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Chiolo I, Altmeyer M, Legube G, Mekhail K. Nuclear and genome dynamics underlying DNA double-strand break repair. Nat Rev Mol Cell Biol 2025:10.1038/s41580-025-00828-1. [PMID: 40097581 DOI: 10.1038/s41580-025-00828-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/21/2025] [Indexed: 03/19/2025]
Abstract
Changes in nuclear shape and in the spatial organization of chromosomes in the nucleus commonly occur in cancer, ageing and other clinical contexts that are characterized by increased DNA damage. However, the relationship between nuclear architecture, genome organization, chromosome stability and health remains poorly defined. Studies exploring the connections between the positioning and mobility of damaged DNA relative to various nuclear structures and genomic loci have revealed nuclear and cytoplasmic processes that affect chromosome stability. In this Review, we discuss the dynamic mechanisms that regulate nuclear and genome organization to promote DNA double-strand break (DSB) repair, genome stability and cell survival. Genome dynamics that support DSB repair rely on chromatin states, repair-protein condensates, nuclear or cytoplasmic microtubules and actin filaments, kinesin or myosin motor proteins, the nuclear envelope, various nuclear compartments, chromosome topology, chromatin loop extrusion and diverse signalling cues. These processes are commonly altered in cancer and during natural or premature ageing. Indeed, the reshaping of the genome in nuclear space during DSB repair points to new avenues for therapeutic interventions that may take advantage of new cancer cell vulnerabilities or aim to reverse age-associated defects.
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Affiliation(s)
- Irene Chiolo
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA.
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich (UZH), Zurich, Switzerland.
| | - Gaëlle Legube
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France.
| | - Karim Mekhail
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.
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2
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Pae S, Sedukhina AS, Sugiyama R, Atanacio SJ, Ohara T, Ishii M, Minagawa K, Akichjev R, Go F, Chandankeri Z, Janjetic ZMM, Sato E, Yamaura A, Meguro R, Palanisamy K, Maeda I, Takeuchi O, Suzuki N, Yudo K, Bernal JA, Sato K. PLK1 overexpression suppresses homologous recombination and confers cellular sensitivity to PARP inhibition. Sci Rep 2024; 14:31276. [PMID: 39732958 PMCID: PMC11682379 DOI: 10.1038/s41598-024-82724-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Accepted: 12/09/2024] [Indexed: 12/30/2024] Open
Abstract
The overexpression of Polo-like kinase 1 (PLK1) is associated with poor clinical outcomes in various malignancies, making it an attractive target for anticancer therapies. Although recent studies suggest PLK1's involvement in homologous recombination (HR), the impact of its overexpression on HR remains unclear. In this study, we investigated the effect of PLK1 overexpression on HR using bioinformatics and experimental approaches. Analyzing The Cancer Genome Atlas (TCGA) and Cancer Cell Line Encyclopedia (CCLE) datasets with the Homologous Recombination Deficiency (HRD) score, we found a positive correlation between PLK1 expression and HRD score, indicating that increased PLK1 expression suppresses HR. To validate these findings, we performed cell line-based experiments, demonstrating that PLK1 overexpression attenuates RAD51 focus formation and HR, as measured by ASHRA in T47D cells. Since HR-deficient cells are hypersensitive to PARP inhibitors, we further confirmed that PLK1 overexpression increases sensitivity to PARP inhibitors, both in CCLE dataset analysis and experiments using T47D cells. Additionally, we found that the effects of PLK1 overexpression on HR suppression and increased PARP inhibitor sensitivity were mitigated by either a PLK1 kinase inhibitor or the kinase-dead mutant [T210A]. This suggests that PLK1's impact on HR and PARP inhibitor sensitivity is mediated through its kinase activity. Moreover, analysis of clinical ovarian cancer samples revealed that higher PLK1 expression correlates with increased sensitivity to PARP inhibitors. Our results suggest that PLK1 overexpression suppresses homologous recombination, leading to enhanced sensitivity to PARP inhibition, presenting a potential therapeutic strategy for targeting cancers with overexpression of PLK1.
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Affiliation(s)
- Sookhee Pae
- Department of Frontier Medicine, Institute of Medical Science, Graduate School of Medicine, St. Marianna University, Kawasaki, 2168511, Japan
| | - Anna S Sedukhina
- Department of Frontier Medicine, Institute of Medical Science, Graduate School of Medicine, St. Marianna University, Kawasaki, 2168511, Japan
- Shirokane Sanko Clinic Research Centre, Minato, 1080072, Japan
| | - Runa Sugiyama
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, St. Marianna University, Kawasaki, 216-8511, Japan
| | | | - Tatsuru Ohara
- Department of Obstetrics and Gynecology, St. Marianna University School of Medicine, Kawasaki, 216-8511, Japan
| | - Masato Ishii
- Department of Obstetrics and Gynecology, St. Marianna University School of Medicine, Kawasaki, 216-8511, Japan
| | - Kimino Minagawa
- Division of Genomic Epidemiology and Clinical Trials, Clinical Trials Research Center, Nihon University School of Medicine, Tokyo, Japan
| | - Romaan Akichjev
- Shirokane Sanko Clinic Research Centre, Minato, 1080072, Japan
- Katholieke Universiteit Leuven, 3000, Leuven, Belgium
| | - Fumie Go
- Shirokane Sanko Clinic Research Centre, Minato, 1080072, Japan
- K International School Tokyo, Koto, 1350021, Japan
| | - Zayan Chandankeri
- Shirokane Sanko Clinic Research Centre, Minato, 1080072, Japan
- K International School Tokyo, Koto, 1350021, Japan
| | - Zoran M M Janjetic
- Shirokane Sanko Clinic Research Centre, Minato, 1080072, Japan
- K International School Tokyo, Koto, 1350021, Japan
| | - Eri Sato
- Shirokane Sanko Clinic Research Centre, Minato, 1080072, Japan
| | - Ayako Yamaura
- Shirokane Sanko Clinic Research Centre, Minato, 1080072, Japan
| | - Rei Meguro
- Shirokane Sanko Clinic Research Centre, Minato, 1080072, Japan
- University of Michigan Ann Arbor, Ann Arbor, MI, 48109, USA
| | - Kishore Palanisamy
- Shirokane Sanko Clinic Research Centre, Minato, 1080072, Japan
- School of Medicine, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Ichiro Maeda
- Department of Pathology, Kitasato University Kitasato Institute Hospital, Minato, 1080072, Japan
- Department of Pathology, Kitasato University School of Medicine, Sagamihara, 2520374, Japan
| | - Osamu Takeuchi
- Biomedical Laboratory, Department of Research, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Nao Suzuki
- Department of Obstetrics and Gynecology, St. Marianna University School of Medicine, Kawasaki, 216-8511, Japan
| | - Kazuo Yudo
- Department of Frontier Medicine, Institute of Medical Science, Graduate School of Medicine, St. Marianna University, Kawasaki, 2168511, Japan
| | - Juan A Bernal
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Ko Sato
- Department of Frontier Medicine, Institute of Medical Science, Graduate School of Medicine, St. Marianna University, Kawasaki, 2168511, Japan.
- Shirokane Sanko Clinic Research Centre, Minato, 1080072, Japan.
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3
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Sokolova V, Miratsky J, Svetlov V, Brenowitz M, Vant J, Lewis TS, Dryden K, Lee G, Sarkar S, Nudler E, Singharoy A, Tan D. Structural mechanism of HP1⍺-dependent transcriptional repression and chromatin compaction. Structure 2024; 32:2094-2106.e6. [PMID: 39383876 PMCID: PMC11560701 DOI: 10.1016/j.str.2024.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 08/12/2024] [Accepted: 09/12/2024] [Indexed: 10/11/2024]
Abstract
Heterochromatin protein 1 (HP1) plays a central role in establishing and maintaining constitutive heterochromatin. However, the mechanisms underlying HP1-nucleosome interactions and their contributions to heterochromatin functions remain elusive. Here, we present the cryoelectron microscopy (cryo-EM) structure of an HP1α dimer bound to an H2A.Z-nucleosome, revealing two distinct HP1α-nucleosome interfaces. The primary HP1α binding site is located at the N terminus of histone H3, specifically at the trimethylated lysine 9 (K9me3) region, while a secondary binding site is situated near histone H2B, close to nucleosome superhelical location 4 (SHL4). Our biochemical data further demonstrates that HP1α binding influences the dynamics of DNA on the nucleosome. It promotes DNA unwrapping near the nucleosome entry and exit sites while concurrently restricting DNA accessibility in the vicinity of SHL4. Our study offers a model for HP1α-mediated heterochromatin maintenance and gene silencing. It also sheds light on the H3K9me-independent role of HP1 in responding to DNA damage.
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Affiliation(s)
- Vladyslava Sokolova
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Jacob Miratsky
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Vladimir Svetlov
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Michael Brenowitz
- Departments of Biochemistry and Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - John Vant
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Tyler S Lewis
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Kelly Dryden
- Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA
| | - Gahyun Lee
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Shayan Sarkar
- Department of Pathology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | - Dongyan Tan
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, USA.
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Song J, Feng Y, Yan J, Wang Y, Yan W, Yang N, Wu T, Liu S, Wang Y, Zheng N, He L, Zhang Y. Computed Tomography Imaging Guided Microenvironment-Responsive Ir@WO 3-x Dual-Catalytic Nanoreactor for Selective Radiosensitization. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2405192. [PMID: 39102342 PMCID: PMC11481196 DOI: 10.1002/advs.202405192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/28/2024] [Indexed: 08/07/2024]
Abstract
Radiotherapy (RT) is often administered, either alone or in combination with other therapies, for most malignancies. However, the degree of tumor oxygenation, damage to adjacent healthy tissues, and inaccurate guidance remain issues that result in discontinuation or failure of RT. Here, a multifunctional therapeutic platform based on Ir@WO3-x is developed which simultaneously addresses these critical issues above for precision radiosensitization. Ir@WO3-x nanoreactors exhibit strong absorption of X-ray, acting as radiosensitizers. Moreover, ultrasmall Ir enzyme-mimic nanocrystals (NCs) are decorated onto the surface of the nanoreactor, where NCs have catalyst-like activity and are sensitive to H2O2 in the tumor microenvironment (TME) under near infrared-II (NIR-II) light stimulation. They efficiently catalyze the conversion of H2O2 to O2, thereby ameliorating hypoxia, inhibiting the expression of HIF-1α, and enhancing RT-induced DNA damage in cancerous tissue, further improving the efficiency of RT. Additionally, in response to high H2O2 levels in TME, the Ir@WO3-x nanoreactor also exerts peroxidase-like activity, boosting exogenous ROS, which increases oxidative damage and enhances ROS-dependent death signaling. Furthermore, Ir@WO3-x can serve as a high-quality computed tomography contrast agent due to its high X-ray attenuation coefficient and generation of pronounced tumor-tissue contrast. This report highlights the potential of advanced health materials to enhance precision therapeutic modalities.
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Affiliation(s)
- Jiayu Song
- Department of Gynecological RadiotherapyHarbin Medical University Cancer HospitalHarbin150001China
- School of Medicine and HealthKey Laboratory of Microsystems and Microstructures ManufacturingHarbin Institute of TechnologyHarbin150001China
| | - Yue Feng
- Department of Gynecological OncologyZhejiang Cancer HospitalZhengzhouZhejiang310022China
| | - Jiazhuo Yan
- Department of Gynecological RadiotherapyHarbin Medical University Cancer HospitalHarbin150001China
| | - Ying Wang
- Department of Gynecological RadiotherapyHarbin Medical University Cancer HospitalHarbin150001China
| | - Weixiao Yan
- School of Medicine and HealthKey Laboratory of Microsystems and Microstructures ManufacturingHarbin Institute of TechnologyHarbin150001China
| | - Nan Yang
- Department of Gynecological RadiotherapyHarbin Medical University Cancer HospitalHarbin150001China
| | - Tusheng Wu
- Department of Gynecological RadiotherapyHarbin Medical University Cancer HospitalHarbin150001China
| | - Sijia Liu
- Department of Gynecological RadiotherapyHarbin Medical University Cancer HospitalHarbin150001China
| | - Yuan Wang
- Department of Gynecological RadiotherapyHarbin Medical University Cancer HospitalHarbin150001China
| | - Nannan Zheng
- School of Medicine and HealthKey Laboratory of Microsystems and Microstructures ManufacturingHarbin Institute of TechnologyHarbin150001China
- Zhengzhou Research InstituteHarbin Institute of TechnologyZhengzhouHenan450000China
| | - Liangcan He
- School of Medicine and HealthKey Laboratory of Microsystems and Microstructures ManufacturingHarbin Institute of TechnologyHarbin150001China
- Zhengzhou Research InstituteHarbin Institute of TechnologyZhengzhouHenan450000China
| | - Yunyan Zhang
- Department of Gynecological RadiotherapyHarbin Medical University Cancer HospitalHarbin150001China
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Zhang J, Sun P, Wu Z, Wu J, Jia J, Zou H, Mo Y, Zhou Z, Liu B, Ao Y, Wang Z. Targeting CK2 eliminates senescent cells and prolongs lifespan in Zmpste24-deficient mice. Cell Death Dis 2024; 15:380. [PMID: 38816370 PMCID: PMC11139886 DOI: 10.1038/s41419-024-06760-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 05/13/2024] [Accepted: 05/17/2024] [Indexed: 06/01/2024]
Abstract
Senescent cell clearance is emerging as a promising strategy for treating age-related diseases. Senolytics are small molecules that promote the clearance of senescent cells; however, senolytics are uncommon and their underlying mechanisms remain largely unknown. Here, we investigated whether genomic instability is a potential target for senolytic. We screened small-molecule kinase inhibitors involved in the DNA damage response (DDR) in Zmpste24-/- mouse embryonic fibroblasts, a progeroid model characterized with impaired DDR and DNA repair. 4,5,6,7-tetrabromo-2-azabenzamidazole (TBB), which specifically inhibits casein kinase 2 (CK2), was selected and discovered to preferentially trigger apoptosis in Zmpste24-/- cells. Mechanistically, inhibition of CK2 abolished the phosphorylation of heterochromatin protein 1α (HP1α), which retarded the dynamic HP1α dissociation from repressive histone mark H3K9me3 and its relocalization with γH2AX to DNA damage sites, suggesting that disrupting heterochromatin remodeling in the initiation of DDR accelerates apoptosis in senescent cells. Furthermore, feeding Zmpste24-deficient mice with TBB alleviated progeroid features and extended their lifespan. Our study identified TBB as a new class senolytic compound that can reduce age-related symptoms and prolong lifespan in progeroid mice.
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Affiliation(s)
- Jie Zhang
- Guangdong Key Laboratory of Genome Stability and Human Disease Prevention, Carson International Cancer Center, Department of Biochemistry & Molecular Biology, School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen, 518055, China
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, 518060, China
- Shenzhen Key Laboratory for Systemic Aging and Intervention, National Engineering Research Center for Biotechnology (Shenzhen), Shenzhen University, Shenzhen, 518055, China
| | - Pengfei Sun
- Guangdong Key Laboratory of Genome Stability and Human Disease Prevention, Carson International Cancer Center, Department of Biochemistry & Molecular Biology, School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen, 518055, China
| | - Zhuping Wu
- Guangdong Key Laboratory of Genome Stability and Human Disease Prevention, Carson International Cancer Center, Department of Biochemistry & Molecular Biology, School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen, 518055, China
| | - Jie Wu
- Guangdong Key Laboratory of Genome Stability and Human Disease Prevention, Carson International Cancer Center, Department of Biochemistry & Molecular Biology, School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen, 518055, China
| | - Jiali Jia
- Guangdong Key Laboratory of Genome Stability and Human Disease Prevention, Carson International Cancer Center, Department of Biochemistry & Molecular Biology, School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen, 518055, China
| | - Haoman Zou
- Guangdong Key Laboratory of Genome Stability and Human Disease Prevention, Carson International Cancer Center, Department of Biochemistry & Molecular Biology, School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen, 518055, China
| | - Yanzhen Mo
- Guangdong Key Laboratory of Genome Stability and Human Disease Prevention, Carson International Cancer Center, Department of Biochemistry & Molecular Biology, School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen, 518055, China
| | - Zhongjun Zhou
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong
| | - Baohua Liu
- Guangdong Key Laboratory of Genome Stability and Human Disease Prevention, Carson International Cancer Center, Department of Biochemistry & Molecular Biology, School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen, 518055, China
- Shenzhen Key Laboratory for Systemic Aging and Intervention, National Engineering Research Center for Biotechnology (Shenzhen), Shenzhen University, Shenzhen, 518055, China
| | - Ying Ao
- Guangdong Key Laboratory of Genome Stability and Human Disease Prevention, Carson International Cancer Center, Department of Biochemistry & Molecular Biology, School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen, 518055, China.
- Shenzhen Key Laboratory for Systemic Aging and Intervention, National Engineering Research Center for Biotechnology (Shenzhen), Shenzhen University, Shenzhen, 518055, China.
| | - Zimei Wang
- Guangdong Key Laboratory of Genome Stability and Human Disease Prevention, Carson International Cancer Center, Department of Biochemistry & Molecular Biology, School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen, 518055, China.
- Shenzhen Key Laboratory for Systemic Aging and Intervention, National Engineering Research Center for Biotechnology (Shenzhen), Shenzhen University, Shenzhen, 518055, China.
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Feng P, Wang Y, Liu N, Chen Y, Hu Y, Huang Z, Liu Y, Zheng S, Jiang T, Xiao X, Dai W, Huang P, Xia Y. High expression of PPP1CC promotes NHEJ-mediated DNA repair leading to radioresistance and poor prognosis in nasopharyngeal carcinoma. Cell Death Differ 2024; 31:683-696. [PMID: 38589496 PMCID: PMC11094031 DOI: 10.1038/s41418-024-01287-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/10/2024] Open
Abstract
Protein phosphatase 1 catalytic subunit gamma (PPP1CC) promotes DNA repair and tumor development and progression, however, its underlying mechanisms remain unclear. This study investigated the molecular mechanism of PPP1CC's involvement in DNA repair and the potential clinical implications. High expression of PPP1CC was significantly correlated with radioresistance and poor prognosis in human nasopharyngeal carcinoma (NPC) patients. The mechanistic study revealed that PPP1CC bound to Ku70/Ku80 heterodimers and activated DNA-PKcs by promoting DNA-PK holoenzyme formation, which enhanced nonhomologous end junction (NHEJ) -mediated DNA repair and led to radioresistance. Importantly, BRCA1-BRCA2-containing complex subunit 3 (BRCC3) interacted with PPP1CC to enhance its stability by removing the K48-linked polyubiquitin chain at Lys234 to prevent PPP1CC degradation. Therefore, BRCC3 helped the overexpressed PPP1CC to maintain its high protein level, thereby sustaining the elevation of DNA repair capacity and radioresistance. Our study identified the molecular mechanism by which PPP1CC promotes NHEJ-mediated DNA repair and radioresistance, suggesting that the BRCC3-PPP1CC-Ku70 axis is a potential therapeutic target to improve the efficacy of radiotherapy.
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Affiliation(s)
- Ping Feng
- State Key Laboratory of Oncology in South China; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy; Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Ying Wang
- State Key Laboratory of Oncology in South China; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy; Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Na Liu
- State Key Laboratory of Oncology in South China; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy; Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Yanming Chen
- The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Yujun Hu
- State Key Laboratory of Oncology in South China; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy; Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Zilu Huang
- State Key Laboratory of Oncology in South China; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy; Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Ya Liu
- State Key Laboratory of Oncology in South China; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy; Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Shuohan Zheng
- State Key Laboratory of Oncology in South China; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy; Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Tongchao Jiang
- State Key Laboratory of Oncology in South China; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy; Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Xiang Xiao
- State Key Laboratory of Oncology in South China; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy; Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Wei Dai
- Department of Clinical Oncology, University of Hong Kong, Hong Kong (SAR), China
- University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Peng Huang
- State Key Laboratory of Oncology in South China; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy; Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
- Metabolic Innovation Center, Sun Yat-sen University, Guangzhou, 510060, China.
| | - Yunfei Xia
- State Key Laboratory of Oncology in South China; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy; Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
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7
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Serafim RB, Cardoso C, Storti CB, da Silva P, Qi H, Parasuram R, Navegante G, Peron JPS, Silva WA, Espreafico EM, Paçó-Larson ML, Price BD, Valente V. HJURP is recruited to double-strand break sites and facilitates DNA repair by promoting chromatin reorganization. Oncogene 2024; 43:804-820. [PMID: 38279062 DOI: 10.1038/s41388-024-02937-1] [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: 03/15/2023] [Revised: 12/21/2023] [Accepted: 01/04/2024] [Indexed: 01/28/2024]
Abstract
HJURP is overexpressed in several cancer types and strongly correlates with patient survival. However, the mechanistic basis underlying the association of HJURP with cancer aggressiveness is not well understood. HJURP promotes the loading of the histone H3 variant, CENP-A, at the centromeric chromatin, epigenetically defining the centromeres and supporting proper chromosome segregation. In addition, HJURP is associated with DNA repair but its function in this process is still scarcely explored. Here, we demonstrate that HJURP is recruited to DSBs through a mechanism requiring chromatin PARylation and promotes epigenetic alterations that favor the execution of DNA repair. Incorporation of HJURP at DSBs promotes turnover of H3K9me3 and HP1, facilitating DNA damage signaling and DSB repair. Moreover, HJURP overexpression in glioma cell lines also affected global structure of heterochromatin independently of DNA damage induction, promoting genome-wide reorganization and assisting DNA damage response. HJURP overexpression therefore extensively alters DNA damage signaling and DSB repair, and also increases radioresistance of glioma cells. Importantly, HJURP expression levels in tumors are also associated with poor response of patients to radiation. Thus, our results enlarge the understanding of HJURP involvement in DNA repair and highlight it as a promising target for the development of adjuvant therapies that sensitize tumor cells to irradiation.
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Affiliation(s)
- Rodolfo B Serafim
- Department of Cellular and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo (USP), Avenida Bandeirantes, 3900, Ribeirão Preto, 14049-900, Brazil
- São Paulo State University (UNESP), School of Pharmaceutical Sciences, Rodovia Araraquara - Jaú, Km 01 - s/n, Campos Ville, Araraquara, SP, 14800-903, Brazil
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Center for Cell-Based Therapy-CEPID/FAPESP, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, 14051-140, Brazil
| | - Cibele Cardoso
- Department of Cellular and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo (USP), Avenida Bandeirantes, 3900, Ribeirão Preto, 14049-900, Brazil
- Center for Cell-Based Therapy-CEPID/FAPESP, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, 14051-140, Brazil
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo (USP), Avenida Bandeirantes, 3900, Ribeirão Preto, 14049-900, Brazil
| | - Camila B Storti
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo (USP), Avenida Bandeirantes, 3900, Ribeirão Preto, 14049-900, Brazil
| | - Patrick da Silva
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Hongyun Qi
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Ramya Parasuram
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Geovana Navegante
- São Paulo State University (UNESP), School of Pharmaceutical Sciences, Rodovia Araraquara - Jaú, Km 01 - s/n, Campos Ville, Araraquara, SP, 14800-903, Brazil
| | - Jean Pierre S Peron
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Wilson A Silva
- Center for Cell-Based Therapy-CEPID/FAPESP, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, 14051-140, Brazil
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo (USP), Avenida Bandeirantes, 3900, Ribeirão Preto, 14049-900, Brazil
| | - Enilza M Espreafico
- Department of Cellular and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo (USP), Avenida Bandeirantes, 3900, Ribeirão Preto, 14049-900, Brazil
| | - Maria L Paçó-Larson
- Department of Cellular and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo (USP), Avenida Bandeirantes, 3900, Ribeirão Preto, 14049-900, Brazil
| | - Brendan D Price
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
| | - Valeria Valente
- Department of Cellular and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo (USP), Avenida Bandeirantes, 3900, Ribeirão Preto, 14049-900, Brazil.
- São Paulo State University (UNESP), School of Pharmaceutical Sciences, Rodovia Araraquara - Jaú, Km 01 - s/n, Campos Ville, Araraquara, SP, 14800-903, Brazil.
- Center for Cell-Based Therapy-CEPID/FAPESP, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, 14051-140, Brazil.
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8
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Sutcu HH, Rassinoux P, Donnio LM, Neuillet D, Vianna F, Gabillot O, Mari PO, Baldeyron C, Giglia-Mari G. Decline of DNA damage response along with myogenic differentiation. Life Sci Alliance 2024; 7:e202302279. [PMID: 37993260 PMCID: PMC10665522 DOI: 10.26508/lsa.202302279] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 11/15/2023] [Accepted: 11/16/2023] [Indexed: 11/24/2023] Open
Abstract
DNA integrity is incessantly confronted to agents inducing DNA lesions. All organisms are equipped with a network of DNA damage response mechanisms that will repair DNA lesions and restore proper cellular activities. Despite DNA repair mechanisms have been revealed in replicating cells, still little is known about how DNA lesions are repaired in postmitotic cells. Muscle fibers are highly specialized postmitotic cells organized in syncytia and they are vulnerable to age-related degeneration and atrophy after radiotherapy treatment. We have studied the DNA repair capacity of muscle fiber nuclei and compared it with the one measured in proliferative myoblasts here. We focused on the DNA repair mechanisms that correct ionizing radiation (IR)-induced lesions, namely the base excision repair, the nonhomologous end joining, and the homologous recombination (HR). We found that in the most differentiated myogenic cells, myotubes, these DNA repair mechanisms present weakened kinetics of recruitment of DNA repair proteins to IR-damaged DNA. For base excision repair and HR, this decline can be linked to reduced steady-state levels of key proteins involved in these processes.
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Affiliation(s)
- Haser H Sutcu
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SERAMED/LRAcc, Fontenay-aux-Roses, France
| | - Phoebe Rassinoux
- Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM) CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, Lyon, France
| | - Lise-Marie Donnio
- Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM) CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, Lyon, France
| | - Damien Neuillet
- Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM) CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, Lyon, France
| | - François Vianna
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LMDN, Saint-Paul-Lez-Durance, France
| | - Olivier Gabillot
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SERAMED/LRAcc, Fontenay-aux-Roses, France
| | - Pierre-Olivier Mari
- Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM) CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, Lyon, France
| | - Céline Baldeyron
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SERAMED/LRAcc, Fontenay-aux-Roses, France
| | - Giuseppina Giglia-Mari
- Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM) CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, Lyon, France
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9
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Guo M, Li X, Li T, Liu R, Pang W, Luo J, Zeng W, Zheng Y. YTHDF2 promotes DNA damage repair by positively regulating the histone methyltransferase SETDB1 in spermatogonia†. Biol Reprod 2024; 110:48-62. [PMID: 37812443 DOI: 10.1093/biolre/ioad136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 09/04/2023] [Accepted: 10/06/2023] [Indexed: 10/10/2023] Open
Abstract
Genomic integrity is critical for sexual reproduction, ensuring correct transmission of parental genetic information to the descendant. To preserve genomic integrity, germ cells have evolved multiple DNA repair mechanisms, together termed as DNA damage response. The RNA N6-methyladenosine is the most abundant mRNA modification in eukaryotic cells, which plays important roles in DNA damage response, and YTH N6-methyladenosine RNA binding protein 2 (YTHDF2) is a well-acknowledged N6-methyladenosine reader protein regulating the mRNA decay and stress response. Despite this, the correlation between YTHDF2 and DNA damage response in germ cells, if any, remains enigmatic. Here, by employing a Ythdf2-conditional knockout mouse model as well as a Ythdf2-null GC-1 mouse spermatogonial cell line, we explored the role and the underlying mechanism for YTHDF2 in spermatogonial DNA damage response. We identified that, despite no evident testicular morphological abnormalities under the normal circumstance, conditional mutation of Ythdf2 in adult male mice sensitized germ cells, including spermatogonia, to etoposide-induced DNA damage. Consistently, Ythdf2-KO GC-1 cells displayed increased sensitivity and apoptosis in response to DNA damage, accompanied by the decreased SET domain bifurcated 1 (SETDB1, a histone methyltransferase) and H3K9me3 levels. The Setdb1 knockdown in GC-1 cells generated a similar phenotype, but its overexpression in Ythdf2-null GC-1 cells alleviated the sensitivity and apoptosis in response to DNA damage. Taken together, these results demonstrate that the N6-methyladenosine reader YTHDF2 promotes DNA damage repair by positively regulating the histone methyltransferase SETDB1 in spermatogonia, which provides novel insights into the mechanisms underlying spermatogonial genome integrity maintenance and therefore contributes to safe reproduction.
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Affiliation(s)
- Ming Guo
- Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xueliang Li
- Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Tianjiao Li
- Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ruifang Liu
- Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Weijun Pang
- Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jun Luo
- Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wenxian Zeng
- Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yi Zheng
- Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
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10
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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] [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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11
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Sokolova V, Miratsky J, Svetlov V, Brenowitz M, Vant J, Lewis T, Dryden K, Lee G, Sarkar S, Nudler E, Singharoy A, Tan D. Structural mechanism of HP1α-dependent transcriptional repression and chromatin compaction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.30.569387. [PMID: 38076844 PMCID: PMC10705452 DOI: 10.1101/2023.11.30.569387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Heterochromatin protein 1 (HP1) plays a central role in establishing and maintaining constitutive heterochromatin. However, the mechanisms underlying HP1-nucleosome interactions and their contributions to heterochromatin functions remain elusive. In this study, we employed a multidisciplinary approach to unravel the interactions between human HP1α and nucleosomes. We have elucidated the cryo-EM structure of an HP1α dimer bound to an H2A.Z nucleosome, revealing that the HP1α dimer interfaces with nucleosomes at two distinct sites. The primary binding site is located at the N-terminus of histone H3, specifically at the trimethylated K9 (K9me3) region, while a novel secondary binding site is situated near histone H2B, close to nucleosome superhelical location 4 (SHL4). Our biochemical data further demonstrates that HP1α binding influences the dynamics of DNA on the nucleosome. It promotes DNA unwrapping near the nucleosome entry and exit sites while concurrently restricting DNA accessibility in the vicinity of SHL4. This study offers a model that explains how HP1α functions in heterochromatin maintenance and gene silencing, particularly in the context of H3K9me-dependent mechanisms. Additionally, it sheds light on the H3K9me-independent role of HP1 in responding to DNA damage.
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Affiliation(s)
- Vladyslava Sokolova
- Department of Pharmacological Sciences, Stony Brook University; Stony Brook, NY, USA
| | - Jacob Miratsky
- School of Molecular Sciences, Arizona State University; Tempe, AZ, USA
| | - Vladimir Svetlov
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Michael Brenowitz
- Departments of Biochemistry and Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - John Vant
- School of Molecular Sciences, Arizona State University; Tempe, AZ, USA
| | - Tyler Lewis
- Department of Pharmacological Sciences, Stony Brook University; Stony Brook, NY, USA
| | - Kelly Dryden
- Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903 USA
| | - Gahyun Lee
- Department of Pharmacological Sciences, Stony Brook University; Stony Brook, NY, USA
| | - Shayan Sarkar
- Department of Pathology, Stony Brook University; Stony Brook, New York, 11794 USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | - Dongyan Tan
- Department of Pharmacological Sciences, Stony Brook University; Stony Brook, NY, USA
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12
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Fischer EF, Pilarczyk G, Hausmann M. Microscopic Analysis of Heterochromatin, Euchromatin and Cohesin in Cancer Cell Models and under Anti-Cancer Treatment. Curr Issues Mol Biol 2023; 45:8152-8172. [PMID: 37886958 PMCID: PMC10605351 DOI: 10.3390/cimb45100515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/01/2023] [Accepted: 10/03/2023] [Indexed: 10/28/2023] Open
Abstract
The spatial organization of euchromatin (EC) and heterochromatin (HC) appears as a cell-type specific network, which seems to have an impact on gene regulation and cell fate. The spatial organization of cohesin should thus also be characteristic for a cell type since it is involved in a TAD (topologically associating domain) formation, and thus in gene regulation or DNA repair processes. Based on the previous hypotheses and results on the general importance of heterochromatin organization on genome functions in particular, the configurations of these organizational units (EC represented by H3K4me3-positive regions, HC represented by H3K9me3-positive regions, cohesins) are investigated in the cell nuclei of different cancer and non-cancerous cell types and under different anti-cancer treatments. Confocal microscopic images of the model cell systems were used and analyzed using analytical processes of quantification created in Fiji, an imaging tool box well established in different fields of science. Human fibroblasts, breast cancer and glioblastoma cells as well as murine embryonal terato-carcinoma cells were used as these cell models and compared according to the different parameters of spatial arrangements. In addition, proliferating, quiescent and from the quiescent state reactivated fibroblasts were analyzed. In some selected cases, the cells were treated with X-rays or azacitidine. Heterogeneous results were obtained by the analyses of the configurations of the three different organizational units: granulation and a loss of H3K4me3-positive regions (EC) occurred after irradiation with 4 Gy or azacitidine treatment. While fibroblasts responded to irradiation with an increase in cohesin and granulation, in breast cancer cells, it resulted in decreases in cohesin and changes in granulation. H3K9me3-positive regions (HC) in fibroblasts experienced increased granulation, whereas in breast cancer cells, the amount of such regions increased. After azacitidine treatment, murine stem cells showed losses of cohesin and granulation and an increase in the granulation of H3K9me3-positive regions. Fibroblasts that were irradiated with 2 Gy only showed irregularities in structural amounts and granulation. Quiescent fibroblasts contained less euchromatin-related H3K4me3-positive signals and cohesin levels as well as higher heterochromatin-related H3K9me3-positive signals than non-quiescent ones. In general, fibroblasts responded more intensely to X-ray irradiation than breast cancer cells. The results indicate the usefulness of model cell systems and show that, in general, characteristic differences initially existing in chromatin and cohesin organizations result in specific responses to anti-cancer treatment.
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Affiliation(s)
| | | | - Michael Hausmann
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany; (E.F.F.); (G.P.)
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13
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Scumaci D, Zheng Q. Epigenetic meets metabolism: novel vulnerabilities to fight cancer. Cell Commun Signal 2023; 21:249. [PMID: 37735413 PMCID: PMC10512595 DOI: 10.1186/s12964-023-01253-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 08/01/2023] [Indexed: 09/23/2023] Open
Abstract
Histones undergo a plethora of post-translational modifications (PTMs) that regulate nucleosome and chromatin dynamics and thus dictate cell fate. Several evidences suggest that the accumulation of epigenetic alterations is one of the key driving forces triggering aberrant cellular proliferation, invasion, metastasis and chemoresistance pathways. Recently a novel class of histone "non-enzymatic covalent modifications" (NECMs), correlating epigenome landscape and metabolic rewiring, have been described. These modifications are tightly related to cell metabolic fitness and are able to impair chromatin architecture. During metabolic reprogramming, the high metabolic flux induces the accumulation of metabolic intermediate and/or by-products able to react with histone tails altering epigenome homeostasis. The accumulation of histone NECMs is a damaging condition that cancer cells counteracts by overexpressing peculiar "eraser" enzymes capable of removing these modifications preserving histones architecture. In this review we explored the well-established NECMs, emphasizing the role of their corresponding eraser enzymes. Additionally, we provide a parterre of drugs aiming to target those eraser enzymes with the intent to propose novel routes of personalized medicine based on the identification of epi-biomarkers which might be selectively targeted for therapy. Video Abstract.
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Affiliation(s)
- Domenica Scumaci
- Research Center On Advanced Biochemistry and Molecular Biology, Magna Græcia University of Catanzaro, 88100, Catanzaro, Italy.
- Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, 88100, Catanzaro, Italy.
| | - Qingfei Zheng
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA.
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA.
- Department of Biological Chemistry and Pharmacology, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA.
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14
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Jiang T, Chen J, Wang Z, Wang X, Ma J, Zhao F, Huang C, Chen Y. miR-4796 enhances the sensitivity of breast cancer cells to ionising radiation by impairing the DNA repair pathway. Breast Cancer 2023; 30:691-702. [PMID: 37460775 DOI: 10.1007/s12282-023-01482-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 07/03/2023] [Indexed: 08/06/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) are important regulators of DNA damage response (DDR) through post-transcriptional regulation on their target genes, which are implicated in DDR and DNA repair (DR). In this study, we investigated the functional roles and target genes of miR-4796 and miR-1287 in breast cancer cells in response to radiation. The molecular mechanism of miR-4796 in regulating the radiosensitivity of breast cancer cells was also elucidated. METHODS Real-time polymerase chain reaction detected miR-4796 and miR-1287 expression; colony formation assay and irradiation therapy tumour xenograft in vivo examined radiosensitising effect; comet assay assessed DNA damage; immunofluorescence imaging determined the formation of γ-H2AX foci; targetscan and RegRNA predicted target mRNAs; luciferase reporter and mutation assays validated target genes; western blotting detected the expression of genes at the protein level; and flow cytometry quantified the activities of nonhomologous end-joining (NHEJ) and homologous recombination (HR). RESULTS The expressions of miR-4796 and miR-1287 were acutely fluctuated in response to ionising radiation. In the absence of radiation, overexpression of miR-1287 dramatically promoted growth of breast cancer cells in vitro and in vivo, whereas overexpression of miR-4796 did not affect cell growth. When under the treatment with radiation, overexpression of miR-4796 suppressed DR and sensitised cancer cells to radiation both in vitro and in vivo. However, such effect was only observed in cell assays in the overexpressed miR-1287 group, and not confirmed in vivo. We therefore further explored the molecular mechanism of action of miR-4796, and found that miR-4796 targeted multiple components of DDR and DR, including ATM, BRCA1, PARP and RAD51. Moreover, overexpression of miR-4796 inhibited the expression of these DDR components at the protein level. In addition, miR-4796 inhibited HR and NHEJ repair pathways and aggravated radiation-induced DNA damage. CONCLUSIONS The findings here suggest that miR-4796 can enhance radiation-induced cell death by directly targeting multiple DDR components, and repress NHEJ and HR DNA repair pathways. miR-4796 can act as an effective radiation sensitising agent.
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Affiliation(s)
- Ting Jiang
- Department of Cell Biology and Genetics, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Jinfeng Chen
- Target Discovery Institute, NDM Research Building, Oxford Ludwig Institute of Cancer Research, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Zhenzhen Wang
- Department of Cell Biology and Genetics, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Xiaofei Wang
- Biomedical Experimental Centre, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Jun Ma
- Department of Radiology, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Fei Zhao
- Department of Cell Biology and Genetics, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
- Institute of Genetics and Developmental Biology, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Chen Huang
- Department of Cell Biology and Genetics, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China.
- Institute of Genetics and Developmental Biology, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China.
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China.
| | - Yanke Chen
- Department of Cell Biology and Genetics, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China.
- Institute of Genetics and Developmental Biology, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China.
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China.
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15
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Kuroda Y, Iwata-Otsubo A, Dias KR, Temple SEL, Nagao K, De Hayr L, Zhu Y, Isobe SY, Nishibuchi G, Fiordaliso SK, Fujita Y, Rippert AL, Baker SW, Leung ML, Koboldt DC, Harman A, Keena BA, Kazama I, Subramanian GM, Manickam K, Schmalz B, Latsko M, Zackai EH, Edwards M, Evans CA, Dulik MC, Buckley MF, Yamashita T, O'Brien WT, Harvey RJ, Obuse C, Roscioli T, Izumi K. Dominant-negative variants in CBX1 cause a neurodevelopmental disorder. Genet Med 2023; 25:100861. [PMID: 37087635 DOI: 10.1016/j.gim.2023.100861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 04/16/2023] [Accepted: 04/16/2023] [Indexed: 04/24/2023] Open
Abstract
PURPOSE This study aimed to establish variants in CBX1, encoding heterochromatin protein 1β (HP1β), as a cause of a novel syndromic neurodevelopmental disorder. METHODS Patients with CBX1 variants were identified, and clinician researchers were connected using GeneMatcher and physician referrals. Clinical histories were collected from each patient. To investigate the pathogenicity of identified variants, we performed in vitro cellular assays and neurobehavioral and cytological analyses of neuronal cells obtained from newly generated Cbx1 mutant mouse lines. RESULTS In 3 unrelated individuals with developmental delay, hypotonia, and autistic features, we identified heterozygous de novo variants in CBX1. The identified variants were in the chromodomain, the functional domain of HP1β, which mediates interactions with chromatin. Cbx1 chromodomain mutant mice displayed increased latency-to-peak response, suggesting the possibility of synaptic delay or myelination deficits. Cytological and chromatin immunoprecipitation experiments confirmed the reduction of mutant HP1β binding to heterochromatin, whereas HP1β interactome analysis demonstrated that the majority of HP1β-interacting proteins remained unchanged between the wild-type and mutant HP1β. CONCLUSION These collective findings confirm the role of CBX1 in developmental disabilities through the disruption of HP1β chromatin binding during neurocognitive development. Because HP1β forms homodimers and heterodimers, mutant HP1β likely sequesters wild-type HP1β and other HP1 proteins, exerting dominant-negative effects.
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Affiliation(s)
- Yukiko Kuroda
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Aiko Iwata-Otsubo
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Kerith-Rae Dias
- Randwick Genomics Laboratory, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW, Australia; Neuroscience Research Australia (NeuRA) and Prince of Wales Clinical School, University of New South Wales, Kensington, NSW, Australia
| | - Suzanna E L Temple
- Randwick Genomics Laboratory, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW, Australia; Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Koji Nagao
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Lachlan De Hayr
- School of Health, University of the Sunshine Coast, Maroochydore, QLD, Australia; Sunshine Coast Health Institute, Birtinya, QLD, Australia
| | - Ying Zhu
- Randwick Genomics Laboratory, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Shin-Ya Isobe
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Gohei Nishibuchi
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Sarah K Fiordaliso
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Yuki Fujita
- Department of Molecular Neuroscience, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Alyssa L Rippert
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Samuel W Baker
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Marco L Leung
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH; Department of Pathology, The Ohio State University College of Medicine, Columbus, OH
| | - Daniel C Koboldt
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH
| | - Adele Harman
- Transgenic core, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Beth A Keena
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Izumi Kazama
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Kandamurugu Manickam
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH; Division of Genetic and Genomic Medicine, Nationwide Children's Hospital, Columbus, OH
| | - Betsy Schmalz
- Division of Genetic and Genomic Medicine, Nationwide Children's Hospital, Columbus, OH
| | - Maeson Latsko
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH
| | - Elaine H Zackai
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA; Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Matt Edwards
- Hunter Genetics, Newcastle, NSW, Australia; University of Western Sydney School of Medicine, Sydney, NSW, Australia
| | - Carey-Anne Evans
- Randwick Genomics Laboratory, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW, Australia; Neuroscience Research Australia (NeuRA) and Prince of Wales Clinical School, University of New South Wales, Kensington, NSW, Australia
| | - Matthew C Dulik
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Michael F Buckley
- Randwick Genomics Laboratory, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Toshihide Yamashita
- Department of Molecular Neuroscience, Graduate School of Medicine, Osaka University, Suita, Japan
| | - W Timothy O'Brien
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Robert J Harvey
- School of Health, University of the Sunshine Coast, Maroochydore, QLD, Australia; Sunshine Coast Health Institute, Birtinya, QLD, Australia
| | - Chikashi Obuse
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Tony Roscioli
- Randwick Genomics Laboratory, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW, Australia; Neuroscience Research Australia (NeuRA) and Prince of Wales Clinical School, University of New South Wales, Kensington, NSW, Australia
| | - Kosuke Izumi
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA; Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA; Roberts Individualized Medical Genetics Center, The Children's Hospital of Philadelphia, Philadelphia, PA; Laboratory of Rare Disease Research, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan; Division of Genetics and Metabolism, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX.
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16
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Na J, Lee CH, Chung JK, Youn H. Overexpression of Both Human Sodium Iodide Symporter (NIS) and BRG1-Bromodomain Synergistically Enhances Radioiodine Sensitivity by Stabilizing p53 through NPM1 Expression. Int J Mol Sci 2023; 24:ijms24032761. [PMID: 36769088 PMCID: PMC9917390 DOI: 10.3390/ijms24032761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/19/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023] Open
Abstract
Improved therapeutic strategies are required to minimize side effects associated with radioiodine gene therapy to avoid unnecessary damage to normal cells and radiation-induced secondary malignancies. We previously reported that codon-optimized sodium iodide symporter (oNIS) enhances absorption of I-131 and that the brahma-associated gene 1 bromodomain (BRG1-BRD) causes inefficient DNA damage repair after high-energy X-ray therapy. To increase the therapeutic effect without applying excessive radiation, we considered the combination of oNIS and BRG1-BRD as gene therapy for the most effective radioiodine treatment. The antitumor effect of I-131 with oNIS or oNIS+BRD expression was examined by tumor xenograft models along with functional assays at the cellular level. The synergistic effect of both BRG1-BRD and oNIS gene overexpression resulted in more DNA double-strand breaks and led to reduced cell proliferation/survival rates after I-131 treatment, which was mediated by the p53/p21 pathway. We found increased p53, p21, and nucleophosmin 1 (NPM1) in oNIS- and BRD-expressing cells following I-131 treatment, even though the remaining levels of citrulline and protein arginine deiminase 4 (PAD4) were unchanged at the protein level.
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Affiliation(s)
- Juri Na
- Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Correspondence: (J.N.); (H.Y.); Tel.: +44-1752-431038 (J.N.); +82-2-3668-7026 (H.Y.)
| | - Chul-Hee Lee
- Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - June-Key Chung
- Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Hyewon Youn
- Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Cancer Imaging Centre, Seoul National University Hospital, Seoul 03080, Republic of Korea
- Correspondence: (J.N.); (H.Y.); Tel.: +44-1752-431038 (J.N.); +82-2-3668-7026 (H.Y.)
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17
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Effectiveness of Flattening-Filter-Free versus Flattened Beams in V79 and Glioblastoma Patient-Derived Stem-like Cells. Int J Mol Sci 2023; 24:ijms24021107. [PMID: 36674623 PMCID: PMC9861147 DOI: 10.3390/ijms24021107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/31/2022] [Accepted: 01/03/2023] [Indexed: 01/09/2023] Open
Abstract
Literature data on the administration of conventional high-dose beams with (FF) or without flattening filters (FFF) show conflicting results on biological effects at the cellular level. To contribute to this field, we irradiated V79 Chinese hamster lung fibroblasts and two patient-derived glioblastoma stem-like cell lines (GSCs-named #1 and #83) using a clinical 10 MV accelerator with FF (at 4 Gy/min) and FFF (at two dose rates 4 and 24 Gy/min). Cell killing and DNA damage induction, determined using the γ-H2AX assay, and gene expression were studied. No significant differences in the early survival of V79 cells were observed as a function of dose rates and FF or FFF beams, while a trend of reduction in late survival was observed at the highest dose rate with the FFF beam. GSCs showed similar survival levels as a function of dose rates, both delivered in the FFF regimen. The amount of DNA damage measured for both dose rates after 2 h was much higher in line #1 than in line #83, with statistically significant differences between the two dose rates only in line #83. The gene expression analysis of the two GSC lines indicates gene signatures mimicking the prognosis of glioblastoma (GBM) patients derived from a public database. Overall, the results support the current use of FFF and highlight the possibility of identifying patients with candidate gene signatures that could benefit from irradiation with FFF beams at a high dose rate.
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18
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Naqvi AAT, Rizvi SAM, Hassan MI. Pan-cancer analysis of Chromobox (CBX) genes for prognostic significance and cancer classification. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166561. [PMID: 36183965 DOI: 10.1016/j.bbadis.2022.166561] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 09/15/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022]
Abstract
Polycomb group of proteins play a significant role in chromatin remodelling essential for epigenetic regulation of transcription. Chromobox (CBX) gene family is an important part of canonical polycomb repressive complex 1 (PRC1), belonging to the polycomb group involved in chromatin remodelling. Aberrations in CBX expression are linked to various cancers. To assess their biomarker significance, we performed a pan-cancer analysis of CBX mRNA levels in 18 cancer types. We also performed cancer classification using CBX genes as distinctive features for machine learning model development. Logistic regression (L.R.), support vector machine (SVM), random forest (R.F.), decision tree (D.T.), and XGBoost (XGB) algorithms for model training and classification. The expression of CBX genes was significantly changed in four cancer types, i.e., cholangiocarcinoma (CHOL), colon adenocarcinoma (COAD), lung adenocarcinoma (LUAD), and lung squamous cell carcinoma (LUSC). The fold change (FC) values suggest that CBX2 was significantly upregulated in CHOL (FC = 1.639), COAD (FC = 1.734), and LUSC (FC = 1.506). On the other hand, CBX7 was found downregulated in COAD (FC = -1.209), LUAD (FC = -1.190), and LUSC (FC = -1.214). The performance of machine learning models for classification was excellent. L.R., R.F., SVM, and XGB obtained a prediction accuracy of 100 % for most cancers. However, D.T. performed comparatively poorly in prediction accuracy. The results suggest that CBX expression is significantly altered in all the cancers studied; therefore, they might be treated as potential biomarkers for therapeutic intervention of these cancers.
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Affiliation(s)
| | | | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India.
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19
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Zhao Y, Huang S, Tan X, Long L, He Q, Liang X, Bai J, Li Q, Lin J, Li Y, Liu N, Ma J, Chen Y. N 6 -Methyladenosine-Modified CBX1 Regulates Nasopharyngeal Carcinoma Progression Through Heterochromatin Formation and STAT1 Activation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2205091. [PMID: 36310139 PMCID: PMC9798977 DOI: 10.1002/advs.202205091] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Indexed: 05/16/2023]
Abstract
Epitranscriptomic remodeling such as N6 -methyladenosine (m6 A) modification plays a critical role in tumor development. However, little is known about the underlying mechanisms connecting m6 A modification and nasopharyngeal carcinoma (NPC) progression. Here, CBX1 is identified, a histone methylation regulator, to be significantly upregulated with m6 A hypomethylation in metastatic NPC tissues. The m6 A-modified CBX1 mRNA transcript is recognized and destabilized by the m6 A reader YTHDF3. Furthermore, it is revealed that CBX1 promotes NPC cell migration, invasion, and proliferation through transcriptional repression of MAP7 via H3K9me3-mediated heterochromatin formation. In addition to its oncogenic effect, CBX1 can facilitate immune evasion through IFN-γ-STAT1 signaling-mediated PD-L1 upregulation. Clinically, CBX1 serves as an independent predictor for unfavorable prognosis in NPC patients. The results reveal a crosstalk between epitranscriptomic and epigenetic regulation in NPC progression, and shed light on the functions of CBX1 in tumorigenesis and immunomodulation, which may provide an appealing therapeutic target in NPC.
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Affiliation(s)
- Yin Zhao
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy651 Dongfeng Road EastGuangzhouGuangdong510060China
| | - Shengyan Huang
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy651 Dongfeng Road EastGuangzhouGuangdong510060China
| | - Xirong Tan
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy651 Dongfeng Road EastGuangzhouGuangdong510060China
| | - Liufen Long
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy651 Dongfeng Road EastGuangzhouGuangdong510060China
| | - Qingmei He
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy651 Dongfeng Road EastGuangzhouGuangdong510060China
| | - Xiaoyu Liang
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy651 Dongfeng Road EastGuangzhouGuangdong510060China
| | - Jiewen Bai
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy651 Dongfeng Road EastGuangzhouGuangdong510060China
| | - Qingjie Li
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy651 Dongfeng Road EastGuangzhouGuangdong510060China
| | - Jiayi Lin
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy651 Dongfeng Road EastGuangzhouGuangdong510060China
| | - Yingqin Li
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy651 Dongfeng Road EastGuangzhouGuangdong510060China
| | - Na Liu
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy651 Dongfeng Road EastGuangzhouGuangdong510060China
| | - Jun Ma
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy651 Dongfeng Road EastGuangzhouGuangdong510060China
| | - Yupei Chen
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy651 Dongfeng Road EastGuangzhouGuangdong510060China
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20
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Hou J, Yang Y, Gao H, Ouyang T, Liu Q, Ding R, Kan H. Systematic investigation of the clinical significance and prognostic value of the CBXs in esophageal cancer. Medicine (Baltimore) 2022; 101:e30888. [PMID: 36221371 PMCID: PMC9542684 DOI: 10.1097/md.0000000000030888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 09/01/2022] [Indexed: 11/05/2022] Open
Abstract
Esophageal cancer (ESCA), one of the most aggressive malignant tumors, has been announced to be the ninth most common cancer and the sixth leading cause of cancer-related death in the world. Chromobox family members (CBXs) are important epigenetic regulators which are related with the transcription of target genes. The role of CBXs in carcinomas has been reported in many studies. However, the function and prognostic value of different CBXs in ESCA are still largely unknown. In this article, we first performed differential expression analysis through several methods including Oncomine and Gene Expression Profiling Interactive Analysis. The results led us to determine the differential expression of CBXs in pan-cancer, especially ESCA. Then we evaluated the prognostic value of different CBX messenger RNA (mRNA) expression in patients with ESCA through the Kaplan-Meier plotter and the Human Protein Atlas database. In addition, we used cBioPortal to explore all genetic alterations and mutations in the CBXs in ESCA. Simultaneously, the correlation between its expression and the level of immune infiltration of ESCA was visualized by TIMER. Finally, the biological function of CBXs in ESCA is obtained through Biological Enrichment Analysis including gene ontology and Kyoto Encyclopedia of Genes and Genomes. The expression levels of CBX3/4/5 and CBX8 in ESCA tissues increased significantly and the expression level of CBX7 decreased through differential expression analysis. Additionally, CBX1 is significantly related to the clinical cancer stage and disease-free survival of ESCA patients. The high mRNA expression of CBX4 is related to the short overall survival of patients with esophageal squamous cell carcinoma, and the high mRNA expression of CBX3/7/8 is related to the short overall survival of patients with esophageal adenocarcinoma, indicating that CBX1/3/4/7/8 may be a potential prognostic biomarker for the survival of ESCA patients. Besides, the expression of CBXs is significantly related to the infiltration of a variety of immune cells, including six types of CD4-positive T-lymphocytes, macrophages, neutrophils, bursindependentlymphocyte, CD8-positive T-lymphocytes cells and dendritic cells in ESCA. Moreover, we found that CBXs are mainly associated with the inhibition of cell cycle and apoptosis pathway. Further, enrichment analysis indicated that CBXs and correlated genes were enriched in mismatch repair, DNA replication, cancer pathways, and spliceosomes. Our research may provide new insights into the choice of prognosis biomarkers of the CBXs in ESCA.
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Affiliation(s)
- Jun Hou
- School of Medical Informatics Engineering, Anhui University of Chinese Medicine, Hefei, China
| | - Yinfeng Yang
- School of Medical Informatics Engineering, Anhui University of Chinese Medicine, Hefei, China
- Anhui Computer Application Research Institute of Chinese Medicine, China Academy of Chinese Medical Sciences, Hefei, China
| | - Honglei Gao
- School of Medical Informatics Engineering, Anhui University of Chinese Medicine, Hefei, China
| | - Ting Ouyang
- School of Medical Informatics Engineering, Anhui University of Chinese Medicine, Hefei, China
| | - Qiwei Liu
- School of Medical Informatics Engineering, Anhui University of Chinese Medicine, Hefei, China
| | - Ran Ding
- School of Medical Informatics Engineering, Anhui University of Chinese Medicine, Hefei, China
| | - Hongxing Kan
- School of Medical Informatics Engineering, Anhui University of Chinese Medicine, Hefei, China
- Anhui Computer Application Research Institute of Chinese Medicine, China Academy of Chinese Medical Sciences, Hefei, China
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21
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Roemer A, Mohammed L, Strickfaden H, Underhill DA, Hendzel MJ. Mechanisms governing the accessibility of DNA damage proteins to constitutive heterochromatin. Front Genet 2022; 13:876862. [PMID: 36092926 PMCID: PMC9458887 DOI: 10.3389/fgene.2022.876862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 07/18/2022] [Indexed: 12/05/2022] Open
Abstract
Chromatin is thought to regulate the accessibility of the underlying DNA sequence to machinery that transcribes and repairs the DNA. Heterochromatin is chromatin that maintains a sufficiently high density of DNA packing to be visible by light microscopy throughout the cell cycle and is thought to be most restrictive to transcription. Several studies have suggested that larger proteins and protein complexes are attenuated in their access to heterochromatin. In addition, heterochromatin domains may be associated with phase separated liquid condensates adding further complexity to the regulation of protein concentration within chromocenters. This provides a solvent environment distinct from the nucleoplasm, and proteins that are not size restricted in accessing this liquid environment may partition between the nucleoplasm and heterochromatin based on relative solubility. In this study, we assessed the accessibility of constitutive heterochromatin in mouse cells, which is organized into large and easily identifiable chromocenters, to fluorescently tagged DNA damage response proteins. We find that proteins larger than the expected 10 nm size limit can access the interior of heterochromatin. We find that the sensor proteins Ku70 and PARP1 enrich in mouse chromocenters. At the same time, MRE11 shows variability within an asynchronous population that ranges from depleted to enriched but is primarily homogeneously distribution between chromocenters and the nucleoplasm. While larger downstream proteins such as ATM, BRCA1, and 53BP1 are commonly depleted in chromocenters, they show a wide range of concentrations, with none being depleted beyond approximately 75%. Contradicting exclusively size-dependent accessibility, many smaller proteins, including EGFP, are also depleted in chromocenters. Our results are consistent with minimal size-dependent selectivity but a distinct solvent environment explaining reduced concentrations of diffusing nucleoplasmic proteins within the volume of the chromocenter.
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22
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ITGA2 overexpression inhibits DNA repair and confers sensitivity to radiotherapies in pancreatic cancer. Cancer Lett 2022; 547:215855. [PMID: 35998796 DOI: 10.1016/j.canlet.2022.215855] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/26/2022] [Accepted: 07/30/2022] [Indexed: 11/20/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a dismal disease with a 5-year survival rate of less than 10%, despite the recent advances in chemoradiotherapy. The sensitivity of the PDAC patients to chemoradiotherapy varies widely, especially to radiotherapy, suggesting the need for more elucidation of the underlying mechanisms. In this study, a novel function of the nuclear ITGA2, the alpha subunit of transmembrane collagen receptor integrin alpha-2/beta-1, regulating the DNA damage response (DDR), was identified. First, analyzing The Cancer Genome Atlas (TCGA) PDAC data set indicated that the expression status of ITGA2 was negatively correlated with the genome stability parameters. The study further demonstrated that ITGA2 specially inhibited the activity of the non-homologous end joining (NHEJ) pathway and conferred the sensitivity to radiotherapy in PDAC by restraining the recruitment of DNA-dependent protein kinase catalytic subunit (DNA-PKcs) to Ku70/80 heterodimer during DDR. Considering the overexpression of ITGA2 and its associated with the poor prognosis of PDAC patients, this study suggested that the ITGA2 expression status could be used as an indicator for radiotherapy and DNA damage reagents, and the radiotherapy in combination with the overexpression of ITGA2 might be a viable treatment strategy for the PDAC patients.
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23
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Firnau MB, Brieger A. CK2 and the Hallmarks of Cancer. Biomedicines 2022; 10:1987. [PMID: 36009534 PMCID: PMC9405757 DOI: 10.3390/biomedicines10081987] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 08/08/2022] [Accepted: 08/10/2022] [Indexed: 11/29/2022] Open
Abstract
Cancer is a leading cause of death worldwide. Casein kinase 2 (CK2) is commonly dysregulated in cancer, impacting diverse molecular pathways. CK2 is a highly conserved serine/threonine kinase, constitutively active and ubiquitously expressed in eukaryotes. With over 500 known substrates and being estimated to be responsible for up to 10% of the human phosphoproteome, it is of significant importance. A broad spectrum of diverse types of cancer cells has been already shown to rely on disturbed CK2 levels for their survival. The hallmarks of cancer provide a rationale for understanding cancer's common traits. They constitute the maintenance of proliferative signaling, evasion of growth suppressors, resisting cell death, enabling of replicative immortality, induction of angiogenesis, the activation of invasion and metastasis, as well as avoidance of immune destruction and dysregulation of cellular energetics. In this work, we have compiled evidence from the literature suggesting that CK2 modulates all hallmarks of cancer, thereby promoting oncogenesis and operating as a cancer driver by creating a cellular environment favorable to neoplasia.
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Affiliation(s)
| | - Angela Brieger
- Department of Internal Medicine I, Biomedical Research Laboratory, University Hospital Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
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24
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Locatelli M, Lawrimore J, Lin H, Sanaullah S, Seitz C, Segall D, Kefer P, Salvador Moreno N, Lietz B, Anderson R, Holmes J, Yuan C, Holzwarth G, Bloom KS, Liu J, Bonin K, Vidi PA. DNA damage reduces heterogeneity and coherence of chromatin motions. Proc Natl Acad Sci U S A 2022; 119:e2205166119. [PMID: 35858349 PMCID: PMC9304018 DOI: 10.1073/pnas.2205166119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/07/2022] [Indexed: 01/14/2023] Open
Abstract
Chromatin motions depend on and may regulate genome functions, in particular the DNA damage response. In yeast, DNA double-strand breaks (DSBs) globally increase chromatin diffusion, whereas in higher eukaryotes the impact of DSBs on chromatin dynamics is more nuanced. We mapped the motions of chromatin microdomains in mammalian cells using diffractive optics and photoactivatable chromatin probes and found a high level of spatial heterogeneity. DNA damage reduces heterogeneity and imposes spatially defined shifts in motions: Distal to DNA breaks, chromatin motions are globally reduced, whereas chromatin retains higher mobility at break sites. These effects are driven by context-dependent changes in chromatin compaction. Photoactivated lattices of chromatin microdomains are ideal to quantify microscale coupling of chromatin motion. We measured correlation distances up to 2 µm in the cell nucleus, spanning chromosome territories, and speculate that this correlation distance between chromatin microdomains corresponds to the physical separation of A and B compartments identified in chromosome conformation capture experiments. After DNA damage, chromatin motions become less correlated, a phenomenon driven by phase separation at DSBs. Our data indicate tight spatial control of chromatin motions after genomic insults, which may facilitate repair at the break sites and prevent deleterious contacts of DSBs, thereby reducing the risk of genomic rearrangements.
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Affiliation(s)
- Maëlle Locatelli
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157
| | - Josh Lawrimore
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Hua Lin
- Department of Physics, Indiana University–Purdue University Indianapolis, Indianapolis, IN 46202
| | - Sarvath Sanaullah
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157
| | - Clayton Seitz
- Department of Physics, Indiana University–Purdue University Indianapolis, Indianapolis, IN 46202
| | - Dave Segall
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109
| | - Paul Kefer
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109
| | - Naike Salvador Moreno
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157
| | - Benton Lietz
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157
| | - Rebecca Anderson
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157
| | - Julia Holmes
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157
| | - Chongli Yuan
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47907
| | - George Holzwarth
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109
| | - Kerry S. Bloom
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Jing Liu
- Department of Physics, Indiana University–Purdue University Indianapolis, Indianapolis, IN 46202
- Melvin and Bren Simon Comprehensive Cancer Center, Indiana University, Indianapolis, IN 46202
- Center for Computational Biology and Bioinformatics, Indiana University, Indianapolis, IN 46202
| | - Keith Bonin
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109
- Atrium Health Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC 27157
| | - Pierre-Alexandre Vidi
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157
- Atrium Health Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC 27157
- Laboratoire InGenO, Institut de Cancérologie de l’Ouest, 49055 Angers, France
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25
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Chomiak AA, Guo Y, Kopsidas CA, McDaniel DP, Lowe CC, Pan H, Zhou X, Zhou Q, Doughty ML, Feng Y. Nde1 is required for heterochromatin compaction and stability in neocortical neurons. iScience 2022; 25:104354. [PMID: 35601919 PMCID: PMC9121328 DOI: 10.1016/j.isci.2022.104354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 03/28/2022] [Accepted: 04/29/2022] [Indexed: 11/20/2022] Open
Abstract
The NDE1 gene encodes a scaffold protein essential for brain development. Although biallelic NDE1 loss of function (LOF) causes microcephaly with profound mental retardation, NDE1 missense mutations and copy number variations are associated with multiple neuropsychiatric disorders. However, the etiology of the diverse phenotypes resulting from NDE1 aberrations remains elusive. Here we demonstrate Nde1 controls neurogenesis through facilitating H4K20 trimethylation-mediated heterochromatin compaction. This mechanism patterns diverse chromatin landscapes and stabilizes constitutive heterochromatin of neocortical neurons. We demonstrate that NDE1 can undergo dynamic liquid-liquid phase separation, partitioning to the nucleus and interacting with pericentromeric and centromeric satellite repeats. Nde1 LOF results in nuclear architecture aberrations and DNA double-strand breaks, as well as instability and derepression of pericentromeric satellite repeats in neocortical neurons. These findings uncover a pivotal role of NDE1/Nde1 in establishing and protecting neuronal heterochromatin. They suggest that heterochromatin instability predisposes a wide range of brain dysfunction.
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Affiliation(s)
- Alison A. Chomiak
- Department of Neurology, Northwestern University Feinberg School of Medicine, 303 E. Superior Street, Chicago, IL 60611, USA
| | - Yan Guo
- Department of Neurology, Northwestern University Feinberg School of Medicine, 303 E. Superior Street, Chicago, IL 60611, USA
| | - Caroline A. Kopsidas
- Department of Biochemistry and Molecular Biology, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Dennis P. McDaniel
- Biomedical Instrumentation Center, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Clara C. Lowe
- Department of Biochemistry and Molecular Biology, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Hongna Pan
- Department of Biochemistry and Molecular Biology, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Xiaoming Zhou
- Department of Medicine, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Qiong Zhou
- Department of Anatomy, Physiology, and Genetics, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Martin L. Doughty
- Department of Anatomy, Physiology, and Genetics, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Yuanyi Feng
- Department of Biochemistry and Molecular Biology, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
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26
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Song H, Shen R, Liu X, Yang X, Xie K, Guo Z, Wang D. Histone post-translational modification and the DNA damage response. Genes Dis 2022. [DOI: 10.1016/j.gendis.2022.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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27
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Rawal CC, Butova NL, Mitra A, Chiolo I. An Expanding Toolkit for Heterochromatin Repair Studies. Genes (Basel) 2022; 13:genes13030529. [PMID: 35328082 PMCID: PMC8955653 DOI: 10.3390/genes13030529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 02/28/2022] [Accepted: 03/02/2022] [Indexed: 12/04/2022] Open
Abstract
Pericentromeric heterochromatin is mostly composed of repetitive DNA sequences prone to aberrant recombination. Cells have developed highly specialized mechanisms to enable ‘safe’ homologous recombination (HR) repair while preventing aberrant recombination in this domain. Understanding heterochromatin repair responses is essential to understanding the critical mechanisms responsible for genome integrity and tumor suppression. Here, we review the tools, approaches, and methods currently available to investigate double-strand break (DSB) repair in pericentromeric regions, and also suggest how technologies recently developed for euchromatin repair studies can be adapted to characterize responses in heterochromatin. With this ever-growing toolkit, we are witnessing exciting progress in our understanding of how the ‘dark matter’ of the genome is repaired, greatly improving our understanding of genome stability mechanisms.
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28
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Jeon YH, Kim GW, Kim SY, Yi SA, Yoo J, Kim JY, Lee SW, Kwon SH. Heterochromatin Protein 1: A Multiplayer in Cancer Progression. Cancers (Basel) 2022; 14:cancers14030763. [PMID: 35159030 PMCID: PMC8833910 DOI: 10.3390/cancers14030763] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 01/28/2022] [Accepted: 01/29/2022] [Indexed: 11/16/2022] Open
Abstract
Dysregulation of epigenetic mechanisms as well as genomic mutations contribute to the initiation and progression of cancer. In addition to histone code writers, including histone lysine methyltransferase (KMT), and histone code erasers, including histone lysine demethylase (KDM), histone code reader proteins such as HP1 are associated with abnormal chromatin regulation in human diseases. Heterochromatin protein 1 (HP1) recognizes histone H3 lysine 9 methylation and broadly affects chromatin biology, such as heterochromatin formation and maintenance, transcriptional regulation, DNA repair, chromatin remodeling, and chromosomal segregation. Molecular functions of HP1 proteins have been extensively studied, although their exact roles in diseases require further study. Here, we comprehensively review the studies that have revealed the altered expression of HP1 and its functions in tumorigenesis. In particular, the distinctive effects of each HP1 subtype, namely HP1α, HP1β, and HP1γ, have been thoroughly explored in various cancer types. We also highlight how HP1 can serve as a potential biomarker for cancer prognosis and therapeutic target for cancer patients.
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Affiliation(s)
- Yu Hyun Jeon
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Korea; (Y.H.J.); (G.W.K.); (S.Y.K.); (J.Y.); (J.Y.K.); (S.W.L.)
| | - Go Woon Kim
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Korea; (Y.H.J.); (G.W.K.); (S.Y.K.); (J.Y.); (J.Y.K.); (S.W.L.)
| | - So Yeon Kim
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Korea; (Y.H.J.); (G.W.K.); (S.Y.K.); (J.Y.); (J.Y.K.); (S.W.L.)
| | - Sang Ah Yi
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea;
| | - Jung Yoo
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Korea; (Y.H.J.); (G.W.K.); (S.Y.K.); (J.Y.); (J.Y.K.); (S.W.L.)
| | - Ji Yoon Kim
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Korea; (Y.H.J.); (G.W.K.); (S.Y.K.); (J.Y.); (J.Y.K.); (S.W.L.)
| | - Sang Wu Lee
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Korea; (Y.H.J.); (G.W.K.); (S.Y.K.); (J.Y.); (J.Y.K.); (S.W.L.)
| | - So Hee Kwon
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Korea; (Y.H.J.); (G.W.K.); (S.Y.K.); (J.Y.); (J.Y.K.); (S.W.L.)
- Correspondence: ; Tel.: +82-32-749-4513
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29
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Kieffer SR, Lowndes NF. Immediate-Early, Early, and Late Responses to DNA Double Stranded Breaks. Front Genet 2022; 13:793884. [PMID: 35173769 PMCID: PMC8841529 DOI: 10.3389/fgene.2022.793884] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/10/2022] [Indexed: 12/18/2022] Open
Abstract
Loss or rearrangement of genetic information can result from incorrect responses to DNA double strand breaks (DSBs). The cellular responses to DSBs encompass a range of highly coordinated events designed to detect and respond appropriately to the damage, thereby preserving genomic integrity. In analogy with events occurring during viral infection, we appropriate the terms Immediate-Early, Early, and Late to describe the pre-repair responses to DSBs. A distinguishing feature of the Immediate-Early response is that the large protein condensates that form during the Early and Late response and are resolved upon repair, termed foci, are not visible. The Immediate-Early response encompasses initial lesion sensing, involving poly (ADP-ribose) polymerases (PARPs), KU70/80, and MRN, as well as rapid repair by so-called ‘fast-kinetic’ canonical non-homologous end joining (cNHEJ). Initial binding of PARPs and the KU70/80 complex to breaks appears to be mutually exclusive at easily ligatable DSBs that are repaired efficiently by fast-kinetic cNHEJ; a process that is PARP-, ATM-, 53BP1-, Artemis-, and resection-independent. However, at more complex breaks requiring processing, the Immediate-Early response involving PARPs and the ensuing highly dynamic PARylation (polyADP ribosylation) of many substrates may aid recruitment of both KU70/80 and MRN to DSBs. Complex DSBs rely upon the Early response, largely defined by ATM-dependent focal recruitment of many signalling molecules into large condensates, and regulated by complex chromatin dynamics. Finally, the Late response integrates information from cell cycle phase, chromatin context, and type of DSB to determine appropriate pathway choice. Critical to pathway choice is the recruitment of p53 binding protein 1 (53BP1) and breast cancer associated 1 (BRCA1). However, additional factors recruited throughout the DSB response also impact upon pathway choice, although these remain to be fully characterised. The Late response somehow channels DSBs into the appropriate high-fidelity repair pathway, typically either ‘slow-kinetic’ cNHEJ or homologous recombination (HR). Loss of specific components of the DSB repair machinery results in cells utilising remaining factors to effect repair, but often at the cost of increased mutagenesis. Here we discuss the complex regulation of the Immediate-Early, Early, and Late responses to DSBs proceeding repair itself.
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30
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Heath J, Cheyou ES, Findlay S, Luo VM, Carpio EP, Lee J, Djerir B, Chen X, Morin T, Lebeau B, Karam M, Bagci H, Grapton D, Ursini‐Siegel J, Côté J, Witcher M, Richard S, Maréchal A, Orthwein A. POGZ promotes homology-directed DNA repair in an HP1-dependent manner. EMBO Rep 2022; 23:e51041. [PMID: 34758190 PMCID: PMC8728601 DOI: 10.15252/embr.202051041] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 10/08/2021] [Accepted: 10/20/2021] [Indexed: 01/07/2023] Open
Abstract
The heterochromatin protein HP1 plays a central role in the maintenance of genome stability but little is known about how HP1 is controlled. Here, we show that the zinc finger protein POGZ promotes the presence of HP1 at DNA double-strand breaks (DSBs) in human cells. POGZ depletion delays the resolution of DSBs and sensitizes cells to different DNA-damaging agents, including cisplatin and talazoparib. Mechanistically, POGZ promotes homology-directed DNA repair by retaining the BRCA1/BARD1 complex at DSBs in an HP1-dependent manner. In vivo CRISPR inactivation of Pogz is embryonically lethal. Pogz haploinsufficiency (Pogz+ /delta) results in developmental delay, impaired intellectual abilities, hyperactive behaviour and a compromised humoral immune response in mice, recapitulating the main clinical features of the White Sutton syndrome (WHSUS). Pogz+ /delta mice are further radiosensitive and accumulate DSBs in diverse tissues, including the spleen and brain. Altogether, our findings identify POGZ as an important player in homology-directed DNA repair both in vitro and in vivo.
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Affiliation(s)
- John Heath
- Lady Davis Institute for Medical Research, Segal Cancer CentreJewish General HospitalMontrealQCCanada
- Division of Experimental MedicineMcGill UniversityMontrealQCCanada
| | - Estelle Simo Cheyou
- Lady Davis Institute for Medical Research, Segal Cancer CentreJewish General HospitalMontrealQCCanada
- Gerald Bronfman Department of OncologyMcGill UniversityMontrealQCCanada
| | - Steven Findlay
- Lady Davis Institute for Medical Research, Segal Cancer CentreJewish General HospitalMontrealQCCanada
- Division of Experimental MedicineMcGill UniversityMontrealQCCanada
| | - Vincent M Luo
- Lady Davis Institute for Medical Research, Segal Cancer CentreJewish General HospitalMontrealQCCanada
- Department of Microbiology and ImmunologyMcGill UniversityMontrealQCCanada
| | - Edgar Pinedo Carpio
- Lady Davis Institute for Medical Research, Segal Cancer CentreJewish General HospitalMontrealQCCanada
- Division of Experimental MedicineMcGill UniversityMontrealQCCanada
| | - Jeesan Lee
- Lady Davis Institute for Medical Research, Segal Cancer CentreJewish General HospitalMontrealQCCanada
| | - Billel Djerir
- Department of BiologyUniversité de SherbrookeSherbrookeQCCanada
| | - Xiaoru Chen
- Lady Davis Institute for Medical Research, Segal Cancer CentreJewish General HospitalMontrealQCCanada
| | - Théo Morin
- Department of BiologyUniversité de SherbrookeSherbrookeQCCanada
| | - Benjamin Lebeau
- Lady Davis Institute for Medical Research, Segal Cancer CentreJewish General HospitalMontrealQCCanada
- Division of Experimental MedicineMcGill UniversityMontrealQCCanada
| | - Martin Karam
- Lady Davis Institute for Medical Research, Segal Cancer CentreJewish General HospitalMontrealQCCanada
- Division of Experimental MedicineMcGill UniversityMontrealQCCanada
| | - Halil Bagci
- Institut de Recherches Cliniques de Montréal (IRCM)MontrealQCCanada
- Département of Anatomy and Cell BiologyMcGill UniversityMontrealQCCanada
- Present address:
Institute of BiochemistryETH ZürichZürichSwitzerland
| | - Damien Grapton
- Lady Davis Institute for Medical Research, Segal Cancer CentreJewish General HospitalMontrealQCCanada
| | - Josie Ursini‐Siegel
- Lady Davis Institute for Medical Research, Segal Cancer CentreJewish General HospitalMontrealQCCanada
- Division of Experimental MedicineMcGill UniversityMontrealQCCanada
- Gerald Bronfman Department of OncologyMcGill UniversityMontrealQCCanada
| | - Jean‐Francois Côté
- Institut de Recherches Cliniques de Montréal (IRCM)MontrealQCCanada
- Département of Anatomy and Cell BiologyMcGill UniversityMontrealQCCanada
- Département de Biochimie et Médecine MoléculaireUniversité de MontréalMontrealQCCanada
- Département de Médecine (Programmes de Biologie Moléculaire)Université de MontréalMontrealQCCanada
| | - Michael Witcher
- Lady Davis Institute for Medical Research, Segal Cancer CentreJewish General HospitalMontrealQCCanada
- Division of Experimental MedicineMcGill UniversityMontrealQCCanada
| | - Stéphane Richard
- Lady Davis Institute for Medical Research, Segal Cancer CentreJewish General HospitalMontrealQCCanada
- Gerald Bronfman Department of OncologyMcGill UniversityMontrealQCCanada
| | | | - Alexandre Orthwein
- Lady Davis Institute for Medical Research, Segal Cancer CentreJewish General HospitalMontrealQCCanada
- Division of Experimental MedicineMcGill UniversityMontrealQCCanada
- Gerald Bronfman Department of OncologyMcGill UniversityMontrealQCCanada
- Department of Microbiology and ImmunologyMcGill UniversityMontrealQCCanada
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31
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Wootton J, Soutoglou E. Chromatin and Nuclear Dynamics in the Maintenance of Replication Fork Integrity. Front Genet 2022; 12:773426. [PMID: 34970302 PMCID: PMC8712883 DOI: 10.3389/fgene.2021.773426] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/24/2021] [Indexed: 11/13/2022] Open
Abstract
Replication of the eukaryotic genome is a highly regulated process and stringent control is required to maintain genome integrity. In this review, we will discuss the many aspects of the chromatin and nuclear environment that play key roles in the regulation of both unperturbed and stressed replication. Firstly, the higher order organisation of the genome into A and B compartments, topologically associated domains (TADs) and sub-nuclear compartments has major implications in the control of replication timing. In addition, the local chromatin environment defined by non-canonical histone variants, histone post-translational modifications (PTMs) and enrichment of factors such as heterochromatin protein 1 (HP1) plays multiple roles in normal S phase progression and during the repair of replicative damage. Lastly, we will cover how the spatial organisation of stalled replication forks facilitates the resolution of replication stress.
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Affiliation(s)
- Jack Wootton
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Evi Soutoglou
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, United Kingdom
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32
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Le PT, Ha N, Tran NK, Newman AG, Esselen KM, Dalrymple JL, Schmelz EM, Bhandoola A, Xue HH, Singh PB, Thai TH. Targeting Cbx3/HP1γ Induces LEF-1 and IL-21R to Promote Tumor-Infiltrating CD8 T-Cell Persistence. Front Immunol 2021; 12:738958. [PMID: 34721405 PMCID: PMC8549513 DOI: 10.3389/fimmu.2021.738958] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/08/2021] [Indexed: 11/13/2022] Open
Abstract
Immune checkpoint blockade (ICB) relieves CD8+ T-cell exhaustion in most mutated tumors, and TCF-1 is implicated in converting progenitor exhausted cells to functional effector cells. However, identifying mechanisms that can prevent functional senescence and potentiate CD8+ T-cell persistence for ICB non-responsive and resistant tumors remains elusive. We demonstrate that targeting Cbx3/HP1γ in CD8+ T cells augments transcription initiation and chromatin remodeling leading to increased transcriptional activity at Lef1 and Il21r. LEF-1 and IL-21R are necessary for Cbx3/HP1γ-deficient CD8+ effector T cells to persist and control ovarian cancer, melanoma, and neuroblastoma in preclinical models. The enhanced persistence of Cbx3/HP1γ-deficient CD8+ T cells facilitates remodeling of the tumor chemokine/receptor landscape ensuring their optimal invasion at the expense of CD4+ Tregs. Thus, CD8+ T cells heightened effector function consequent to Cbx3/HP1γ deficiency may be distinct from functional reactivation by ICB, implicating Cbx3/HP1γ as a viable cancer T-cell-based therapy target for ICB resistant, non-responsive solid tumors.
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Affiliation(s)
- Phuong T Le
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Ngoc Ha
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Ngan K Tran
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Andrew G Newman
- Institute of Cell and Neurobiology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Katharine M Esselen
- Division of Gynecologic Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - John L Dalrymple
- Division of Gynecologic Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Eva M Schmelz
- Department of Human Nutrition, Food, and Exercise, Virginia Tech, Blacksburg, VA, United States
| | - Avinash Bhandoola
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
| | - Hai-Hui Xue
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ, United States
| | - Prim B Singh
- Nazarbayev University School of Medicine, Nur-Sultan, Kazakhstan
| | - To-Ha Thai
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States.,Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
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33
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Ortega P, Gómez-González B, Aguilera A. Heterogeneity of DNA damage incidence and repair in different chromatin contexts. DNA Repair (Amst) 2021; 107:103210. [PMID: 34416542 DOI: 10.1016/j.dnarep.2021.103210] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/02/2021] [Accepted: 08/11/2021] [Indexed: 11/18/2022]
Abstract
It has been long known that some regions of the genome are more susceptible to damage and mutagenicity than others. Recent advances have determined a critical role of chromatin both in the incidence of damage and in its repair. Thus, chromatin arises as a guardian of the stability of the genome, which is altered in cancer cells. In this review, we focus into the mechanisms by which chromatin influences the occurrence and repair of the most cytotoxic DNA lesions, double-strand breaks, in particular at actively transcribed chromatin or related to DNA replication.
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Affiliation(s)
- Pedro Ortega
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Belén Gómez-González
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain.
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
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34
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Merigliano C, Chiolo I. Multi-scale dynamics of heterochromatin repair. Curr Opin Genet Dev 2021; 71:206-215. [PMID: 34717276 DOI: 10.1016/j.gde.2021.09.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 09/16/2021] [Accepted: 09/27/2021] [Indexed: 10/24/2022]
Abstract
Studies across different organisms show that nuclear architecture and dynamics play central roles in different aspects of homologous recombination (HR) repair. Here we review the most recent discoveries in this field, ranging from directed motions mediating relocalization pathways, to global chromatin mobilization, local DNA looping, and changes in repair focus properties associated with clustering and phase separation. We discuss how these dynamics work in different contexts, including molecular mechanisms and regulatory pathways involved. We specifically highlight how they function in pericentromeric heterochromatin, which presents a unique environment for HR repair given the abundance of repeated DNA sequences prone to aberrant recombination, the 'silent' chromatin state, and the phase separation characterizing this domain.
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Affiliation(s)
- Chiara Merigliano
- University of Southern California, Molecular and Computational Biology Department, Los Angeles, CA 90089, USA
| | - Irene Chiolo
- University of Southern California, Molecular and Computational Biology Department, Los Angeles, CA 90089, USA.
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35
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The Sound of Silence: How Silenced Chromatin Orchestrates the Repair of Double-Strand Breaks. Genes (Basel) 2021; 12:genes12091415. [PMID: 34573397 PMCID: PMC8467445 DOI: 10.3390/genes12091415] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/07/2021] [Accepted: 09/13/2021] [Indexed: 12/29/2022] Open
Abstract
The eukaryotic nucleus is continuously being exposed to endogenous and exogenous sources that cause DNA breaks, whose faithful repair requires the activity of dedicated nuclear machineries. DNA is packaged into a variety of chromatin domains, each characterized by specific molecular properties that regulate gene expression and help maintain nuclear structure. These different chromatin environments each demand a tailored response to DNA damage. Silenced chromatin domains in particular present a major challenge to the cell’s DNA repair machinery due to their specific biophysical properties and distinct, often repetitive, DNA content. To this end, we here discuss the interplay between silenced chromatin domains and DNA damage repair, specifically double-strand breaks, and how these processes help maintain genome stability.
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36
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González‐Arzola K, Guerra‐Castellano A, Rivero‐Rodríguez F, Casado‐Combreras MÁ, Pérez‐Mejías G, Díaz‐Quintana A, Díaz‐Moreno I, De la Rosa MA. Mitochondrial cytochrome c shot towards histone chaperone condensates in the nucleus. FEBS Open Bio 2021; 11:2418-2440. [PMID: 33938164 PMCID: PMC8409293 DOI: 10.1002/2211-5463.13176] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/26/2021] [Indexed: 12/15/2022] Open
Abstract
Despite mitochondria being key for the control of cell homeostasis and fate, their role in DNA damage response is usually just regarded as an apoptotic trigger. However, growing evidence points to mitochondrial factors modulating nuclear functions. Remarkably, after DNA damage, cytochrome c (Cc) interacts in the cell nucleus with a variety of well-known histone chaperones, whose activity is competitively inhibited by the haem protein. As nuclear Cc inhibits the nucleosome assembly/disassembly activity of histone chaperones, it might indeed affect chromatin dynamics and histone deposition on DNA. Several histone chaperones actually interact with Cc Lys residues through their acidic regions, which are also involved in heterotypic interactions leading to liquid-liquid phase transitions responsible for the assembly of nuclear condensates, including heterochromatin. This relies on dynamic histone-DNA interactions that can be modulated by acetylation of specific histone Lys residues. Thus, Cc may have a major regulatory role in DNA repair by fine-tuning nucleosome assembly activity and likely nuclear condensate formation.
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Affiliation(s)
- Katiuska González‐Arzola
- Institute for Chemical Research (IIQ)Scientific Research Centre Isla de la Cartuja (cicCartuja)University of Seville – CSICSpain
| | - Alejandra Guerra‐Castellano
- Institute for Chemical Research (IIQ)Scientific Research Centre Isla de la Cartuja (cicCartuja)University of Seville – CSICSpain
| | - Francisco Rivero‐Rodríguez
- Institute for Chemical Research (IIQ)Scientific Research Centre Isla de la Cartuja (cicCartuja)University of Seville – CSICSpain
| | - Miguel Á. Casado‐Combreras
- Institute for Chemical Research (IIQ)Scientific Research Centre Isla de la Cartuja (cicCartuja)University of Seville – CSICSpain
| | - Gonzalo Pérez‐Mejías
- Institute for Chemical Research (IIQ)Scientific Research Centre Isla de la Cartuja (cicCartuja)University of Seville – CSICSpain
| | - Antonio Díaz‐Quintana
- Institute for Chemical Research (IIQ)Scientific Research Centre Isla de la Cartuja (cicCartuja)University of Seville – CSICSpain
| | - Irene Díaz‐Moreno
- Institute for Chemical Research (IIQ)Scientific Research Centre Isla de la Cartuja (cicCartuja)University of Seville – CSICSpain
| | - Miguel A. De la Rosa
- Institute for Chemical Research (IIQ)Scientific Research Centre Isla de la Cartuja (cicCartuja)University of Seville – CSICSpain
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37
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Vodnala M, Choi EB, Fong YW. Low complexity domains, condensates, and stem cell pluripotency. World J Stem Cells 2021; 13:416-438. [PMID: 34136073 PMCID: PMC8176841 DOI: 10.4252/wjsc.v13.i5.416] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/20/2021] [Accepted: 04/28/2021] [Indexed: 02/06/2023] Open
Abstract
Biological reactions require self-assembly of factors in the complex cellular milieu. Recent evidence indicates that intrinsically disordered, low-complexity sequence domains (LCDs) found in regulatory factors mediate diverse cellular processes from gene expression to DNA repair to signal transduction, by enriching specific biomolecules in membraneless compartments or hubs that may undergo liquid-liquid phase separation (LLPS). In this review, we discuss how embryonic stem cells take advantage of LCD-driven interactions to promote cell-specific transcription, DNA damage response, and DNA repair. We propose that LCD-mediated interactions play key roles in stem cell maintenance and safeguarding genome integrity.
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Affiliation(s)
- Munender Vodnala
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, United States
| | - Eun-Bee Choi
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, United States
| | - Yick W Fong
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, United States
- Harvard Stem Cell Institute, Cambridge, MA 02138, United States.
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38
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Pettinato AM, Yoo D, VanOudenhove J, Chen YS, Cohn R, Ladha FA, Yang X, Thakar K, Romano R, Legere N, Meredith E, Robson P, Regnier M, Cotney JL, Murry CE, Hinson JT. Sarcomere function activates a p53-dependent DNA damage response that promotes polyploidization and limits in vivo cell engraftment. Cell Rep 2021; 35:109088. [PMID: 33951429 PMCID: PMC8161465 DOI: 10.1016/j.celrep.2021.109088] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 03/11/2021] [Accepted: 04/14/2021] [Indexed: 12/21/2022] Open
Abstract
Human cardiac regeneration is limited by low cardiomyocyte replicative rates and progressive polyploidization by unclear mechanisms. To study this process, we engineer a human cardiomyocyte model to track replication and polyploidization using fluorescently tagged cyclin B1 and cardiac troponin T. Using time-lapse imaging, in vitro cardiomyocyte replication patterns recapitulate the progressive mononuclear polyploidization and replicative arrest observed in vivo. Single-cell transcriptomics and chromatin state analyses reveal that polyploidization is preceded by sarcomere assembly, enhanced oxidative metabolism, a DNA damage response, and p53 activation. CRISPR knockout screening reveals p53 as a driver of cell-cycle arrest and polyploidization. Inhibiting sarcomere function, or scavenging ROS, inhibits cell-cycle arrest and polyploidization. Finally, we show that cardiomyocyte engraftment in infarcted rat hearts is enhanced 4-fold by the increased proliferation of troponin-knockout cardiomyocytes. Thus, the sarcomere inhibits cell division through a DNA damage response that can be targeted to improve cardiomyocyte replacement strategies.
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Affiliation(s)
- Anthony M Pettinato
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT 06030, USA
| | - Dasom Yoo
- Department of Bioengineering, University of Washington, Seattle, WA 98109, USA
| | | | - Yu-Sheng Chen
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Rachel Cohn
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Feria A Ladha
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT 06030, USA
| | - Xiulan Yang
- Center for Cardiovascular Biology and Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Ketan Thakar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Robert Romano
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Nicolas Legere
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Emily Meredith
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Paul Robson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Michael Regnier
- Department of Bioengineering, University of Washington, Seattle, WA 98109, USA
| | - Justin L Cotney
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT 06030, USA
| | - Charles E Murry
- Department of Bioengineering, University of Washington, Seattle, WA 98109, USA; Center for Cardiovascular Biology and Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; Department of Pathology, University of Washington, Seattle, WA 98109, USA; Department of Medicine/Cardiology, University of Washington, Seattle, WA 98109, USA
| | - J Travis Hinson
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT 06030, USA; The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
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Zhou D, Borsa M, Simon AK. Hallmarks and detection techniques of cellular senescence and cellular ageing in immune cells. Aging Cell 2021; 20:e13316. [PMID: 33524238 PMCID: PMC7884036 DOI: 10.1111/acel.13316] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 01/03/2021] [Accepted: 01/09/2021] [Indexed: 12/15/2022] Open
Abstract
The ageing of the global population brings about unprecedented challenges. Chronic age-related diseases in an increasing number of people represent an enormous burden for health and social care. The immune system deteriorates during ageing and contributes to many of these age-associated diseases due to its pivotal role in pathogen clearance, tissue homeostasis and maintenance. Moreover, in order to develop treatments for COVID-19, we urgently need to acquire more knowledge about the aged immune system, as older adults are disproportionally and more severely affected. Changes with age lead to impaired responses to infections, malignancies and vaccination, and are accompanied by chronic, low-degree inflammation, which together is termed immunosenescence. However, the molecular and cellular mechanisms that underlie immunosenescence, termed immune cell senescence, are mostly unknown. Cellular senescence, characterised by an irreversible cell cycle arrest, is thought to be the cause of tissue and organismal ageing. Thus, better understanding of cellular senescence in immune populations at single-cell level may provide us with insight into how immune cell senescence develops over the life time of an individual. In this review, we will briefly introduce the phenotypic characterisation of aged innate and adaptive immune cells, which also contributes to overall immunosenescence, including subsets and function. Next, we will focus on the different hallmarks of cellular senescence and cellular ageing, and the detection techniques most suitable for immune cells. Applying these techniques will deepen our understanding of immune cell senescence and to discover potential druggable pathways, which can be modulated to reverse immune ageing.
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Affiliation(s)
- Dingxi Zhou
- The Kennedy Institute of RheumatologyUniversity of OxfordOxfordUK
| | - Mariana Borsa
- The Kennedy Institute of RheumatologyUniversity of OxfordOxfordUK
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40
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See C, Arya D, Lin E, Chiolo I. Live Cell Imaging of Nuclear Actin Filaments and Heterochromatic Repair foci in Drosophila and Mouse Cells. Methods Mol Biol 2021; 2153:459-482. [PMID: 32840799 DOI: 10.1007/978-1-0716-0644-5_32] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Pericentromeric heterochromatin is mostly composed of repeated DNA sequences, which are prone to aberrant recombination during double-strand break (DSB) repair. Studies in Drosophila and mouse cells revealed that 'safe' homologous recombination (HR) repair of these sequences relies on the relocalization of repair sites to outside the heterochromatin domain before Rad51 recruitment. Relocalization requires a striking network of nuclear actin filaments (F-actin) and myosins that drive directed motions. Understanding this pathway requires the detection of nuclear actin filaments that are significantly less abundant than those in the cytoplasm, and the imaging and tracking of repair sites for long time periods. Here, we describe an optimized protocol for live cell imaging of nuclear F-actin in Drosophila cells, and for repair focus tracking in mouse cells, including: imaging setup, image processing approaches, and analysis methods. We emphasize approaches that can be applied to identify the most effective fluorescent markers for live cell imaging, strategies to minimize photobleaching and phototoxicity with a DeltaVision deconvolution microscope, and image processing and analysis methods using SoftWoRx and Imaris software. These approaches enable a deeper understanding of the spatial and temporal dynamics of heterochromatin repair and have broad applicability in the fields of nuclear architecture, nuclear dynamics, and DNA repair.
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Affiliation(s)
- Colby See
- Molecular and Computational Biology Department, University of Southern California, Los Angeles, CA, USA
| | - Deepak Arya
- Molecular and Computational Biology Department, University of Southern California, Los Angeles, CA, USA
| | - Emily Lin
- Molecular and Computational Biology Department, University of Southern California, Los Angeles, CA, USA
| | - Irene Chiolo
- Molecular and Computational Biology Department, University of Southern California, Los Angeles, CA, USA.
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41
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Zhou Y, Shao C. Histone methylation can either promote or reduce cellular radiosensitivity by regulating DNA repair pathways. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2020; 787:108362. [PMID: 34083050 DOI: 10.1016/j.mrrev.2020.108362] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 12/03/2020] [Accepted: 12/07/2020] [Indexed: 10/22/2022]
Abstract
Radiotherapy is one of the primary modalities for cancer treatment, and its efficiency usually relies on cellular radiosensitivity. DNA damage repair is a core content of cellular radiosensitivity, and the primary mechanism of which includes non-homologous end-joining (NHEJ) and homologous recombination (HR). By affecting DNA damage repair, histone methylation regulated by histone methyltransferases (HMTs) and histone demethylases (HDMs) participates in the regulation of cellular radiosensitivity via three mechanisms: (a) recruiting DNA repair-related proteins, (b) regulating the expressions of DNA repair genes, and (c) mediating the dynamic change of chromatin. Interestingly, both aberrantly high and low levels of histone methylation could impede DNA repair processes. Here we reviewed the mechanisms of the dual effects of histone methylation on cell response to radiation. Since some inhibitors of HMTs and HDMs are reported to increase cellular radiosensitivity, understanding their molecular mechanisms may be helpful in developing new drugs for the therapy of radioresistant tumors.
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Affiliation(s)
- Yuchuan Zhou
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, No. 2094 Xie-Tu Road, Shanghai, 200032, China
| | - Chunlin Shao
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, No. 2094 Xie-Tu Road, Shanghai, 200032, China.
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42
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Pokorná P, Krepl M, Šponer J. Residues flanking the ARK me3T/S motif allow binding of diverse targets to the HP1 chromodomain: Insights from molecular dynamics simulations. Biochim Biophys Acta Gen Subj 2020; 1865:129771. [PMID: 33153976 DOI: 10.1016/j.bbagen.2020.129771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/15/2020] [Accepted: 10/20/2020] [Indexed: 11/28/2022]
Abstract
BACKGROUND The chromodomain (CD) of HP1 proteins is an established H3K9me3 reader that also binds H1, EHMT2 and H3K23 lysine-methylated targets. Structural experiments have provided atomistic pictures of its recognition of the conserved ARKme3S/T motif, but structural dynamics' contribution to the recognition may have been masked by ensemble averaging. METHODS We acquired ~350 μs of explicit solvent molecular dynamics (MD) simulations of the CD domain interacting with several peptides using the latest AMBER force fields. RESULTS The simulations reproduced the experimentally observed static binding patterns well but also revealed visible structural dynamics at the interfaces. While the buried K0me3 and A-2 target residues are tightly bound, several flanking sidechains sample diverse sites on the CD surface. Different amino acid positions of the targets can substitute for each other by forming mutually replaceable interactions with CD, thereby explaining the lack of strict requirement for cationic H3 target residues at the -3 position. The Q-4 residue of H3 targets further stabilizes the binding. The recognition pattern of the H3K23 ATKme3A motif, for which no structure is available, is predicted. CONCLUSIONS The CD reads a longer target segment than previously thought, ranging from positions -7 to +3. The CD anionic clamp can be neutralized not only by the -3 and -1 residues, but also by -7, -6, -5 and +3 residues. GENERAL SIGNIFICANCE Structural dynamics, not immediately apparent from the structural data, contribute to molecular recognition between the HP1 CD domain and its targets. Mutual replaceability of target residues increases target sequence flexibility.
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Affiliation(s)
- Pavlína Pokorná
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.
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43
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HP1s modulate the S-Adenosyl Methionine synthesis pathway in liver cancer cells. Biochem J 2020; 477:1033-1047. [PMID: 32091571 DOI: 10.1042/bcj20190621] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 02/20/2020] [Accepted: 02/24/2020] [Indexed: 12/24/2022]
Abstract
Hepatocellular carcinoma (HCC) is the most frequent primary liver cancer in adults. Among the altered pathways leading to HCC, an increasing role is attributed to abnormal epigenetic regulation. Members of the Heterochromatin Protein (HP1) 1 family are key players in chromatin organisation, acting as docking sites for chromatin modifiers. Here, we inactivated HP1α in HepG2 human liver carcinoma cells and showed that HP1α participated in cell proliferation. HP1α-depleted cells have a global decrease in DNA methylation and consequently a perturbed chromatin organisation, as exemplified by the reactivation of transcription at centromeric and pericentromeric regions, eventhough the protein levels of chromatin writers depositing methylation marks, such as EZH2, SETDB1, SUV39H1, G9A and DNMT3A remained unaltered. This decrease was attributed mainly to a low S-Adenosyl Methionine (SAM) level, a cofactor involved in methylation processes. Furthermore, we showed that this decrease was due to a modification in the Methionine adenosyl transferase 2A RNA (MAT2A) level, which modifies the ratio of MAT1A/MAT2A, two enzymes that generate SAM. Importantly, HP1α reintroduction into HP1α-depleted cells restored the MAT2A protein to its initial level. Finally, we demonstrated that this transcriptional deregulation of MAT2A in HP1α-depleted cells relied on a lack of recruitment of HP1β and HP1γ to MAT2A promoter where an improper non-CpG methylation site was promoted in the vicinity of the transcription start site where HP1β and HP1γ bound. Altogether, these results highlight an unanticipated link between HP1 and the SAM synthesis pathway, and emphasise emerging functions of HP1s as sensors of some aspects of liver cell metabolism.
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44
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Chen Y, Jiang T, Zhang H, Gou X, Han C, Wang J, Chen AT, Ma J, Liu J, Chen Z, Jing X, Lei H, Wang Z, Bao Y, Baqri M, Zhu Y, Bindra RS, Hansen JE, Dou J, Huang C, Zhou J. LRRC31 inhibits DNA repair and sensitizes breast cancer brain metastasis to radiation therapy. Nat Cell Biol 2020; 22:1276-1285. [PMID: 33005030 PMCID: PMC7962994 DOI: 10.1038/s41556-020-00586-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 08/28/2020] [Indexed: 12/27/2022]
Abstract
Breast cancer brain metastasis (BCBM) is a devastating disease. Radiation therapy remains the mainstay for treatment of this disease. Unfortunately, its efficacy is limited by the dose that can be safely applied. One promising approach to overcoming this limitation is to sensitize BCBMs to radiation by inhibiting their ability to repair DNA damage. Here, we report a DNA repair suppressor, leucine-rich repeat-containing protein 31 (LRRC31), that was identified through a genome-wide CRISPR screen. We found that overexpression of LRRC31 suppresses DNA repair and sensitizes BCBMs to radiation. Mechanistically, LRRC31 interacts with Ku70/Ku80 and the ataxia telangiectasia mutated and RAD3-related (ATR) at the protein level, resulting in inhibition of DNA-dependent protein kinase, catalytic subunit (DNA-PKcs) recruitment and activation, and disruption of the MutS homologue 2 (MSH2)-ATR module. We demonstrate that targeted delivery of the LRRC31 gene via nanoparticles improves the survival of tumour-bearing mice after irradiation. Collectively, our study suggests LRRC31 as a major DNA repair suppressor that can be targeted for cancer radiosensitizing therapy.
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Affiliation(s)
- Yanke Chen
- Department of Cell Biology and Genetics, Xi'an Jiaotong University, Xi'an, Shaanxi, China.,Department of Neurosurgery, Yale University, New Haven, CT, USA
| | - Ting Jiang
- Department of Cell Biology and Genetics, Xi'an Jiaotong University, Xi'an, Shaanxi, China.,Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Hongyi Zhang
- Department of Neurosurgery, Yale University, New Haven, CT, USA.,Department of Microbiology and Immunology, School of Medicine, Jinan University, Guangzhou, China
| | - Xingchun Gou
- Department of Neurosurgery, Yale University, New Haven, CT, USA.,Shaanxi Key Laboratory of Brain Disorders & Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an, China
| | - Cong Han
- Department of Cell Biology and Genetics, Xi'an Jiaotong University, Xi'an, Shaanxi, China.,Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Jianhui Wang
- Department of Pathology, Yale University, New Haven, CT, USA
| | - Ann T Chen
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Jun Ma
- Department of Radiology in the First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Jun Liu
- Department of Neurosurgery, Yale University, New Haven, CT, USA
| | - Zeming Chen
- Department of Neurosurgery, Yale University, New Haven, CT, USA
| | - Xintao Jing
- Department of Cell Biology and Genetics, Xi'an Jiaotong University, Xi'an, Shaanxi, China.,Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Hong Lei
- Shaanxi Key Laboratory of Brain Disorders & Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an, China
| | - Zhenzhen Wang
- Department of Cell Biology and Genetics, Xi'an Jiaotong University, Xi'an, Shaanxi, China.,Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Youmei Bao
- Department of Neurosurgery, Yale University, New Haven, CT, USA
| | - Mehdi Baqri
- Department of Neurosurgery, Yale University, New Haven, CT, USA
| | - Yong Zhu
- School of Public Health, Yale University, New Haven, CT, USA
| | - Ranjit S Bindra
- Department of Therapeutic Radiology, Yale University, New Haven, CT, USA
| | - James E Hansen
- Department of Therapeutic Radiology, Yale University, New Haven, CT, USA
| | - Jun Dou
- Department of Pathogenic Biology and Immunology, School of Medicine, Southeast University, Nanjing, China
| | - Chen Huang
- Department of Cell Biology and Genetics, Xi'an Jiaotong University, Xi'an, Shaanxi, China. .,Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Xi'an, Shaanxi, China.
| | - Jiangbing Zhou
- Department of Neurosurgery, Yale University, New Haven, CT, USA. .,Department of Biomedical Engineering, Yale University, New Haven, CT, USA.
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45
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Farsani ZA, Schmid VJ. Co-localization analysis in fluorescence microscopy via maximum entropy copula. Int J Biostat 2020; 17:165-175. [PMID: 32946417 DOI: 10.1515/ijb-2019-0019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 08/08/2020] [Indexed: 11/15/2022]
Abstract
Co-localization analysis is a popular method for quantitative analysis in fluorescence microscopy imaging. The localization of marked proteins in the cell nucleus allows a deep insight into biological processes in the nucleus. Several metrics have been developed for measuring the co-localization of two markers, however, they depend on subjective thresholding of background and the assumption of linearity. We propose a robust method to estimate the bivariate distribution function of two color channels. From this, we can quantify their co- or anti-colocalization. The proposed method is a combination of the Maximum Entropy Method (MEM) and a Gaussian Copula, which we call the Maximum Entropy Copula (MEC). This new method can measure the spatial and nonlinear correlation of signals to determine the marker colocalization in fluorescence microscopy images. The proposed method is compared with MEM for bivariate probability distributions. The new colocalization metric is validated on simulated and real data. The results show that MEC can determine co- and anti-colocalization even in high background settings. MEC can, therefore, be used as a robust tool for colocalization analysis.
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Affiliation(s)
- Zahra Amini Farsani
- Statistics Department, School of Science, Lorestan University, 68151-44316 Khorramabad, Islamic Republic of Iran.,Bioimaging Group, Department of Statistics, Ludwig-Maximilians-Universität München, Ludwigstraße 33, 80539 Munich, Germany
| | - Volker J Schmid
- Bioimaging Group, Department of Statistics, Ludwig-Maximilians-Universität München, Ludwigstraße 33, 80539 Munich, Germany
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46
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Miné-Hattab J, Chiolo I. Complex Chromatin Motions for DNA Repair. Front Genet 2020; 11:800. [PMID: 33061931 PMCID: PMC7481375 DOI: 10.3389/fgene.2020.00800] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/06/2020] [Indexed: 12/26/2022] Open
Abstract
A number of studies across different model systems revealed that chromatin undergoes significant changes in dynamics in response to DNA damage. These include local motion changes at damage sites, increased nuclear exploration of both damaged and undamaged loci, and directed motions to new nuclear locations associated with certain repair pathways. These studies also revealed the need for new analytical methods to identify directed motions in a context of mixed trajectories, and the importance of investigating nuclear dynamics over different time scales to identify diffusion regimes. Here we provide an overview of the current understanding of this field, including imaging and analytical methods developed to investigate nuclear dynamics in different contexts. These dynamics are essential for genome integrity. Identifying the molecular mechanisms responsible for these movements is key to understanding how their misregulation contributes to cancer and other genome instability disorders.
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Affiliation(s)
- Judith Miné-Hattab
- UMR 3664, CNRS, Institut Curie, PSL Research University, Paris, France
- UMR 3664, CNRS, Institut Curie, Sorbonne Université, Paris, France
| | - Irene Chiolo
- Molecular and Computational Biology Department, University of Southern California, Los Angeles, CA, United States
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47
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Singh PB, Belyakin SN, Laktionov PP. Biology and Physics of Heterochromatin- Like Domains/Complexes. Cells 2020; 9:E1881. [PMID: 32796726 PMCID: PMC7465696 DOI: 10.3390/cells9081881] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 07/29/2020] [Accepted: 08/04/2020] [Indexed: 11/17/2022] Open
Abstract
The hallmarks of constitutive heterochromatin, HP1 and H3K9me2/3, assemble heterochromatin-like domains/complexes outside canonical constitutively heterochromatic territories where they regulate chromatin template-dependent processes. Domains are more than 100 kb in size; complexes less than 100 kb. They are present in the genomes of organisms ranging from fission yeast to human, with an expansion in size and number in mammals. Some of the likely functions of domains/complexes include silencing of the donor mating type region in fission yeast, preservation of DNA methylation at imprinted germline differentially methylated regions (gDMRs) and regulation of the phylotypic progression during vertebrate development. Far cis- and trans-contacts between micro-phase separated domains/complexes in mammalian nuclei contribute to the emergence of epigenetic compartmental domains (ECDs) detected in Hi-C maps. A thermodynamic description of micro-phase separation of heterochromatin-like domains/complexes may require a gestalt shift away from the monomer as the "unit of incompatibility" that determines the sign and magnitude of the Flory-Huggins parameter, χ. Instead, a more dynamic structure, the oligo-nucleosomal "clutch", consisting of between 2 and 10 nucleosomes is both the long sought-after secondary structure of chromatin and its unit of incompatibility. Based on this assumption we present a simple theoretical framework that enables an estimation of χ for domains/complexes flanked by euchromatin and thereby an indication of their tendency to phase separate. The degree of phase separation is specified by χN, where N is the number of "clutches" in a domain/complex. Our approach could provide an additional tool for understanding the biophysics of the 3D genome.
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Affiliation(s)
- Prim B. Singh
- Nazarbayev University School of Medicine, Nur-Sultan City 010000, Kazakhstan
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
| | - Stepan N. Belyakin
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
- Genomics laboratory, Institute of molecular and cellular biology SD RAS, Lavrentyev ave, 8/2, 630090 Novosibirsk, Russia; (S.N.B.); (P.P.L.)
| | - Petr P. Laktionov
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
- Genomics laboratory, Institute of molecular and cellular biology SD RAS, Lavrentyev ave, 8/2, 630090 Novosibirsk, Russia; (S.N.B.); (P.P.L.)
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48
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Aleksandrov R, Hristova R, Stoynov S, Gospodinov A. The Chromatin Response to Double-Strand DNA Breaks and Their Repair. Cells 2020; 9:cells9081853. [PMID: 32784607 PMCID: PMC7464352 DOI: 10.3390/cells9081853] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/03/2020] [Accepted: 08/04/2020] [Indexed: 02/07/2023] Open
Abstract
Cellular DNA is constantly being damaged by numerous internal and external mutagenic factors. Probably the most severe type of insults DNA could suffer are the double-strand DNA breaks (DSBs). They sever both DNA strands and compromise genomic stability, causing deleterious chromosomal aberrations that are implicated in numerous maladies, including cancer. Not surprisingly, cells have evolved several DSB repair pathways encompassing hundreds of different DNA repair proteins to cope with this challenge. In eukaryotic cells, DSB repair is fulfilled in the immensely complex environment of the chromatin. The chromatin is not just a passive background that accommodates the multitude of DNA repair proteins, but it is a highly dynamic and active participant in the repair process. Chromatin alterations, such as changing patterns of histone modifications shaped by numerous histone-modifying enzymes and chromatin remodeling, are pivotal for proficient DSB repair. Dynamic chromatin changes ensure accessibility to the damaged region, recruit DNA repair proteins, and regulate their association and activity, contributing to DSB repair pathway choice and coordination. Given the paramount importance of DSB repair in tumorigenesis and cancer progression, DSB repair has turned into an attractive target for the development of novel anticancer therapies, some of which have already entered the clinic.
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49
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Charaka V, Tiwari A, Pandita RK, Hunt CR, Pandita TK. Role of HP1β during spermatogenesis and DNA replication. Chromosoma 2020; 129:215-226. [PMID: 32651609 DOI: 10.1007/s00412-020-00739-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 06/28/2020] [Accepted: 06/29/2020] [Indexed: 11/25/2022]
Abstract
Heterochromatin protein 1β (HP1β), encoded by the Cbx1 gene, has been functionally linked to chromatin condensation, transcriptional regulation, and DNA damage repair. Here we report that testis-specific Cbx1 conditional knockout (Cbx1 cKO) impairs male germ cell development in mice. Depletion of HP1β negatively affected sperm maturation and increased seminiferous tubule degeneration in Cbx1 cKO mice. In addition, the spermatogonia have elevated γ-H2AX foci levels as do Cbx1 deficient mouse embryonic fibroblasts (MEFs) as compared to wild-type (WT) control MEFs. The increase in γ-H2AX foci in proliferating Cbx1 cKO cells indicates defective replication-dependent DNA damage repair. Depletion or loss of HP1β from human cells and MEFs increased DNA replication fork stalling and firing of new origins of replication, indicating defective DNA synthesis. Taken together, these results suggest that loss of HP1β in proliferating cells leads to DNA replication defects with associated DNA damage that impact spermatogenesis.
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Affiliation(s)
- Vijay Charaka
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX, 77030, USA
| | - Anjana Tiwari
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX, 77030, USA
| | - Raj K Pandita
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX, 77030, USA
- Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Clayton R Hunt
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX, 77030, USA
| | - Tej K Pandita
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX, 77030, USA.
- Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.
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Wang M, Li R, Feng X, Dang C, Dai F, Yin X, He M, Liu D, Qi H. Cellulose Nanofiber-Reinforced Ionic Conductors for Multifunctional Sensors and Devices. ACS APPLIED MATERIALS & INTERFACES 2020; 12:27545-27554. [PMID: 32458678 DOI: 10.1021/acsami.0c04907] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Ionic conductors are normally prepared from water-based materials in the solid form and feature a combination of intrinsic transparency and stretchability. The sensitivity toward humidity inevitably leads to dehydration or deliquescence issues, which will limit the long-term use of ionic conductors. Here, a novel ionic conductor based on natural bacterial cellulose (BC) and polymerizable deep eutectic solvents (PDESs) is developed for addressing the abovementioned drawbacks. The superstrong three-dimensional nanofiber network and strong interfacial interaction endow the BC-PDES ionic conductor with significantly enhanced mechanical properties (tensile strength of 8 × 105 Pa and compressive strength of 6.68 × 106 Pa). Furthermore, compared to deliquescent PDESs, BC-PDES composites showed obvious mechanical stability, which maintain good mechanical properties even when exposed to high humidity for 120 days. These materials were demonstrated to possess multiple sensitivity to external stimulus, such as strain, pressure, bend, and temperature. Thus, they can easily serve as supersensitive sensors to recognize physical activity of humans such as limb movements, throat vibrations, and handwriting. Moreover, the BC-PDES ionic conductors can be used in flexible, patterned electroluminescent devices. This work provides an efficient strategy for making cellulose-based sustainable and functional ionic conductors which have broad application in artificial flexible electronics and other products.
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Affiliation(s)
- Ming Wang
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510641, China
| | - Renai Li
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510641, China
| | - Xiao Feng
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510641, China
| | - Chao Dang
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510641, China
| | - Fanglin Dai
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510641, China
| | - Xueqiong Yin
- Provincial Fine Chemical Engineering Research Center, Hainan University, Haikou, Hainan 570228, P. R. China
| | - Minghui He
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510641, China
| | - Detao Liu
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510641, China
| | - Haisong Qi
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510641, China
- Guangdong Engineering Research Center for Green Fine Chemicals, Guangzhou 510640, China
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