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Li Q, Wang X, Xu S, Chen B, Wu T, Liu J, Zhao G, Wu L. Remodeling of Chromatin Accessibility Regulates the Radiological Responses of NSCLC A549 Cells to High-LET Carbon Ions. Radiat Res 2023; 200:474-488. [PMID: 37815204 DOI: 10.1667/rade-23-00097.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 09/19/2023] [Indexed: 10/11/2023]
Abstract
Carbon-ion radiation therapy (CIRT) may offer remarkable advantages in cancer treatment with its unique physical and biological characteristics. However, the underlying epigenetic regulatory mechanisms of cancer response to CIRT remain to be identified. In this study, we showed consistent but different degrees of biological effects induced in NSCLC A549 cells by carbon ions of different LET. The genome-wide chromatin accessibility and transcriptional profiles of carbon ion-treated A549 cells were performed using transposase-accessible chromatin sequencing (ATAC-seq) and RNA-seq, respectively, and further gene regulatory network analysis was performed by integrating the two sets of genomic data. Alterations in chromatin accessibility by carbon ions of different LET predominantly occurred in intron, distal intergenic and promoter regions of differential chromatin accessibility regions. The transcriptional changes were mainly regulated by proximal chromatin accessibility. Notably, CCCTC-binding factor (CTCF) was identified as a key transcription factor in the cellular response to carbon ions. The target genes regulated by CTCF in response to carbon ions were found to be closely associated with the LET of carbon ions, particularly in the regulation of gene transcription within the DNA replication- and metabolism-related signaling pathways. This study provides a regulatory profile of genes involved in key signaling pathways and highlighted key regulatory elements in NSCLC A549 cells during CIRT, which expands our understanding of the epigenetic mechanisms of carbon ion-induced biological effects and reveals an important role for LET in the regulation of changes in chromatin accessibility, although further research is needed.
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Affiliation(s)
- Qian Li
- School of Environmental Science and Optoelectronic Technology, University of Science and Technology of China, Hefei, Anhui, 230026, PR China
| | - Xiaofei Wang
- School of Biology, Food and Environment, Hefei University, Hefei 230601, P. R. China
| | - Shengmin Xu
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, PR China
| | - Biao Chen
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, PR China
| | - Tao Wu
- School of Environmental Science and Optoelectronic Technology, University of Science and Technology of China, Hefei, Anhui, 230026, PR China
| | - Jie Liu
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, PR China
| | - Guoping Zhao
- School of Environmental Science and Optoelectronic Technology, University of Science and Technology of China, Hefei, Anhui, 230026, PR China
| | - Lijun Wu
- School of Environmental Science and Optoelectronic Technology, University of Science and Technology of China, Hefei, Anhui, 230026, PR China
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, PR China
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Lei T, Du S, Peng Z, Chen L. Multifaceted regulation and functions of 53BP1 in NHEJ‑mediated DSB repair (Review). Int J Mol Med 2022; 50:90. [PMID: 35583003 PMCID: PMC9162042 DOI: 10.3892/ijmm.2022.5145] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/29/2022] [Indexed: 12/02/2022] Open
Abstract
The repair of DNA double-strand breaks (DSBs) is crucial for the preservation of genomic integrity and the maintenance of cellular homeostasis. Non-homologous DNA end joining (NHEJ) is the predominant repair mechanism for any type of DNA DSB during the majority of the cell cycle. NHEJ defects regulate tumor sensitivity to ionizing radiation and anti-neoplastic agents, resulting in immunodeficiencies and developmental abnormalities in malignant cells. p53-binding protein 1 (53BP1) is a key mediator involved in DSB repair, which functions to maintain a balance in the repair pathway choices and in preserving genomic stability. 53BP1 promotes DSB repair via NHEJ and antagonizes DNA end overhang resection. At present, novel lines of evidence have revealed the molecular mechanisms underlying the recruitment of 53BP1 and DNA break-responsive effectors to DSB sites, and the promotion of NHEJ-mediated DSB repair via 53BP1, while preventing homologous recombination. In the present review article, recent advances made in the elucidation of the structural and functional characteristics of 53BP1, the mechanisms of 53BP1 recruitment and interaction with the reshaping of the chromatin architecture around DSB sites, the post-transcriptional modifications of 53BP1, and the up- and downstream pathways of 53BP1 are discussed. The present review article also focuses on the application perspectives, current challenges and future directions of 53BP1 research.
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Affiliation(s)
- Tiantian Lei
- Department of Pharmacy, Women and Children's Hospital of Chongqing Medical University, Chongqing 401147, P.R. China
| | - Suya Du
- Department of Clinical Pharmacy, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan 610041, P.R. China
| | - Zhe Peng
- Department of Pharmacy, Women and Children's Hospital of Chongqing Medical University, Chongqing 401147, P.R. China
| | - Lin Chen
- Department of Pharmacy, Women and Children's Hospital of Chongqing Medical University, Chongqing 401147, P.R. China
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Brunner S, Varga D, Bozó R, Polanek R, Tőkés T, Szabó ER, Molnár R, Gémes N, Szebeni GJ, Puskás LG, Erdélyi M, Hideghéty K. Analysis of Ionizing Radiation Induced DNA Damage by Superresolution dSTORM Microscopy. Pathol Oncol Res 2022; 27:1609971. [PMID: 35370480 PMCID: PMC8966514 DOI: 10.3389/pore.2021.1609971] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/12/2021] [Indexed: 11/17/2022]
Abstract
The quantitative detection of radiation caused DNA double-strand breaks (DSB) by immunostained γ-H2AX foci using direct stochastic optical reconstruction microscopy (dSTORM) provides a deeper insight into the DNA repair process at nanoscale in a time-dependent manner. Glioblastoma (U251) cells were irradiated with 250 keV X-ray at 0, 2, 5, 8 Gy dose levels. Cell cycle phase distribution and apoptosis of U251 cells upon irradiation was assayed by flow cytometry. We studied the density, topology and volume of the γ-H2AX foci with 3D confocal microscopy and the dSTORM superresolution method. A pronounced increase in γ-H2AX foci and cluster density was detected by 3D confocal microscopy after 2 Gy, at 30 min postirradiation, but both returned to the control level at 24 h. Meanwhile, at 24 h a considerable amount of residual foci could be measured from 5 Gy, which returned to the normal level 48 h later. The dSTORM based γ-H2AX analysis revealed that the micron-sized γ-H2AX foci are composed of distinct smaller units with a few tens of nanometers. The density of these clusters, the epitope number and the dynamics of γ-H2AX foci loss could be analyzed. Our findings suggest a discrete level of repair enzyme capacity and the restart of the repair process for the residual DSBs, even beyond 24 h. The dSTORM superresolution technique provides a higher precision over 3D confocal microscopy to study radiation induced γ-H2AX foci and molecular rearrangements during the repair process, opening a novel perspective for radiation research.
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Affiliation(s)
- Szilvia Brunner
- Biomedical Applications Group, ELI-ALPS Research Institute, ELI-HU Non-Profit Ltd., Szeged, Hungary
| | - Dániel Varga
- Department of Optics and Quantum Electronics, University of Szeged, Szeged, Hungary
| | - Renáta Bozó
- Department of Dermatology and Allergology, University of Szeged, Szeged, Hungary
| | - Róbert Polanek
- Biomedical Applications Group, ELI-ALPS Research Institute, ELI-HU Non-Profit Ltd., Szeged, Hungary.,Department of Oncotherapy, University of Szeged, Szeged, Hungary
| | - Tünde Tőkés
- Biomedical Applications Group, ELI-ALPS Research Institute, ELI-HU Non-Profit Ltd., Szeged, Hungary.,Department of Oncotherapy, University of Szeged, Szeged, Hungary
| | - Emília Rita Szabó
- Biomedical Applications Group, ELI-ALPS Research Institute, ELI-HU Non-Profit Ltd., Szeged, Hungary.,Department of Oncotherapy, University of Szeged, Szeged, Hungary
| | - Réka Molnár
- Biomedical Applications Group, ELI-ALPS Research Institute, ELI-HU Non-Profit Ltd., Szeged, Hungary.,Department of Oncotherapy, University of Szeged, Szeged, Hungary
| | - Nikolett Gémes
- Laboratory of Functional Genomics, Biological Research Centre, Szeged, Hungary
| | - Gábor J Szebeni
- Laboratory of Functional Genomics, Biological Research Centre, Szeged, Hungary
| | - László G Puskás
- Laboratory of Functional Genomics, Biological Research Centre, Szeged, Hungary
| | - Miklós Erdélyi
- Department of Optics and Quantum Electronics, University of Szeged, Szeged, Hungary
| | - Katalin Hideghéty
- Biomedical Applications Group, ELI-ALPS Research Institute, ELI-HU Non-Profit Ltd., Szeged, Hungary.,Department of Oncotherapy, University of Szeged, Szeged, Hungary
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Berzsenyi I, Pantazi V, Borsos BN, Pankotai T. Systematic overview on the most widespread techniques for inducing and visualizing the DNA double-strand breaks. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2021; 788:108397. [PMID: 34893162 DOI: 10.1016/j.mrrev.2021.108397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 12/18/2022]
Abstract
DNA double-strand breaks (DSBs) are one of the most frequent causes of initiating cancerous malformations, therefore, to reduce the risk, cells have developed sophisticated DNA repair mechanisms. These pathways ensure proper cellular function and genome integrity. However, any alteration or malfunction during DNA repair can influence cellular homeostasis, as improper recognition of the DNA damage or dysregulation of the repair process can lead to genome instability. Several powerful methods have been established to extend our current knowledge in the field of DNA repair. For this reason, in this review, we focus on the methods used to study DSB repair, and we summarize the advantages and disadvantages of the most commonly used techniques currently available for the site-specific induction of DSBs and the subsequent tracking of the repair processes in human cells. We highlight methods that are suitable for site-specific DSB induction (by restriction endonucleases, CRISPR-mediated DSB induction and laser microirradiation) as well as approaches [e.g., fluorescence-, confocal- and super-resolution microscopy, chromatin immunoprecipitation (ChIP), DSB-labeling and sequencing techniques] to visualize and follow the kinetics of DSB repair.
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Affiliation(s)
- Ivett Berzsenyi
- Institute of Pathology, Albert Szent-Györgyi Medical School, University of Szeged, 1 Állomás Street H-6725, Szeged, Hungary.
| | - Vasiliki Pantazi
- Institute of Pathology, Albert Szent-Györgyi Medical School, University of Szeged, 1 Állomás Street H-6725, Szeged, Hungary.
| | - Barbara N Borsos
- Institute of Pathology, Albert Szent-Györgyi Medical School, University of Szeged, 1 Állomás Street H-6725, Szeged, Hungary.
| | - Tibor Pankotai
- Institute of Pathology, Albert Szent-Györgyi Medical School, University of Szeged, 1 Állomás Street H-6725, Szeged, Hungary.
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