idea that fragmentation causes TLD, by peaking before the onset of TLD and disappearing by the time TLD accelerates. Quantity and kinetics of fragmentation also stays unchanged in hyper-TLD-exhibiting recBCD mutant, making its faster and deeper TLD independent of fragmentation as well. Elimination of fragmentation without affecting cellular metabolism did not abolish TLD in the thyA mutant, but reduced early TLD in the thyA recBCD mutant, suggesting replication-dependent, but undetectable by pulsed field gel, double-strand breaks contributed to TLD. Chromosomal fragmentation, but not TLD, was eliminated in both the thyA and thyA recBCD mutants harboring deoCABD operon. Expression of a single gene, deoA, encoding thymidine phosphorylase, was sufficient to abolish fragmentation, suggesting thymidine-to-thymine interconversion during T-starvation being a key factor. Overall, this study reveals that chromosomal fragmentation, a direct consequence of T-starvation, is either dispensable or redundant for the overall TLD pathology, including hyper-TLD in the recBCD mutant. Replication forks, unlike chromosomal fragmentation, may provide minor contribution to TLD, but only in the repair-deficient thyA deoCABD recBCD mutant.
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Affiliation(s)
- Sharik R Khan
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Andrei Kuzminov
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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12
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Deshpande RA, Paull TT. Characterization of DNA-PK-Bound End Fragments Using GLASS-ChIP. Methods Mol Biol 2022; 2444:171-182. [PMID: 35290638 DOI: 10.1007/978-1-0716-2063-2_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Endonucleolytic cleavage of DNA ends by the human Mre11-Rad50-Nbs1 (MRN) complex occurs in a manner that is promoted by DNA-dependent protein kinase (DNA-PK). A method is described to isolate DNA-PK-bound fragments released from chromatin in human cells using a modified Gentle Lysis and Size Selection chromatin immunoprecipitation (GLASS-ChIP) protocol. This method, combined with real-time PCR or next-generation sequencing, can identify sites of MRN endonucleolytic cutting adjacent to DNA-PK binding sites in human cells.
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Affiliation(s)
- Rajashree A Deshpande
- The Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Tanya T Paull
- The Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
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13
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Liu H, Gordon SG, Rog O. Heterologous synapsis in C. elegans is regulated by meiotic double-strand breaks and crossovers. Chromosoma 2021; 130:237-250. [PMID: 34608541 PMCID: PMC8671313 DOI: 10.1007/s00412-021-00763-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/21/2021] [Accepted: 09/23/2021] [Indexed: 10/20/2022]
Abstract
Alignment of the parental chromosomes during meiotic prophase is key to the formation of genetic exchanges, or crossovers, and consequently to the successful production of gametes. In almost all studied organisms, alignment involves synapsis: the assembly of a conserved inter-chromosomal interface called the synaptonemal complex (SC). While the SC usually synapses homologous sequences, it can assemble between heterologous sequences. However, little is known about the regulation of heterologous synapsis. Here, we study the dynamics of heterologous synapsis in the nematode C. elegans. We characterize two experimental scenarios: SC assembly onto a folded-back chromosome that cannot pair with its homologous partner; and synapsis of pseudo-homologs, a fusion chromosome partnering with an unfused chromosome half its size. We observed elevated levels of heterologous synapsis when the number of meiotic double-strand breaks or crossovers were reduced, indicating that the promiscuity of synapsis is regulated by break formation or repair. In addition, our data suggests the existence of both chromosome-specific and nucleus-wide regulation on heterologous synapsis.
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Affiliation(s)
- Hanwenheng Liu
- School of Biological Sciences and Center for Cell and Genome Sciences, University of Utah, 257 South 1400 East, Salt Lake City, UT, 84112-0840, USA
- The Division of Biology & Biomedical Sciences, Washington University in St. Louis, 660 South Euclid Avenue, Missouri, 63110, USA
| | - Spencer G Gordon
- School of Biological Sciences and Center for Cell and Genome Sciences, University of Utah, 257 South 1400 East, Salt Lake City, UT, 84112-0840, USA
| | - Ofer Rog
- School of Biological Sciences and Center for Cell and Genome Sciences, University of Utah, 257 South 1400 East, Salt Lake City, UT, 84112-0840, USA.
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14
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Roy IM, Nadar PS, Khurana S. Neutral Comet Assay to Detect and Quantitate DNA Double-Strand Breaksin Hematopoietic Stem Cells. Bio Protoc 2021; 11:e4130. [PMID: 34541048 DOI: 10.21769/bioprotoc.4130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 04/09/2021] [Accepted: 05/10/2021] [Indexed: 11/02/2022] Open
Abstract
In vertebrates, hematopoietic stem cells (HSCs) regulate the supply of blood cells throughout the lifetime and help to maintain homeostasis. Due to their long lifespan, genetic integrity is paramount for these cells, and accordingly, a number of stem cell-specific mechanisms are employed. However, HSCs tend to show more DNA damage with increasing age due to an imbalance between proliferation rates and DNA damage responses. The comet assay is the most common and reliable method to study DNA strand breaks at the single-cell level. This procedure is based on the electrophoresis of agarose-embedded lysed cells. Following the electrophoretic mobilization of DNA, it is stained with fluorescent DNA-binding dye. Broken DNA strands migrate based on fragment size and form a tail-like structure called "the comet," whereas intact nuclear DNA remains a part of the head of the comet. Since the alkaline comet assay fails to differentiate between single and double-strand breaks (DSBs), we used a neutral comet assay to quantitate the DSBs in HSCs upon aging and other physiological stresses. The protocol presented here provides procedural details on this highly sensitive, rapid, and cost-effective assay, which can be used for rare populations of cells such as HSCs. Graphical abstract: The neutral comet assay is an extremely useful tool that allows the detection and quantitation of double-strand DNA breaks at the single-cell level. The graphical abstract represents a flowchart for the neutral comet assay procedure.
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Affiliation(s)
- Irene Mariam Roy
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Kerala, 695 551, India
| | - Pon Sowbhagya Nadar
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Kerala, 695 551, India
| | - Satish Khurana
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Kerala, 695 551, India
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15
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Kot P, Yasuhara T, Shibata A, Hirakawa M, Abe Y, Yamauchi M, Matsuda N. Mechanism of chromosome rearrangement arising from single-strand breaks. Biochem Biophys Res Commun 2021; 572:191-196. [PMID: 34375929 DOI: 10.1016/j.bbrc.2021.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 08/02/2021] [Indexed: 10/20/2022]
Abstract
Chromosome rearrangements, which are structural chromosomal abnormalities commonly found in human cancer, result from the misrejoining between two or more DNA double-strand breaks arising at different genomic regions. Consequently, chromosome rearrangements can generate fusion genes that promote tumorigenesis. The mechanisms of chromosome rearrangement have been studied using exogenous double-strand break inducers, such as radiation and nucleases. However, the mechanism underlying the occurrence of chromosome rearrangements in the absence of exogenous double-strand break-inducing stimuli is unclear. This study aimed to identify the major source of chromosome rearrangements and the DNA repair pathway that suppresses them. DNA repair factors that potentially suppress gene fusion were screened using The Cancer Genome Atlas dataset. In total, 22 repair factors whose expression levels were negatively correlated with the frequency of gene fusion were identified. More than 60% of these repair factors are involved in homologous recombination, a major double-strand break repair pathway. We hypothesized that DNA single-strand breaks are the source of double-strand breaks that lead to chromosome rearrangements. This study demonstrated that hydrogen peroxide (H2O2)-induced single-strand breaks gave rise to double-strand breaks in a replication-dependent manner. Additionally, H2O2 induced the formation of RPA and RAD51 foci, which indicated that double-strand breaks derived from single-strand breaks were repaired through homologous recombination. Moreover, treatment with H2O2 promoted the formation of radial chromosomes, a type of chromosome rearrangements, only upon the downregulation of homologous recombination factors, such as BRCA1 and CtIP. Thus, single-strand breaks are the major source of chromosome rearrangements when the expression of homologous recombination factors is downregulated.
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Affiliation(s)
- Palina Kot
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8523, Japan
| | - Takaaki Yasuhara
- Laboratory of Molecular Radiology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Atsushi Shibata
- Gunma University Initiative for Advanced Research, Maebashi, Gunma, 371-8511, Japan
| | - Miyako Hirakawa
- Radioisotope Research Center, Life Science Support Center, Nagasaki University, Nagasaki, 852-8523, Japan
| | - Yu Abe
- Department of Radiation Biology and Protection, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, 852-8523, Japan
| | - Motohiro Yamauchi
- Department of Radiation Biology and Protection, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, 852-8523, Japan.
| | - Naoki Matsuda
- Department of Radiation Biology and Protection, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, 852-8523, Japan
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16
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Liang S, Chaplin AK, Stavridi AK, Appleby R, Hnizda A, Blundell TL. Stages, scaffolds and strings in the spatial organisation of non-homologous end joining: Insights from X-ray diffraction and Cryo-EM. Prog Biophys Mol Biol 2021; 163:60-73. [PMID: 33285184 PMCID: PMC8224183 DOI: 10.1016/j.pbiomolbio.2020.11.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 11/26/2020] [Indexed: 01/10/2023]
Abstract
Non-homologous end joining (NHEJ) is the preferred pathway for the repair of DNA double-strand breaks in humans. Here we describe three structural aspects of the repair pathway: stages, scaffolds and strings. We discuss the orchestration of DNA repair to guarantee robust and efficient NHEJ. We focus on structural studies over the past two decades, not only using X-ray diffraction, but also increasingly exploiting cryo-EM to investigate the macromolecular assemblies.
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Affiliation(s)
- Shikang Liang
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, Cambridgeshire, UK
| | - Amanda K Chaplin
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, Cambridgeshire, UK
| | - Antonia Kefala Stavridi
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, Cambridgeshire, UK
| | - Robert Appleby
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, Cambridgeshire, UK
| | - Ales Hnizda
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, Cambridgeshire, UK
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, Cambridgeshire, UK.
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17
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Gowtham Kumar G, Paul SFD, Martin J, Manickavasagam M, Sundersingh S, Ganesan N, Ramya R, Usha Rani G, Andrea Mary F. Association between RAD51, XRCC2 and XRCC3 gene polymorphisms and risk of ovarian cancer: a case control and an in silico study. Mol Biol Rep 2021; 48:4209-20. [PMID: 34097201 DOI: 10.1007/s11033-021-06434-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/21/2021] [Indexed: 12/28/2022]
Abstract
Homologous recombination (HR) is one of the important mechanisms in repairing double-strand breaks to maintain genomic integrity and DNA stability from the cytotoxic effects and mutations. Various studies have reported that single nucleotide polymorphisms (SNPs) in the HR-associated genes may have a significant association with ovarian cancer (OCa) risk but the results were inconclusive. In the present study, five polymorphisms of HR-associated genes (RAD51, XRCC2 and XRCC3) were genotyped by allelic discrimination assay in 200 OCa cases and 200 healthy individuals. The association with OCa risk was evaluated by unconditional logistic regression analyses. The results revealed that the mutant allele in both rs1801320 (CC) and rs1801321 (TT) of RAD51 gene was associated with increased risk of OCa (odds ratio [OR] 3.79, 95% confidence interval [CI] 1.21-11.78, p = 0.014 and OR 1.61, 95% CI 1.06-2.45, p = 0.025, respectively). Moreover, a significant association of TT allele (OR 4.68, 95% CI 1.27-17.15, p = 0.011) of rs3218536 of XRCC2 gene with OCa was observed. Stratified analysis results showed that patients with early menarche and stages 3 and 4 were found to be associated with rs1801321 of RAD51 gene and rs1799794 of XRCC3 gene. In silico analysis predicted that the two missense SNPs (rs3218536 and rs1799794) were found to have an impact on the protein structure, stability and function. The present study suggested that RAD51 and XRCC2 gene polymorphisms might have an impact on the OCa risk in the South Indian population. However, studies with a larger sample and on different populations are needed to support the conclusions.
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18
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Niazi Y, Thomsen H, Smolkova B, Vodickova L, Vodenkova S, Kroupa M, Vymetalkova V, Kazimirova A, Barancokova M, Volkovova K, Staruchova M, Hoffmann P, Nöthen MM, Dusinska M, Musak L, Vodicka P, Försti A, Hemminki K. DNA repair gene polymorphisms and chromosomal aberrations in healthy, nonsmoking population. DNA Repair (Amst) 2021; 101:103079. [PMID: 33676360 DOI: 10.1016/j.dnarep.2021.103079] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 02/21/2021] [Accepted: 02/24/2021] [Indexed: 02/05/2023]
Abstract
Nonspecific structural chromosomal aberrations (CAs) can be found at around 1% of circulating lymphocytes from healthy individuals but the frequency may be higher after exposure to carcinogenic chemicals or radiation. The frequency of CAs has been measured in occupational monitoring and an increased frequency of CAs has also been associated with cancer risk. Alterations in DNA damage repair and telomere maintenance are thought to contribute to the formation of CAs, which include chromosome type of aberrations and chromatid type of aberrations. In the present study, we used the result of our published genome-wide association studies to extract data on 153 DNA repair genes from 866 nonsmoking persons who had no known occupational exposure to genotoxic substances. Considering an arbitrary cut-off level of P< 5 × 10-3, single nucleotide polymorphisms (SNPs) tagging 22 DNA repair genes were significantly associated with CAs and they remained significant at P < 0.05 when adjustment for multiple comparisons was done by the Binomial Sequential Goodness of Fit test. Nucleotide excision repair pathway genes showed most associations with 6 genes. Among the associated genes were several in which mutations manifest CA phenotype, including Fanconi anemia, WRN, BLM and genes that are important in maintaining genome stability, as well as PARP2 and mismatch repair genes. RPA2 and RPA3 may participate in telomere maintenance through the synthesis of the C strand of telomeres. Errors in NHEJ1 function may lead to translocations. The present results show associations with some genes with known CA phenotype and suggest other pathways with mechanistic rationale for the formation of CAs in healthy nonsmoking population.
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Affiliation(s)
- Yasmeen Niazi
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; Hopp Children's Cancer Center (KiTZ), 69120, Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120, Heidelberg, Germany.
| | - Hauke Thomsen
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; GeneWerk GmbH, Im Neuenheimer Feld 582, 6910 Heidelberg, Germany
| | - Bozena Smolkova
- Department of Molecular Oncology, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 84505 Bratislava, Slovakia
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, 30605 Pilsen, Czech Republic
| | - Soňa Vodenkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic
| | - Michal Kroupa
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, 30605 Pilsen, Czech Republic
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, 30605 Pilsen, Czech Republic
| | - Alena Kazimirova
- Department of Biology, Faculty of Medicine, Slovak Medical University, Limbova 12, 833 03 Bratislava, Slovakia
| | - Magdalena Barancokova
- Department of Biology, Faculty of Medicine, Slovak Medical University, Limbova 12, 833 03 Bratislava, Slovakia
| | - Katarina Volkovova
- Department of Biology, Faculty of Medicine, Slovak Medical University, Limbova 12, 833 03 Bratislava, Slovakia
| | - Marta Staruchova
- Department of Biology, Faculty of Medicine, Slovak Medical University, Limbova 12, 833 03 Bratislava, Slovakia
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn School of Medicine & University Hospital Bonn, Bonn, Germany; Division of Medical Genetics, Department of Biomedicine, University of Basel, 4003 Basel, Switzerland
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Maria Dusinska
- Health Effects Laboratory, Department of Environmental Chemistry, NILU-Norwegian Institute for Air Research, Instituttveien 18, 2007 Kjeller, Norway
| | - Ludovit Musak
- Biomedical Center Martin, Comenius University in Bratislava, Jessenius Faculty of Medicine, Malá Hora 4D, 03601 Martin, Slovakia
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, 30605 Pilsen, Czech Republic
| | - Asta Försti
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; Hopp Children's Cancer Center (KiTZ), 69120, Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
| | - Kari Hemminki
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, 30605 Pilsen, Czech Republic; Division of Cancer Epidemiology, German Cancer Research Centre (DKFZ), 69120 Heidelberg, Germany
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Lara-Cerrillo S, Ribas-Maynou J, Rosado-Iglesias C, Lacruz-Ruiz T, Benet J, García-Peiró A. Sperm selection during ICSI treatments reduces single- but not double-strand DNA break values compared to the semen sample. J Assist Reprod Genet 2021; 38:1187-96. [PMID: 33660206 DOI: 10.1007/s10815-021-02129-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/23/2021] [Indexed: 12/12/2022] Open
Abstract
PURPOSE To detect a possible bias in sperm DNA fragmentation (SDF) testing when performed on semen samples or on those few spermatozoa selected for Intracytoplasmic Sperm Injection (ICSI) treatments. METHODS A multimethodological analysis of Single- and Double-Strand DNA Breaks (SSB and DSB, respectively) was performed through the Neutral Comet, the Alkaline Comet, the Sperm Chromatin Dispersion (SCD) and the Terminal deoxynucleotidyl transferase dUTP Nick End Labelling (TUNEL) assays. SDF was evaluated in (i) semen samples from 23 infertile patients (not achieving pregnancy or suffering recurrent miscarriage); (ii) samples after a Swim-up and (iii) spermatozoa microselected for ICSI (ICSI-S). RESULTS The analysis of 3217 ICSI-S revealed a significant reduction of SSB values compared to the Ejaculate and the Swim-up samples. On the contrary, DSB values were not reduced after any sperm selection method. The No-pregnancy group presented poorer semen parameters and higher SSB values. The Recurrent miscarriage group presented better semen parameters but also higher DSB values. CONCLUSION The analysis of SDF on semen samples may not be fully representative of those few spermatozoa selected for ICSI. Since oxidative stress impairs sperm motility and causes SSB, selecting a motile sperm may intrinsically imply choosing a sperm not affected by this damage. DSB have an enzymatic origin which does not affect motility, making it difficult to select a sperm without this damage. Therefore, ICSI treatments could be effective in patients presenting high SSB values. Patients presenting high DSB values should expect bad ICSI results if this damage is not reduced through other specific methods.
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20
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Yates LA. Regulation of DNA break repair by RNA. Prog Biophys Mol Biol 2021; 163:23-33. [PMID: 33385412 DOI: 10.1016/j.pbiomolbio.2020.12.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/25/2020] [Accepted: 12/17/2020] [Indexed: 12/19/2022]
Abstract
Genomic stability is critical for cell survival and its effective repair when damaged is a vital process for preserving genetic information. Failure to correctly repair the genome can lead to the accumulation of mutations that ultimately drives carcinogenesis. Life has evolved sophisticated surveillance, repair pathways, and mechanisms to recognize and mend genomic lesions to preserve its integrity. Many of these pathways involve a cascade of protein effectors that act to identify the type of damage, such as double-strand (ds) DNA breaks, propagate the damage signal, and recruit an array of other protein factors to resolve the damage without loss of genetic information. It is now becoming increasingly clear that there are a number of RNA processing factors, such as the transcriptional machinery, and microRNA biogenesis components, as well as RNA itself, that facilitate the repair of DNA damage. Here, some of the recent work unravelling the role of RNA in the DNA Damage Response (DDR), in particular the dsDNA break repair pathway, will be reviewed.
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21
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Abstract
Meiosis is a specialized reductional cell division responsible for the formation of gametes and the generation of genetic diversity. A fundamental feature of the meiotic process is the initiation of homologous recombination (HR) by the programmed induction of DNA double-strand breaks (DSBs). Caenorhabditis elegans is a powerful experimental organism, which is used to study meiotic processes mainly due to the germline that allows for visualization of sequential stages of meiosis. C. elegans meiosis-programed DSBs are resolved through HR; hence, the germline provides a suitable model to study DSB repair. Classically direct procedures to detect and study intermediate steps in DSB repair by HR in the nematode rely on germline immunofluorescence against the strand exchange protein RAD-51.
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22
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Abstract
DNA double-strand breaks (DSBs) are the most deleterious type of DNA damage and a cause of genetic instability as they can lead to mutations, genome rearrangements, or loss of genetic material when not properly repaired. Eukaryotes from budding yeast to mammalian cells respond to the formation of DSBs with the immediate phosphorylation of a histone H2A isoform. The modified histone, phosphorylated in serine 139 in mammals (S129 in yeast), is named γ-H2AX. Detection of DSBs is of high relevance in research on DNA repair, aging, tumorigenesis, and cancer drug development, given the tight association of DSBs with different diseases and its potential to kill cells. DSB levels can be obtained by measuring levels of γ-H2AX in extracts of cell populations or by counting foci in individual nuclei. In this chapter some techniques to detect γ-H2AX are described.
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Affiliation(s)
- Sonia I Barroso
- Centro Andaluz de Biología Molecular y Medicina Regenerativa, CABIMER, University of Seville-CSIC-UPO, Seville, Spain
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa, CABIMER, University of Seville-CSIC-UPO, Seville, Spain.
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23
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Mehta K, Laimins L. High-Risk Human Papillomaviruses and DNA Repair. Recent Results Cancer Res 2021; 217:141-55. [PMID: 33200365 DOI: 10.1007/978-3-030-57362-1_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
Human papillomaviruses (HPVs) are small DNA viruses that infect basal epithelial cells and are the causative agents of cervical, anogenital, as well as oral cancers. High-risk HPVs are responsible for nearly half of all virally induced cancers. Viral replication and amplification are intimately linked to the stratified epithelium differentiation program. The E6 and E7 proteins contribute to the development of cancers in HPV positive individuals by hijacking cellular processes and causing genetic instability. This genetic instability induces a robust DNA damage response and activating both ATM and ATR repair pathways. These pathways are critical for the productive replication of high-risk HPVs, and understanding how they contribute to the viral life cycle can provide important insights into HPV's role in oncogenesis. This review will discuss the role that differentiation and the DNA damage responses play in productive replication of high-risk HPVs as well as in the development of cancer.
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Lerch S, Berthold S, Ziemann F, Dreffke K, Subtil FSB, Senger Y, Jensen A, Engenhart-Cabillic R, Dikomey E, Wittig A, Eberle F, Schötz U. HPV-positive HNSCC cell lines show strongly enhanced radiosensitivity after photon but not after carbon ion irradiation. Radiother Oncol 2020; 151:134-140. [PMID: 32717362 DOI: 10.1016/j.radonc.2020.07.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/29/2020] [Accepted: 07/20/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND AND PURPOSE HPV positive (pos.) HNSCC cells are significantly more radiosensitive to photon irradiation as compared to HPV negative (neg.) cells. Functionally, this is considered to result from a reduced DSB repair capacity. It was now tested, whether such a difference is also observed when using carbon ion (12C) irradiation. MATERIAL AND METHODS Five HPV pos. and five HPV neg. HNSCC cell lines were irradiated with photons or 12C-ions using 2D or 3D cell culture conditions. Clonogenic survival was determined by colony formation assay and DSB repair by immunofluorescence using co-staining of γH2AX and 53BP1 foci. RESULTS The pronounced difference in radiosensitivity known for these two entities when exposed to photons in 2D cell culture, was reduced when treated under 3D conditions. Irradiation with 12C-ions strongly enhanced cell killing, whereby increase was more pronounced for the HPV neg. when compared to the HPV pos. cell line (RBE = 2.81 vs. 2.14). As a consequence, after 12C-irradiation clonogenic survival was almost identical for the two entities as was demonstrated for all cell lines at a dose of 3 Gy. In line with this, the significant difference in DSB repair capacity between HPV pos. and neg. HNSCC cells, as seen after photon irradiation, was abrogated after 12C-irradiation. CONCLUSION While HPV pos. cells are significantly more radiosensitive to photons than HPV neg. cells, no significant difference was seen after 12C-irradiation. This needs to be considered when planning new clinical protocols for the treatment of HPV neg. and pos. tumors with 12C-ions.
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Affiliation(s)
- Stefan Lerch
- Department of Radiotherapy and Radiooncology, Philipps-University Marburg, Germany
| | - Sophie Berthold
- Department of Radiotherapy and Radiooncology, Philipps-University Marburg, Germany
| | - Frank Ziemann
- Department of Radiotherapy and Radiooncology, Philipps-University Marburg, Germany
| | - Kristin Dreffke
- Department of Radiotherapy and Radiooncology, Philipps-University Marburg, Germany
| | | | | | - Alexandra Jensen
- Department of Radiotherapy and Radiooncology, Philipps-University Marburg, Germany
| | | | - Ekkehard Dikomey
- Department of Radiotherapy and Radiooncology, Philipps-University Marburg, Germany; Laboratory of Radiobiology & Experimental Radiooncology, University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Andrea Wittig
- Department of Radiotherapy and Radiooncology, Philipps-University Marburg, Germany; Department of Radiotherapy and Radiation Oncology, University Hospital Jena, Friedrich-Schiller-University, Germany
| | - Fabian Eberle
- Department of Radiotherapy and Radiooncology, Philipps-University Marburg, Germany
| | - Ulrike Schötz
- Department of Radiotherapy and Radiooncology, Philipps-University Marburg, Germany.
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25
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Massonneau J, Lacombe-Burgoyne C, Boissonneault G. pH-induced variations in the TK1 gene model. Mutat Res Genet Toxicol Environ Mutagen 2020; 849:503128. [PMID: 32087849 DOI: 10.1016/j.mrgentox.2019.503128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 11/09/2019] [Accepted: 11/25/2019] [Indexed: 12/31/2022]
Abstract
A physiological decrease in extracellular pH (pHe) alters the efficiency of DNA repair and increases formation of DNA double-strand breaks (DSBs). Whether this could translate into genetic instability and variations, was investigated using the TK6 cell model, in which positive selection of the TK1 gene loss-of-function mutations can be achieved from resistance to trifluorothymidine. Cell exposure to suboptimal pH (down to 6.9) for 3 weeks resulted in the 100 % frequency of a stronger frameshift mutation that has spread to both TK1 alleles, whereas weaker frameshift mutations within the 3'exon were eliminated during the selection. Suboptimal pHe values were also found to alter the proportion of the TK1 splicing variant expressed as percent spliced in index values and promote selection of truncated exons as well as intron retention. Although recovery at pH 7.4 did not reverse the selected frameshift mutation, reversal of splice variants and exon truncation towards control values were observed. Hence, suboptimal pHe can induce a combination of mutational events and splicing alterations within the same gene in the resistant clones. This model of positive selection for loss-of-function clearly demonstrates that suboptimal pHe may confer a similar growth advantage when such instability occurs within tumor suppressor genes.
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Affiliation(s)
- Julien Massonneau
- Dept of Biochemistry and Functional Genomics, Faculty of Medicine & Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Chloë Lacombe-Burgoyne
- Dept of Biochemistry and Functional Genomics, Faculty of Medicine & Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Guylain Boissonneault
- Dept of Biochemistry and Functional Genomics, Faculty of Medicine & Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada.
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26
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Abstract
Double-strand DNA break (DSB) formation is a key feature of apoptosis called chromosomal DNA fragmentation. However, some apoptosis inducers introduce DNA damage-induced DSBs prior to induction of apoptotic chromosomal DNA fragmentation. To analyze these distinct breaks, we have developed a method using pulsed-field gel electrophoresis (PFGE) with a rotating gel electrophoresis system (RGE) that enables us to distinguish between apoptotic DSBs and DNA damaging agent-induced DSBs based on their mobility in the electrophoresis gel. Apoptotic DSBs appear as smeared low-molecular weight bands (less than 500 kb), while damage-induced DSBs result in a compact single band (more than 500 kb). Furthermore, using a caspase inhibitor, Z-VAD-FMK, we can confirm whether broken DNA fragments are produced as part of an apoptotic response. Overall, we succeeded in characterizing two individual apoptosis inducers and showed the different effects of those compounds on the induction of DNA breaks.
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Affiliation(s)
- Takeshi Terabayashi
- Department of Pharmacology, Faculty of Medicine, Oita University, Yufu, Oita, Japan.
| | - Asako Tokumaru
- Department of Pharmacology, Faculty of Medicine, Oita University, Yufu, Oita, Japan
| | - Toshimasa Ishizaki
- Department of Pharmacology, Faculty of Medicine, Oita University, Yufu, Oita, Japan
| | - Katsuhiro Hanada
- Clinical Engineering Research Center, Faculty of Medicine, Oita University, Yufu, Oita, Japan.
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27
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Guo W, Lobachev KS. Genetic Screens to Study GAA/TTC and Inverted Repeat Instability in Saccharomyces cerevisiae. Methods Mol Biol 2020; 2056:103-112. [PMID: 31586343 PMCID: PMC7098163 DOI: 10.1007/978-1-4939-9784-8_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Instability of trinucleotide and inverted repeats is a causative factor in the development of a number of neurological diseases, hereditary syndromes, and cancer. To understand the mechanisms that lead to repeat-induced genome destabilization it is important to identify factors that affect repeat metabolism. Here we present an approach that utilizes systematic and unbiased genome-wide screen in yeast Saccharomyces cerevisiae aimed to find genes that govern GAA/TTC and inverted repeat instability. These screens allowed for the identification of more than 30 mutants with increased fragility of both repeat motifs.
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Affiliation(s)
- Wenying Guo
- Institute for Bioengineering and Bioscience, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Kirill S Lobachev
- Institute for Bioengineering and Bioscience, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
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28
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Abstract
Carcinogenesis is caused by genome instability, one of the major causes of which is double-strand DNA breaks (DSBs). Interestingly, infection by particular species of bacteria can induce DSBs in host cells. For example, several reports suggest an association between periodontal disease and oral cancer. Aggregatibacter actinomycetemcomitans, a common periodontal pathogen, causes DSBs in the host cell. Pulsed-field gel electrophoresis (PFGE) is often used to identify DSBs in host cells. However, as established during investigation of A. actinomycetemcomitans infection, it is often difficult to determine whether broken DNA fragments are indeed from human chromosomes or whether they are bacterial in origin using PFGE-based methods. Because the method involves the coculture of human cells with bacteria, both bacterial and human DNA fragments may be present in the broken DNA fraction. To address this problem, we have developed a method to detect only human chromosomal DNA upon PFGE analysis. Human chromosomes were prelabeled with halogenated deoxyuridine (e.g., BrdU and IdU) before being fractionated by PFGE and visualized by immunoblotting. As proof of concept, we successfully used this method to investigate the mechanism of DSB formation in host chromosomes following infection with genotoxic bacterial species.
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Affiliation(s)
- Rie Teshima
- Shirokuma Dental Clinic, Beppu, Oita, Japan.
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29
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Critchley WR, Reid A, Morris J, Naish JH, Stone JP, Ball AL, Major T, Clark D, Waldron N, Fortune C, Lagan J, Lewis GA, Ainslie M, Schelbert EB, Davis DM, Schmitt M, Fildes JE, Miller CA. The effect of 1.5 T cardiac magnetic resonance on human circulating leucocytes. Eur Heart J 2019; 39:305-312. [PMID: 29165554 DOI: 10.1093/eurheartj/ehx646] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 10/20/2017] [Indexed: 12/25/2022] Open
Abstract
Aims Investigators have proposed that cardiovascular magnetic resonance (CMR) should have restrictions similar to those of ionizing imaging techniques. We aimed to investigate the acute effect of 1.5 T CMR on leucocyte DNA integrity, cell counts, and function in vitro, and in a large cohort of patients in vivo. Methods and results In vitro study: peripheral blood mononuclear cells (PBMCs) were isolated from healthy volunteers, and histone H2AX phosphorylation (γ-H2AX) expression, leucocyte counts, and functional parameters were quantified using flow cytometry under the following conditions: (i) immediately following PBMC isolation, (ii) after standing on the benchside as a temperature and time control, (iii) after a standard CMR scan. In vivo study: blood samples were taken from 64 consecutive consenting patients immediately before and after a standard clinical scan. Samples were analysed for γ-H2AX expression and leucocyte counts. CMR was not associated with a significant change in γ-H2AX expression in vitro or in vivo, although there were significant inter-patient variations. In vitro cell integrity and function did not change with CMR. There was a significant reduction in circulating T cells in vivo following CMR. Conclusion 1.5 T CMR was not associated with DNA damage in vitro or in vivo. Histone H2AX phosphorylation expression varied markedly between individuals; therefore, small studies using γ-H2AX as a marker of DNA damage should be interpreted with caution. Cardiovascular magnetic resonance was not associated with loss of leucocyte viability or function in vitro. Cardiovascular magnetic resonance was associated with a statistically significant reduction in viable leucocytes in vivo.
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Affiliation(s)
- William R Critchley
- Manchester Collaborative Centre for Inflammation Research (MCCIR), Division of Infection, Immunity and Respiratory Research, School of Biology, Medicine and Health, Manchester Academic Health Science Centre, Room 2.12 Core Technology Facility, Grafton Street, University of Manchester, M13 9NT Manchester, UK.,The Transplant Centre, Manchester University Hospitals NHS Foundation Trust, Southmoor Road, Wythenshawe, M23 9LT Manchester, UK
| | - Anna Reid
- North West Heart Centre, Manchester University Hospitals NHS Foundation Trust, Southmoor Road, Wythenshawe, M23 9LT Manchester, UK.,Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, 3rd Floor-Core Technology Facility, 46 Grafton Street, M13 9PL Manchester UK
| | - Julie Morris
- Department of Medical Statistics, Manchester University Hospitals NHS Foundation Trust, Southmoor Road, Wythenshawe, M23 9LT Manchester, UK
| | - Josephine H Naish
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, 3rd Floor-Core Technology Facility, 46 Grafton Street, M13 9PL Manchester UK
| | - John P Stone
- Manchester Collaborative Centre for Inflammation Research (MCCIR), Division of Infection, Immunity and Respiratory Research, School of Biology, Medicine and Health, Manchester Academic Health Science Centre, Room 2.12 Core Technology Facility, Grafton Street, University of Manchester, M13 9NT Manchester, UK.,The Transplant Centre, Manchester University Hospitals NHS Foundation Trust, Southmoor Road, Wythenshawe, M23 9LT Manchester, UK
| | - Alexandra L Ball
- Manchester Collaborative Centre for Inflammation Research (MCCIR), Division of Infection, Immunity and Respiratory Research, School of Biology, Medicine and Health, Manchester Academic Health Science Centre, Room 2.12 Core Technology Facility, Grafton Street, University of Manchester, M13 9NT Manchester, UK.,The Transplant Centre, Manchester University Hospitals NHS Foundation Trust, Southmoor Road, Wythenshawe, M23 9LT Manchester, UK
| | - Triin Major
- Manchester Collaborative Centre for Inflammation Research (MCCIR), Division of Infection, Immunity and Respiratory Research, School of Biology, Medicine and Health, Manchester Academic Health Science Centre, Room 2.12 Core Technology Facility, Grafton Street, University of Manchester, M13 9NT Manchester, UK.,The Transplant Centre, Manchester University Hospitals NHS Foundation Trust, Southmoor Road, Wythenshawe, M23 9LT Manchester, UK
| | - David Clark
- Wythenshawe Alliance Medical Cardiac MRI Unit, Wythenshawe Hospital, Southmoor Road, Wythenshawe, M23 9LT Manchester, UK
| | - Nick Waldron
- North West Heart Centre, Manchester University Hospitals NHS Foundation Trust, Southmoor Road, Wythenshawe, M23 9LT Manchester, UK
| | - Christien Fortune
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, 3rd Floor-Core Technology Facility, 46 Grafton Street, M13 9PL Manchester UK
| | - Jakub Lagan
- North West Heart Centre, Manchester University Hospitals NHS Foundation Trust, Southmoor Road, Wythenshawe, M23 9LT Manchester, UK.,Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, 3rd Floor-Core Technology Facility, 46 Grafton Street, M13 9PL Manchester UK
| | - Gavin A Lewis
- North West Heart Centre, Manchester University Hospitals NHS Foundation Trust, Southmoor Road, Wythenshawe, M23 9LT Manchester, UK.,Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, 3rd Floor-Core Technology Facility, 46 Grafton Street, M13 9PL Manchester UK
| | - Mark Ainslie
- North West Heart Centre, Manchester University Hospitals NHS Foundation Trust, Southmoor Road, Wythenshawe, M23 9LT Manchester, UK
| | - Erik B Schelbert
- Department of Medicine, University of Pittsburgh School of Medicine, 3550 Terrace St, Pittsburgh, PA 15213, USA.,Cardiovascular Magnetic Resonance Center, UPMC, 200 Lothrop St., Pittsburgh, PA 15213, USA
| | - Daniel M Davis
- Manchester Collaborative Centre for Inflammation Research (MCCIR), Division of Infection, Immunity and Respiratory Research, School of Biology, Medicine and Health, Manchester Academic Health Science Centre, Room 2.12 Core Technology Facility, Grafton Street, University of Manchester, M13 9NT Manchester, UK
| | - Matthias Schmitt
- North West Heart Centre, Manchester University Hospitals NHS Foundation Trust, Southmoor Road, Wythenshawe, M23 9LT Manchester, UK
| | - James E Fildes
- Manchester Collaborative Centre for Inflammation Research (MCCIR), Division of Infection, Immunity and Respiratory Research, School of Biology, Medicine and Health, Manchester Academic Health Science Centre, Room 2.12 Core Technology Facility, Grafton Street, University of Manchester, M13 9NT Manchester, UK.,The Transplant Centre, Manchester University Hospitals NHS Foundation Trust, Southmoor Road, Wythenshawe, M23 9LT Manchester, UK
| | - Christopher A Miller
- North West Heart Centre, Manchester University Hospitals NHS Foundation Trust, Southmoor Road, Wythenshawe, M23 9LT Manchester, UK.,Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, 3rd Floor-Core Technology Facility, 46 Grafton Street, M13 9PL Manchester UK.,Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biology, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, M13 9PT Manchester, UK
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30
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Sharma V, Mohan V. Detection of DNA Double-Strand Breaks Using Pulsed-Field Gel Electrophoresis. Methods Mol Biol 2019; 2031:301-11. [PMID: 31473967 DOI: 10.1007/978-1-4939-9646-9_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
DNA is one of the most biologically important targets of exogenous and endogenous toxicants as well as carcinogens. Damage to DNA can be of different types (e.g., DNA adducts, DNA protein cross-links, single-strand breaks, oxidized bases, abasic sites, and double-strand breaks (DSBs)). DSBs are considered the most lethal form of DNA damage for eukaryotic cells, and if left unrepaired or misrepaired, can cause cell death, chromosome instability, and cancer. DSBs can arise in the cells through different sources and can be distinguished as endogenous or exogenous DSBs. Exogenous sources can be chemotherapeutic drugs, irradiation, and environmental chemicals. The endogenous causes of DNA DSBs in the cells are mainly reactive oxygen species and faulty repair of oxidative clustered DNA lesions. Qualitative and quantitative analysis of DNA DSBs is of utmost importance to understand physiologically relevant cellular processes as well as to investigate the genotoxic or clastogenic effects of toxicants. Pulsed-field gel electrophoresis (PFGE) is a widely used method for direct quantification of DNA DSBs. In this method, the cells exposed to DSB-inducing agents are embedded in the agarose blocks and lysed. These agarose blocks containing DNA are then run under multiple electric fields which are at 120° angle, to aid in the movement of large DNA strands. It gives a direct and specific measure of DSBs unlike the foci-based assays. This chapter provides a brief overview of the various commonly used approaches to analyze DNA DSBs and describes the theory, advantages and method of PFGE, for use in cells exposed to DNA DSB inducing agents.
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31
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Frit P, Ropars V, Modesti M, Charbonnier JB, Calsou P. Plugged into the Ku-DNA hub: The NHEJ network. Prog Biophys Mol Biol 2019; 147:62-76. [PMID: 30851288 DOI: 10.1016/j.pbiomolbio.2019.03.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 02/26/2019] [Accepted: 03/01/2019] [Indexed: 12/16/2022]
Abstract
In vertebrates, double-strand breaks in DNA are primarily repaired by Non-Homologous End-Joining (NHEJ). The ring-shaped Ku heterodimer rapidly senses and threads onto broken DNA ends forming a recruiting hub. Through protein-protein contacts eventually reinforced by protein-DNA interactions, the Ku-DNA hub attracts a series of specialized proteins with scaffolding and/or enzymatic properties. To shed light on these dynamic interplays, we review here current knowledge on proteins directly interacting with Ku and on the contact points involved, with a particular accent on the different classes of Ku-binding motifs identified in several Ku partners. An integrated structural model of the core NHEJ network at the synapsis step is proposed.
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32
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Gospodinov A, Ugrinova I. Chromatin control in double strand break repair. Adv Protein Chem Struct Biol 2019; 115:69-94. [PMID: 30798938 DOI: 10.1016/bs.apcsb.2018.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Abstract
DNA double strand breaks (DSB) are the most deleterious type of damage inflicted on DNA by various environmental factors and as consequences of normal cellular metabolism. The multistep nature of DSB repair and the need to assemble large protein complexes at repair sites necessitate multiple chromatin changes there. This review focuses on the key findings of how chromatin regulators exert temporal and spatial control on DSB repair. These mechanisms coordinate repair with cell cycle progression, lead to DSB repair pathway choice, provide accessibility of repair machinery to damaged sites and move the lesions to nuclear environments permissive for repair.
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Abstract
Background During the last decade, genome sequencing projects in cancer genomes as well as in patients with congenital diseases and healthy individuals have led to the identification of new types of massive chromosomal rearrangements arising during single chaotic cellular events. These unanticipated catastrophic phenomenon are termed chromothripsis, chromoanasynthesis and chromoplexis., and are grouped under the name of “chromoanagenesis”. Results For each process, several specific features have been described, allowing each phenomenon to be distinguished from each other and to understand its mechanism of formation and to better understand its aetiology. Thus, chromothripsis derives from chromosome shattering followed by the random restitching of chromosomal fragments with low copy-number change whereas chromoanasynthesis results from erroneous DNA replication of a chromosome through serial fork stalling and template switching with variable copy-number gains, and chromoplexy refers to the occurrence of multiple inter-and intra-chromosomal translocations and deletions with little or no copy-number alterations in prostate cancer. Cumulating data and experimental models have shown that chromothripsis and chromoanasynthesis may essentially result from lagging chromosome encapsulated in micronuclei or telomere attrition and end-to-end telomere fusion. Conclusion The concept of chromanagenesis has provided new insight into the aetiology of complex structural rearrangements, the connection between defective cell cycle progression and genomic instability, and the complexity of cancer evolution. Increasing reported chromoanagenesis events suggest that these chaotic mechanisms are probably much more frequent than anticipated.
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Affiliation(s)
- Franck Pellestor
- Unit of Chromosomal Genetics, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHRU, 371, avenue du Doyen Gaston Giraud, 34295 Montpellier cedex 5, France.,INSERM 1183 Unit «Genome and Stem Cell Plasticity in Development and Aging », Institute of Regenerative Medicine and Biotherapies, St Eloi Hospital, Montpellier, France
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Azorín-Vega E, Aranda-Lara L, Torres-García E, Santiago-Bañuelos JA. Effect of 177Lu-iPSMA on viability and DNA damage of human glioma cells subjected to hypoxia-mimetic conditions. Appl Radiat Isot 2019; 146:24-8. [PMID: 30743222 DOI: 10.1016/j.apradiso.2019.01.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/24/2019] [Accepted: 01/24/2019] [Indexed: 01/22/2023]
Abstract
The therapeutic potential of 177Lu-iPSMA on hypoxic cancer cells has not been yet demonstrated. The aim of this work was to evaluate the radiation dose effect of 177Lu-iPSMA on viability and DNA damage in U87MG human glioma cells subjected to hypoxia-mimetic conditions. U87MG cells treated with 177Lu-iPSMA were incubated with CoCl2 in order to induce hypoxia-mimetic conditions. The cytotoxic and genotoxic effect was evaluated with an in vitro viability test and a neutral comet assay. 177Lu-iPSMA decreased the cell viability and induced DNA double strand breaks in U87MG human glioma cells under hypoxia-mimetic conditions. 177Lu-iPSMA produced the maximum effect at 48 h, suggesting that this radiopharmaceutical could be used as a strategy for the treatment of human glioma hypoxic cells.
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Abstract
DNA damage possesses the capacity to threaten the genomic integrity of an organism. A multitude of proteins are involved in the detection and repair of DNA double-strand breaks (DSBs), a severe kind of DNA damage. The function of DNA repair proteins can be examined by biochemical assays in vitro as well as in cell-based studies. The Ca2+-binding protein S100A11 shows functional interactions with factors involved in the repair of DSBs by homologous recombination (HR), a high-fidelity DNA repair pathway, such as RAD51 and RAD54B. The key enzyme of the homologous recombination repair is RAD51 that catalyzes the invasion of single-stranded DNA (ssDNA) into double-stranded DNA (dsDNA) containing homologous regions and the exchange of these DNA molecules generating heteroduplex DNA (hDNA). In this chapter, we describe a protocol for the purification of S100A11 to near homogeneity. Using purified proteins, we show the ability of S100A11 to stimulate RAD51 in a DNA strand exchange assay. Additionally, we describe a protocol how S100A11 can be localized in sites of DNA repair by immunofluorescence staining. Furthermore, we present a protocol for assessment of chromosomal aberrations after depletion of S100A11 that illustrate the apparent involvement of S100A11 in genome integrity.
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36
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Abstract
Human biomonitoring studies aim to identify potential exposures to environmental, occupational, or lifestyle toxicants in human populations and are commonly used by public health decision makers to predict disease risk. The Comet assay measures changes in genomic stability and is one of the most reliable biomarkers to indicate early biological effects and therefore accepted by various governmental regulatory agencies. The appeal of the Comet assay lies in its relative simplicity, rapidity, sensitivity, and economic efficiency. Furthermore, the assay is known for its broad versatility, as it can be applied to virtually any human cell and easily adapted in order to detect particular biomarkers of interest, such as DNA repair capacity or single and double-strand breaks. In a standard experiment, isolated single cells are first embedded in agarose, and then lysed in high-salt solutions in order to remove all cellular contents except the DNA attached to a nuclear scaffold. Subsequent electrophoresis results in accumulation of undamaged DNA sequences at the proximity of the nuclear scaffold, while damaged sequences migrate toward the anode. When visualized with fluorochromes, these migrated DNA fragments resemble a Comet tail and can be quantified for their intensity and shape according to internationally drafted guidelines.
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Affiliation(s)
- Diana Anderson
- Faculty of Life Sciences, University of Bradford, Bradford, UK.
| | - Alok Dhawan
- Nanomaterial Toxicology Group, CSIR-Indian Institute of Toxicology Research, Lucknow, Uttar Pradesh, India
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Abstract
DNA double-strand breaks (DSBs), one of the most severe lesions of DNA damage triggered by various genotoxic insults, can lead to chromosome change, genomic instability, and even tumorigenesis if not repaired efficiently. In response to DNA damage, histone H2AX molecules are rapidly phosphorylated at serine 139 near the site of DNA DSBs and form γ-H2AX foci. As an early important cellular event linked to DNA damage and repair, γ-H2AX is a highly sensitive biomarker for "monitoring" DNA damage and consequently is a useful tool in genetic toxicology screen. We and other researchers have used γ-H2AX as a marker to assess the potential genotoxic effects of some nanoparticles in vitro and in vivo. In this chapter, we describe several useful methods for γ-H2AX detection, which can be used to evaluate the potential genotoxic effects of nanoparticles.
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Affiliation(s)
- Rong Wan
- Department of Pathology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, People's Republic of China.,Department of Environmental and Occupational Health Sciences, School of Public Health and Information Sciences, University of Louisville, Louisville, KY, USA
| | - Yiqun Mo
- Department of Environmental and Occupational Health Sciences, School of Public Health and Information Sciences, University of Louisville, Louisville, KY, USA
| | - Ruirui Tong
- Department of Pathology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, People's Republic of China
| | - Meiqin Gao
- Department of Pathology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, People's Republic of China
| | - Qunwei Zhang
- Department of Environmental and Occupational Health Sciences, School of Public Health and Information Sciences, University of Louisville, Louisville, KY, USA.
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38
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Kotlajich MV, Xia J, Zhai Y, Lin HY, Bradley CC, Shen X, Mei Q, Wang AZ, Lynn EJ, Shee C, Chen LT, Li L, Miller KM, Herman C, Hastings PJ, Rosenberg SM. Fluorescent fusions of the N protein of phage Mu label DNA damage in living cells. DNA Repair (Amst) 2018; 72:86-92. [PMID: 30268364 PMCID: PMC6287932 DOI: 10.1016/j.dnarep.2018.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 09/09/2018] [Accepted: 09/10/2018] [Indexed: 01/06/2023]
Abstract
The N protein of phage Mu was indicated from studies in Escherichia coli to hold linear Mu chromosomes in a circular conformation by non-covalent association, and thus suggested potentially to bind DNA double-stranded ends. Because of its role in association with linear Mu DNA, we tested whether fluorescent-protein fusions to N might provide a useful tool for labeling DNA damage including double-strand break (DSB) ends in single cells. We compared N-GFP with a biochemically well documented DSB-end binding protein, the Gam protein of phage Mu, also fused to GFP. We find that N-GFP produced in live E. coli forms foci in response to DNA damage induced by radiomimetic drug phleomycin, indicating that it labels damaged DNA. N-GFP also labels specific DSBs created enzymatically by I-SceI double-strand endonuclease, and by X-rays, with the numbers of foci corresponding with the numbers of DSBs generated, indicating DSB labeling. However, whereas N-GFP forms about half as many foci as GamGFP with phleomycin, its labeling of I-SceI- and X-ray-induced DSBs is far less efficient than that of GamGFP. The data imply that N-GFP binds and labels DNA damage including DSBs, but may additionally label phleomycin-induced non-DSB damage, with which DSB-specific GamGFP does not interact. The data indicate that N-GFP labels DNA damage, and may be useful for general, not DSB-specific, DNA-damage detection.
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Affiliation(s)
- Matthew V Kotlajich
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jun Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Yin Zhai
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Hsin-Yu Lin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Catherine C Bradley
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas 77030, USA; Robert and Janice McNair Foundation/McNair Medical Institute M.D./Ph.D. Scholars Program, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Xi Shen
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Qian Mei
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA; Systems, Synthetic and Physical Biology Program, Rice University, Houston, Texas 77030, USA
| | - Anthony Z Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Erica J Lynn
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Chandan Shee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Li-Tzu Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Lei Li
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Kyle M Miller
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712 USA
| | - Christophe Herman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - P J Hastings
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Susan M Rosenberg
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA; Systems, Synthetic and Physical Biology Program, Rice University, Houston, Texas 77030, USA.
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Gorlas A, Catchpole R, Marguet E, Forterre P. Increase of positive supercoiling in a hyperthermophilic archaeon after UV irradiation. Extremophiles 2019; 23:141-9. [PMID: 30467661 DOI: 10.1007/s00792-018-1068-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 11/14/2018] [Indexed: 10/27/2022]
Abstract
Diverse DNA repair mechanisms are essential to all living organisms. Some of the most widespread repair systems allow recovery of genome integrity in the face of UV radiation. Here, we show that the hyperthermophilic archaeon Thermococcus nautili possesses a remarkable ability to recovery from extreme chromosomal damage. Immediately following UV irradiation, chromosomal DNA of T. nautili is fragmented beyond recognition. However, the extensive UV-induced double-stranded breaks (DSB) are repaired over the course of several hours, allowing restoration of growth. DSBs also disrupted plasmid DNA in this species. Similar to the chromosome, plasmid integrity was restored during an outgrowth period. Intriguingly, the topology of recovered pTN1 plasmids differed from control strain by being more positively supercoiled. As reverse gyrase (RG) is the only enzyme capable of inducing positive supercoiling, our results suggest the activation of RG activity by UV-induced stress. We suggest simple UV stress could be used to study archaeal DNA repair and responses to DSB.
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Tal E, Alfo M, Zha S, Barzilai A, De Zeeuw CI, Ziv Y, Shiloh Y. Inactive Atm abrogates DSB repair in mouse cerebellum more than does Atm loss, without causing a neurological phenotype. DNA Repair (Amst) 2018; 72:10-17. [PMID: 30348496 DOI: 10.1016/j.dnarep.2018.10.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 09/22/2018] [Accepted: 10/04/2018] [Indexed: 12/11/2022]
Abstract
The genome instability syndrome, ataxia-telangiectasia (A-T) is caused by null mutations in the ATM gene, that lead to complete loss or inactivation of the gene's product, the ATM protein kinase. ATM is the primary mobilizer of the cellular response to DNA double-strand breaks (DSBs) - a broad signaling network in which many components are ATM targets. The major clinical feature of A-T is cerebellar atrophy, characterized by relentless loss of Purkinje and granule cells. In Atm-knockout (Atm-KO) mice, complete loss of Atm leads to a very mild neurological phenotype, suggesting that Atm loss is not sufficient to markedly abrogate cerebellar structure and function in this organism. Expression of inactive ("kinase-dead") Atm (AtmKD) in mice leads to embryonic lethality, raising the question of whether conditional expression of AtmKD in the murine nervous system would lead to a more pronounced neurological phenotype than Atm loss. We generated two mouse strains in which AtmKD was conditionally expressed as the sole Atm species: one in the CNS and one specifically in Purkinje cells. Focusing our analysis on Purkinje cells, the dynamics of DSB readouts indicated that DSB repair was delayed longer in the presence of AtmKD compared to Atm loss. However, both strains exhibited normal life span and displayed no gross cerebellar histological abnormalities or significant neurological phenotype. We conclude that the presence of AtmKD is indeed more harmful to DSB repair than Atm loss, but the murine central nervous system can reasonably tolerate the extent of this DSB repair impairment. Greater pressure needs to be exerted on genome stability to obtain a mouse model that recapitulates the severe A-T neurological phenotype.
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Affiliation(s)
- Efrat Tal
- The David and Inez Myers Laboratory for Cancer Research, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, New York, United States
| | - Marina Alfo
- The David and Inez Myers Laboratory for Cancer Research, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, New York, United States
| | - Shan Zha
- Institute for Cancer Genetics, Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY, United States
| | - Ari Barzilai
- Department of Neurobiology, George S. Wise Faculty of Life Sciences, and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Chris I De Zeeuw
- Department of Neuroscience, Erasmus Medical Center, Rotterdam, and the Royal Netherlands Academy of Art & Science, Amsterdam, Netherlands
| | - Yael Ziv
- The David and Inez Myers Laboratory for Cancer Research, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, New York, United States
| | - Yosef Shiloh
- The David and Inez Myers Laboratory for Cancer Research, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, New York, United States.
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Elbakry A, Juhász S, Mathes A, Löbrich M. DNA repair synthesis and histone deposition partner during homologous recombination. Mol Cell Oncol 2018; 5:e1511210. [PMID: 30263950 PMCID: PMC6154852 DOI: 10.1080/23723556.2018.1511210] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 08/01/2018] [Accepted: 08/09/2018] [Indexed: 11/25/2022]
Abstract
Chromatin remodeling is critical for the regulation of the DNA damage response. We highlight findings from our recent study showing that the deposition of the histone variant H3.3 by the alpha-thalassemia mental retardation X-linked protein (ATRX) and the death domain associated protein (DAXX) chromatin remodeling complex regulates DNA repair synthesis during homologous recombination.
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Affiliation(s)
- Amira Elbakry
- Radiation Biology and DNA Repair, Darmstadt University of Technology, Darmstadt, Germany
| | - Szilvia Juhász
- Radiation Biology and DNA Repair, Darmstadt University of Technology, Darmstadt, Germany
| | - Arthur Mathes
- Radiation Biology and DNA Repair, Darmstadt University of Technology, Darmstadt, Germany
| | - Markus Löbrich
- Radiation Biology and DNA Repair, Darmstadt University of Technology, Darmstadt, Germany
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Mourad R, Ginalski K, Legube G, Cuvier O. Predicting double-strand DNA breaks using epigenome marks or DNA at kilobase resolution. Genome Biol 2018; 19:34. [PMID: 29544533 PMCID: PMC5856001 DOI: 10.1186/s13059-018-1411-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 02/22/2018] [Indexed: 12/18/2022] Open
Abstract
Double-strand breaks (DSBs) result from the attack of both DNA strands by multiple sources, including radiation and chemicals. DSBs can cause the abnormal chromosomal rearrangements associated with cancer. Recent techniques allow the genome-wide mapping of DSBs at high resolution, enabling the comprehensive study of their origins. However, these techniques are costly and challenging. Hence, we devise a computational approach to predict DSBs using the epigenomic and chromatin context, for which public data are readily available from the ENCODE project. We achieve excellent prediction accuracy at high resolution. We identify chromatin accessibility, activity, and long-range contacts as the best predictors.
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Affiliation(s)
- Raphaël Mourad
- LBME, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 118, route de Narbonne, Toulouse, 31062, France.
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, Warsaw, 02-089, Poland
| | - Gaëlle Legube
- LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 118, route de Narbonne, Toulouse, 31062, France
| | - Olivier Cuvier
- LBME, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 118, route de Narbonne, Toulouse, 31062, France
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Siddiqui MS, Francois M, Hecker J, Faunt J, Fenech MF, Leifert WR. γH2AX is increased in peripheral blood lymphocytes of Alzheimer's disease patients in the South Australian Neurodegeneration, Nutrition and DNA Damage (SAND) study of aging. Mutat Res Genet Toxicol Environ Mutagen 2018; 829-830:6-18. [PMID: 29704994 DOI: 10.1016/j.mrgentox.2018.03.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 03/06/2018] [Accepted: 03/07/2018] [Indexed: 12/27/2022]
Abstract
An early cellular response to DNA double-strand breaks is the phosphorylation of histone H2AX to form γH2AX. Although increased levels of γH2AX have been reported in neuronal nuclei of Alzheimer's disease (AD) patients, γH2AX responses in the lymphocytes of individuals with mild cognitive impairment (MCI) and AD remain unexplored. In this study, the endogenous γH2AX level was measured, using laser scanning cytometry (LSC) and visual scoring, in lymphocyte nuclei from MCI (n = 18), or AD (n = 20) patients and healthy controls (n = 40). Levels were significantly elevated in nuclei of the AD group compared to the MCI and control groups, and there was a concomitant increase, with a significant trend, from the control group through MCI to the AD group. A significant negative correlation was seen between γH2AX and the mini mental state examination (MMSE) score, when the analysis included all subjects. Receiver Operation Characteristic curves were carried out for different γH2AX parameters; visually scored percent cells containing overlapping γH2AX foci displayed the best area under the curve value of 0.9081 with 85% sensitivity and 92% specificity for the identification of AD patients versus control. Plasma homocysteine, creatinine, and chitinase-3-like protein 1 (CHI3L1) were positively correlated with lymphocyte γH2AX signals, while glomerular filtration rate (GFR) was negatively correlated. Finally, there was a diminished γH2AX response to X-rays in lymphocytes of the MCI and AD groups compared to the control group. Our results indicate that lymphocyte γH2AX levels are a potential marker for identifying individuals at increased risk of developing AD. Prospective studies with normal healthy individuals are needed to test whether there is indeed a link between γH2AX levels and AD risk.
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Affiliation(s)
- Mohammad Sabbir Siddiqui
- CSIRO Food and Nutrition, Personalised Nutrition and DNA Damage, Adelaide, South Australia, 5000, Australia; University of Adelaide, School of Agriculture, Food & Wine, Urrbrae, South Australia, 5064, Australia
| | - Maxime Francois
- CSIRO Food and Nutrition, Personalised Nutrition and DNA Damage, Adelaide, South Australia, 5000, Australia
| | - Jane Hecker
- Department of Internal Medicine, Royal Adelaide Hospital, Adelaide, South Australia, 5000, Australia
| | - Jeffrey Faunt
- Department of General Medicine, Royal Adelaide Hospital, Adelaide, South Australia, 5000, Australia
| | - Michael F Fenech
- CSIRO Food and Nutrition, Personalised Nutrition and DNA Damage, Adelaide, South Australia, 5000, Australia
| | - Wayne R Leifert
- CSIRO Food and Nutrition, Personalised Nutrition and DNA Damage, Adelaide, South Australia, 5000, Australia.
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Moiani D, Ronato DA, Brosey CA, Arvai AS, Syed A, Masson JY, Petricci E, Tainer JA. Targeting Allostery with Avatars to Design Inhibitors Assessed by Cell Activity: Dissecting MRE11 Endo- and Exonuclease Activities. Methods Enzymol 2018. [PMID: 29523233 DOI: 10.1016/bs.mie.2017.11.030] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
For inhibitor design, as in most research, the best system is question dependent. We suggest structurally defined allostery to design specific inhibitors that target regions beyond active sites. We choose systems allowing efficient quality structures with conformational changes as optimal for structure-based design to optimize inhibitors. We maintain that evolutionarily related targets logically provide molecular avatars, where this Sanskrit term for descent includes ideas of functional relationships and of being a physical embodiment of the target's essential features without requiring high sequence identity. Appropriate biochemical and cell assays provide quantitative measurements, and for biomedical impacts, any inhibitor's activity should be validated in human cells. Specificity is effectively shown empirically by testing if mutations blocking target activity remove cellular inhibitor impact. We propose this approach to be superior to experiments testing for lack of cross-reactivity among possible related enzymes, which is a challenging negative experiment. As an exemplary avatar system for protein and DNA allosteric conformational controls, we focus here on developing separation-of-function inhibitors for meiotic recombination 11 nuclease activities. This was achieved not by targeting the active site but rather by geometrically impacting loop motifs analogously to ribosome antibiotics. These loops are neighboring the dimer interface and active site act in sculpting dsDNA and ssDNA into catalytically competent complexes. One of our design constraints is to preserve DNA substrate binding to geometrically block competing enzymes and pathways from the damaged site. We validate our allosteric approach to controlling outcomes in human cells by reversing the radiation sensitivity and genomic instability in BRCA mutant cells.
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Affiliation(s)
- Davide Moiani
- The University of Texas, M.D. Anderson Cancer Center, Houston, TX, United States
| | - Daryl A Ronato
- Genome Stability Laboratory, CHU de Québec Research Center, Québec City, QC, Canada; Laval University Cancer Research Center, Québec City, QC, Canada
| | - Chris A Brosey
- The University of Texas, M.D. Anderson Cancer Center, Houston, TX, United States
| | - Andrew S Arvai
- The Scripps Research Institute, La Jolla, CA, United States
| | - Aleem Syed
- The University of Texas, M.D. Anderson Cancer Center, Houston, TX, United States
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Québec Research Center, Québec City, QC, Canada; Laval University Cancer Research Center, Québec City, QC, Canada
| | | | - John A Tainer
- The University of Texas, M.D. Anderson Cancer Center, Houston, TX, United States; Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
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Tao SM, Li X, Schoepf UJ, Nance JW, Jacobs BE, Zhou CS, Gu HF, Lu MJ, Lu GM, Zhang LJ. Comparison of the effect of radiation exposure from dual-energy CT versus single-energy CT on double-strand breaks at CT pulmonary angiography. Eur J Radiol 2018; 101:92-96. [PMID: 29571808 DOI: 10.1016/j.ejrad.2018.02.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 11/19/2017] [Accepted: 02/03/2018] [Indexed: 11/19/2022]
Abstract
PURPOSE To compare the effect of dual-source dual-energy CT versus single-energy CT on DNA double-strand breaks (DSBs) in blood lymphocytes at CT pulmonary angiography (CTPA). METHODS AND MATERIALS Sixty-two patients underwent either dual-energy CTPA (Group 1: n = 21, 80/Sn140 kVp, 89/38 mAs; Group 2: n = 20, 100/Sn140 kVp, 89/76 mAs) or single-energy CTPA (Group 3: n = 21, 120 kVp, 110 mAs). Blood samples were obtained before and 5 min after CTPA. DSBs were assessed with fluorescence microscopy and Kruskal-Walls tests were used to compare DSBs levels among groups. Volume CT dose index (CTDIvol), dose length product (DLP) and organ radiation dose were compared using ANOVA. RESULTS There were increased excess DSB foci per lymphocyte 5 min after CTPA examinations in three groups (Group 1: P = .001; Group 2: P = .001; Group 3: P = .006). There were no differences among groups regarding excess DSB foci/cell and percentage of excess DSBs (Group 1, 23%; Group 2, 24%; Group 3, 20%; P = .932). CTDIvol, DLP and organ radiation dose in Group 1 were the lowest among the groups (all P < .001). CONCLUSION DSB is increased following dual-source and single-source CTPA, while dual-source dual-energy CT protocols do not increase the estimated radiation dose and also do not result in a higher incidence of DNA DSBs in patients undergoing CTPA.
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Affiliation(s)
- Shu Min Tao
- Department of Medical Imaging, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, 210002, China
| | - Xie Li
- Department of Medical Imaging, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, 210002, China
| | - U Joseph Schoepf
- Department of Medical Imaging, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, 210002, China; Division of Cardiovascular Imaging, Department of Radiology and Radiological Science, Medical University of South Carolina, Ashley River Tower, MSC 226, 25 Courtenay Dr. Charleston, SC 29401, United States
| | - John W Nance
- Division of Cardiovascular Imaging, Department of Radiology and Radiological Science, Medical University of South Carolina, Ashley River Tower, MSC 226, 25 Courtenay Dr. Charleston, SC 29401, United States
| | - Brian E Jacobs
- Division of Cardiovascular Imaging, Department of Radiology and Radiological Science, Medical University of South Carolina, Ashley River Tower, MSC 226, 25 Courtenay Dr. Charleston, SC 29401, United States
| | - Chang Sheng Zhou
- Department of Medical Imaging, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, 210002, China
| | - Hai Feng Gu
- Department of Medical Imaging, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, 210002, China
| | - Meng Jie Lu
- Department of Medical Imaging, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, 210002, China
| | - Guang Ming Lu
- Department of Medical Imaging, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, 210002, China
| | - Long Jiang Zhang
- Department of Medical Imaging, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, 210002, China.
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Abstract
Homology-directed DNA repair (HDR) is an evolutionary conserved mechanism that is required for genome integrity and organismal fitness across species. While a myriad of different factors and mechanisms are able to execute HDR, all forms necessitate common steps of DNA damage recognition, homology search and capture, and assembly of a DNA polymerase complex to conduct templated DNA synthesis. The central question of what determines HDR mechanism utilization in mammalian cells has been limited by an inability to directly monitor the DNA damage response and products of repair as they arise from a defined genomic lesion. In this chapter, we describe several methodologies to delineate major steps of HDR during alternative lengthening of telomeres in human cells. This includes procedures to visualize interchromosomal telomere homology searches in real time and quantitatively detect HDR synthesis of nascent telomeres emanating from synchronous activation of telomere DNA double-strand breaks. We highlight the critical details of these methods and their applicability to monitoring HDR at telomeres in a broad variety of mammalian cell types.
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Affiliation(s)
- Priyanka Verma
- Basser Research Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Robert L Dilley
- Basser Research Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Melina T Gyparaki
- Basser Research Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Roger A Greenberg
- Basser Research Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.
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Abstract
DNA strand breaks arise from normal cellular processes such as replication, transcription, and DNA repair as well as spontaneous DNA damage caused by cell metabolic activities. In addition, strand breaks occur due to direct or indirect DNA damage produced by various abiotic and biotic stresses. Strand breaks are among the most problematic DNA lesions because unrepaired strand breaks may lead to cell cycle arrest, gross chromosome rearrangements, or even cell death. Thus, the measurement of the relative number of strand breaks can provide an informative picture of genome stability of a given cell, tissue, or organism. Here, we describe the use of random oligonucleotide-primed synthesis (ROPS) assay for the detection and quantification of the level of strand breaks in tissue samples. The applications of the assay for a quantitative detection of 3'OH, 3'P, or DNA strand breaks at a cleavage site of the deoxyribose residue are discussed.
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Affiliation(s)
- Andriy Bilichak
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, 4401 University Drive, Lethbridge, AB, Canada, T1K 3M4.
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48
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Abstract
The nucleolytic degradation of the 5'-ending strand of a Double-Strand DNA break (DSB) is necessary to initiate homologous recombination to correctly repair the break. This process is called DNA end resection and it is finely regulated to prevent genome rearrangements. Here, we describe a protocol to quantify DSB resection rate by qPCR, which could be applied to every organisms whenever the break site and its flanking region sequences are known.
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Affiliation(s)
- Matteo Ferrari
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Shyam Twayana
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Federica Marini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Achille Pellicioli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy.
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49
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Abstract
DNA double-strand breaks (DSBs) are toxic lesions that every cell must accurately repair in order to survive. The repair of DSBs is an integral part of a cell life cycle and can lead to lethality if repaired incorrectly. Laser microirradiation is an established technique which has been used in yeast, mammalian cell culture, and Drosophila cell culture to study the regulation of DSB repair. Up to our studies, this method has not been adapted for use in a whole, live, multicellular organism to study this repair in vivo. We have recently shown that this system can be used for study of the recruitment of vital repair proteins to microirradiation-induced breaks in the transparent nematode Caenorhabditis elegans. With the integration of microirradiation and imaging technology, we can precisely induce DSBs in target nuclei and study the recruitment of fluorescently tagged repair proteins from the time of damage induction. Whole, live worms are plated and immobilized for targeting of nuclei, and immediately following induction the targeted region can be imaged for up to an hour and a half post-microirradiation. This method is the first that allows for study of DNA repair protein kinetics in vivo in an intact organism, which can be adapted in numerous ways to allow for study of repair kinetics in various aspects of the repair process.
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Affiliation(s)
| | - Emily Koury
- Department of Biology, University of Iowa, Iowa City, USA
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Ren X, Tang Y, Sun J, Feng J, Chen L, Chen H, Zeng S, Chen C, Li X, Zhu H, Zeng Z. Flavone protects HBE cells from DNA double-strand breaks caused by PM2.5. Hum Cell 2017; 31:116-126. [PMID: 29168129 DOI: 10.1007/s13577-017-0193-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 11/06/2017] [Indexed: 12/29/2022]
Abstract
Ambient air particulate matter 2.5 (PM2.5) contains many harmful components that can enter the circulatory system and produce reactive oxygen species (ROS) in body. Oxidative stress and DNA damage induced by ROS may affect any cellular macromolecule and lead to DNA double-strand breaks (DSBs). Flavonoids, widely distributed in some herbs and berries, have been proved having anti-oxidative or anti-cancer efficacy. In this study, we investigated whether Flavone, a kind of flavonoids, can protect human bronchial epithelial cells (HBE) from DSBs caused by PM2.5 and how this function is probably implemented. We found that cells exposed to PM2.5 obviously induced viability inhibition, DNA damage and part of apoptosis. However, Flavone treatment prior to PM2.5 apparently improved cell viability, and mitigated the formation of 8-hydroxy-2-deoxyguanosine, the expression of DNA damage-relative protein and cell apoptosis. Our studies demonstrated that PM2.5 induced oxidative DSBs while Flavone ameliorated the DNA damage and increased cell viability probably through influencing DNA repair mechanism of cells.
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Affiliation(s)
- Xing Ren
- School of Life Sciences, Central South University, Xiangya Road No. 110, Changsha, 410078, Hunan, People's Republic of China
| | - Yong Tang
- School of Life Sciences, Central South University, Xiangya Road No. 110, Changsha, 410078, Hunan, People's Republic of China
| | - Jiameng Sun
- School of Life Sciences, Central South University, Xiangya Road No. 110, Changsha, 410078, Hunan, People's Republic of China
| | - Jianbo Feng
- Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, 410078, People's Republic of China
| | - Leilei Chen
- Xiangya School of Medicine, Central South University, Changsha, 410078, People's Republic of China
| | - Huixi Chen
- Xiangya School of Medicine, Central South University, Changsha, 410078, People's Republic of China
| | - Sijing Zeng
- School of Life Sciences, Central South University, Xiangya Road No. 110, Changsha, 410078, Hunan, People's Republic of China
| | - Changhui Chen
- School of Life Sciences, Central South University, Xiangya Road No. 110, Changsha, 410078, Hunan, People's Republic of China
| | - Xinqiu Li
- Xiangya School of Medicine, Central South University, Changsha, 410078, People's Republic of China
| | - Haixia Zhu
- The Third Hospital of Xiangya, Central South University, Tongzipo Road No. 138, Changsha, 410013, Hunan, People's Republic of China
| | - Zhaojun Zeng
- School of Life Sciences, Central South University, Xiangya Road No. 110, Changsha, 410078, Hunan, People's Republic of China. .,State Key Laboratory of Medical Genetics, Central South University, Changsha, People's Republic of China.
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