1
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Lim B, Matsui Y, Jung S, Djekidel MN, Qi W, Yuan ZF, Wang X, Yang X, Connolly N, Pilehroud AS, Pan H, Wang F, Pruett-Miller SM, Kavdia K, Pagala V, Fan Y, Peng J, Xu B, Peng JC. Phosphorylation of the DNA damage repair factor 53BP1 by ATM kinase controls neurodevelopmental programs in cortical brain organoids. PLoS Biol 2024; 22:e3002760. [PMID: 39226322 PMCID: PMC11398655 DOI: 10.1371/journal.pbio.3002760] [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: 08/25/2023] [Revised: 09/13/2024] [Accepted: 07/19/2024] [Indexed: 09/05/2024] Open
Abstract
53BP1 is a well-established DNA damage repair factor that has recently emerged to critically regulate gene expression for tumor suppression and neural development. However, its precise function and regulatory mechanisms remain unclear. Here, we showed that phosphorylation of 53BP1 at serine 25 by ATM is required for neural progenitor cell proliferation and neuronal differentiation in cortical brain organoids. Dynamic phosphorylation of 53BP1-serine 25 controls 53BP1 target genes governing neuronal differentiation and function, cellular response to stress, and apoptosis. Mechanistically, ATM and RNF168 govern 53BP1's binding to gene loci to directly affect gene regulation, especially at genes for neuronal differentiation and maturation. 53BP1 serine 25 phosphorylation effectively impedes its binding to bivalent or H3K27me3-occupied promoters, especially at genes regulating H3K4 methylation, neuronal functions, and cell proliferation. Beyond 53BP1, ATM-dependent phosphorylation displays wide-ranging effects, regulating factors in neuronal differentiation, cytoskeleton, p53 regulation, as well as key signaling pathways such as ATM, BDNF, and WNT during cortical organoid differentiation. Together, our data suggest that the interplay between 53BP1 and ATM orchestrates essential genetic programs for cell morphogenesis, tissue organization, and developmental pathways crucial for human cortical development.
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Affiliation(s)
- Bitna Lim
- Department of Developmental Neurobiology, St Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Yurika Matsui
- Department of Developmental Neurobiology, St Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Seunghyun Jung
- Department of Developmental Neurobiology, St Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Mohamed Nadhir Djekidel
- Center for Applied Bioinformatics, St Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Wenjie Qi
- Center for Applied Bioinformatics, St Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Zuo-Fei Yuan
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Xusheng Wang
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Xiaoyang Yang
- Department of Developmental Neurobiology, St Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Nina Connolly
- Department of Developmental Neurobiology, St Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Abbas Shirinifard Pilehroud
- Department of Developmental Neurobiology, St Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Haitao Pan
- Department of Biostatistics, St Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Fang Wang
- Department of Biostatistics, St Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Shondra M. Pruett-Miller
- Department of Cell & Molecular Biology, St Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Kanisha Kavdia
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Vishwajeeth Pagala
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Yiping Fan
- Center for Applied Bioinformatics, St Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Junmin Peng
- Department of Developmental Neurobiology, St Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
- Department of Structural Biology, St Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Beisi Xu
- Center for Applied Bioinformatics, St Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Jamy C. Peng
- Department of Developmental Neurobiology, St Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
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2
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Xuan H, Xu L, Li K, Xuan F, Xu T, Wen H, Shi X. Hotspot Cancer Mutation Impairs KAT8-mediated Nucleosomal Histone Acetylation. J Mol Biol 2024; 436:168413. [PMID: 38135180 PMCID: PMC10957314 DOI: 10.1016/j.jmb.2023.168413] [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: 10/20/2023] [Revised: 12/13/2023] [Accepted: 12/18/2023] [Indexed: 12/24/2023]
Abstract
KAT8 is an evolutionarily conserved lysine acetyltransferase that catalyzes histone acetylation at H4K16 or H4K5 and H4K8 through distinct protein complexes. It plays a pivotal role in male X chromosome dosage compensation in Drosophila and is implicated in the regulation of diverse cellular processes in mammals. Mutations and dysregulation of KAT8 have been reported in human neurodevelopmental disorders and various cancers. However, the precise mechanisms by which these mutations disrupt KAT8's normal function, leading to disease pathogenesis, remain largely unknown. In this study, we focus on a hotspot missense cancer mutation, the R98W point mutation within the Tudor-knot domain. Our study reveals that the R98W mutation leads to a reduction in global H4K16ac levels in cells and downregulates the expression of target genes. Mechanistically, we demonstrate that R98 is essential for KAT8-mediated acetylation of nucleosomal histones by modulating substrate accessibility.
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Affiliation(s)
- Hongwen Xuan
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Longxia Xu
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Kuai Li
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Fan Xuan
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Tinghai Xu
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Hong Wen
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Xiaobing Shi
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA.
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3
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Kodavati M, Wang H, Guo W, Mitra J, Hegde PM, Provasek V, Rao VHM, Vedula I, Zhang A, Mitra S, Tomkinson AE, Hamilton DJ, Van Den Bosch L, Hegde ML. FUS unveiled in mitochondrial DNA repair and targeted ligase-1 expression rescues repair-defects in FUS-linked motor neuron disease. Nat Commun 2024; 15:2156. [PMID: 38461154 PMCID: PMC10925063 DOI: 10.1038/s41467-024-45978-6] [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: 07/08/2023] [Accepted: 02/08/2024] [Indexed: 03/11/2024] Open
Abstract
This study establishes the physiological role of Fused in Sarcoma (FUS) in mitochondrial DNA (mtDNA) repair and highlights its implications to the pathogenesis of FUS-associated neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS). Endogenous FUS interacts with and recruits mtDNA Ligase IIIα (mtLig3) to DNA damage sites within mitochondria, a relationship essential for maintaining mtDNA repair and integrity in healthy cells. Using ALS patient-derived FUS mutant cell lines, a transgenic mouse model, and human autopsy samples, we discovered that compromised FUS functionality hinders mtLig3's repair role, resulting in increased mtDNA damage and mutations. These alterations cause various manifestations of mitochondrial dysfunction, particularly under stress conditions relevant to disease pathology. Importantly, rectifying FUS mutations in patient-derived induced pluripotent cells (iPSCs) preserves mtDNA integrity. Similarly, targeted introduction of human DNA Ligase 1 restores repair mechanisms and mitochondrial activity in FUS mutant cells, suggesting a potential therapeutic approach. Our findings unveil FUS's critical role in mitochondrial health and mtDNA repair, offering valuable insights into the mechanisms underlying mitochondrial dysfunction in FUS-associated motor neuron disease.
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Affiliation(s)
- Manohar Kodavati
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX, USA
| | - Haibo Wang
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX, USA
| | - Wenting Guo
- KU Leuven-Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), Leuven, Belgium
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, Leuven, Belgium
- INSERM, UMR-S1118, Mécanismes Centraux et Périphériques de la Neurodégénérescence, Université de Strasbourg, CRBS, Strasbourg, France
| | - Joy Mitra
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX, USA
| | - Pavana M Hegde
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX, USA
| | - Vincent Provasek
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX, USA
- College of Medicine, Texas A&M University, College Station, TX, USA
| | - Vikas H Maloji Rao
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX, USA
| | - Indira Vedula
- Center for Bioenergetics, Houston Methodist Research Institute, Houston, TX, USA
| | - Aijun Zhang
- Center for Bioenergetics, Houston Methodist Research Institute, Houston, TX, USA
- Department of Medicine, Houston Methodist, Weill Cornell Medicine affiliate, Houston, TX, USA
| | - Sankar Mitra
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX, USA
| | - Alan E Tomkinson
- Departments of Internal Medicine, and Molecular Genetics and Microbiology and University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, USA
| | - Dale J Hamilton
- Center for Bioenergetics, Houston Methodist Research Institute, Houston, TX, USA
- Department of Medicine, Houston Methodist, Weill Cornell Medicine affiliate, Houston, TX, USA
| | - Ludo Van Den Bosch
- KU Leuven-Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), Leuven, Belgium
- VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven, Belgium
| | - Muralidhar L Hegde
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX, USA.
- Department of Neuroscience, Weill Cornell Medical College, New York, NY, USA.
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4
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Wang ZX, Liu Y, Li YL, Wei Q, Lin RR, Kang R, Ruan Y, Lin ZH, Xue NJ, Zhang BR, Pu JL. Nuclear DJ-1 Regulates DNA Damage Repair via the Regulation of PARP1 Activity. Int J Mol Sci 2023; 24:ijms24108651. [PMID: 37239999 DOI: 10.3390/ijms24108651] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 04/03/2023] [Accepted: 04/06/2023] [Indexed: 05/28/2023] Open
Abstract
DNA damage and defective DNA repair are extensively linked to neurodegeneration in Parkinson's disease (PD), but the underlying molecular mechanisms remain poorly understood. Here, we determined that the PD-associated protein DJ-1 plays an essential role in modulating DNA double-strand break (DSB) repair. Specifically, DJ-1 is a DNA damage response (DDR) protein that can be recruited to DNA damage sites, where it promotes DSB repair through both homologous recombination and nonhomologous end joining. Mechanistically, DJ-1 interacts directly with PARP1, a nuclear enzyme essential for genomic stability, and stimulates its enzymatic activity during DNA repair. Importantly, cells from PD patients with the DJ-1 mutation also have defective PARP1 activity and impaired repair of DSBs. In summary, our findings uncover a novel function of nuclear DJ-1 in DNA repair and genome stability maintenance, and suggest that defective DNA repair may contribute to the pathogenesis of PD linked to DJ-1 mutations.
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Affiliation(s)
- Zhong-Xuan Wang
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Yi Liu
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Yao-Lin Li
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Qiao Wei
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Rong-Rong Lin
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Ruiqing Kang
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Yang Ruan
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Zhi-Hao Lin
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Nai-Jia Xue
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Bao-Rong Zhang
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Jia-Li Pu
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
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5
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Lim B, Djekidel MN, Matsui Y, Jung S, Yuan ZF, Wang X, Yang X, Pilehroud AS, Pan H, Wang F, Pruett-Miller S, Kavdia K, Pagala V, Fan Y, Peng J, Xu B, Peng JC. Phosphorylation of 53BP1 by ATM enforce neurodevelopmental programs in cortical organoids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.04.539457. [PMID: 37205560 PMCID: PMC10187281 DOI: 10.1101/2023.05.04.539457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
53BP1 is a well-established DNA damage repair factor recently shown to regulate gene expression and critically influence tumor suppression and neural development. For gene regulation, how 53BP1 is regulated remains unclear. Here, we showed that 53BP1-serine 25 phosphorylation by ATM is required for neural progenitor cell proliferation and neuronal differentiation in cortical organoids. 53BP1-serine 25 phosphorylation dynamics controls 53BP1 target genes for neuronal differentiation and function, cellular response to stress, and apoptosis. Beyond 53BP1, ATM is required for phosphorylation of factors in neuronal differentiation, cytoskeleton, p53 regulation, and ATM, BNDF, and WNT signaling pathways for cortical organoid differentiation. Overall, our data suggest that 53BP1 and ATM control key genetic programs required for human cortical development.
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6
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KAT8 acetylation-controlled lipolysis affects the invasive and migratory potential of colorectal cancer cells. Cell Death Dis 2023; 14:164. [PMID: 36849520 PMCID: PMC9970984 DOI: 10.1038/s41419-023-05582-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 12/18/2022] [Accepted: 01/11/2023] [Indexed: 03/01/2023]
Abstract
Epigenetic mechanisms involved in gene expression play an essential role in various cellular processes, including lipid metabolism. Lysine acetyltransferase 8 (KAT8), a histone acetyltransferase, has been reported to mediate de novo lipogenesis by acetylating fatty acid synthase. However, the effect of KAT8 on lipolysis is unclear. Here, we report a novel mechanism of KAT8 on lipolysis involving in its acetylation by general control non-repressed protein 5 (GCN5) and its deacetylation by Sirtuin 6 (SIRT6). KAT8 acetylation at K168/175 residues attenuates the binding activity of KAT8 and inhibits the recruitment of RNA pol II to the promoter region of the lipolysis-related genes adipose triglyceride lipase (ATGL) and hormone-sensitive lipase (HSL), subsequently down-regulating lipolysis to affect the invasive and migratory potential of colorectal cancer cells. Our findings uncover a novel mechanism that KAT8 acetylation-controlled lipolysis affects invasive and migratory potential in colorectal cancer cells.
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7
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Zhao P, Malik S. The phosphorylation to acetylation/methylation cascade in transcriptional regulation: how kinases regulate transcriptional activities of DNA/histone-modifying enzymes. Cell Biosci 2022; 12:83. [PMID: 35659740 PMCID: PMC9164400 DOI: 10.1186/s13578-022-00821-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 05/27/2022] [Indexed: 11/30/2022] Open
Abstract
Transcription factors directly regulate gene expression by recognizing and binding to specific DNA sequences, involving the dynamic alterations of chromatin structure and the formation of a complex with different kinds of cofactors, like DNA/histone modifying-enzymes, chromatin remodeling factors, and cell cycle factors. Despite the significance of transcription factors, it remains unclear to determine how these cofactors are regulated to cooperate with transcription factors, especially DNA/histone modifying-enzymes. It has been known that DNA/histone modifying-enzymes are regulated by post-translational modifications. And the most common and important modification is phosphorylation. Even though various DNA/histone modifying-enzymes have been classified and partly explained how phosphorylated sites of these enzymes function characteristically in recent studies. It still needs to find out the relationship between phosphorylation of these enzymes and the diseases-associated transcriptional regulation. Here this review describes how phosphorylation affects the transcription activity of these enzymes and other functions, including protein stability, subcellular localization, binding to chromatin, and interaction with other proteins.
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8
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Li J, Lin J, Huang S, Li M, Yu W, Zhao Y, Guo J, Zhang P, Huang X, Qiao Y. Functional Phosphoproteomics in Cancer Chemoresistance Using CRISPR-Mediated Base Editors. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2200717. [PMID: 36045417 PMCID: PMC9596822 DOI: 10.1002/advs.202200717] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 07/19/2022] [Indexed: 06/15/2023]
Abstract
Selective inhibition of targeted protein kinases is an effective therapeutic approach for treatment of human malignancies, which interferes phosphorylation of cellular substrates. However, a drug-imposed selection creates pressures for tumor cells to acquire chemoresistance-conferring mutations or activating alternative pathways, which can bypass the inhibitory effects of kinase inhibitors. Thus, identifying downstream phospho-substrates conferring drug resistance is of great importance for developing poly-pharmacological and targeted therapies. To identify functional phosphorylation sites involved in 5-fluorouracil (5-FU) resistance during its treatment of colorectal cancer cells, CRISPR-mediated cytosine base editor (CBE) and adenine base editor (ABE) are utilized for functional screens by mutating phosphorylated amino acids with two libraries specifically targeting 7779 and 10 149 phosphorylation sites. Among the top enriched gRNAs-induced gain-of-function mutants, the target genes are involved in cell cycle and post-translational covalent modifications. Moreover, several substrates of RSK2 and PAK4 kinases are discovered as main effectors in responding to 5-FU chemotherapy, and combinational treatment of colorectal cancer cells with 5-FU and RSK2 inhibitor or PAK4 inhibitor can largely inhibit cell growth and enhance cell apoptosis through a RSK2/TP53BP1/γ-H2AX phosphorylation signaling axis. It is proposed that this screen approach can be used for functional phosphoproteomics in chemotherapy of various human diseases.
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Affiliation(s)
- Jianan Li
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
- Zhejiang LabHangzhouZhejiang311121China
| | - Jianxiang Lin
- Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghai200125China
- Shanghai Institute of Precision MedicineShanghai200125China
| | | | - Min Li
- Precise Genome Engineering CenterSchool of Life SciencesGuangzhou UniversityGuangzhou510006China
| | - Wenxia Yu
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Yuting Zhao
- Precise Genome Engineering CenterSchool of Life SciencesGuangzhou UniversityGuangzhou510006China
| | - Junfan Guo
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Pumin Zhang
- Zhejiang Provincial Key Laboratory of Pancreatic DiseaseThe First Affiliated Hospitaland Institute of Translational MedicineZhejiang University School of MedicineHangzhou310029China
| | - Xingxu Huang
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
- Zhejiang Provincial Key Laboratory of Pancreatic DiseaseThe First Affiliated Hospitaland Institute of Translational MedicineZhejiang University School of MedicineHangzhou310029China
| | - Yunbo Qiao
- Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghai200125China
- Shanghai Institute of Precision MedicineShanghai200125China
- Precise Genome Engineering CenterSchool of Life SciencesGuangzhou UniversityGuangzhou510006China
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9
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Mattoo AR, Jessup JM. MCL‐1 interacts with MOF and BID to regulate H4K16 acetylation and homologous recombination repair. Cell Biol Int 2022; 46:1196-1203. [DOI: 10.1002/cbin.11831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 02/05/2022] [Accepted: 02/15/2022] [Indexed: 11/06/2022]
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10
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Van HT, Harkins PR, Patel A, Jain AK, Lu Y, Bedford MT, Santos MA. Methyl-lysine readers PHF20 and PHF20L1 define two distinct gene expression-regulating NSL complexes. J Biol Chem 2022; 298:101588. [PMID: 35033534 PMCID: PMC8867114 DOI: 10.1016/j.jbc.2022.101588] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 01/06/2022] [Accepted: 01/08/2022] [Indexed: 11/16/2022] Open
Abstract
The methyl-lysine readers plant homeodomain finger protein 20 (PHF20) and its homolog PHF20-like protein 1 (PHF20L1) are known components of the nonspecific lethal (NSL) complex that regulates gene expression through its histone acetyltransferase activity. In the current model, both PHF homologs coexist in the same NSL complex, although this was not formally tested; nor have the functions of PHF20 and PHF20L1 regarding NSL complex integrity and transcriptional regulation been investigated. Here, we perform an in-depth biochemical and functional characterization of PHF20 and PHF20L1 in the context of the NSL complex. Using mass spectrometry, genome-wide chromatin analysis, and protein-domain mapping, we identify the existence of two distinct NSL complexes that exclusively contain either PHF20 or PHF20L1. We show that the C-terminal domains of PHF20 and PHF20L1 are essential for complex formation with NSL, and the Tudor 2 domains are required for chromatin binding. The genome-wide chromatin landscape of PHF20-PHF20L1 shows that these proteins bind mostly to the same genomic regions, at promoters of highly expressed/housekeeping genes. Yet, deletion of PHF20 and PHF20L1 does not abrogate gene expression or impact the recruitment of the NSL complex to those target gene promoters, suggesting the existence of an alternative mechanism that compensates for the transcription of genes whose sustained expression is important for critical cellular functions. This work shifts the current paradigm and lays the foundation for studies on the differential roles of PHF20 and PHF20L1 in regulating NSL complex activity in physiological and diseases states.
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Affiliation(s)
- Hieu T Van
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA; Graduate Program in Genetics & Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Peter R Harkins
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Avni Patel
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Abhinav K Jain
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Margarida A Santos
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
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11
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Pandita TK, Hunt CR, Singh V, Adhikary S, Pandita S, Roy S, Ramos K, Das C. Role of the Histone Acetyl Transferase MOF and the Histone Deacetylase Sirtuins in Regulation of H4K16ac During DNA Damage Repair and Metabolic Programming: Implications in Cancer and Aging. Subcell Biochem 2022; 100:115-141. [PMID: 36301493 DOI: 10.1007/978-3-031-07634-3_4] [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] [Indexed: 06/16/2023]
Abstract
The accurate repair of genomic damage mediated by ionizing radiation (IR), chemo- or radiomimetic drugs, or other exogenous agents, is necessary for maintenance of genome integrity, preservation of cellular viability and prevention of oncogenic transformation. Eukaryotes have conserved mechanisms designed to perceive and repair the damaged DNA quite efficiently. Among the different types of DNA damage, double strand breaks (DSB) are the most detrimental. The cellular DNA DSB response is a hierarchical signaling network that integrates damage sensing and repair with chromatin structural changes that involve a range of pre-existing and induced covalent modifications. Recent studies have revealed that pre-existing histone modifications are important contributors within this signaling/repair network. This chapter discusses the role of a critical histone acetyl transferase (HAT) known as MOF (males absent on the first) and the histone deacetylases (HDACs) Sirtuins on histone H4K16 acetylation (H4K16ac) and DNA damage repair. We also discuss the role of this important histone modification in light of metabolic rewiring and its role in regulating human pathophysiologic states.
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Affiliation(s)
- Tej K Pandita
- The Houston Methodist Research Institute, Houston, TX, USA.
- Department of Cellular and Molecular Biology, Baylor College of Medicine, Houston, TX, USA.
- Center for Genomics and Precision Medicine, Texas A&M College of Medicine, Houston, TX, USA.
| | - Clayton R Hunt
- The Houston Methodist Research Institute, Houston, TX, USA
| | - Vipin Singh
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
- Homi Bhaba National Institute, Mumbai, India
| | - Santanu Adhikary
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Shruti Pandita
- Department of Internal Medicine, Division of Hematology, Oncology and Cellular Therapy, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Siddhartha Roy
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
| | - Kenneth Ramos
- Center for Genomics and Precision Medicine, Texas A&M College of Medicine, Houston, TX, USA
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
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12
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Wang X, Zhao J. Targeted Cancer Therapy Based on Acetylation and Deacetylation of Key Proteins Involved in Double-Strand Break Repair. Cancer Manag Res 2022; 14:259-271. [PMID: 35115826 PMCID: PMC8800007 DOI: 10.2147/cmar.s346052] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 01/13/2022] [Indexed: 12/22/2022] Open
Abstract
DNA double-strand breaks (DSBs) play an important role in promoting genomic instability and cell death. The precise repair of DSBs is essential for maintaining genome integrity during cancer progression, and inducing genomic instability or blocking DNA repair is an important mechanism through which chemo/radiotherapies exert killing effects on cancer cells. The two main pathways that facilitate the repair of DSBs in cancer cells are homologous recombination (HR) and non-homologous end-joining (NHEJ). Accumulating data suggest that the acetylation and deacetylation of DSB repair proteins regulate the initiation and progression of the cellular response to DNA DSBs, which may further affect the chemosensitivity or radiosensitivity of cancer cells. Here, we focus on the role of acetylation/deacetylation in the regulation of ataxia-telangiectasia mutated, Rad51, and 53BP1 in the HR pathway, as well as the relevant roles of PARP1 and Ku70 in NHEJ. Notably, several histone deacetylase (HDAC) inhibitors targeting HR or NHEJ have been demonstrated to enhance chemo/radiosensitivity in preclinical studies. This review highlights the essential role of acetylation/deacetylation in the regulation of DSB repair proteins, suggesting that HDAC inhibitors targeting the HR or NHEJ pathways that downregulate DNA DSB repair genes may be worthwhile cancer therapeutic agents.
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Affiliation(s)
- Xiwen Wang
- Department of Thoracic Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People’s Republic of China
| | - Jungang Zhao
- Department of Thoracic Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People’s Republic of China
- Correspondence: Jungang Zhao, Department of Thoracic Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People’s Republic of China, Tel/Fax +86 13889311066, Email
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13
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Mir US, Bhat A, Mushtaq A, Pandita S, Altaf M, Pandita TK. Role of histone acetyltransferases MOF and Tip60 in genome stability. DNA Repair (Amst) 2021; 107:103205. [PMID: 34399315 DOI: 10.1016/j.dnarep.2021.103205] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 08/01/2021] [Accepted: 08/05/2021] [Indexed: 01/23/2023]
Abstract
The accurate repair of DNA damage specifically the chromosomal double-strand breaks (DSBs) arising from exposure to physical or chemical agents, such as ionizing radiation (IR) and radiomimetic drugs is critical in maintaining genomic integrity. The DNA DSB response and repair is facilitated by hierarchical signaling networks that orchestrate chromatin structural changes specifically histone modifications which impact cell-cycle checkpoints through enzymatic activities to repair the broken DNA ends. Various histone posttranslational modifications such as phosphorylation, acetylation, methylation and ubiquitylation have been shown to play a role in DNA damage repair. Recent studies have provided important insights into the role of histone-specific modifications in sensing DNA damage and facilitating the DNA repair. Histone modifications have been shown to determine the pathway choice for repair of DNA DSBs. This review will summarize the role of important histone acetyltransferases MOF and Tip60 mediated acetylation in repair of DNA DSBs in eukaryotic cells.
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Affiliation(s)
- Ulfat Syed Mir
- Chromatin and Epigenetics Lab, Department of Biotechnology, University of Kashmir, Srinagar, Jammu and Kashmir, 190006, India
| | - Audesh Bhat
- Centre for Molecular Biology, Central University of Jammu, 181143, India
| | - Arjamand Mushtaq
- Chromatin and Epigenetics Lab, Department of Biotechnology, University of Kashmir, Srinagar, Jammu and Kashmir, 190006, India
| | - Shruti Pandita
- Department of Internal Medicine, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Mohammad Altaf
- Chromatin and Epigenetics Lab, Department of Biotechnology, University of Kashmir, Srinagar, Jammu and Kashmir, 190006, India; Centre for Interdisciplinary Research and Innovations, University of Kashmir, Srinagar, Jammu and Kashmir, 190006, India.
| | - Tej K Pandita
- Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
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14
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Banday S, Pandita RK, Mushtaq A, Bacolla A, Mir US, Singh DK, Jan S, Bhat KP, Hunt CR, Rao G, Charaka VK, Tainer JA, Pandita TK, Altaf M. Autism-Associated Vigilin Depletion Impairs DNA Damage Repair. Mol Cell Biol 2021; 41:e0008221. [PMID: 33941620 PMCID: PMC8224237 DOI: 10.1128/mcb.00082-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/17/2021] [Accepted: 04/28/2021] [Indexed: 12/24/2022] Open
Abstract
Vigilin (Vgl1) is essential for heterochromatin formation, chromosome segregation, and mRNA stability and is associated with autism spectrum disorders and cancer: vigilin, for example, can suppress proto-oncogene c-fms expression in breast cancer. Conserved from yeast to humans, vigilin is an RNA-binding protein with 14 tandemly arranged nonidentical hnRNP K-type homology (KH) domains. Here, we report that vigilin depletion increased cell sensitivity to cisplatin- or ionizing radiation (IR)-induced cell death and genomic instability due to defective DNA repair. Vigilin depletion delayed dephosphorylation of IR-induced γ-H2AX and elevated levels of residual 53BP1 and RIF1 foci, while reducing Rad51 and BRCA1 focus formation, DNA end resection, and double-strand break (DSB) repair. We show that vigilin interacts with the DNA damage response (DDR) proteins RAD51 and BRCA1, and vigilin depletion impairs their recruitment to DSB sites. Transient hydroxyurea (HU)-induced replicative stress in vigilin-depleted cells increased replication fork stalling and blocked restart of DNA synthesis. Furthermore, histone acetylation promoted vigilin recruitment to DSBs preferentially in the transcriptionally active genome. These findings uncover a novel vigilin role in DNA damage repair with implications for autism and cancer-related disorders.
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Affiliation(s)
- Shahid Banday
- Chromatin and Epigenetics Lab, Department of Biotechnology, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Raj K. Pandita
- Houston Methodist Research Institute, Houston, Texas, USA
- Baylor College of Medicine, Houston, Texas, USA
| | - Arjamand Mushtaq
- Chromatin and Epigenetics Lab, Department of Biotechnology, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Albino Bacolla
- Department of Molecular and Cellular Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas, USA
| | - Ulfat Syed Mir
- Chromatin and Epigenetics Lab, Department of Biotechnology, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | | | - Sadaf Jan
- Chromatin and Epigenetics Lab, Department of Biotechnology, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Krishna P. Bhat
- Department of Pathology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas, USA
| | | | - Ganesh Rao
- Baylor College of Medicine, Houston, Texas, USA
| | | | - John A. Tainer
- Department of Molecular and Cellular Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas, USA
- Department of Cancer Biology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas, USA
| | - Tej K. Pandita
- Houston Methodist Research Institute, Houston, Texas, USA
- Baylor College of Medicine, Houston, Texas, USA
| | - Mohammad Altaf
- Chromatin and Epigenetics Lab, Department of Biotechnology, University of Kashmir, Srinagar, Jammu and Kashmir, India
- Centre for Interdisciplinary Research and Innovations, University of Kashmir, Srinagar, Jammu and Kashmir, India
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15
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Bogdanova NV, Jguburia N, Ramachandran D, Nischik N, Stemwedel K, Stamm G, Werncke T, Wacker F, Dörk T, Christiansen H. Persistent DNA Double-Strand Breaks After Repeated Diagnostic CT Scans in Breast Epithelial Cells and Lymphocytes. Front Oncol 2021; 11:634389. [PMID: 33968734 PMCID: PMC8103218 DOI: 10.3389/fonc.2021.634389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 03/22/2021] [Indexed: 12/14/2022] Open
Abstract
DNA double-strand break (DSB) induction and repair have been widely studied in radiation therapy (RT); however little is known about the impact of very low exposures from repeated computed tomography (CT) scans for the efficiency of repair. In our current study, DSB repair and kinetics were investigated in side-by-side comparison of RT treatment (2 Gy) with repeated diagnostic CT scans (≤20 mGy) in human breast epithelial cell lines and lymphoblastoid cells harboring different mutations in known DNA damage repair proteins. Immunocytochemical analysis of well known DSB markers γH2AX and 53BP1, within 48 h after each treatment, revealed highly correlated numbers of foci and similar appearance/disappearance profiles. The levels of γH2AX and 53BP1 foci after CT scans were up to 30% of those occurring 0.5 h after 2 Gy irradiation. The DNA damage repair after diagnostic CT scans was monitored and quantitatively assessed by both γH2AX and 53BP1 foci in different cell types. Subsequent diagnostic CT scans in 6 and/or 12 weeks intervals resulted in elevated background levels of repair foci, more pronounced in cells that were prone to genomic instability due to mutations in known regulators of DNA damage response (DDR). The levels of persistent foci remained enhanced for up to 6 months. This “memory effect” may reflect a radiation-induced long-term response of cells after low-dose x-ray exposure.
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Affiliation(s)
- Natalia V Bogdanova
- Radiation Oncology Research Unit, Hannover Medical School, Hannover, Germany
| | - Nina Jguburia
- Radiation Oncology Research Unit, Hannover Medical School, Hannover, Germany
| | | | - Nora Nischik
- Radiation Oncology Research Unit, Hannover Medical School, Hannover, Germany.,Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Katharina Stemwedel
- Radiation Oncology Research Unit, Hannover Medical School, Hannover, Germany
| | - Georg Stamm
- Department of Radiology, Hannover Medical School, Hannover, Germany.,Department of Diagnostic and Interventional Radiology, University Medical Center, Göttingen, Germany
| | - Thomas Werncke
- Department of Radiology, Hannover Medical School, Hannover, Germany
| | - Frank Wacker
- Department of Radiology, Hannover Medical School, Hannover, Germany
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Hans Christiansen
- Radiation Oncology Research Unit, Hannover Medical School, Hannover, Germany
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16
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Murashko MM, Stasevich EM, Schwartz AM, Kuprash DV, Uvarova AN, Demin DE. The Role of RNA in DNA Breaks, Repair and Chromosomal Rearrangements. Biomolecules 2021; 11:biom11040550. [PMID: 33918762 PMCID: PMC8069526 DOI: 10.3390/biom11040550] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 03/31/2021] [Accepted: 04/07/2021] [Indexed: 12/28/2022] Open
Abstract
Incorrect reparation of DNA double-strand breaks (DSB) leading to chromosomal rearrangements is one of oncogenesis's primary causes. Recently published data elucidate the key role of various types of RNA in DSB formation, recognition and repair. With growing interest in RNA biology, increasing RNAs are classified as crucial at the different stages of the main pathways of DSB repair in eukaryotic cells: nonhomologous end joining (NHEJ) and homology-directed repair (HDR). Gene mutations or variation in expression levels of such RNAs can lead to local DNA repair defects, increasing the chromosome aberration frequency. Moreover, it was demonstrated that some RNAs could stimulate long-range chromosomal rearrangements. In this review, we discuss recent evidence demonstrating the role of various RNAs in DSB formation and repair. We also consider how RNA may mediate certain chromosomal rearrangements in a sequence-specific manner.
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Affiliation(s)
- Matvey Mikhailovich Murashko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (M.M.M.); (E.M.S.); (A.M.S.); (D.V.K.); (A.N.U.)
| | - Ekaterina Mikhailovna Stasevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (M.M.M.); (E.M.S.); (A.M.S.); (D.V.K.); (A.N.U.)
| | - Anton Markovich Schwartz
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (M.M.M.); (E.M.S.); (A.M.S.); (D.V.K.); (A.N.U.)
- Moscow Institute of Physics and Technology, Department of Molecular and Biological Physics, 141701 Moscow, Russia
| | - Dmitriy Vladimirovich Kuprash
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (M.M.M.); (E.M.S.); (A.M.S.); (D.V.K.); (A.N.U.)
| | - Aksinya Nicolaevna Uvarova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (M.M.M.); (E.M.S.); (A.M.S.); (D.V.K.); (A.N.U.)
| | - Denis Eriksonovich Demin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (M.M.M.); (E.M.S.); (A.M.S.); (D.V.K.); (A.N.U.)
- Correspondence:
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17
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Singh M, Bacolla A, Chaudhary S, Hunt CR, Pandita S, Chauhan R, Gupta A, Tainer JA, Pandita TK. Histone Acetyltransferase MOF Orchestrates Outcomes at the Crossroad of Oncogenesis, DNA Damage Response, Proliferation, and Stem Cell Development. Mol Cell Biol 2020; 40:e00232-20. [PMID: 32661120 PMCID: PMC7459263 DOI: 10.1128/mcb.00232-20] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The DNA and protein complex known as chromatin is subject to posttranslational modifications (PTMs) that regulate cellular functions such that PTM dysregulation can lead to disease, including cancer. One critical PTM is acetylation/deacetylation, which is being investigated as a means to develop targeted cancer therapies. The histone acetyltransferase (HAT) family of proteins performs histone acetylation. In humans, MOF (hMOF), a member of the MYST family of HATs, acetylates histone H4 at lysine 16 (H4K16ac). MOF-mediated acetylation plays a critical role in the DNA damage response (DDR) and embryonic stem cell development. Functionally, MOF is found in two distinct complexes: NSL (nonspecific lethal) in humans and MSL (male-specific lethal) in flies. The NSL complex is also able to acetylate additional histone H4 sites. Dysregulation of MOF activity occurs in multiple cancers, including ovarian cancer, medulloblastoma, breast cancer, colorectal cancer, and lung cancer. Bioinformatics analysis of KAT8, the gene encoding hMOF, indicated that it is highly overexpressed in kidney tumors as part of a concerted gene coexpression program that can support high levels of chromosome segregation and cell proliferation. The linkage between MOF and tumor proliferation suggests that there are additional functions of MOF that remain to be discovered.
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Affiliation(s)
- Mayank Singh
- Department of Medical Oncology, BRAIRCH, All India Institute of Medical Sciences Delhi, New Delhi, India
| | - Albino Bacolla
- Department of Cancer Biology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas, USA
- Department of Molecular and Cellular Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas, USA
| | - Shilpi Chaudhary
- Department of Medical Oncology, BRAIRCH, All India Institute of Medical Sciences Delhi, New Delhi, India
| | - Clayton R Hunt
- The Houston Methodist Research Institute, Houston, Texas, USA
| | - Shruti Pandita
- Department of Internal Medicine, Division of Hematology, Oncology and Cellular Therapy, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Ravi Chauhan
- Department of Medical Oncology, BRAIRCH, All India Institute of Medical Sciences Delhi, New Delhi, India
| | - Ashna Gupta
- Department of Medical Oncology, BRAIRCH, All India Institute of Medical Sciences Delhi, New Delhi, India
| | - John A Tainer
- Department of Cancer Biology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas, USA
- Department of Molecular and Cellular Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas, USA
| | - Tej K Pandita
- The Houston Methodist Research Institute, Houston, Texas, USA
- Department of Cellular and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
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18
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Francica P, Mutlu M, Blomen VA, Oliveira C, Nowicka Z, Trenner A, Gerhards NM, Bouwman P, Stickel E, Hekkelman ML, Lingg L, Klebic I, van de Ven M, de Korte-Grimmerink R, Howald D, Jonkers J, Sartori AA, Fendler W, Chapman JR, Brummelkamp T, Rottenberg S. Functional Radiogenetic Profiling Implicates ERCC6L2 in Non-homologous End Joining. Cell Rep 2020; 32:108068. [PMID: 32846126 DOI: 10.1016/j.celrep.2020.108068] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 04/27/2020] [Accepted: 08/04/2020] [Indexed: 12/20/2022] Open
Abstract
Using genome-wide radiogenetic profiling, we functionally dissect vulnerabilities of cancer cells to ionizing radiation (IR). We identify ERCC6L2 as a major determinant of IR response, together with classical DNA damage response genes and members of the recently identified shieldin and CTC1-STN1-TEN1 (CST) complexes. We show that ERCC6L2 contributes to non-homologous end joining (NHEJ), and it may exert this function through interactions with SFPQ. In addition to causing radiosensitivity, ERCC6L2 loss restores DNA end resection and partially rescues homologous recombination (HR) in BRCA1-deficient cells. As a consequence, ERCC6L2 deficiency confers resistance to poly (ADP-ribose) polymerase (PARP) inhibition in tumors deficient for both BRCA1 and p53. Moreover, we show that ERCC6L2 mutations are found in human tumors and correlate with a better overall survival in patients treated with radiotherapy (RT); this finding suggests that ERCC6L2 is a predictive biomarker of RT response.
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Affiliation(s)
- Paola Francica
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | - Merve Mutlu
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | - Vincent A Blomen
- Division of Biochemistry, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Catarina Oliveira
- Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Zuzanna Nowicka
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, 92-215 Lodz, Poland
| | - Anika Trenner
- Institute of Molecular Cancer Research, University of Zurich, 8057 Zurich, Switzerland
| | - Nora M Gerhards
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | - Peter Bouwman
- Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Division of Molecular Pathology, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Elmer Stickel
- Division of Biochemistry, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Maarten L Hekkelman
- Division of Biochemistry, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Lea Lingg
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | - Ismar Klebic
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | - Marieke van de Ven
- Mouse Clinic for Cancer and Aging Research (MCCA), Preclinical Intervention Unit, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Renske de Korte-Grimmerink
- Mouse Clinic for Cancer and Aging Research (MCCA), Preclinical Intervention Unit, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Denise Howald
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | - Jos Jonkers
- Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Division of Molecular Pathology, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Alessandro A Sartori
- Institute of Molecular Cancer Research, University of Zurich, 8057 Zurich, Switzerland
| | - Wojciech Fendler
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, 92-215 Lodz, Poland; Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - J Ross Chapman
- Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Thijn Brummelkamp
- Division of Biochemistry, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Sven Rottenberg
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland; Division of Molecular Pathology, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Bern Center for Precision Medicine, University of Bern, 3012 Bern, Switzerland.
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19
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denDekker AD, Davis FM, Joshi AD, Wolf SJ, Allen R, Lipinski J, Nguyen B, Kirma J, Nycz D, Bermick J, Moore BB, Gudjonsson JE, Kunkel SL, Gallagher KA. TNF-α regulates diabetic macrophage function through the histone acetyltransferase MOF. JCI Insight 2020; 5:132306. [PMID: 32069267 DOI: 10.1172/jci.insight.132306] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 02/12/2020] [Indexed: 12/18/2022] Open
Abstract
A critical component of wound healing is the transition from the inflammatory phase to the proliferation phase to initiate healing and remodeling of the wound. Macrophages are critical for the initiation and resolution of the inflammatory phase during wound repair. In diabetes, macrophages display a sustained inflammatory phenotype in late wound healing characterized by elevated production of inflammatory cytokines, such as TNF-α. Previous studies have shown that an altered epigenetic program directs diabetic macrophages toward a proinflammatory phenotype, contributing to a sustained inflammatory phase. Males absent on the first (MOF) is a histone acetyltransferase (HAT) that has been shown be a coactivator of TNF-α signaling and promote NF-κB-mediated gene transcription in prostate cancer cell lines. Based on MOF's role in TNF-α/NF-κB-mediated gene expression, we hypothesized that MOF influences macrophage-mediated inflammation during wound repair. We used myeloid-specific Mof-knockout (Lyz2Cre Moffl/fl) and diet-induced obese (DIO) mice to determine the function of MOF in diabetic wound healing. MOF-deficient mice exhibited reduced inflammatory cytokine gene expression. Furthermore, we found that wound macrophages from DIO mice had elevated MOF levels and higher levels of acetylated histone H4K16, MOF's primary substrate of HAT activity, on the promoters of inflammatory genes. We further identified that MOF expression could be stimulated by TNF-α and that treatment with etanercept, an FDA-approved TNF-α inhibitor, reduced MOF levels and improved wound healing in DIO mice. This report is the first to our knowledge to define an important role for MOF in regulating macrophage-mediated inflammation in wound repair and identifies TNF-α inhibition as a potential therapy for the treatment of chronic inflammation in diabetic wounds.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Bethany B Moore
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | | | | | - Katherine A Gallagher
- Department of Surgery.,Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
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20
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Onn L, Portillo M, Ilic S, Cleitman G, Stein D, Kaluski S, Shirat I, Slobodnik Z, Einav M, Erdel F, Akabayov B, Toiber D. SIRT6 is a DNA double-strand break sensor. eLife 2020; 9:51636. [PMID: 31995034 PMCID: PMC7051178 DOI: 10.7554/elife.51636] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 01/23/2020] [Indexed: 12/18/2022] Open
Abstract
DNA double-strand breaks (DSB) are the most deleterious type of DNA damage. In this work, we show that SIRT6 directly recognizes DNA damage through a tunnel-like structure that has high affinity for DSB. SIRT6 relocates to sites of damage independently of signaling and known sensors. It activates downstream signaling for DSB repair by triggering ATM recruitment, H2AX phosphorylation and the recruitment of proteins of the homologous recombination and non-homologous end joining pathways. Our findings indicate that SIRT6 plays a previously uncharacterized role as a DNA damage sensor, a critical factor in initiating the DNA damage response (DDR). Moreover, other Sirtuins share some DSB-binding capacity and DDR activation. SIRT6 activates the DDR before the repair pathway is chosen, and prevents genomic instability. Our findings place SIRT6 as a sensor of DSB, and pave the road to dissecting the contributions of distinct DSB sensors in downstream signaling. DNA is a double-stranded molecule in which the two strands run in opposite directions, like the lanes on a two-lane road. Also like a road, DNA can be damaged by use and adverse conditions. Double-strand breaks – where both strands of DNA snap at once – are the most dangerous type of DNA damage, so cells have systems in place to rapidly detect and repair this kind of damage. There are three confirmed sensors for double-strand break in human cells. A fourth protein, known as SIRT6, arrives within five seconds of DNA damage, and was known to make the DNA more accessible so that it can be repaired. However, it was unclear whether SIRT6 could detect the double-strand break itself, or whether it was recruited to the damage by another double-strand break sensor. To address this issue, Onn et al. blocked the three other sensors in human cells and watched the response to DNA damage. Even when all the other sensors were inactive, SIRT6 still arrived at damaged DNA and activated the DNA damage response. To find out how SIRT6 sensed DNA damage, Onn et al. examined how purified SIRT6 interacts with different kinds of DNA. This revealed that SIRT6 sticks to broken DNA ends, especially if the end of one strand slightly overhangs the other – a common feature of double-strand breaks. A closer look at the structure of the SIRT6 protein revealed that it contains a narrow tube, which fits over the end of one broken DNA strand. When both strands break at once, two SIRT6 molecules cap the broken ends, joining together to form a pair. This pair not only protects the open ends of the DNA from further damage, it also sends signals to initiating repairs. In this way, SIRT6 could be thought of acting like a paramedic who arrives first on the scene of an accident and works to treat the injured while waiting for more specialized help to arrive. Understanding the SIRT6 sensor could improve knowledge about how cells repair their DNA. SIRT6 arrives before the cell chooses how to fix its broken DNA, so studying it further could reveal how that critical decision happens. This is important for medical research because DNA damage builds up in age-related diseases like cancer and neurodegeneration. In the long term, these findings can help us develop new treatments that target different types of DNA damage sensors.
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Affiliation(s)
- Lior Onn
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.,The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Miguel Portillo
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.,The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Stefan Ilic
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Gal Cleitman
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.,The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Daniel Stein
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.,The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Shai Kaluski
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.,The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Ido Shirat
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.,The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Zeev Slobodnik
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.,The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Monica Einav
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.,The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Fabian Erdel
- Division of Chromatin Networks, German Cancer Research Center (DKFZ), BioQuant, Heidelberg, Germany.,Centre de Biologie Intégrative, CNRS UPS, Toulouse, France
| | - Barak Akabayov
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Debra Toiber
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.,The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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21
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Mohseni-Salehi FS, Zare-Mirakabad F, Sadeghi M, Ghafouri-Fard S. A Stochastic Model of DNA Double-Strand Breaks Repair Throughout the Cell Cycle. Bull Math Biol 2020; 82:11. [PMID: 31933029 DOI: 10.1007/s11538-019-00692-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 12/20/2019] [Indexed: 01/15/2023]
Abstract
Cell cycle phase is a decisive factor in determining the repair pathway of DNA double-strand breaks (DSBs) by non-homologous end joining (NHEJ) or homologous recombination (HR). Recent experimental studies revealed that 53BP1 and BRCA1 are the key mediators of the DNA damage response (DDR) with antagonizing roles in choosing the appropriate DSB repair pathway in G1, S, and G2 phases. Here, we present a stochastic model of biochemical kinetics involved in detecting and repairing DNA DSBs induced by ionizing radiation during the cell cycle progression. A three-dimensional stochastic process is defined to monitor the cell cycle phase and DSBs repair at times after irradiation. To estimate the model parameters, a Metropolis Monte Carlo method is applied to perform maximum likelihood estimation utilizing the kinetics of γ-H2AX and RAD51 foci formation in G1, S, and G2 phases. The recruitment of DSB repair proteins is verified by comparing our model predictions with the corresponding experimental data on human cells after exposure to X and γ-radiation. Furthermore, the interaction between 53BP1 and BRCA1 is simulated for G1 and S/G2 phases determining the competition between NHEJ and HR pathways in repairing induced DSBs throughout the cell cycle. In accordance with recent biological data, the numerical results demonstrate that the maximum proportion of HR occurs in S phase cells and the high level of NHEJ takes place in G1 and G2 phases. Moreover, the stochastic realizations of the total yield of simple and complex DSBs ligation are compared for G1 and S/G2 damaged cells. Finally, the proposed stochastic model is validated when DSBs induced by different particle radiation such as iron, silicon, oxygen, proton, and carbon.
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Affiliation(s)
- Fazeleh S Mohseni-Salehi
- Mathematics and Computer Science Department, Amirkabir University of Technology (Tehran Polytechinc), Tehran, Iran
| | - Fatemeh Zare-Mirakabad
- Mathematics and Computer Science Department, Amirkabir University of Technology (Tehran Polytechinc), Tehran, Iran.
| | - Mehdi Sadeghi
- School of Biological Science, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
- National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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22
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Dong Z, Zou J, Li J, Pang Y, Liu Y, Deng C, Chen F, Cui H. MYST1/KAT8 contributes to tumor progression by activating EGFR signaling in glioblastoma cells. Cancer Med 2019; 8:7793-7808. [PMID: 31691527 PMCID: PMC6912028 DOI: 10.1002/cam4.2639] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 09/30/2019] [Accepted: 10/10/2019] [Indexed: 12/18/2022] Open
Abstract
With short survival time, glioblastoma (GBM) is the most malignant tumor in the central nervous system. Recently, epigenetic enzymes play essential roles in the regulation of tumorigenesis and cancer development of GBM. However, little is known about MYST1/KAT8/MOF, a histone acetylation enzyme, in GBM. The present study shows that MYST1 promotes GBM progression through activating epidermal growth factor receptor (EGFR) signaling. MYST1 expression was increased in GBM and was negatively correlated with prognosis in patients with glioma and GBM. Knockdown of MYST1 reduced cell proliferation and BrdU incorporation in LN229, U87, and A172 GBM cells. Besides, MYST1 downregulation also induced cell cycle arrest at G2M phase, as well as the reduced expression of CDK1, Cyclin A, Cyclin B1, and increased expression of p21CIP1/Waf1. Meanwhile, Self‐renewal capability in vitro and tumorigenecity in vivo were also impaired after MYST1 knockdown. Importantly, MYST1 expression was lowly expressed in mesenchymal subtype of GBM and was positively correlated with EGFR expression in a cohort from The Cancer Genome Atlas. Western blot subsequently confirmed that phosphorylation and activation of p‐Try1068 of EGFR, p‐Ser473 of AKT and p‐Thr202/Tyr204 of Erk1/2 were also decreased by MYST1 knockdown. Consistent with the results above, overexpression of MYST1 promoted GBM growth and activated EGFR signaling in vitro and in vivo. In addition, erlotinib, a US Food and Drug Administration approved cancer drug which targets EGFR, was able to rescue MYST1‐promoted cell proliferation and EGFR signaling pathway. Furthermore, the transcription of EGF, an EFGR ligand, was shown to be positively regulated by MYST1 possibly via H4K16 acetylation. Our findings elucidate MYST1 as a tumor promoter in GBM and an EGFR activator, and may be a potential drug target for GBM treatment.
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Affiliation(s)
- Zhen Dong
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing, China.,Cancer Center, Medical Research Institute, Southwest University, Chongqing, China.,Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, China.,Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Chongqing, China
| | - Jiahua Zou
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing, China
| | - Jifu Li
- College of Biotechnology, Southwest University, Chongqing, China
| | - Yi Pang
- Chongqing Engineering Research Center of Antitumor Natural Drugs, Chongqing Three Gorges Medical College, Chongqing, China
| | - Yudong Liu
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing, China.,Cancer Center, Medical Research Institute, Southwest University, Chongqing, China.,Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, China.,Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Chongqing, China
| | - Chaowei Deng
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing, China.,Cancer Center, Medical Research Institute, Southwest University, Chongqing, China.,Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, China.,Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Chongqing, China
| | - Fei Chen
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, USA
| | - Hongjuan Cui
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing, China.,Cancer Center, Medical Research Institute, Southwest University, Chongqing, China.,Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, China.,Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Chongqing, China
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23
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Horikoshi N, Sharma D, Leonard F, Pandita RK, Charaka VK, Hambarde S, Horikoshi NT, Gaur Khaitan P, Chakraborty S, Cote J, Godin B, Hunt CR, Pandita TK. Pre-existing H4K16ac levels in euchromatin drive DNA repair by homologous recombination in S-phase. Commun Biol 2019; 2:253. [PMID: 31286070 PMCID: PMC6611875 DOI: 10.1038/s42003-019-0498-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 05/29/2019] [Indexed: 12/22/2022] Open
Abstract
The homologous recombination (HR) repair pathway maintains genetic integrity after DNA double-strand break (DSB) damage and is particularly crucial for maintaining fidelity of expressed genes. Histone H4 acetylation on lysine 16 (H4K16ac) is associated with transcription, but how pre-existing H4K16ac directly affects DSB repair is not known. To answer this question, we used CRISPR/Cas9 technology to introduce I-SceI sites, or repair pathway reporter cassettes, at defined locations within gene-rich (high H4K16ac/euchromatin) and gene-poor (low H4K16ac/heterochromatin) regions. The frequency of DSB repair by HR is higher in gene-rich regions. Interestingly, artificially targeting H4K16ac at specific locations using gRNA/dCas9-MOF increases HR frequency in euchromatin. Finally, inhibition/depletion of RNA polymerase II or Cockayne syndrome B protein leads to decreased recruitment of HR factors at DSBs. These results indicate that the pre-existing H4K16ac status at specific locations directly influences the repair of local DNA breaks, favoring HR in part through the transcription machinery.
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Affiliation(s)
- Nobuo Horikoshi
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX 77030 USA
- Present Address: Department of Radiation Oncology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Dharmendra Sharma
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX 77030 USA
| | - Fransisca Leonard
- Department of Nanomedicine, 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
| | - Vijaya K. Charaka
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX 77030 USA
| | - Shashank Hambarde
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX 77030 USA
| | - Nobuko T. Horikoshi
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX 77030 USA
| | - Puja Gaur Khaitan
- Department of Surgery, The Houston Methodist Research Institute, Houston, TX 77030 USA
- Present Address: Department of Surgery, Medstar Washington Hospital Center, Washington, DC 20010 USA
| | - Sharmistha Chakraborty
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX 77030 USA
| | - Jacques Cote
- St. Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Quebec City, QC G1V4G2 Canada
| | - Biana Godin
- Department of Nanomedicine, The Houston Methodist Research Institute, 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
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24
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Ketchum CC, Larsen CD, McNeil A, Meyer-Ficca ML, Meyer RG. Early histone H4 acetylation during chromatin remodeling in equine spermatogenesis. Biol Reprod 2019; 98:115-129. [PMID: 29186293 DOI: 10.1093/biolre/iox159] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 11/23/2017] [Indexed: 01/08/2023] Open
Abstract
Chromatin remodeling during spermatogenesis culminates in the exchange of nucleosomes for transition proteins and protamines as an important part of spermatid development to give rise to healthy sperm. Comparative immunofluorescence analyses of equine and murine testis histological sections were used to characterize nucleoprotein exchange in the stallion. Histone H4 hyperacetylation is considered a key event of histone removal during the nucleoprotein transition to a protamine-based sperm chromatin structure. In the stallion, but not the mouse, H4 was already highly acetylated in lysine residues K5, K8, and K12 in round spermatids almost immediately after meiotic division. Time courses of transition protein 1 (TP1), protamine 1, H2A histone family member Z (H2AFZ), and testis-specific histone H2B variant (TH2B) expression in stallion spermatogenesis were similar to the mouse where protamine 1 and TP1 were only expressed in elongating spermatids much later in spermatid development. The additional acetylation of H4 in K16 position (H4K16ac) was detected during a brief phase of spermatid elongation in both species, concomitant with the phosphorylation of the noncanonical histone variant H2AFX resulting from DNA strand break-mediated DNA relaxation. The results suggest that H4K16 acetylation, which is dependent on DNA damage signaling, may be more important for nucleosome replacement in spermiogenesis than indicated by data obtained in rodents and highlight the value of the stallion as an alternative animal model for investigating human spermatogenesis. A revised classification system of the equine spermatogenic cycle for simplified comparison with the mouse is proposed to this end.
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Affiliation(s)
- Chelsea C Ketchum
- Department of Animal, Dairy and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah Experimental Station, Utah State University, Logan, Utah, USA.,Utah Experimental Station, Utah State University, Logan, Utah, USA
| | - Casey D Larsen
- School of Veterinary Medicine (Washington-Idaho-Montana-Utah Regional Veterinary Medical Program, WIMU), Utah State University, Logan, Utah, USA
| | - Alexis McNeil
- Department of Animal, Dairy and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah Experimental Station, Utah State University, Logan, Utah, USA
| | - Mirella L Meyer-Ficca
- Department of Animal, Dairy and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah Experimental Station, Utah State University, Logan, Utah, USA.,School of Veterinary Medicine (Washington-Idaho-Montana-Utah Regional Veterinary Medical Program, WIMU), Utah State University, Logan, Utah, USA
| | - Ralph G Meyer
- Department of Animal, Dairy and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah Experimental Station, Utah State University, Logan, Utah, USA.,Utah Experimental Station, Utah State University, Logan, Utah, USA.,School of Veterinary Medicine (Washington-Idaho-Montana-Utah Regional Veterinary Medical Program, WIMU), Utah State University, Logan, Utah, USA
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25
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Abstract
The timely and precise repair of DNA damage, or more specifically DNA double-strand breaks (DSBs) - the most deleterious DNA lesions, is crucial for maintaining genome integrity and cellular homeostasis. An appropriate cellular response to DNA DSBs requires the integration of various factors, including the post-translational modifications (PTMs) of chromatin and chromatin-associated proteins. Notably, the PTMs of histones have been shown to play a fundamental role in initiating and regulating cellular responses to DNA DSBs. Here we review the role of the major histone PTMs, including phosphorylation, ubiquitination, methylation and acetylation, and their interactions during DNA DSB-induced responses.
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Affiliation(s)
- Hieu T Van
- a Department of Epigenetics and Molecular Carcinogenesis , University of Texas M.D. Anderson Cancer Center , Houston , TX , USA
| | - Margarida A Santos
- a Department of Epigenetics and Molecular Carcinogenesis , University of Texas M.D. Anderson Cancer Center , Houston , TX , USA
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26
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Sharma AK, Hendzel MJ. The relationship between histone posttranslational modification and DNA damage signaling and repair. Int J Radiat Biol 2018; 95:382-393. [PMID: 30252564 DOI: 10.1080/09553002.2018.1516911] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
PURPOSE The cellular response to DNA damage occurs in the context of an organized chromatin environment in order to maintain genome integrity. Immediately after DNA damage, an array of histone modifications are induced to relieve the physical constraints of the chromatin environment, mark the site as damaged, and function as a platform for the assembly of mediator and effector proteins of DNA damage response signaling pathway. Changes in chromatin structure in the vicinity of the DNA double-strand break (DSB) facilitates the efficient initiation of the DNA damage signaling cascade. Failure of induction of DNA damage responsive histone modifications may lead to genome instability and cancer. Here we will discuss our current understanding of the DNA damage responsive histone modifications and their role in DNA repair as well as their implications for genome stability. We further discuss recent studies which highlight not only how histone modification has involved in the signaling and remodeling at the DSB but also how it influences the DNA repair pathway choice. CONCLUSIONS Histone modifications pattern alter during the induction of DNA DSBs induction as well as during the repair and recovery phase of DNA damage response. It will be interesting to understand more precisely, how DSBs within chromatin are repaired by HR and NHEJ. The emergence of proteomic and genomic technologies in combination with advanced microscopy and imaging methods will help in better understanding the role of chromatin environment in the regulation of genome stability.
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Affiliation(s)
- Ajit K Sharma
- a Departments of Cell Biology and Oncology, Faculty of Medicine and Dentistry , University of Alberta , Edmonton , Canada
| | - Michael J Hendzel
- a Departments of Cell Biology and Oncology, Faculty of Medicine and Dentistry , University of Alberta , Edmonton , Canada
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27
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Mutant FUS causes DNA ligation defects to inhibit oxidative damage repair in Amyotrophic Lateral Sclerosis. Nat Commun 2018; 9:3683. [PMID: 30206235 PMCID: PMC6134028 DOI: 10.1038/s41467-018-06111-6] [Citation(s) in RCA: 131] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 08/14/2018] [Indexed: 01/17/2023] Open
Abstract
Genome damage and defective repair are etiologically linked to neurodegeneration. However, the specific mechanisms involved remain enigmatic. Here, we identify defects in DNA nick ligation and oxidative damage repair in a subset of amyotrophic lateral sclerosis (ALS) patients. These defects are caused by mutations in the RNA/DNA-binding protein FUS. In healthy neurons, FUS protects the genome by facilitating PARP1-dependent recruitment of XRCC1/DNA Ligase IIIα (LigIII) to oxidized genome sites and activating LigIII via direct interaction. We discover that loss of nuclear FUS caused DNA nick ligation defects in motor neurons due to reduced recruitment of XRCC1/LigIII to DNA strand breaks. Moreover, DNA ligation defects in ALS patient-derived iPSC lines carrying FUS mutations and in motor neurons generated therefrom are rescued by CRISPR/Cas9-mediated correction of mutation. Our findings uncovered a pathway of defective DNA ligation in FUS-linked ALS and suggest that LigIII-targeted therapies may prevent or slow down disease progression.
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28
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Mattoo AR, Joun A, Jessup JM. Repurposing of mTOR Complex Inhibitors Attenuates MCL-1 and Sensitizes to PARP Inhibition. Mol Cancer Res 2018; 17:42-53. [DOI: 10.1158/1541-7786.mcr-18-0650] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Revised: 08/09/2018] [Accepted: 08/30/2018] [Indexed: 11/16/2022]
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29
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Sunavala-Dossabhoy G. Preserving salivary gland physiology against genotoxic damage - the Tousled way. Oral Dis 2018; 24:1390-1398. [PMID: 29383801 DOI: 10.1111/odi.12836] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 01/23/2018] [Accepted: 01/23/2018] [Indexed: 12/23/2022]
Abstract
Tousled and its homologs are evolutionarily conserved serine/threonine kinases present in plants and animals. Human Tousled-like kinases, TLK1 and TLK2, are implicated in chromatin assembly during DNA replication, chromosome segregation during mitosis, as well as in DNA damage response and repair. They share a high degree of sequence similarity, but have few non-redundant functions. Our laboratory has studied TLK1 and found that it increases the resistance of cells to ionizing radiation (IR) damage through expedited double-strand break (DSB) repair. DSBs are life-threatening lesions which when repaired restore DNA integrity and promote cell survival. A major focus in our laboratory is to dissect TLK1's role in DSB response and repair and study its usefulness in averting salivary gland hypofunction, a condition that invariably afflicts patients undergoing regional radiotherapy. The identification of anti-silencing factor 1 (ASF1), histone H3, and Rad9 as substrates of TLK1 links the protein to chromatin organization and DNA damage response and repair. However, recent findings of new interacting partners that include NEK1 suggest that TLK1 may play a broader role in DSB repair. This review provides a brief overview of the DNA damage response and DSB repair, and it highlights our current understanding of TLK1 in the process.
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Affiliation(s)
- G Sunavala-Dossabhoy
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA, USA
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30
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Jiang H, Gao Q, Zheng W, Yin S, Wang L, Zhong L, Ali A, Khan T, Hao Q, Fang H, Sun X, Xu P, Pandita TK, Jiang X, Shi Q. MOF influences meiotic expansion of H2AX phosphorylation and spermatogenesis in mice. PLoS Genet 2018; 14:e1007300. [PMID: 29795555 PMCID: PMC6019819 DOI: 10.1371/journal.pgen.1007300] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 06/26/2018] [Accepted: 03/07/2018] [Indexed: 12/11/2022] Open
Abstract
Three waves of H2AX phosphorylation (γH2AX) have been observed in male meiotic prophase I: the first is ATM-dependent and occurs at leptonema, while the second and third are ATR-dependent, occuring at zygonema and pachynema, respectively. The third wave of H2AX phosphorylation marks and silences unsynapsed chromosomes. Little is known about H2AX phosphorylation expands to chromatin-wide regions in spermatocytes. Here, we report that histone acetyltransferase (HAT) MOF is involved in all three waves of H2AX phosphorylation expansion. Germ cell-specific deletion of Mof in spermatocytes by Stra8-Cre (Mof cKO) caused global loss of H4K16ac. In leptotene and zygotene spermatocytes of cKO mice, the γH2AX signals were observed only along the chromosomal axes, and chromatin-wide H2AX phosphorylation was lost. In almost 40% of early-mid pachytene spermatocytes from Mof cKO mice, γH2AX and MDC1 were detected along the unsynapsed axes of the sex chromosomes, but failed to expand, which consequently caused meiotic sex chromosome inactivation (MSCI) failure. Furthermore, though RAD51 was proficiently recruited to double-strand break (DSB) sites, defects in DSB repair and crossover formation were observed in Mof cKO spermatocytes, indicating that MOF facilitates meiotic DSB repair after RAD51 recruitment. We propose that MOF regulates male meiosis and is involved in the expansion of all three waves of H2AX phosphorylation from the leptotene to pachytene stages, initiated by ATM and ATR, respectively.
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Affiliation(s)
- Hanwei Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale, USTC-SJH Joint Center for Human Reproduction and Genetics, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China (USTC), Collaborative Innovation Center of Genetics and Development, Hefei, Anhui, China
| | - Qian Gao
- Hefei National Laboratory for Physical Sciences at the Microscale, USTC-SJH Joint Center for Human Reproduction and Genetics, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China (USTC), Collaborative Innovation Center of Genetics and Development, Hefei, Anhui, China
| | - Wei Zheng
- Hefei National Laboratory for Physical Sciences at the Microscale, USTC-SJH Joint Center for Human Reproduction and Genetics, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China (USTC), Collaborative Innovation Center of Genetics and Development, Hefei, Anhui, China
| | - Shi Yin
- Hefei National Laboratory for Physical Sciences at the Microscale, USTC-SJH Joint Center for Human Reproduction and Genetics, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China (USTC), Collaborative Innovation Center of Genetics and Development, Hefei, Anhui, China
| | - Liu Wang
- Hefei National Laboratory for Physical Sciences at the Microscale, USTC-SJH Joint Center for Human Reproduction and Genetics, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China (USTC), Collaborative Innovation Center of Genetics and Development, Hefei, Anhui, China
| | - Liangwen Zhong
- Hefei National Laboratory for Physical Sciences at the Microscale, USTC-SJH Joint Center for Human Reproduction and Genetics, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China (USTC), Collaborative Innovation Center of Genetics and Development, Hefei, Anhui, China
| | - Asim Ali
- Hefei National Laboratory for Physical Sciences at the Microscale, USTC-SJH Joint Center for Human Reproduction and Genetics, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China (USTC), Collaborative Innovation Center of Genetics and Development, Hefei, Anhui, China
| | - Teka Khan
- Hefei National Laboratory for Physical Sciences at the Microscale, USTC-SJH Joint Center for Human Reproduction and Genetics, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China (USTC), Collaborative Innovation Center of Genetics and Development, Hefei, Anhui, China
| | - Qiaomei Hao
- Hefei National Laboratory for Physical Sciences at the Microscale, USTC-SJH Joint Center for Human Reproduction and Genetics, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China (USTC), Collaborative Innovation Center of Genetics and Development, Hefei, Anhui, China
| | - Hui Fang
- Hefei National Laboratory for Physical Sciences at the Microscale, USTC-SJH Joint Center for Human Reproduction and Genetics, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China (USTC), Collaborative Innovation Center of Genetics and Development, Hefei, Anhui, China
| | - Xiaoling Sun
- Hefei National Laboratory for Physical Sciences at the Microscale, USTC-SJH Joint Center for Human Reproduction and Genetics, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China (USTC), Collaborative Innovation Center of Genetics and Development, Hefei, Anhui, China
| | - Peng Xu
- Hefei National Laboratory for Physical Sciences at the Microscale, USTC-SJH Joint Center for Human Reproduction and Genetics, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China (USTC), Collaborative Innovation Center of Genetics and Development, Hefei, Anhui, China
| | - Tej K. Pandita
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, United States
| | - Xiaohua Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale, USTC-SJH Joint Center for Human Reproduction and Genetics, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China (USTC), Collaborative Innovation Center of Genetics and Development, Hefei, Anhui, China
| | - Qinghua Shi
- Hefei National Laboratory for Physical Sciences at the Microscale, USTC-SJH Joint Center for Human Reproduction and Genetics, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China (USTC), Collaborative Innovation Center of Genetics and Development, Hefei, Anhui, China
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31
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Chakraborty S, Pandita RK, Hambarde S, Mattoo AR, Charaka V, Ahmed KM, Iyer SP, Hunt CR, Pandita TK. SMARCAD1 Phosphorylation and Ubiquitination Are Required for Resection during DNA Double-Strand Break Repair. iScience 2018; 2:123-135. [PMID: 29888761 PMCID: PMC5993204 DOI: 10.1016/j.isci.2018.03.016] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 01/16/2018] [Accepted: 02/28/2018] [Indexed: 02/08/2023] Open
Abstract
The chromatin remodeling factor SMARCAD1, an SWI/SNF ATPase family member, has a role in 5' end resection at DNA double-strand breaks (DSBs) to produce single-strand DNA (ssDNA), a critical step for subsequent checkpoint and repair factor loading to remove DNA damage. However, the mechanistic details of SMARCAD1 coupling to the DNA damage response and repair pathways remains unknown. Here we report that SMARCAD1 is recruited to DNA DSBs through an ATM-dependent process. Depletion of SMARCAD1 reduces ionizing radiation (IR)-induced repairosome foci formation and DSB repair by homologous recombination (HR). IR induces SMARCAD1 phosphorylation at a conserved T906 by ATM kinase, a modification essential for SMARCAD1 recruitment to DSBs. Interestingly, T906 phosphorylation is also important for SMARCAD1 ubiquitination by RING1 at K905. Both these post-translational modifications are critical for regulating the role of SMARCAD1 in DNA end resection, HR-mediated repair, and cell survival after DNA damage.
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Affiliation(s)
- Sharmistha Chakraborty
- Department of Radiation Oncology, Houston Methodist Cancer Center, The Houston Methodist Research Institute, Weill Cornell Medical College, Houston, TX 77030, USA.
| | - Raj K Pandita
- Department of Radiation Oncology, Houston Methodist Cancer Center, The Houston Methodist Research Institute, Weill Cornell Medical College, Houston, TX 77030, USA
| | - Shashank Hambarde
- Department of Radiation Oncology, Houston Methodist Cancer Center, The Houston Methodist Research Institute, Weill Cornell Medical College, Houston, TX 77030, USA
| | - Abid R Mattoo
- Department of Radiation Oncology, Houston Methodist Cancer Center, The Houston Methodist Research Institute, Weill Cornell Medical College, Houston, TX 77030, USA
| | - Vijaya Charaka
- Department of Radiation Oncology, Houston Methodist Cancer Center, The Houston Methodist Research Institute, Weill Cornell Medical College, Houston, TX 77030, USA
| | - Kazi M Ahmed
- Department of Radiation Oncology, Houston Methodist Cancer Center, The Houston Methodist Research Institute, Weill Cornell Medical College, Houston, TX 77030, USA
| | - Swaminathan P Iyer
- Department of Hematology, Houston Methodist Cancer Center, The Houston Methodist Research Institute, Weill Cornell Medical College, Houston, TX 77030, USA
| | - Clayton R Hunt
- Department of Radiation Oncology, Houston Methodist Cancer Center, The Houston Methodist Research Institute, Weill Cornell Medical College, Houston, TX 77030, USA
| | - Tej K Pandita
- Department of Radiation Oncology, Houston Methodist Cancer Center, The Houston Methodist Research Institute, Weill Cornell Medical College, Houston, TX 77030, USA.
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32
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Wang H, Peng B, Pandita RK, Engler DA, Matsunami RK, Xu X, Hegde PM, Butler BE, Pandita TK, Mitra S, Xu B, Hegde ML. Aurora kinase B dependent phosphorylation of 53BP1 is required for resolving merotelic kinetochore-microtubule attachment errors during mitosis. Oncotarget 2018; 8:48671-48687. [PMID: 28415769 PMCID: PMC5564716 DOI: 10.18632/oncotarget.16225] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 03/03/2017] [Indexed: 01/11/2023] Open
Abstract
Defects in resolving kinetochore-microtubule attachment mistakes during mitosis is linked to chromosome instability associated with carcinogenesis as well as resistance to cancer therapy. Here we report for the first time that tumor suppressor p53-binding protein 1 (53BP1) is phosphorylated at serine 1342 (S1342) by Aurora kinase B both in vitro and in human cells, which is required for optimal recruitment of 53BP1 at kinetochores. Furthermore, 53BP1 staining normally localized on the outer kinetochore, extended to the whole kinetochore when it is merotelically-attached, in concert with mitotic centromere-associated kinesin. Kinetochore-binding of pS1342-53BP1 is essential for efficient resolving of merotelic attachment, a spontaneous kinetochore-microtubule connection error that usually causes aneuploidy. Consistently, loss of 53BP1 results in significant increase in lagging chromosome events, micronuclei formation and aneuploidy, due to the unresolved merotely in both cancer and primary cells, which is prevented by ectopic wild type 53BP1 but not by the nonphophorylable S1342A mutant. We thus document a novel DNA damage-independent function of 53BP1 in maintaining faithful chromosome segregation during mitosis.
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Affiliation(s)
- Haibo Wang
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA.,Houston Methodist Neurological Institute, Houston, TX, USA
| | - Bin Peng
- Beijing Key Laboratory of DNA Damage Response and College of Life Science, Capital Normal University, Beijing, China
| | - Raj K Pandita
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA
| | - David A Engler
- Proteomics Programmatic Core Laboratory, Houston Methodist Research Institute, Houston, TX, USA
| | - Risë K Matsunami
- Proteomics Programmatic Core Laboratory, Houston Methodist Research Institute, Houston, TX, USA
| | - Xingzhi Xu
- Beijing Key Laboratory of DNA Damage Response and College of Life Science, Capital Normal University, Beijing, China
| | - Pavana M Hegde
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA
| | - Brian E Butler
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA
| | - Tej K Pandita
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA.,Weill Medical College of Cornell University, New York, NY, USA
| | - Sankar Mitra
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA.,Weill Medical College of Cornell University, New York, NY, USA
| | - Bo Xu
- Department of Oncology, Southern Research Institute, Birmingham, AL, USA
| | - Muralidhar L Hegde
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA.,Houston Methodist Neurological Institute, Houston, TX, USA.,Weill Medical College of Cornell University, New York, NY, USA
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33
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Chen CC, Feng W, Lim PX, Kass EM, Jasin M. Homology-Directed Repair and the Role of BRCA1, BRCA2, and Related Proteins in Genome Integrity and Cancer. ANNUAL REVIEW OF CANCER BIOLOGY 2018; 2:313-336. [PMID: 30345412 PMCID: PMC6193498 DOI: 10.1146/annurev-cancerbio-030617-050502] [Citation(s) in RCA: 201] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Germ-line and somatic mutations in genes that promote homology-directed repair (HDR), especially BRCA1 and BRCA2, are frequently observed in several cancers, in particular, breast and ovary but also prostate and other cancers. HDR is critical for the error-free repair of DNA double-strand breaks and other lesions, and HDR factors also protect stalled replication forks. As a result, loss of BRCA1 or BRCA2 poses significant risks to genome integrity, leading not only to cancer predisposition but also to sensitivity to DNA-damaging agents, affecting therapeutic approaches. Here we review recent advances in our understanding of BRCA1 and BRCA2, including how they genetically interact with other repair factors, how they protect stalled replication forks, how they affect the response to aldehydes, and how loss of their functions links to mutation signatures. Importantly, given the recent advances with poly(ADP-ribose) polymerase inhibitors (PARPi) for the treatment of HDR-deficient tumors, we discuss mechanisms by which BRCA-deficient tumors acquire resistance to PARPi and other agents.
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Affiliation(s)
- Chun-Chin Chen
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY 10065
| | - Weiran Feng
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Pei Xin Lim
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Elizabeth M Kass
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY 10065
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065
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34
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MOF Suppresses Replication Stress and Contributes to Resolution of Stalled Replication Forks. Mol Cell Biol 2018; 38:MCB.00484-17. [PMID: 29298824 DOI: 10.1128/mcb.00484-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 12/05/2017] [Indexed: 01/13/2023] Open
Abstract
The human MOF (hMOF) protein belongs to the MYST family of histone acetyltransferases and plays a critical role in transcription and the DNA damage response. MOF is essential for cell proliferation; however, its role during replication and replicative stress is unknown. Here we demonstrate that cells depleted of MOF and under replicative stress induced by cisplatin, hydroxyurea, or camptothecin have reduced survival, a higher frequency of S-phase-specific chromosome damage, and increased R-loop formation. MOF depletion decreased replication fork speed and, when combined with replicative stress, also increased stalled replication forks as well as new origin firing. MOF interacted with PCNA, a key coordinator of replication and repair machinery at replication forks, and affected its ubiquitination and recruitment to the DNA damage site. Depletion of MOF, therefore, compromised the DNA damage repair response as evidenced by decreased Mre11, RPA70, Rad51, and PCNA focus formation, reduced DNA end resection, and decreased CHK1 phosphorylation in cells after exposure to hydroxyurea or cisplatin. These results support the argument that MOF plays an important role in suppressing replication stress induced by genotoxic agents at several stages during the DNA damage response.
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35
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Bakr A, Köcher S, Volquardsen J, Petersen C, Borgmann K, Dikomey E, Rothkamm K, Mansour WY. Impaired 53BP1/RIF1 DSB mediated end-protection stimulates CtIP-dependent end resection and switches the repair to PARP1-dependent end joining in G1. Oncotarget 2018; 7:57679-57693. [PMID: 27494840 PMCID: PMC5295381 DOI: 10.18632/oncotarget.11023] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 07/23/2016] [Indexed: 01/30/2023] Open
Abstract
End processing at DNA double strand breaks (DSB) is a decisive step in repair pathway selection. Here, we investigated the role of 53BP1/RIF1 in limiting BRCA1/CtIP-mediated end resection to control DSB repair pathway choice. ATM orchestrates this process through 53BP1 phosphorylation to promote RIF1 recruitment. As cells enter S/G2-phase, end resection is activated, which displaces pATM from DSB sites and diminishes 53BP1 phosphorylation and RIF1 recruitment. Consistently, the kinetics of ATM and 53BP1 phosphorylation in S/G2-phase concur. We show that defective 53BP1/RIF1-mediated DSB end-protection in G1-phase stimulates CtIP/MRE11-dependent end-resection, which requires Polo-like kinase 3. This end resection activity in G1 was shown to produce only short tracks of ssDNA overhangs, as evidenced by the findings that in 53BP1 depleted cells, (i) RPA focus intensity was significantly lower in G1 compared to that in S/G2 phase, and (ii) EXO1 knockdown did not alter either number or intensity of RPA foci in G1 but significantly decreased the RPA focus intensity in S/G2 phase. Importantly, we report that the observed DSB end resection in G1 phase inhibits DNA-PK-dependent nonhomologous end joining but is not sufficient to stimulate HR. Instead, it switches the repair to the alternative PARP1-dependent end joining pathway.
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Affiliation(s)
- Ali Bakr
- Laboratory of Radiobiology & Experimental Radiooncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sabrina Köcher
- Laboratory of Radiobiology & Experimental Radiooncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jennifer Volquardsen
- Laboratory of Radiobiology & Experimental Radiooncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Cordula Petersen
- Department of Radiotherapy and Radiooncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kerstin Borgmann
- Laboratory of Radiobiology & Experimental Radiooncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ekkehard Dikomey
- Laboratory of Radiobiology & Experimental Radiooncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kai Rothkamm
- Laboratory of Radiobiology & Experimental Radiooncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Wael Y Mansour
- Laboratory of Radiobiology & Experimental Radiooncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Tumor Biology Department, National Cancer Institute, Cairo University, Egypt
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36
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Hegde ML, Dutta A, Yang C, Mantha AK, Hegde PM, Pandey A, Sengupta S, Yu Y, Calsou P, Chen D, Lees-Miller SP, Mitra S. Scaffold attachment factor A (SAF-A) and Ku temporally regulate repair of radiation-induced clustered genome lesions. Oncotarget 2018; 7:54430-54444. [PMID: 27303920 PMCID: PMC5342353 DOI: 10.18632/oncotarget.9914] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 05/26/2016] [Indexed: 12/22/2022] Open
Abstract
Ionizing radiation (IR) induces highly cytotoxic double-strand breaks (DSBs) and also clustered oxidized bases in mammalian genomes. Base excision repair (BER) of bi-stranded oxidized bases could generate additional DSBs as repair intermediates in the vicinity of direct DSBs, leading to loss of DNA fragments. This could be avoided if DSB repair via DNA-PK-mediated nonhomologous end joining (NHEJ) precedes BER initiated by NEIL1 and other DNA glycosylases (DGs). Here we show that DNA-PK subunit Ku inhibits DGs via direct interaction. The scaffold attachment factor (SAF)-A, (also called hnRNP-U), phosphorylated at Ser59 by DNA-PK early after IR treatment, is linked to transient release of chromatin-bound NEIL1, thus preventing BER. SAF-A is subsequently dephosphorylated. Ku inhibition of DGs in vitro is relieved by unphosphorylated SAF-A, but not by the phosphomimetic Asp59 mutant. We thus propose that SAF-A, in concert with Ku, temporally regulates base damage repair in irradiated cell genome.
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Affiliation(s)
- Muralidhar L Hegde
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA.,Houston Methodist Neurological Institute, Houston, TX, USA.,Weill Medical College of Cornell University, Ithaca, NY, USA
| | - Arijit Dutta
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA.,Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX , USA
| | - Chunying Yang
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA
| | - Anil K Mantha
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX , USA.,Center for Animal Sciences, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Pavana M Hegde
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA
| | - Arvind Pandey
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA
| | - Shiladitya Sengupta
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA.,Weill Medical College of Cornell University, Ithaca, NY, USA
| | - Yaping Yu
- Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, Canada
| | - Patrick Calsou
- Institut de Pharmacologie et de Biologie Structurale, CNRS, Université de Toulouse-Université Paul Sabatier, Equipe Labellisée Ligue contre le Cancer, Toulouse, France
| | - David Chen
- UT Southwestern Medical Center, Dallas, TX, USA
| | - Susan P Lees-Miller
- Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, Canada
| | - Sankar Mitra
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA.,Weill Medical College of Cornell University, Ithaca, NY, USA.,Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX , USA
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37
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Horikoshi N, Pandita RK, Mujoo K, Hambarde S, Sharma D, Mattoo AR, Chakraborty S, Charaka V, Hunt CR, Pandita TK. β2-spectrin depletion impairs DNA damage repair. Oncotarget 2018; 7:33557-70. [PMID: 27248179 PMCID: PMC5085102 DOI: 10.18632/oncotarget.9677] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 05/20/2016] [Indexed: 12/22/2022] Open
Abstract
β2-Spectrin (β2SP/SPTBN1, gene SPTBN1) is a key TGF-β/SMAD3/4 adaptor and transcriptional cofactor that regulates TGF-β signaling and can contribute to liver cancer development. Here we report that cells deficient in β2-Spectrin (β2SP) are moderately sensitive to ionizing radiation (IR) and extremely sensitive to agents that cause interstrand cross-links (ICLs) or replication stress. In response to treatment with IR or ICL agents (formaldehyde, cisplatin, camptothecin, mitomycin), β2SP deficient cells displayed a higher frequency of cells with delayed γ-H2AX removal and a higher frequency of residual chromosome aberrations. Following hydroxyurea (HU)-induced replication stress, β2SP-deficient cells displayed delayed disappearance of γ-H2AX foci along with defective repair factor recruitment (MRE11, CtIP, RAD51, RPA, and FANCD2) as well as defective restart of stalled replication forks. Repair factor recruitment is a prerequisite for initiation of DNA damage repair by the homologous recombination (HR) pathway, which was also defective in β2SP deficient cells. We propose that β2SP is required for maintaining genomic stability following replication fork stalling, whether induced by either ICL damage or replicative stress, by facilitating fork regression as well as DNA damage repair by homologous recombination.
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Affiliation(s)
- Nobuo Horikoshi
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA.,Department of Radiation Oncology, University of Texas Southwestern Medical School, Dallas, TX, USA
| | - Raj K Pandita
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA.,Department of Radiation Oncology, University of Texas Southwestern Medical School, Dallas, TX, USA
| | - Kalpana Mujoo
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA
| | - Shashank Hambarde
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA.,Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Dharmendra Sharma
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA
| | - Abid R Mattoo
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA
| | - Sharmistha Chakraborty
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA.,Department of Radiation Oncology, University of Texas Southwestern Medical School, Dallas, TX, USA
| | - Vijaya Charaka
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA
| | - Clayton R Hunt
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA.,Department of Radiation Oncology, University of Texas Southwestern Medical School, Dallas, TX, USA
| | - Tej K Pandita
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA.,Department of Radiation Oncology, University of Texas Southwestern Medical School, Dallas, TX, USA
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38
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Mujoo K, Pandita RK, Tiwari A, Charaka V, Chakraborty S, Singh DK, Hambarde S, Hittelman WN, Horikoshi N, Hunt CR, Khanna KK, Kots AY, Butler EB, Murad F, Pandita TK. Differentiation of Human Induced Pluripotent or Embryonic Stem Cells Decreases the DNA Damage Repair by Homologous Recombination. Stem Cell Reports 2017; 9:1660-1674. [PMID: 29103969 PMCID: PMC5831054 DOI: 10.1016/j.stemcr.2017.10.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 10/04/2017] [Accepted: 10/05/2017] [Indexed: 12/16/2022] Open
Abstract
The nitric oxide (NO)-cyclic GMP pathway contributes to human stem cell differentiation, but NO free radical production can also damage DNA, necessitating a robust DNA damage response (DDR) to ensure cell survival. How the DDR is affected by differentiation is unclear. Differentiation of stem cells, either inducible pluripotent or embryonic derived, increased residual DNA damage as determined by γ-H2AX and 53BP1 foci, with increased S-phase-specific chromosomal aberration after exposure to DNA-damaging agents, suggesting reduced homologous recombination (HR) repair as supported by the observation of decreased HR-related repair factor foci formation (RAD51 and BRCA1). Differentiated cells also had relatively increased fork stalling and R-loop formation after DNA replication stress. Treatment with NO donor (NOC-18), which causes stem cell differentiation has no effect on double-strand break (DSB) repair by non-homologous end-joining but reduced DSB repair by HR. Present studies suggest that DNA repair by HR is impaired in differentiated cells. Spontaneous and S-phase-specific chromosome aberrations in differentiated cells Higher frequency of residual γ-H2AX foci after exposure to DNA-damaging agents Higher frequency of cells with 53BP1 and RIF1 co-localization in differentiated cells Higher frequency of cells with a reduced number of RAD51 or BRCA1 foci
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Affiliation(s)
- Kalpana Mujoo
- Department of Radiation Oncology, Weill Cornell Medical College, The Houston Methodist Hospital Research Institute, Houston, TX 77030, USA; Institute of Molecular Medicine, University of Texas Health at Houston, Houston, TX 77030, USA.
| | - Raj K Pandita
- Department of Radiation Oncology, Weill Cornell Medical College, The Houston Methodist Hospital Research Institute, Houston, TX 77030, USA
| | - Anjana Tiwari
- Department of Radiation Oncology, Weill Cornell Medical College, The Houston Methodist Hospital Research Institute, Houston, TX 77030, USA
| | - Vijay Charaka
- Department of Radiation Oncology, Weill Cornell Medical College, The Houston Methodist Hospital Research Institute, Houston, TX 77030, USA
| | - Sharmistha Chakraborty
- Department of Radiation Oncology, Weill Cornell Medical College, The Houston Methodist Hospital Research Institute, Houston, TX 77030, USA
| | - Dharmendra Kumar Singh
- Department of Radiation Oncology, Weill Cornell Medical College, The Houston Methodist Hospital Research Institute, Houston, TX 77030, USA
| | - Shashank Hambarde
- Department of Radiation Oncology, Weill Cornell Medical College, The Houston Methodist Hospital Research Institute, Houston, TX 77030, USA
| | - Walter N Hittelman
- Department of Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nobuo Horikoshi
- Department of Radiation Oncology, Weill Cornell Medical College, The Houston Methodist Hospital Research Institute, Houston, TX 77030, USA
| | - Clayton R Hunt
- Department of Radiation Oncology, Weill Cornell Medical College, The Houston Methodist Hospital Research Institute, Houston, TX 77030, USA
| | - Kum Kum Khanna
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4029, Australia
| | | | - E Brian Butler
- Department of Radiation Oncology, Weill Cornell Medical College, The Houston Methodist Hospital Research Institute, Houston, TX 77030, USA
| | - Ferid Murad
- The George Washington University, Washington, DC 20037, USA
| | - Tej K Pandita
- Department of Radiation Oncology, Weill Cornell Medical College, The Houston Methodist Hospital Research Institute, Houston, TX 77030, USA.
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39
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Meyer RG, Ketchum CC, Meyer-Ficca ML. Heritable sperm chromatin epigenetics: a break to remember†. Biol Reprod 2017; 97:784-797. [DOI: 10.1093/biolre/iox137] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 10/31/2017] [Indexed: 02/07/2023] Open
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40
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Patel N, Garikapati KR, Pandita RK, Singh DK, Pandita TK, Bhadra U, Bhadra MP. miR-15a/miR-16 down-regulates BMI1, impacting Ub-H2A mediated DNA repair and breast cancer cell sensitivity to doxorubicin. Sci Rep 2017; 7:4263. [PMID: 28655885 PMCID: PMC5487337 DOI: 10.1038/s41598-017-02800-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 04/18/2017] [Indexed: 12/18/2022] Open
Abstract
The B-lymphoma Moloney murine leukemia virus insertion region-1 protein (BMI1) acts as an oncogene in various cancers, including breast cancer. Recent evidence suggests that BMI1 is rapidly recruited to sites of DNA double strand breaks where it facilitates histone H2A ubiquitination and DNA double strand break repair by homologous recombination. Here we show that miR-15a and miR-16 expressionis decreased during the initial period after DNA damage where it would otherwise down-regulate BMI1, impairing DNA repair. Elevated miR-15a and miR-16 levels down-regulated BMI1 and other polycomb group proteins like RING1A, RING1B, EZH2 and also altered the expression of proteins associated with the BMI1 dependent ubiquitination pathway. Antagonizing the expression of miR-15a and miR-16, enhanced BMI1 protein levels and increased DNA repair. Further, overexpression of miR-15a and miR-16 sensitized breast cancer cells to DNA damage induced by the chemotherapeutic drug doxorubicin. Our results suggest that miR-15a and miR-16 mediate the down-regulation of BMI1, which impedes DNA repair while elevated levels can sensitize breast cancer cells to doxorubicin leading to apoptotic cell death. This data identifies a new target for manipulating DNA damage response that could impact the development of improved therapeutics for breast cancer.
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Affiliation(s)
- Nibedita Patel
- Centre for Chemical Biology, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, Telangana State, 500007, India
| | - Koteswara Rao Garikapati
- Centre for Chemical Biology, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, Telangana State, 500007, India.,Academy of Scientific and Innovative Research (AcSIR), Training and Development Complex, CSIR Campus, CSIR Road, Taramani, Chennai, 600 113, India
| | - Raj K Pandita
- Department of Radiation Oncology, Weill Cornell Medical College, The Methodist Hospital Research Institute, Houston, TX, 77030, USA
| | - Dharmendra Kumar Singh
- Department of Radiation Oncology, Weill Cornell Medical College, The Methodist Hospital Research Institute, Houston, TX, 77030, USA
| | - Tej K Pandita
- Department of Radiation Oncology, Weill Cornell Medical College, The Methodist Hospital Research Institute, Houston, TX, 77030, USA
| | - Utpal Bhadra
- Gene Silencing Group, Centre for Cellular and Molecular Biology, Hyderabad, Telangana State, 500007, India
| | - Manika Pal Bhadra
- Centre for Chemical Biology, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, Telangana State, 500007, India.
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41
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Yin S, Jiang X, Jiang H, Gao Q, Wang F, Fan S, Khan T, Jabeen N, Khan M, Ali A, Xu P, Pandita TK, Fan HY, Zhang Y, Shi Q. Histone acetyltransferase KAT8 is essential for mouse oocyte development by regulating reactive oxygen species levels. Development 2017; 144:2165-2174. [PMID: 28506985 DOI: 10.1242/dev.149518] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 04/29/2017] [Indexed: 12/22/2022]
Abstract
Proper oocyte development is crucial for female fertility and requires timely and accurate control of gene expression. K (lysine) acetyltransferase 8 (KAT8), an important component of the X chromosome dosage compensation system in Drosophila, regulates gene activity by acetylating histone H4 preferentially at lysine 16. To explore the function of KAT8 during mouse oocyte development, we crossed Kat8flox/flox mice with Gdf9-Cre mice to specifically delete Kat8 in oocytes. Oocyte Kat8 deletion resulted in female infertility, with follicle development failure in the secondary and preantral follicle stages. RNA-seq analysis revealed that Kat8 deficiency in oocytes results in significant downregulation of antioxidant genes, with a consequent increase in reactive oxygen species. Intraperitoneal injection of the antioxidant N-acetylcysteine rescued defective follicle and oocyte development resulting from Kat8 deficiency. Chromatin immunoprecipitation assays indicated that KAT8 regulates antioxidant gene expression by direct binding to promoter regions. Taken together, our findings demonstrate that KAT8 is essential for female fertility by regulating antioxidant gene expression and identify KAT8 as the first histone acetyltransferase with an essential function in oogenesis.
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Affiliation(s)
- Shi Yin
- Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Collaborative Innovation Center of Genetics and Development, Collaborative Innovation Center for Cancer Medicine, Hefei, Anhui 230027, China
| | - Xiaohua Jiang
- Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Collaborative Innovation Center of Genetics and Development, Collaborative Innovation Center for Cancer Medicine, Hefei, Anhui 230027, China
| | - Hanwei Jiang
- Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Collaborative Innovation Center of Genetics and Development, Collaborative Innovation Center for Cancer Medicine, Hefei, Anhui 230027, China
| | - Qian Gao
- Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Collaborative Innovation Center of Genetics and Development, Collaborative Innovation Center for Cancer Medicine, Hefei, Anhui 230027, China
| | - Fang Wang
- Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Collaborative Innovation Center of Genetics and Development, Collaborative Innovation Center for Cancer Medicine, Hefei, Anhui 230027, China
| | - Suixing Fan
- Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Collaborative Innovation Center of Genetics and Development, Collaborative Innovation Center for Cancer Medicine, Hefei, Anhui 230027, China
| | - Teka Khan
- Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Collaborative Innovation Center of Genetics and Development, Collaborative Innovation Center for Cancer Medicine, Hefei, Anhui 230027, China
| | - Nazish Jabeen
- Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Collaborative Innovation Center of Genetics and Development, Collaborative Innovation Center for Cancer Medicine, Hefei, Anhui 230027, China
| | - Manan Khan
- Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Collaborative Innovation Center of Genetics and Development, Collaborative Innovation Center for Cancer Medicine, Hefei, Anhui 230027, China
| | - Asim Ali
- Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Collaborative Innovation Center of Genetics and Development, Collaborative Innovation Center for Cancer Medicine, Hefei, Anhui 230027, China
| | - Peng Xu
- USTC-Shenyang Jinghua Hospital Joint Center of Human Reproduction and Genetics, Shenyang, Liaoning 110000, China
| | - Tej K Pandita
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 75390, USA
| | - Heng-Yu Fan
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yuanwei Zhang
- Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Collaborative Innovation Center of Genetics and Development, Collaborative Innovation Center for Cancer Medicine, Hefei, Anhui 230027, China
| | - Qinghua Shi
- Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Collaborative Innovation Center of Genetics and Development, Collaborative Innovation Center for Cancer Medicine, Hefei, Anhui 230027, China
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42
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Ssb1 and Ssb2 cooperate to regulate mouse hematopoietic stem and progenitor cells by resolving replicative stress. Blood 2017; 129:2479-2492. [PMID: 28270450 DOI: 10.1182/blood-2016-06-725093] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 02/26/2017] [Indexed: 12/14/2022] Open
Abstract
Hematopoietic stem and progenitor cells (HSPCs) are vulnerable to endogenous damage and defects in DNA repair can limit their function. The 2 single-stranded DNA (ssDNA) binding proteins SSB1 and SSB2 are crucial regulators of the DNA damage response; however, their overlapping roles during normal physiology are incompletely understood. We generated mice in which both Ssb1 and Ssb2 were constitutively or conditionally deleted. Constitutive Ssb1/Ssb2 double knockout (DKO) caused early embryonic lethality, whereas conditional Ssb1/Ssb2 double knockout (cDKO) in adult mice resulted in acute lethality due to bone marrow failure and intestinal atrophy featuring stem and progenitor cell depletion, a phenotype unexpected from the previously reported single knockout models of Ssb1 or Ssb2 Mechanistically, cDKO HSPCs showed altered replication fork dynamics, massive accumulation of DNA damage, genome-wide double-strand breaks enriched at Ssb-binding regions and CpG islands, together with the accumulation of R-loops and cytosolic ssDNA. Transcriptional profiling of cDKO HSPCs revealed the activation of p53 and interferon (IFN) pathways, which enforced cell cycling in quiescent HSPCs, resulting in their apoptotic death. The rapid cell death phenotype was reproducible in in vitro cultured cDKO-hematopoietic stem cells, which were significantly rescued by nucleotide supplementation or after depletion of p53. Collectively, Ssb1 and Ssb2 control crucial aspects of HSPC function, including proliferation and survival in vivo by resolving replicative stress to maintain genomic stability.
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43
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Valerio DG, Xu H, Chen CW, Hoshii T, Eisold ME, Delaney C, Cusan M, Deshpande AJ, Huang CH, Lujambio A, Zheng YG, Zuber J, Pandita TK, Lowe SW, Armstrong SA. Histone Acetyltransferase Activity of MOF Is Required for MLL-AF9 Leukemogenesis. Cancer Res 2017; 77:1753-1762. [PMID: 28202522 DOI: 10.1158/0008-5472.can-16-2374] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Revised: 12/22/2016] [Accepted: 12/31/2016] [Indexed: 01/16/2023]
Abstract
Chromatin-based mechanisms offer therapeutic targets in acute myeloid leukemia (AML) that are of great current interest. In this study, we conducted an RNAi-based screen to identify druggable chromatin regulator-based targets in leukemias marked by oncogenic rearrangements of the MLL gene. In this manner, we discovered the H4K16 histone acetyltransferase (HAT) MOF to be important for leukemia cell growth. Conditional deletion of Mof in a mouse model of MLL-AF9-driven leukemogenesis reduced tumor burden and prolonged host survival. RNA sequencing showed an expected downregulation of genes within DNA damage repair pathways that are controlled by MOF, as correlated with a significant increase in yH2AX nuclear foci in Mof-deficient MLL-AF9 tumor cells. In parallel, Mof loss also impaired global H4K16 acetylation in the tumor cell genome. Rescue experiments with catalytically inactive mutants of MOF showed that its enzymatic activity was required to maintain cancer pathogenicity. In support of the role of MOF in sustaining H4K16 acetylation, a small-molecule inhibitor of the HAT component MYST blocked the growth of both murine and human MLL-AF9 leukemia cell lines. Furthermore, Mof inactivation suppressed leukemia development in an NUP98-HOXA9-driven AML model. Taken together, our results establish that the HAT activity of MOF is required to sustain MLL-AF9 leukemia and may be important for multiple AML subtypes. Blocking this activity is sufficient to stimulate DNA damage, offering a rationale to pursue MOF inhibitors as a targeted approach to treat MLL-rearranged leukemias. Cancer Res; 77(7); 1753-62. ©2017 AACR.
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Affiliation(s)
- Daria G Valerio
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York.,Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Haiming Xu
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York.,Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Chun-Wei Chen
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York.,Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Takayuki Hoshii
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York.,Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Meghan E Eisold
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York.,Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Christopher Delaney
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York.,Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Monica Cusan
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York.,Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Aniruddha J Deshpande
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York.,Tumor Initiation and Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Chun-Hao Huang
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Amaia Lujambio
- Department of Oncological Sciences, Mount Sinai School of Medicine, New York, New York
| | - YuJun George Zheng
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia, Athens, Georgia
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Tej K Pandita
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, Texas
| | - Scott W Lowe
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Scott A Armstrong
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York. .,Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
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44
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MCL-1 Depletion Impairs DNA Double-Strand Break Repair and Reinitiation of Stalled DNA Replication Forks. Mol Cell Biol 2017; 37:MCB.00535-16. [PMID: 27821478 DOI: 10.1128/mcb.00535-16] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 10/24/2016] [Indexed: 12/31/2022] Open
Abstract
Myeloid cell leukemia 1 (MCL-1) is a prosurvival BCL-2 protein family member highly expressed in hematopoietic stem cells (HSCs) and regulated by growth factor signals that manifest antiapoptotic activity. Here we report that depletion of MCL-1 but not its isoform MCL-1S increases genomic instability and cell sensitivity to ionizing radiation (IR)-induced death. MCL-1 association with genomic DNA increased postirradiation, and the protein colocalized with 53BP1 foci. Postirradiation, MCL-1-depleted cells exhibited decreased γ-H2AX foci, decreased phosphorylation of ATR, and higher levels of residual 53BP1 and RIF1 foci, suggesting that DNA double-strand break (DSB) repair by homologous recombination (HR) was compromised. Consistent with this model, MCL-1-depleted cells had a reduced frequency of IR-induced BRCA1, RPA, and Rad51 focus formation, decreased DNA end resection, and decreased HR repair in the DR-GFP DSB repair model. Similarly, after HU induction of stalled replication forks in MCL-1-depleted cells, there was a decreased ability to subsequently restart DNA synthesis, which is normally dependent upon HR-mediated resolution of collapsed forks. Therefore, the present data support a model whereby MCL-1 depletion increases 53BP1 and RIF1 colocalization at DSBs, which inhibits BRCA1 recruitment, and sensitizes cells to DSBs from IR or stalled replication forks that require HR for repair.
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45
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Abramowicz I, Carpenter G, Alfieri M, Colnaghi R, Outwin E, Parent P, Thauvin-Robinet C, Iaconis D, Franco B, O'Driscoll M. Oral-facial-digital syndrome type I cells exhibit impaired DNA repair; unanticipated consequences of defective OFD1 outside of the cilia network. Hum Mol Genet 2017; 26:19-32. [PMID: 27798113 DOI: 10.1093/hmg/ddw364] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 10/18/2016] [Indexed: 02/11/2024] Open
Abstract
Defects in OFD1 underlie the clinically complex ciliopathy, Oral-Facial-Digital syndrome Type I (OFD Type I). Our understanding of the molecular, cellular and clinical consequences of impaired OFD1 originates from its characterised roles at the centrosome/basal body/cilia network. Nonetheless, the first described OFD1 interactors were components of the TIP60 histone acetyltransferase complex. We find that OFD1 can also localise to chromatin and its reduced expression is associated with mis-localization of TIP60 in patient-derived cell lines. TIP60 plays important roles in controlling DNA repair. OFD Type I cells exhibit reduced histone acetylation and altered chromatin dynamics in response to DNA double strand breaks (DSBs). Furthermore, reduced OFD1 impaired DSB repair via homologous recombination repair (HRR). OFD1 loss also adversely impacted upon the DSB-induced G2-M checkpoint, inducing a hypersensitive and prolonged arrest. Our findings show that OFD Type I patient cells have pronounced defects in the DSB-induced histone modification, chromatin remodelling and DSB-repair via HRR; effectively phenocopying loss of TIP60. These data extend our knowledge of the molecular and cellular consequences of impaired OFD1, demonstrating that loss of OFD1 can negatively impact upon important nuclear events; chromatin plasticity and DNA repair.
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Affiliation(s)
- Iga Abramowicz
- Human DNA damage Response Disorders Group, Genome Damage & Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Gillian Carpenter
- Human DNA damage Response Disorders Group, Genome Damage & Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | | | - Rita Colnaghi
- Human DNA damage Response Disorders Group, Genome Damage & Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Emily Outwin
- Human DNA damage Response Disorders Group, Genome Damage & Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Philippe Parent
- Service de Génétique, Centre Hospitalier Universitaire de Brest, France
| | | | | | - Brunella Franco
- Telethon Institute of Genetics and Medicine, Naples, Italy
- Department of Medical Translational Sciences, Federico II University, Naples, Italy
| | - Mark O'Driscoll
- Human DNA damage Response Disorders Group, Genome Damage & Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
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46
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Histone acetyltransferase activity of MOF is required for adult but not early fetal hematopoiesis in mice. Blood 2016; 129:48-59. [PMID: 27827827 DOI: 10.1182/blood-2016-05-714568] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 09/16/2016] [Indexed: 12/26/2022] Open
Abstract
K(lysine) acetyltransferase 8 (KAT8, also known as MOF) mediates the acetylation of histone H4 at lysine 16 (H4K16ac) and is crucial for murine embryogenesis. Lysine acetyltransferases have been shown to regulate various stages of normal hematopoiesis. However, the function of MOF in hematopoietic stem cell (HSC) development has not yet been elucidated. We set out to study the role of MOF in general hematopoiesis by using a Vav1-cre-induced conditional murine Mof knockout system and found that MOF is critical for hematopoietic cell maintenance and HSC engraftment capacity in adult hematopoiesis. Rescue experiments with a MOF histone acetyltransferase domain mutant illustrated the requirement for MOF acetyltransferase activity in the clonogenic capacity of HSCs and progenitors. In stark contrast, fetal steady-state hematopoiesis at embryonic day (E) 14.5 was not affected by homozygous Mof deletion despite dramatic loss of global H4K16ac. Hematopoietic defects start manifesting in late gestation at E17.5. The discovery that MOF and its H4K16ac activity are required for adult but not early and midgestational hematopoiesis supports the notion that multiple chromatin regulators may be crucial for hematopoiesis at varying stages of development. MOF is therefore a developmental-stage-specific chromatin regulator found to be essential for adult but not early fetal hematopoiesis.
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47
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Zhong J, Li X, Cai W, Wang Y, Dong S, Yang J, Zhang J, Wu N, Li Y, Mao F, Zeng C, Wu J, Xu X, Sun ZS. TET1 modulates H4K16 acetylation by controlling auto-acetylation of hMOF to affect gene regulation and DNA repair function. Nucleic Acids Res 2016; 45:672-684. [PMID: 27733505 PMCID: PMC5314799 DOI: 10.1093/nar/gkw919] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 09/30/2016] [Accepted: 10/04/2016] [Indexed: 12/14/2022] Open
Abstract
The Ten Eleven Translocation 1 (TET1) protein is a DNA demethylase that regulates gene expression through altering statue of DNA methylation. However, recent studies have demonstrated that TET1 could modulate transcriptional expression independent of its DNA demethylation activity; yet, the detailed mechanisms underlying TET1's role in such transcriptional regulation remain not well understood. Here, we uncovered that Tet1 formed a chromatin complex with histone acetyltransferase Mof and scaffold protein Sin3a in mouse embryonic stem cells by integrative genomic analysis using publicly available ChIP-seq data sets and a series of in vitro biochemical studies in human cell lines. Mechanistically, the TET1 facilitated chromatin affinity and enzymatic activity of hMOF against acetylation of histone H4 at lysine 16 via preventing auto-acetylation of hMOF, to regulate expression of the downstream genes, including DNA repair genes. We found that Tet1 knockout MEF cells exhibited an accumulation of DNA damage and genomic instability and Tet1 deficient mice were more sensitive to x-ray exposure. Taken together, our findings reveal that TET1 forms a complex with hMOF to modulate its function and the level of H4K16Ac ultimately affect gene expression and DNA repair.
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Affiliation(s)
- Jianing Zhong
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325035, China
| | - Xianfeng Li
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wanshi Cai
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Wang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shanshan Dong
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325035, China
| | - Jie Yang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325035, China
| | - Jian'an Zhang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325035, China
| | - Nana Wu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325035, China
| | - Yuanyuan Li
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fengbiao Mao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cheng Zeng
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinyu Wu
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xingzhi Xu
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100049, China
| | - Zhong Sheng Sun
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325035, China .,Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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48
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Chakraborty A, Tapryal N, Venkova T, Horikoshi N, Pandita RK, Sarker AH, Sarkar PS, Pandita TK, Hazra TK. Classical non-homologous end-joining pathway utilizes nascent RNA for error-free double-strand break repair of transcribed genes. Nat Commun 2016; 7:13049. [PMID: 27703167 PMCID: PMC5059474 DOI: 10.1038/ncomms13049] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 08/30/2016] [Indexed: 12/30/2022] Open
Abstract
DNA double-strand breaks (DSBs) leading to loss of nucleotides in the transcribed region can be lethal. Classical non-homologous end-joining (C-NHEJ) is the dominant pathway for DSB repair (DSBR) in adult mammalian cells. Here we report that during such DSBR, mammalian C-NHEJ proteins form a multiprotein complex with RNA polymerase II and preferentially associate with the transcribed genes after DSB induction. Depletion of C-NHEJ factors significantly abrogates DSBR in transcribed but not in non-transcribed genes. We hypothesized that nascent RNA can serve as a template for restoring the missing sequences, thus allowing error-free DSBR. We indeed found pre-mRNA in the C-NHEJ complex. Finally, when a DSB-containing plasmid with several nucleotides deleted within the E. coli lacZ gene was allowed time to repair in lacZ-expressing mammalian cells, a functional lacZ plasmid could be recovered from control but not C-NHEJ factor-depleted cells, providing important mechanistic insights into C-NHEJ-mediated error-free DSBR of the transcribed genome. Most adult mammalian cells prefer to repair double-strand DNA breaks though the classical nonhomologous end-joining pathway. Here the authors present evidence that a nascent RNA transcript can serve as a template to facilitate error-free repair.
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Affiliation(s)
- Anirban Chakraborty
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - Nisha Tapryal
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - Tatiana Venkova
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - Nobuo Horikoshi
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, Texas 77030, USA
| | - Raj K Pandita
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, Texas 77030, USA
| | - Altaf H Sarker
- Division of Life Sciences, Department of Cancer and DNA Damage Responses, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Partha S Sarkar
- Department of Neurology and Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - Tej K Pandita
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, Texas 77030, USA
| | - Tapas K Hazra
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, Texas 77555, USA
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49
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Gong F, Chiu LY, Miller KM. Acetylation Reader Proteins: Linking Acetylation Signaling to Genome Maintenance and Cancer. PLoS Genet 2016; 12:e1006272. [PMID: 27631103 PMCID: PMC5025232 DOI: 10.1371/journal.pgen.1006272] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Chromatin-based DNA damage response (DDR) pathways are fundamental for preventing genome and epigenome instability, which are prevalent in cancer. Histone acetyltransferases (HATs) and histone deacetylases (HDACs) catalyze the addition and removal of acetyl groups on lysine residues, a post-translational modification important for the DDR. Acetylation can alter chromatin structure as well as function by providing binding signals for reader proteins containing acetyl-lysine recognition domains, including the bromodomain (BRD). Acetylation dynamics occur upon DNA damage in part to regulate chromatin and BRD protein interactions that mediate key DDR activities. In cancer, DDR and acetylation pathways are often mutated or abnormally expressed. DNA damaging agents and drugs targeting epigenetic regulators, including HATs, HDACs, and BRD proteins, are used or are being developed to treat cancer. Here, we discuss how histone acetylation pathways, with a focus on acetylation reader proteins, promote genome stability and the DDR. We analyze how acetylation signaling impacts the DDR in the context of cancer and its treatments. Understanding the relationship between epigenetic regulators, the DDR, and chromatin is integral for obtaining a mechanistic understanding of genome and epigenome maintenance pathways, information that can be leveraged for targeting acetylation signaling, and/or the DDR to treat diseases, including cancer.
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Affiliation(s)
- Fade Gong
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Li-Ya Chiu
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Kyle M. Miller
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- * E-mail:
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50
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Li J, Xu X. DNA double-strand break repair: a tale of pathway choices. Acta Biochim Biophys Sin (Shanghai) 2016; 48:641-6. [PMID: 27217474 DOI: 10.1093/abbs/gmw045] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 04/15/2016] [Indexed: 11/15/2022] Open
Abstract
Deoxyribonucleic acid double-strand breaks (DSBs) are cytotoxic lesions that must be repaired either through homologous recombination (HR) or non-homologous end-joining (NHEJ) pathways. DSB repair is critical for genome integrity, cellular homeostasis and also constitutes the biological foundation for radiotherapy and the majority of chemotherapy. The choice between HR and NHEJ is a complex yet not completely understood process that will entail more future efforts. Herein we review our current understandings about how the choice is made over an antagonizing balance between p53-binding protein 1 and breast cancer 1 in the context of cell cycle stages, downstream effects, and distinct chromosomal histone marks. These exciting areas of research will surely bring more mechanistic insights about DSB repair and be utilized in the clinical settings.
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Affiliation(s)
- Jing Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Xingzhi Xu
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
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