1
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Belal H, Ying Ng EF, Meitinger F. 53BP1-mediated activation of the tumor suppressor p53. Curr Opin Cell Biol 2024; 91:102424. [PMID: 39244835 DOI: 10.1016/j.ceb.2024.102424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 08/13/2024] [Accepted: 08/13/2024] [Indexed: 09/10/2024]
Abstract
In recent years, the role of 53BP1 as a cell cycle regulator has come into the spotlight. 53BP1 is best understood for its role in controlling DNA double-strand break repair. However, 53BP1 was initially discovered as an interaction partner of the tumor suppressor p53, which proved to be independent of DNA repair. The importance of this interaction is becoming increasingly clear. 53BP1 responds to mitotic stress, which prolongs mitosis, or to DNA damage and triggers the stabilization of p53 by the deubiquitinase USP28 to stop the proliferation of potentially damaged cells. The ability of 53BP1 to respond to mitotic stress or DNA damage is controlled by cell cycle-specific post-translational modifications and is therefore restricted to specific cell cycle phases. 53BP1-mediated p53 activation is likely involved in tumor suppression and is associated with genetic diseases such as primary microcephaly. This review emphasizes the importance of these mechanisms for the development and maintenance of healthy tissues.
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Affiliation(s)
- Hazrat Belal
- Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Esther Feng Ying Ng
- Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Franz Meitinger
- Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan.
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2
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Yu T, Lok BH. PARP inhibitor resistance mechanisms and PARP inhibitor derived imaging probes. Expert Rev Anticancer Ther 2024:1-20. [PMID: 39199000 DOI: 10.1080/14737140.2024.2398494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Revised: 08/19/2024] [Accepted: 08/27/2024] [Indexed: 09/01/2024]
Abstract
INTRODUCTION Poly(ADP-ribose) polymerase 1 (PARP1) inhibition has become a major target in anticancer therapy. While PARP inhibitors (PARPi) are approved for homologous recombination (HR) deficient cancers, therapeutic resistance is a challenge and PARPi are now being investigated in cancers lacking HR deficiencies. This creates a need to develop molecular and imaging biomarkers of PARPi response to improve patient selection and circumvent therapeutic resistance. AREAS COVERED PubMed and clinicaltrials.gov were queried for studies on PARPi resistance and imaging. This review summarizes established and emerging resistance mechanisms to PARPi, and the current state of imaging and theragnostic probes for PARPi, including fluorescently labeled and radiolabeled probes. EXPERT OPINION While progress has been made in understanding PARPi therapeutic resistance, clinical evidence remains lacking and relatively little is known regarding PARPi response outside of HR deficiencies. Continued research will clarify the importance of known biomarkers and resistance mechanisms in patient cohorts and the broader utility of PARPi. Progress has also been made in PARPi imaging, particularly with radiolabeled probes, and both imaging and theragnostic probes have now reached clinical validation. Reducing abdominal background signal from probe clearance will broaden their applicability, and improvements to molecular synthesis and radiation delivery will increase their utility.
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Affiliation(s)
- Tony Yu
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Benjamin H Lok
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Radiation Medicine Program, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Radiation Oncology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Institute of Medical Science, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
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3
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Glossop MS, Chelysheva I, Ketley RF, Alagia A, Gullerova M. TIRR regulates mRNA export and association with P-bodies in response to DNA damage. Nucleic Acids Res 2024:gkae688. [PMID: 39119906 DOI: 10.1093/nar/gkae688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 07/15/2024] [Accepted: 07/25/2024] [Indexed: 08/10/2024] Open
Abstract
To ensure the integrity of our genetic code, a coordinated network of signalling and repair proteins, known as the DNA damage response (DDR), detects and repairs DNA insults, the most toxic being double-strand breaks (DSBs). Tudor interacting repair regulator (TIRR) is a key factor in DSB repair, acting through its interaction with p53 binding protein 1 (53BP1). TIRR is also an RNA binding protein, yet its role in RNA regulation during the DDR remains elusive. Here, we show that TIRR selectively binds to a subset of messenger RNAs (mRNAs) in response to DNA damage. Upon DNA damage, TIRR interacts with the nuclear export protein Exportin-1 through a nuclear export signal. Furthermore, TIRR plays a crucial role in the modulation of RNA processing bodies (PBs). TIRR itself and TIRR-bound RNA co-localize with PBs, and TIRR depletion results in nuclear RNA retention and impaired PB formation. We also suggest a potential link between TIRR-regulated RNA export and efficient DDR. This work reveals intricate involvement of TIRR in orchestrating mRNA nuclear export and storage within PBs, emphasizing its significance in the regulation of RNA-mediated DDR.
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Affiliation(s)
- Michelle S Glossop
- Sir William Dunn School of Pathology, Medical Sciences Division, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Irina Chelysheva
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford OX3 7LE, UK
| | - Ruth F Ketley
- Sir William Dunn School of Pathology, Medical Sciences Division, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Adele Alagia
- Sir William Dunn School of Pathology, Medical Sciences Division, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Monika Gullerova
- Sir William Dunn School of Pathology, Medical Sciences Division, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
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4
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Sun Y, Patterson-Fortin J, Han S, Li Z, Nowicka Z, Hirohashi Y, Kilgas S, Yi JK, Spektor A, Fendler W, Konstantinopoulos PA, Chowdhury D. 53BP1 loss elicits cGAS-STING-dependent antitumor immunity in ovarian and pancreatic cancer. Nat Commun 2024; 15:6676. [PMID: 39107288 PMCID: PMC11303708 DOI: 10.1038/s41467-024-50999-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 07/29/2024] [Indexed: 08/10/2024] Open
Abstract
53BP1 nucleates the anti-end resection machinery at DNA double-strand breaks, thereby countering BRCA1 activity. Loss of 53BP1 leads to DNA end processing and homologous recombination in BRCA1-deficient cells. Consequently, BRCA1-mutant tumors, typically sensitive to PARP inhibitors (PARPi), become resistant in the absence of 53BP1. Here, we demonstrate that the 'leaky' DNA end resection in the absence of 53BP1 results in increased micronuclei and cytoplasmic double-stranded DNA, leading to activation of the cGAS-STING pathway and pro-inflammatory signaling. This enhances CD8+ T cell infiltration, activates macrophages and natural killer cells, and impedes tumor growth. Loss of 53BP1 correlates with a response to immune checkpoint blockade (ICB) and improved overall survival. Immunohistochemical assessment of 53BP1 in two malignancies, high grade serous ovarian cancer and pancreatic ductal adenocarcinoma, which are refractory to ICBs, reveals that lower 53BP1 levels correlate with an increased adaptive and innate immune response. Finally, BRCA1-deficient tumors that develop resistance to PARPi due to the loss of 53BP1 are susceptible to ICB. Therefore, we conclude that 53BP1 is critical for tumor immunogenicity and underpins the response to ICB. Our results support including 53BP1 expression as an exploratory biomarker in ICB trials for malignancies typically refractory to immunotherapy.
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MESH Headings
- Tumor Suppressor p53-Binding Protein 1/metabolism
- Tumor Suppressor p53-Binding Protein 1/genetics
- Female
- Nucleotidyltransferases/metabolism
- Nucleotidyltransferases/genetics
- Membrane Proteins/metabolism
- Membrane Proteins/genetics
- Humans
- Animals
- Ovarian Neoplasms/immunology
- Ovarian Neoplasms/genetics
- Ovarian Neoplasms/pathology
- Ovarian Neoplasms/metabolism
- Pancreatic Neoplasms/immunology
- Pancreatic Neoplasms/genetics
- Pancreatic Neoplasms/pathology
- Pancreatic Neoplasms/metabolism
- Mice
- Cell Line, Tumor
- DNA Breaks, Double-Stranded
- BRCA1 Protein/metabolism
- BRCA1 Protein/genetics
- Signal Transduction
- CD8-Positive T-Lymphocytes/immunology
- Immune Checkpoint Inhibitors/therapeutic use
- Immune Checkpoint Inhibitors/pharmacology
- Poly(ADP-ribose) Polymerase Inhibitors/pharmacology
- Poly(ADP-ribose) Polymerase Inhibitors/therapeutic use
- Mice, Inbred C57BL
- Killer Cells, Natural/immunology
- Killer Cells, Natural/metabolism
- Mice, Knockout
- Carcinoma, Pancreatic Ductal/immunology
- Carcinoma, Pancreatic Ductal/genetics
- Carcinoma, Pancreatic Ductal/pathology
- Immunity, Innate
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Affiliation(s)
- Yajie Sun
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
| | - Jeffrey Patterson-Fortin
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Sen Han
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Zhe Li
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Zuzanna Nowicka
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, Lodz, Poland
| | - Yuna Hirohashi
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Susan Kilgas
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Jae Kyo Yi
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Alexander Spektor
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Wojciech Fendler
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, Lodz, Poland
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | - Dipanjan Chowdhury
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
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5
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Tsaousidou E, Chrzanowski J, Drané P, Lee GY, Bahour N, Wang ZB, Deng S, Cao Z, Huang K, He Y, Kaminski M, Michalek D, Güney E, Parmar K, Fendler W, Chowdhury D, Hotamışlıgil GS. Endogenous p53 inhibitor TIRR dissociates systemic metabolic health from oncogenic activity. Cell Rep 2024; 43:114337. [PMID: 38861384 PMCID: PMC11325268 DOI: 10.1016/j.celrep.2024.114337] [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: 07/25/2022] [Revised: 04/25/2024] [Accepted: 05/23/2024] [Indexed: 06/13/2024] Open
Abstract
It is unclear whether metabolic health corresponds to reduced oncogenesis or vice versa. We study Tudor-interacting repair regulator (TIRR), an inhibitor of p53 binding protein 1 (53BP1)-mediated p53 activation, and the physiological consequences of enhancing tumor suppressor activity. Deleting TIRR selectively activates p53, significantly protecting against cancer but leading to a systemic metabolic imbalance in mice. TIRR-deficient mice are overweight and insulin resistant, even under normal chow diet. Similarly, reduced TIRR expression in human adipose tissue correlates with higher BMI and insulin resistance. Despite the metabolic challenges, TIRR loss improves p53 heterozygous (p53HET) mouse survival and correlates with enhanced progression-free survival in patients with various p53HET carcinomas. Finally, TIRR's oncoprotective and metabolic effects are dependent on p53 and lost upon p53 deletion in TIRR-deficient mice, with glucose homeostasis and orexigenesis being primarily regulated by TIRR expression in the adipose tissue and the CNS, respectively, as evidenced by tissue-specific models. In summary, TIRR deletion provides a paradigm of metabolic deregulation accompanied by reduced oncogenesis.
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Affiliation(s)
- Eva Tsaousidou
- Sabri Ülker Center for Metabolic Research, Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Jędrzej Chrzanowski
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, 92-215 Lodz, Poland
| | - Pascal Drané
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Grace Y Lee
- Sabri Ülker Center for Metabolic Research, Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Nadine Bahour
- Sabri Ülker Center for Metabolic Research, Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Zeqiu Branden Wang
- Sabri Ülker Center for Metabolic Research, Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Shijun Deng
- Sabri Ülker Center for Metabolic Research, Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Zhe Cao
- Sabri Ülker Center for Metabolic Research, Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Kaimeng Huang
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Yizhou He
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Mateusz Kaminski
- Department of General Surgery, Medical University of Lodz, 90-153 Lodz, Poland
| | - Dominika Michalek
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, 92-215 Lodz, Poland
| | - Ekin Güney
- Sabri Ülker Center for Metabolic Research, Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Kalindi Parmar
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Wojciech Fendler
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biostatistics and Translational Medicine, Medical University of Lodz, 92-215 Lodz, Poland
| | - Dipanjan Chowdhury
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
| | - Gökhan S Hotamışlıgil
- Sabri Ülker Center for Metabolic Research, Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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6
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Zhao B, Xia Z, Yang B, Guo Y, Zhou R, Gu M, Liu M, Li Q, Bai W, Huang J, Zhang X, Zhu C, Leung KT, Chen C, Dong J. USP7 promotes IgA class switching through stabilizing RUNX3 for germline transcription activation. Cell Rep 2024; 43:114194. [PMID: 38735043 DOI: 10.1016/j.celrep.2024.114194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 03/04/2024] [Accepted: 04/18/2024] [Indexed: 05/14/2024] Open
Abstract
Class switch recombination (CSR) diversifies the effector functions of antibodies and involves complex regulation of transcription and DNA damage repair. Here, we show that the deubiquitinase USP7 promotes CSR to immunoglobulin A (IgA) and suppresses unscheduled IgG switching in mature B cells independent of its role in DNA damage repair, but through modulating switch region germline transcription. USP7 depletion impairs Sα transcription, leading to abnormal activation of Sγ germline transcription and increased interaction with the CSR center via loop extrusion for unscheduled IgG switching. Rescue of Sα transcription by transforming growth factor β (TGF-β) in USP7-deleted cells suppresses Sγ germline transcription and prevents loop extrusion toward IgG CSR. Mechanistically, USP7 protects transcription factor RUNX3 from ubiquitination-mediated degradation to promote Sα germline transcription. Our study provides evidence for active transcription serving as an anchor to impede loop extrusion and reveals a functional interplay between USP7 and TGF-β signaling in promoting RUNX3 expression for efficient IgA CSR.
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Affiliation(s)
- Bo Zhao
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Department of Pediatrics, the Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
| | - Zhigang Xia
- Department of Pediatrics, the Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Beibei Yang
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
| | - Yao Guo
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
| | - Ruizhi Zhou
- Department of Pediatrics, the Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Mingyu Gu
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
| | - Meiling Liu
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
| | - Qingcheng Li
- Department of Pediatrics, the Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Wanyu Bai
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Department of Pediatrics, the Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
| | - Junbin Huang
- Department of Pediatrics, the Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Xuefei Zhang
- Biomedical Pioneering Innovation Center, Innovation Center for Genomics, Peking University, Beijing 100871, China
| | - Chengming Zhu
- Center for Scientific Research, the Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Kam Tong Leung
- Department of Paediatrics, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Chun Chen
- Department of Pediatrics, the Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China.
| | - Junchao Dong
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Department of Pediatrics, the Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China.
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7
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Zhao F, Deng Y, Yang F, Yan Y, Feng F, Peng B, Gao J, Bedford MT, Li H. Molecular Basis for SPINDOC-Spindlin1 Engagement and Its Role in Transcriptional Attenuation. J Mol Biol 2024; 436:168371. [PMID: 37977297 DOI: 10.1016/j.jmb.2023.168371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/11/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
Spindlin1 is a histone reader with three Tudor-like domains and its transcriptional co-activator activity could be attenuated by SPINDOC. The first two Tudors are involved in histone methylation readout, while the function of Tudor 3 is largely unknown. Here our structural and binding studies revealed an engagement mode of SPINDOC-Spindlin1, in which a hydrophobic motif of SPINDOC, DOCpep3, stably interacts with Spindlin1 Tudor 3, and two neighboring K/R-rich motifs, DOCpep1 and DOCpep2, bind to the acidic surface of Spindlin1 Tudor 2. Although DOCpep3-Spindlin1 engagement is compatible with histone readout, an extended SPINDOC fragment containing the K/R-rich region attenuates histone or TCF4 binding by Spindlin1 due to introduced competition. This inhibitory effect is more pronounced for weaker binding targets but not for strong ones such as H3 "K4me3-K9me3" bivalent mark. Further ChIP-seq and RT-qPCR indicated that SPINDOC could promote genomic relocation of Spindlin1, thus modulate downstream gene transcription. Collectively, we revealed multivalent engagement between SPINDOC and Spindlin1, in which a hydrophobic motif acts as the primary binding site for stable SPINDOC-Spindlin1 association, while K/R-rich region modulates the target selectivity of Spindlin1 via competitive inhibition, therefore attenuating the transcriptional co-activator activity of Spindlin1.
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Affiliation(s)
- Fan Zhao
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yafang Deng
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Fen Yang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing 211166, China
| | - Yan Yan
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing 100084, China
| | - Fan Feng
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Bo Peng
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Juntao Gao
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing 100084, China.
| | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.
| | - Haitao Li
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua University, Beijing 100084, China; SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, MOE Key Laboratory of Coal Environmental Pathogenesis and Prevention, Shanxi Medical University, Taiyuan, Shanxi Province 030001, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.
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8
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Harvey-Jones E, Raghunandan M, Robbez-Masson L, Magraner-Pardo L, Alaguthurai T, Yablonovitch A, Yen J, Xiao H, Brough R, Frankum J, Song F, Yeung J, Savy T, Gulati A, Alexander J, Kemp H, Starling C, Konde A, Marlow R, Cheang M, Proszek P, Hubank M, Cai M, Trendell J, Lu R, Liccardo R, Ravindran N, Llop-Guevara A, Rodriguez O, Balmana J, Lukashchuk N, Dorschner M, Drusbosky L, Roxanis I, Serra V, Haider S, Pettitt SJ, Lord CJ, Tutt ANJ. Longitudinal profiling identifies co-occurring BRCA1/2 reversions, TP53BP1, RIF1 and PAXIP1 mutations in PARP inhibitor-resistant advanced breast cancer. Ann Oncol 2024; 35:364-380. [PMID: 38244928 DOI: 10.1016/j.annonc.2024.01.003] [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] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Resistance to therapies that target homologous recombination deficiency (HRD) in breast cancer limits their overall effectiveness. Multiple, preclinically validated, mechanisms of resistance have been proposed, but their existence and relative frequency in clinical disease are unclear, as is how to target resistance. PATIENTS AND METHODS Longitudinal mutation and methylation profiling of circulating tumour (ct)DNA was carried out in 47 patients with metastatic BRCA1-, BRCA2- or PALB2-mutant breast cancer treated with HRD-targeted therapy who developed progressive disease-18 patients had primary resistance and 29 exhibited response followed by resistance. ctDNA isolated at multiple time points in the patient treatment course (before, on-treatment and at progression) was sequenced using a novel >750-gene intron/exon targeted sequencing panel. Where available, matched tumour biopsies were whole exome and RNA sequenced and also used to assess nuclear RAD51. RESULTS BRCA1/2 reversion mutations were present in 60% of patients and were the most prevalent form of resistance. In 10 cases, reversions were detected in ctDNA before clinical progression. Two new reversion-based mechanisms were identified: (i) intragenic BRCA1/2 deletions with intronic breakpoints; and (ii) intragenic BRCA1/2 secondary mutations that formed novel splice acceptor sites, the latter being confirmed by in vitro minigene reporter assays. When seen before commencing subsequent treatment, reversions were associated with significantly shorter time to progression. Tumours with reversions retained HRD mutational signatures but had functional homologous recombination based on RAD51 status. Although less frequent than reversions, nonreversion mechanisms [loss-of-function (LoF) mutations in TP53BP1, RIF1 or PAXIP1] were evident in patients with acquired resistance and occasionally coexisted with reversions, challenging the notion that singular resistance mechanisms emerge in each patient. CONCLUSIONS These observations map the prevalence of candidate drivers of resistance across time in a clinical setting, information with implications for clinical management and trial design in HRD breast cancers.
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Affiliation(s)
- E Harvey-Jones
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK; The Breast Cancer Now Research Unit, Guy's Hospital Cancer Centre, King's College London, UK; The City of London Cancer Research UK Centre at King's College London, UK
| | - M Raghunandan
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - L Robbez-Masson
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - L Magraner-Pardo
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - T Alaguthurai
- The Breast Cancer Now Research Unit, Guy's Hospital Cancer Centre, King's College London, UK
| | | | - J Yen
- Guardant Health Inc., Redwood City, USA
| | - H Xiao
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - R Brough
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - J Frankum
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - F Song
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - J Yeung
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - T Savy
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - A Gulati
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - J Alexander
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - H Kemp
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - C Starling
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - A Konde
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - R Marlow
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - M Cheang
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, UK
| | - P Proszek
- Clinical Genomics, The Royal Marsden Hospital, London, UK
| | - M Hubank
- Clinical Genomics, The Royal Marsden Hospital, London, UK
| | - M Cai
- Guardant Health Inc., Redwood City, USA
| | - J Trendell
- The Breast Cancer Now Research Unit, Guy's Hospital Cancer Centre, King's College London, UK
| | - R Lu
- The Breast Cancer Now Research Unit, Guy's Hospital Cancer Centre, King's College London, UK
| | - R Liccardo
- The Breast Cancer Now Research Unit, Guy's Hospital Cancer Centre, King's College London, UK
| | - N Ravindran
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | | | - O Rodriguez
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - J Balmana
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | | | | | | | - I Roxanis
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - V Serra
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - S Haider
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - S J Pettitt
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
| | - C J Lord
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
| | - A N J Tutt
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK; The Breast Cancer Now Research Unit, Guy's Hospital Cancer Centre, King's College London, UK; The City of London Cancer Research UK Centre at King's College London, UK.
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9
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Sheng X, Xia Z, Yang H, Hu R. The ubiquitin codes in cellular stress responses. Protein Cell 2024; 15:157-190. [PMID: 37470788 PMCID: PMC10903993 DOI: 10.1093/procel/pwad045] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 07/04/2023] [Indexed: 07/21/2023] Open
Abstract
Ubiquitination/ubiquitylation, one of the most fundamental post-translational modifications, regulates almost every critical cellular process in eukaryotes. Emerging evidence has shown that essential components of numerous biological processes undergo ubiquitination in mammalian cells upon exposure to diverse stresses, from exogenous factors to cellular reactions, causing a dazzling variety of functional consequences. Various forms of ubiquitin signals generated by ubiquitylation events in specific milieus, known as ubiquitin codes, constitute an intrinsic part of myriad cellular stress responses. These ubiquitination events, leading to proteolytic turnover of the substrates or just switch in functionality, initiate, regulate, or supervise multiple cellular stress-associated responses, supporting adaptation, homeostasis recovery, and survival of the stressed cells. In this review, we attempted to summarize the crucial roles of ubiquitination in response to different environmental and intracellular stresses, while discussing how stresses modulate the ubiquitin system. This review also updates the most recent advances in understanding ubiquitination machinery as well as different stress responses and discusses some important questions that may warrant future investigation.
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Affiliation(s)
- Xiangpeng Sheng
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- State Key Laboratory of Animal Disease Control, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Zhixiong Xia
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hanting Yang
- Department of Neurology, State Key Laboratory of Medical Neurobiology, Institute for Translational Brain Research, MOE Frontiers Center for Brain Science, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Ronggui Hu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
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10
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Kanev PB, Atemin A, Stoynov S, Aleksandrov R. PARP1 roles in DNA repair and DNA replication: The basi(c)s of PARP inhibitor efficacy and resistance. Semin Oncol 2024; 51:2-18. [PMID: 37714792 DOI: 10.1053/j.seminoncol.2023.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 08/10/2023] [Indexed: 09/17/2023]
Abstract
Genome integrity is under constant insult from endogenous and exogenous sources. In order to cope, eukaryotic cells have evolved an elaborate network of DNA repair that can deal with diverse lesion types and exhibits considerable functional redundancy. PARP1 is a major sensor of DNA breaks with established and putative roles in a number of pathways within the DNA repair network, including repair of single- and double-strand breaks as well as protection of the DNA replication fork. Importantly, PARP1 is the major target of small-molecule PARP inhibitors (PARPi), which are employed in the treatment of homologous recombination (HR)-deficient tumors, as the latter are particularly susceptible to the accumulation of DNA damage due to an inability to efficiently repair highly toxic double-strand DNA breaks. The clinical success of PARPi has fostered extensive research into PARP biology, which has shed light on the involvement of PARP1 in various genomic transactions. A major goal within the field has been to understand the relationship between catalytic inhibition and PARP1 trapping. The specific consequences of inhibition and trapping on genomic stability as a basis for the cytotoxicity of PARP inhibitors remain a matter of debate. Finally, PARP inhibition is increasingly recognized for its capacity to elicit/modulate anti-tumor immunity. The clinical potential of PARP inhibition is, however, hindered by the development of resistance. Hence, extensive efforts are invested in identifying factors that promote resistance or sensitize cells to PARPi. The current review provides a summary of advances in our understanding of PARP1 biology, the mechanistic nature, and molecular consequences of PARP inhibition, as well as the mechanisms that give rise to PARPi resistance.
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Affiliation(s)
- Petar-Bogomil Kanev
- Laboratory of Genomic Stability, Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Aleksandar Atemin
- Laboratory of Genomic Stability, Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Stoyno Stoynov
- Laboratory of Genomic Stability, Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria.
| | - Radoslav Aleksandrov
- Laboratory of Genomic Stability, Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria.
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11
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Swift ML, Zhou R, Syed A, Moreau LA, Tomasik B, Tainer JA, Konstantinopoulos PA, D'Andrea AD, He YJ, Chowdhury D. Dynamics of the DYNLL1-MRE11 complex regulate DNA end resection and recruitment of Shieldin to DSBs. Nat Struct Mol Biol 2023; 30:1456-1467. [PMID: 37696958 PMCID: PMC10686051 DOI: 10.1038/s41594-023-01074-9] [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: 01/31/2023] [Accepted: 07/21/2023] [Indexed: 09/13/2023]
Abstract
The extent and efficacy of DNA end resection at DNA double-strand breaks (DSB) determine the repair pathway choice. Here we describe how the 53BP1-associated protein DYNLL1 works in tandem with the Shieldin complex to protect DNA ends. DYNLL1 is recruited to DSBs by 53BP1, where it limits end resection by binding and disrupting the MRE11 dimer. The Shieldin complex is recruited to a fraction of 53BP1-positive DSBs hours after DYNLL1, predominantly in G1 cells. Shieldin localization to DSBs depends on MRE11 activity and is regulated by the interaction of DYNLL1 with MRE11. BRCA1-deficient cells rendered resistant to PARP inhibitors by the loss of Shieldin proteins can be resensitized by the constitutive association of DYNLL1 with MRE11. These results define the temporal and functional dynamics of the 53BP1-centric DNA end resection factors in cells.
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Affiliation(s)
- Michelle L Swift
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Rui Zhou
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Aleem Syed
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Lisa A Moreau
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Bartłomiej Tomasik
- Department of Biostatistics and Translational Medicine, Medical University of Łódź, Łódź, Poland
- Department of Oncology and Radiotherapy, Medical University of Gdańsk, Faculty of Medicine, Gdańsk, Poland
| | - John A Tainer
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Molecular and Cellular Oncology and Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Alan D D'Andrea
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Yizhou Joseph He
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
| | - Dipanjan Chowdhury
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
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12
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Cui G, Botuyan MV, Drané P, Hu Q, Bragantini B, Thompson JR, Schuller DJ, Detappe A, Perfetti MT, James LI, Frye SV, Chowdhury D, Mer G. An autoinhibited state of 53BP1 revealed by small molecule antagonists and protein engineering. Nat Commun 2023; 14:6091. [PMID: 37773238 PMCID: PMC10541411 DOI: 10.1038/s41467-023-41821-6] [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: 03/20/2023] [Accepted: 09/20/2023] [Indexed: 10/01/2023] Open
Abstract
The recruitment of 53BP1 to chromatin, mediated by its recognition of histone H4 dimethylated at lysine 20 (H4K20me2), is important for DNA double-strand break repair. Using a series of small molecule antagonists, we demonstrate a conformational equilibrium between an open and a pre-existing lowly populated closed state of 53BP1 in which the H4K20me2 binding surface is buried at the interface between two interacting 53BP1 molecules. In cells, these antagonists inhibit the chromatin recruitment of wild type 53BP1, but do not affect 53BP1 variants unable to access the closed conformation despite preservation of the H4K20me2 binding site. Thus, this inhibition operates by shifting the conformational equilibrium toward the closed state. Our work therefore identifies an auto-associated form of 53BP1-autoinhibited for chromatin binding-that can be stabilized by small molecule ligands encapsulated between two 53BP1 protomers. Such ligands are valuable research tools to study the function of 53BP1 and have the potential to facilitate the development of new drugs for cancer therapy.
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Affiliation(s)
- Gaofeng Cui
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | | | - Pascal Drané
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Qi Hu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Benoît Bragantini
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | | | - David J Schuller
- Cornell High Energy Synchrotron Source, Cornell University, Ithaca, NY, USA
| | | | - Michael T Perfetti
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lindsey I James
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Stephen V Frye
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Dipanjan Chowdhury
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Georges Mer
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA.
- Department of Cancer Biology, Mayo Clinic, Rochester, MN, USA.
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13
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Satyamitra MM, Cassatt DR, Molinar-Inglis O, Rios CI, Taliaferro LP, Winters TA, DiCarlo AL. The NIAID/RNCP Biodosimetry Program: An Overview. Cytogenet Genome Res 2023; 163:89-102. [PMID: 37742625 PMCID: PMC10946631 DOI: 10.1159/000534213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 09/18/2023] [Indexed: 09/26/2023] Open
Abstract
Established in 2004, the Radiation and Nuclear Countermeasures Program (RNCP), within the National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health has the central mission to advance medical countermeasure mitigators/therapeutics, and biomarkers and technologies to assess, triage, and inform medical management of patients experiencing acute radiation syndrome and/or the delayed effects of acute radiation exposure. The RNCP biodosimetry mission space encompasses: (1) basic research to elucidate novel approaches for rapid and accurate assessment of radiation exposure, (2) studies to support advanced development for US Food and Drug Administration (FDA) clearance of promising triage or treatment devices/approaches, (3) characterization of biomarkers and/or assays to determine degree of tissue or organ dose that can predict outcome of radiation injuries (i.e., organ failure, morbidity, and/or mortality), and (4) outreach efforts to facilitate interactions with researchers developing cutting edge biodosimetry approaches. Thus far, no biodosimetry device has been FDA cleared for use during a radiological/nuclear incident. At NIAID, advancement of radiation biomarkers and biodosimetry approaches is facilitated by a variety of funding mechanisms (grants, contracts, cooperative and interagency agreements, and Small Business Innovation Research awards), with the objective of advancing devices and assays toward clearance, as outlined in the FDA's Radiation Biodosimetry Medical Countermeasure Devices Guidance. The ultimate goal of the RNCP biodosimetry program is to develop and establish accurate and reliable biodosimetry tools that will improve radiation preparedness and ultimately save lives during a radiological or nuclear incident.
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Affiliation(s)
- Merriline M Satyamitra
- Radiation and Nuclear Countermeasures Program (RNCP), Division of Allergy, Immunology, and Transplantation (DAIT), U.S. Department of Health and Human Services (HHS), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Rockville, Maryland, USA
| | - David R Cassatt
- Radiation and Nuclear Countermeasures Program (RNCP), Division of Allergy, Immunology, and Transplantation (DAIT), U.S. Department of Health and Human Services (HHS), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Rockville, Maryland, USA
| | - Olivia Molinar-Inglis
- Radiation and Nuclear Countermeasures Program (RNCP), Division of Allergy, Immunology, and Transplantation (DAIT), U.S. Department of Health and Human Services (HHS), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Rockville, Maryland, USA
| | - Carmen I Rios
- Radiation and Nuclear Countermeasures Program (RNCP), Division of Allergy, Immunology, and Transplantation (DAIT), U.S. Department of Health and Human Services (HHS), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Rockville, Maryland, USA
| | - Lanyn P Taliaferro
- Radiation and Nuclear Countermeasures Program (RNCP), Division of Allergy, Immunology, and Transplantation (DAIT), U.S. Department of Health and Human Services (HHS), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Rockville, Maryland, USA
| | - Thomas A Winters
- Radiation and Nuclear Countermeasures Program (RNCP), Division of Allergy, Immunology, and Transplantation (DAIT), U.S. Department of Health and Human Services (HHS), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Rockville, Maryland, USA
| | - Andrea L DiCarlo
- Radiation and Nuclear Countermeasures Program (RNCP), Division of Allergy, Immunology, and Transplantation (DAIT), U.S. Department of Health and Human Services (HHS), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Rockville, Maryland, USA
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14
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Cui G, Botuyan MV, Drané P, Hu Q, Bragantini B, Thompson JR, Schuller DJ, Detappe A, Perfetti MT, James LI, Frye SV, Chowdhury D, Mer G. An autoinhibited state of 53BP1 revealed by small molecule antagonists and protein engineering. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.20.534960. [PMID: 37131705 PMCID: PMC10153216 DOI: 10.1101/2023.04.20.534960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The recruitment of 53BP1 to chromatin, mediated by its recognition of histone H4 dimethylated at lysine 20 (H4K20me2), is important for DNA double-strand break repair. Using a series of small molecule antagonists, we demonstrate a conformational equilibrium between an open and a pre-existing lowly populated closed state of 53BP1 in which the H4K20me2 binding surface is buried at the interface between two interacting 53BP1 molecules. In cells, these antagonists inhibit the chromatin recruitment of wild type 53BP1, but do not affect 53BP1 variants unable to access the closed conformation despite preservation of the H4K20me2 binding site. Thus, this inhibition operates by shifting the conformational equilibrium toward the closed state. Our work therefore identifies an auto-associated form of 53BP1 - autoinhibited for chromatin binding - that can be stabilized by small molecule ligands encapsulated between two 53BP1 protomers. Such ligands are valuable research tools to study the function of 53BP1 and have the potential to facilitate the development of new drugs for cancer therapy.
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15
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Ma J, Zhou Y, Pan P, Yu H, Wang Z, Li LL, Wang B, Yan Y, Pan Y, Ye Q, Liu T, Feng X, Xu S, Wang K, Wang X, Jian Y, Ma B, Fan Y, Gao Y, Huang H, Li L. TRABID overexpression enables synthetic lethality to PARP inhibitor via prolonging 53BP1 retention at double-strand breaks. Nat Commun 2023; 14:1810. [PMID: 37002234 PMCID: PMC10066190 DOI: 10.1038/s41467-023-37499-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 03/17/2023] [Indexed: 04/03/2023] Open
Abstract
53BP1 promotes nonhomologous end joining (NHEJ) over homologous recombination (HR) repair by mediating inactivation of DNA end resection. Ubiquitination plays an important role in regulating dissociation of 53BP1 from DNA double-strand breaks (DSBs). However, how this process is regulated remains poorly understood. Here, we demonstrate that TRABID deubiquitinase binds to 53BP1 at endogenous level and regulates 53BP1 retention at DSB sites. TRABID deubiquitinates K29-linked polyubiquitination of 53BP1 mediated by E3 ubiquitin ligase SPOP and prevents 53BP1 dissociation from DSBs, consequently inducing HR defects and chromosomal instability. Prostate cancer cells with TRABID overexpression exhibit a high sensitivity to poly (ADP-ribose) polymerase (PARP) inhibitors. Our work shows that TRABID facilitates NHEJ repair over HR during DNA repair by inducing prolonged 53BP1 retention at DSB sites, suggesting that TRABID overexpression may predict HR deficiency and the potential therapeutic use of PARP inhibitors in prostate cancer.
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Affiliation(s)
- Jian Ma
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, 710061, Xi'an, P. R. China
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, 55905, USA
| | - Yingke Zhou
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, 55905, USA
- Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Penglin Pan
- Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Haixin Yu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Zixi Wang
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, 710061, Xi'an, P. R. China
| | - Lei Lily Li
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, 710061, Xi'an, P. R. China
| | - Bing Wang
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, 710061, Xi'an, P. R. China
| | - Yuqian Yan
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, 55905, USA
| | - Yunqian Pan
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, 55905, USA
| | - Qi Ye
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, 710061, Xi'an, P. R. China
| | - Tianjie Liu
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, 710061, Xi'an, P. R. China
| | - Xiaoyu Feng
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, 710061, Xi'an, P. R. China
| | - Shan Xu
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, 710061, Xi'an, P. R. China
| | - Ke Wang
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, 710061, Xi'an, P. R. China
| | - Xinyang Wang
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, 710061, Xi'an, P. R. China
| | - Yanlin Jian
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, 710061, Xi'an, P. R. China
| | - Bohan Ma
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, 710061, Xi'an, P. R. China
| | - Yizeng Fan
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, 710061, Xi'an, P. R. China
| | - Yang Gao
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, 710061, Xi'an, P. R. China
| | - Haojie Huang
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, 55905, USA.
- Mayo Clinic Cancer Center, Mayo Clinic College of Medicine and Science, Rochester, MN, 55905, USA.
- Department of Urology, Mayo Clinic College of Medicine and Science, Rochester, MN, 55905, USA.
| | - Lei Li
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, 710061, Xi'an, P. R. China.
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16
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Zhou R, Swift ML, Syed A, Huang K, Moreau L, Tainer JA, Konstantinopoulos PA, Dâ Andrea AD, He YJ, Chowdhury D. Dynamics of the DYNLL1/MRE11 complex regulates DNA end resection and recruitment of the Shieldin complex to DSBs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.27.534416. [PMID: 37034578 PMCID: PMC10081242 DOI: 10.1101/2023.03.27.534416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Extent and efficacy of DNA end resection at DNA double strand break (DSB)s determines the choice of repair pathway. Here we describe how the 53BP1 associated protein DYNLL1 works in tandem with Shieldin and the CST complex to protect DNA ends. DYNLL1 is recruited to DSBs by 53BP1 where it limits end resection by binding and disrupting the MRE11 dimer. The Shieldin complex is recruited to a fraction of 53BP1-positive DSBs hours after DYNLL1 predominantly in the G1 cells. Shieldin localization to DSBs is dependent on MRE11 activity and is regulated by the interaction of DYNLL1 with MRE11. BRCA1-deficient cells rendered resistant to PARP inhibitors by the loss of Shieldin proteins can be re-sensitized by the constitutive association of DYNLL1 with MRE11. These results define the temporal and functional dynamics of the 53BP1-centric DNA end resection factors in cells.
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17
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Zhang Z, Samsa WE, De Y, Zhang F, Reizes O, Almasan A, Gong Z. HDGFRP3 interaction with 53BP1 promotes DNA double-strand break repair. Nucleic Acids Res 2023; 51:2238-2256. [PMID: 36794849 PMCID: PMC10018360 DOI: 10.1093/nar/gkad073] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 01/11/2023] [Accepted: 01/24/2023] [Indexed: 02/17/2023] Open
Abstract
The 53BP1-dependent end-joining pathway plays a critical role in double-strand break (DSB) repair. However, the regulators of 53BP1 in chromatin remain incompletely characterized. In this study, we identified HDGFRP3 (hepatoma-derived growth factor related protein 3) as a 53BP1-interacting protein. The HDGFRP3-53BP1 interaction is mediated by the PWWP domain of HDGFRP3 and the Tudor domain of 53BP1. Importantly, we observed that the HDGFRP3-53BP1 complex co-localizes with 53BP1 or γH2AX at sites of DSB and participates in the response to DNA damage repair. Loss of HDGFRP3 impairs classical non-homologous end-joining repair (NHEJ), curtails the accumulation of 53BP1 at DSB sites, and enhances DNA end-resection. Moreover, the HDGFRP3-53BP1 interaction is required for cNHEJ repair, 53BP1 recruitment at DSB sites, and inhibition of DNA end resection. In addition, loss of HDGFRP3 renders BRCA1-deficient cells resistant to PARP inhibitors by facilitating end-resection in BRCA1 deficient cells. We also found that the interaction of HDGFRP3 with methylated H4K20 was dramatically decreased; in contrast, the 53BP1-methylated H4K20 interaction was increased after ionizing radiation, which is likely regulated by protein phosphorylation and dephosphorylation. Taken together, our data reveal a dynamic 53BP1-methylated H4K20-HDGFRP3 complex that regulates 53BP1 recruitment at DSB sites, providing new insights into our understanding of the regulation of 53BP1-mediated DNA repair pathway.
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Affiliation(s)
- Zhen Zhang
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - William E Samsa
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - Yanyan De
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - Fan Zhang
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - Ofer Reizes
- Department of Cardiovascular & Metabolic Sciences, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - Alexandru Almasan
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - Zihua Gong
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
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18
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Huang Z, Li X, Tang B, Li H, Zhang J, Sun R, Ma J, Pan Y, Yan B, Zhou Y, Ding D, Yan Y, Jimenez R, Orme JJ, Jin X, Yang J, Huang H, Jia Z. SETDB1 Modulates Degradation of Phosphorylated RB and Anticancer Efficacy of CDK4/6 Inhibitors. Cancer Res 2023; 83:875-889. [PMID: 36637424 DOI: 10.1158/0008-5472.can-22-0264] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 08/14/2022] [Accepted: 01/06/2023] [Indexed: 01/14/2023]
Abstract
Retinoblastoma (RB) protein can exert tumor suppressor functions even when it becomes phosphorylated. It is thus essential to understand how phosphorylated RB (p-RB) expression and function are regulated. Here, we demonstrated that RING finger domain protein TRIM28 bound and promoted ubiquitination and degradation of CDK4/6-phosphorylated RB protein. SETDB1, a known TRIM28 binding partner, protected p-RB from degradation through the binding of methylated RB by its Tudor domain independent of its methyltransferase activity. SETDB1 was found to be frequently overexpressed due to gene amplification and positively correlated with p-RB in prostate cancer patient specimens. Inhibition of SETDB1 expression using a gene-specific antisense oligonucleotide (ASO) reduced tumor growth but accelerated RB protein degradation, limiting the therapeutic efficacy. However, coadministration of the CDK4/6 inhibitor palbociclib blocked ASO-induced RB degradation and resulted in a much greater cancer-inhibitory effect than each inhibitor alone both in vitro and in vivo. This study identified CDK4/6-dependent, TRIM28-mediated proteasomal degradation as a mechanism of RB inactivation and reveals SETDB1 as a key inhibitor of this process. Our findings suggest that combined targeting of SETDB1 and CDK4/6 represents a viable approach for the treatment of cancers with SETDB1 gene amplification or overexpression. SIGNIFICANCE The identification of a role for TRIM28 and SETDB1 in regulating CDK4/6-phosphorylated RB stability uncovers a combination strategy using CDK4/6 and SETDB1 inhibition to decrease RB degradation and inhibit cancer growth.
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Affiliation(s)
- Zhenlin Huang
- Department of Urology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - Xiang Li
- Department of Urology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - Bo Tang
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Hao Li
- Department of Urology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - Jianong Zhang
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - Rui Sun
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - Jian Ma
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - Yunqian Pan
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - Binyuan Yan
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
- Department of Urology, Kidney and Urology Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Yingke Zhou
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - Donglin Ding
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - Yuqian Yan
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - Rafael Jimenez
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - Jacob J Orme
- Division of Medical Oncology, Department of Internal Medicine, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - Xin Jin
- Department of Urology, The Second Xiangya Hospital, Central South University, Changsha, Human, China
| | - Jinjian Yang
- Department of Urology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Haojie Huang
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
- Department of Urology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
- Mayo Clinic Comprehensive Cancer Center, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - Zhankui Jia
- Department of Urology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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19
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Lu J, Li D, Jiang H, Li Y, Lu C, Chen T, Wang Y, Wang X, Sun W, Pu Z, Qiao C, Ma J, Xu G. The aryl sulfonamide indisulam inhibits gastric cancer cell migration by promoting the ubiquitination and degradation of the transcription factor ZEB1. J Biol Chem 2023; 299:103025. [PMID: 36805336 PMCID: PMC10040736 DOI: 10.1016/j.jbc.2023.103025] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/20/2023] [Accepted: 01/22/2023] [Indexed: 02/17/2023] Open
Abstract
Gastric cancer is one of the cancers with high morbidity and mortality worldwide. The aryl sulfonamide indisulam inhibits the proliferation of several types of cancer cells through its function as a molecular glue to promote the ubiquitination and degradation of RNA-binding motif protein 39 (RBM39). However, it is unknown whether and how indisulam regulates the migration of cancer cells. In this work, using label-free quantitative proteomics, we discover that indisulam significantly attenuates N-cadherin, a marker for epithelial to mesenchymal transition and migration of cancer cells. Our bioinformatics analysis and biochemical experiments reveal that indisulam promotes the interaction between the zinc finger E-box-binding homeobox 1 (ZEB1), a transcription factor of N-cadherin, and DCAF15, a substrate receptor of CRL4 E3 ubiquitin ligase, and enhances ZEB1 ubiquitination and proteasomal degradation. In addition, our cell line-based experiments demonstrate that indisulam inhibits the migration of gastric cancer cells in a ZEB1-dependent manner. Analyses of patient samples and datasets in public databases reveal that tumor tissues from patients with gastric cancer express high ZEB1 mRNA and this high expression reduces patient survival rate. Finally, we show that treatment of gastric tumor samples with indisulam significantly reduces ZEB1 protein levels. Therefore, this work discloses a new mechanism by which indisulam inhibits the migration of gastric cancer cells, indicating that indisulam exhibits different biological functions through distinct signaling molecules.
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Affiliation(s)
- Jiaqi Lu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, Jiangsu, China
| | - Dan Li
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, Jiangsu, China
| | - Honglv Jiang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, Jiangsu, China
| | - Yue Li
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, Jiangsu, China
| | - Chengpiao Lu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, Jiangsu, China
| | - Tao Chen
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Yuhong Wang
- Department of Pathology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Xiaohui Wang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, Jiangsu, China
| | - Wenzhao Sun
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, Jiangsu, China
| | - Zhongjian Pu
- Department of Oncology, Haian Hospital of Traditional Chinese Medicine, Haian, Jiangsu, China
| | - Chunhua Qiao
- College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Jingjing Ma
- Department of Pharmacy, Medical Center of Soochow University, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, Jiangsu, China.
| | - Guoqiang Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, Jiangsu, China.
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20
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Rass E, Willaume S, Bertrand P. 53BP1: Keeping It under Control, Even at a Distance from DNA Damage. Genes (Basel) 2022; 13:genes13122390. [PMID: 36553657 PMCID: PMC9778356 DOI: 10.3390/genes13122390] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/02/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
Double-strand breaks (DSBs) are toxic lesions that can be generated by exposure to genotoxic agents or during physiological processes, such as during V(D)J recombination. The repair of these DSBs is crucial to prevent genomic instability and to maintain cellular homeostasis. Two main pathways participate in repairing DSBs, namely, non-homologous end joining (NHEJ) and homologous recombination (HR). The P53-binding protein 1 (53BP1) plays a pivotal role in the choice of DSB repair mechanism, promotes checkpoint activation and preserves genome stability upon DSBs. By preventing DSB end resection, 53BP1 promotes NHEJ over HR. Nonetheless, the balance between DSB repair pathways remains crucial, as unscheduled NHEJ or HR events at different phases of the cell cycle may lead to genomic instability. Therefore, the recruitment of 53BP1 to chromatin is tightly regulated and has been widely studied. However, less is known about the mechanism regulating 53BP1 recruitment at a distance from the DNA damage. The present review focuses on the mechanism of 53BP1 recruitment to damage and on recent studies describing novel mechanisms keeping 53BP1 at a distance from DSBs.
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Affiliation(s)
- Emilie Rass
- Université Paris Cité, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, LREV/iRCM/IBFJ, F-92260 Fontenay-aux-Roses, France
- Université Paris-Saclay, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, LREV/iRCM/IBFJ, F-92260 Fontenay-aux-Roses, France
- Correspondence:
| | - Simon Willaume
- Université Paris Cité, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, LREV/iRCM/IBFJ, F-92260 Fontenay-aux-Roses, France
- Université Paris-Saclay, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, LREV/iRCM/IBFJ, F-92260 Fontenay-aux-Roses, France
| | - Pascale Bertrand
- Université Paris Cité, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, LREV/iRCM/IBFJ, F-92260 Fontenay-aux-Roses, France
- Université Paris-Saclay, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, LREV/iRCM/IBFJ, F-92260 Fontenay-aux-Roses, France
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21
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Martín-Rufo R, de la Vega-Barranco G, Lecona E. Ubiquitin and SUMO as timers during DNA replication. Semin Cell Dev Biol 2022; 132:62-73. [PMID: 35210137 DOI: 10.1016/j.semcdb.2022.02.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 02/12/2022] [Accepted: 02/14/2022] [Indexed: 12/14/2022]
Abstract
Every time a cell copies its DNA the genetic material is exposed to the acquisition of mutations and genomic alterations that corrupt the information passed on to daughter cells. A tight temporal regulation of DNA replication is necessary to ensure the full copy of the DNA while preventing the appearance of genomic instability. Protein modification by ubiquitin and SUMO constitutes a very complex and versatile system that allows the coordinated control of protein stability, activity and interactome. In chromatin, their action is complemented by the AAA+ ATPase VCP/p97 that recognizes and removes ubiquitylated and SUMOylated factors from specific cellular compartments. The concerted action of the ubiquitin/SUMO system and VCP/p97 determines every step of DNA replication enforcing the ordered activation/inactivation, loading/unloading and stabilization/destabilization of replication factors. Here we analyze the mechanisms used by ubiquitin/SUMO and VCP/p97 to establish molecular timers throughout DNA replication and their relevance in maintaining genome stability. We propose that these PTMs are the main molecular watch of DNA replication from origin recognition to replisome disassembly.
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Affiliation(s)
- Rodrigo Martín-Rufo
- Chromatin, Cancer and the Ubiquitin System lab, Centre for Molecular Biology Severo Ochoa (CBMSO, CSIC-UAM), Department of Genome Dynamics and Function, Madrid 28049, Spain
| | - Guillermo de la Vega-Barranco
- Chromatin, Cancer and the Ubiquitin System lab, Centre for Molecular Biology Severo Ochoa (CBMSO, CSIC-UAM), Department of Genome Dynamics and Function, Madrid 28049, Spain
| | - Emilio Lecona
- Chromatin, Cancer and the Ubiquitin System lab, Centre for Molecular Biology Severo Ochoa (CBMSO, CSIC-UAM), Department of Genome Dynamics and Function, Madrid 28049, Spain.
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22
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Stubbs FE, Flynn BP, Rivers CA, Birnie MT, Herman A, Swinstead EE, Baek S, Fang H, Temple J, Carroll JS, Hager GL, Lightman SL, Conway-Campbell BL. Identification of a novel GR-ARID1a-P53BP1 protein complex involved in DNA damage repair and cell cycle regulation. Oncogene 2022; 41:5347-5360. [PMID: 36344675 PMCID: PMC9734058 DOI: 10.1038/s41388-022-02516-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 10/02/2022] [Accepted: 10/17/2022] [Indexed: 11/09/2022]
Abstract
ARID1a (BAF250), a component of human SWI/SNF chromatin remodeling complexes, is frequently mutated across numerous cancers, and its loss of function has been putatively linked to glucocorticoid resistance. Here, we interrogate the impact of siRNA knockdown of ARID1a compared to a functional interference approach in the HeLa human cervical cancer cell line. We report that ARID1a knockdown resulted in a significant global decrease in chromatin accessibility in ATAC-Seq analysis, as well as affecting a subset of genome-wide GR binding sites determined by analyzing GR ChIP-Seq data. Interestingly, the specific effects on gene expression were limited to a relatively small subset of glucocorticoid-regulated genes, notably those involved in cell cycle regulation and DNA repair. The vast majority of glucocorticoid-regulated genes were largely unaffected by ARID1a knockdown or functional interference, consistent with a more specific role for ARID1a in glucocorticoid function than previously speculated. Using liquid chromatography-mass spectrometry, we have identified a chromatin-associated protein complex comprising GR, ARID1a, and several DNA damage repair proteins including P53 binding protein 1 (P53BP1), Poly(ADP-Ribose) Polymerase 1 (PARP1), DNA damage-binding protein 1 (DDB1), DNA mismatch repair protein MSH6 and splicing factor proline and glutamine-rich protein (SFPQ), as well as the histone acetyltransferase KAT7, an epigenetic regulator of steroid-dependent transcription, DNA damage repair and cell cycle regulation. Not only was this protein complex ablated with both ARID1a knockdown and functional interference, but spontaneously arising DNA damage was also found to accumulate in a manner consistent with impaired DNA damage repair mechanisms. Recovery from dexamethasone-dependent cell cycle arrest was also significantly impaired. Taken together, our data demonstrate that although glucocorticoids can still promote cell cycle arrest in the absence of ARID1a, the purpose of this arrest to allow time for DNA damage repair is hindered.
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Affiliation(s)
- Felicity E Stubbs
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, Translational Health Sciences, Faculty of Health Sciences, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol, BS1 3NY, UK
- Laboratory of Receptor Biology and Gene Expression, The National Cancer Institute, US National Institutes of Health, 41 Medlars Drive, Bethesda, MD, 20892, USA
| | - Benjamin P Flynn
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, Translational Health Sciences, Faculty of Health Sciences, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol, BS1 3NY, UK
| | - Caroline A Rivers
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, Translational Health Sciences, Faculty of Health Sciences, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol, BS1 3NY, UK
| | - Matthew T Birnie
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, Translational Health Sciences, Faculty of Health Sciences, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol, BS1 3NY, UK
| | - Andrew Herman
- Flow Cytometry Facility, Faculty of Life Sciences, School of Cellular & Molecular Medicine, Biomedical Sciences Building, University of Bristol, Bristol, BS8 1TD, UK
| | - Erin E Swinstead
- Laboratory of Receptor Biology and Gene Expression, The National Cancer Institute, US National Institutes of Health, 41 Medlars Drive, Bethesda, MD, 20892, USA
| | - Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, The National Cancer Institute, US National Institutes of Health, 41 Medlars Drive, Bethesda, MD, 20892, USA
| | - Hai Fang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jillian Temple
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Jason S Carroll
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, The National Cancer Institute, US National Institutes of Health, 41 Medlars Drive, Bethesda, MD, 20892, USA
| | - Stafford L Lightman
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, Translational Health Sciences, Faculty of Health Sciences, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol, BS1 3NY, UK
| | - Becky L Conway-Campbell
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, Translational Health Sciences, Faculty of Health Sciences, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol, BS1 3NY, UK.
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23
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Pre-Existing and Acquired Resistance to PARP Inhibitor-Induced Synthetic Lethality. Cancers (Basel) 2022; 14:cancers14235795. [PMID: 36497275 PMCID: PMC9741207 DOI: 10.3390/cancers14235795] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/17/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022] Open
Abstract
The advanced development of synthetic lethality has opened the doors for specific anti-cancer medications of personalized medicine and efficient therapies against cancers. One of the most popular approaches being investigated is targeting DNA repair pathways as the implementation of the PARP inhibitor (PARPi) into individual or combinational therapeutic schemes. Such treatment has been effectively employed against homologous recombination-defective solid tumors as well as hematopoietic malignancies. However, the resistance to PARPi has been observed in both preclinical research and clinical treatment. Therefore, elucidating the mechanisms responsible for the resistance to PARPi is pivotal for the further success of this intervention. Apart from mechanisms of acquired resistance, the bone marrow microenvironment provides a pre-existing mechanism to induce the inefficiency of PARPi in leukemic cells. Here, we describe the pre-existing and acquired mechanisms of the resistance to PARPi-induced synthetic lethality. We also discuss the potential rationales for developing effective therapies to prevent/repress the PARPi resistance in cancer cells.
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24
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Baxter JS, Zatreanu D, Pettitt SJ, Lord CJ. Resistance to DNA repair inhibitors in cancer. Mol Oncol 2022; 16:3811-3827. [PMID: 35567571 PMCID: PMC9627783 DOI: 10.1002/1878-0261.13224] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/25/2022] [Accepted: 05/12/2022] [Indexed: 12/24/2022] Open
Abstract
The DNA damage response (DDR) represents a complex network of proteins which detect and repair DNA damage, thereby maintaining the integrity of the genome and preventing the transmission of mutations and rearranged chromosomes to daughter cells. Faults in the DDR are a known driver and hallmark of cancer. Furthermore, inhibition of DDR enzymes can be used to treat the disease. This is exemplified by PARP inhibitors (PARPi) used to treat cancers with defects in the homologous recombination DDR pathway. A series of novel DDR targets are now also under pre-clinical or clinical investigation, including inhibitors of ATR kinase, WRN helicase or the DNA polymerase/helicase Polθ (Pol-Theta). Drug resistance is a common phenomenon that impairs the overall effectiveness of cancer treatments and there is already some understanding of how resistance to PARPi occurs. Here, we discuss how an understanding of PARPi resistance could inform how resistance to new drugs targeting the DDR emerges. We also discuss potential strategies that could limit the impact of these therapy resistance mechanisms in cancer.
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Affiliation(s)
- Joseph S. Baxter
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research CentreThe Institute of Cancer ResearchLondonUK
| | - Diana Zatreanu
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research CentreThe Institute of Cancer ResearchLondonUK
| | - Stephen J. Pettitt
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research CentreThe Institute of Cancer ResearchLondonUK
| | - Christopher J. Lord
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research CentreThe Institute of Cancer ResearchLondonUK
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25
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Ketley RF, Battistini F, Alagia A, Mondielli C, Iehl F, Balikçi E, Huber KVM, Orozco M, Gullerova M. DNA double-strand break-derived RNA drives TIRR/53BP1 complex dissociation. Cell Rep 2022; 41:111526. [PMID: 36288694 PMCID: PMC9638026 DOI: 10.1016/j.celrep.2022.111526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/11/2022] [Accepted: 09/28/2022] [Indexed: 11/25/2022] Open
Abstract
Tudor-interacting repair regulator (TIRR) is an RNA-binding protein and a negative regulator of the DNA-repair factor p53-binding protein 1 (53BP1). In non-damage conditions, TIRR is bound to 53BP1. After DNA damage, TIRR and 53BP1 dissociate, and 53BP1 binds the chromatin at the double-strand break (DSB) to promote non-homologous end joining (NHEJ)-mediated repair. However, the exact mechanistic details of this dissociation after damage are unknown. Increasing evidence has implicated RNA as a crucial factor in the DNA damage response (DDR). Here, we show that RNA can separate TIRR/53BP1. Specifically, RNA with a hairpin secondary structure, transcribed at the DSB by RNA polymerase II (RNAPII), promotes TIRR/53BP1 complex separation. This hairpin RNA binds to the same residues on TIRR as 53BP1. Our results uncover a role of DNA-damage-derived RNA in modulating a protein-protein interaction and contribute to our understanding of DSB repair.
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Affiliation(s)
- Ruth F Ketley
- Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK
| | - Federica Battistini
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science, and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain; Department of Biochemistry and Molecular Biology. University of Barcelona, 08028 Barcelona, Spain
| | - Adele Alagia
- Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK
| | - Clémence Mondielli
- HTBS - Biophysics Group, Evotec (France) SAS, Campus Curie, 195 Route d'Espagne, 31036 Toulouse Cedex, France
| | - Florence Iehl
- HTBS - Biophysics Group, Evotec (France) SAS, Campus Curie, 195 Route d'Espagne, 31036 Toulouse Cedex, France
| | - Esra Balikçi
- Centre for Medicines Discovery, Nuffield Department of Medicine, Oxford OX3 7FZ, UK; Target Discovery Institute, Nuffield Department of Medicine, Oxford OX3 7FZ, UK
| | - Kilian V M Huber
- Centre for Medicines Discovery, Nuffield Department of Medicine, Oxford OX3 7FZ, UK; Target Discovery Institute, Nuffield Department of Medicine, Oxford OX3 7FZ, UK
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science, and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain; Department of Biochemistry and Molecular Biology. University of Barcelona, 08028 Barcelona, Spain
| | - Monika Gullerova
- Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK.
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26
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González-Bermúdez L, Genescà A, Terradas M, Martín M. Role of H4K16 acetylation in 53BP1 recruitment to double-strand break sites in in vitro aged cells. Biogerontology 2022; 23:499-514. [PMID: 35851632 PMCID: PMC9388460 DOI: 10.1007/s10522-022-09979-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 06/29/2022] [Indexed: 12/20/2022]
Abstract
AbstractIncreased frequency of DNA double strand breaks (DSBs) with aging suggests an age-associated decline in DSB repair efficiency, which is also influenced by the epigenetic landscape. H4 acetylation at lysine 16 (H4K16Ac) has been related to DSB repair since deacetylation of this mark is required for efficient 53BP1 recruitment to DSBs. Although age-associated changes in H4K16Ac levels have been studied, their contribution to age-related DSB accumulation remains unknown. In vitro aged Human Dermal Fibroblasts (HDFs) display lower levels of H4K16A that correlate with reduced recruitment of 53BP1 to basal DSBs. Following DNA damage induction, early passage (EP) cells suffered from a transient H4K16 deacetylation that allowed proper 53BP1 recruitment to DSBs. In contrast, to reach this specific and optimum level, aged cells responded by increasing their overall lower H4K16Ac levels. Induced hyperacetylation of late passage (LP) cells using trichostatin A increased H4K16Ac levels but did not ameliorate 53BP1 recruitment. Instead, deacetylation induced by MOF silencing reduced H4K16Ac levels and compromised 53BP1 recruitment in both EP and LP cells. Age-associated decrease of H4K16Ac levels contributes to the repair defect displayed by in vitro aged cells. H4K16Ac responds to DNA damage in order to reach a specific, optimum level that allows proper 53BP1 recruitment. This response may be compromised with age, as LP cells depart from lower H4K16Ac levels. Variations in H4K16Ac following the activation of the DNA damage response and aging point at this histone mark as a key mediator between DNA repair and age-associated chromatin alterations.
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Affiliation(s)
- Lourdes González-Bermúdez
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Anna Genescà
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Spain
| | - Mariona Terradas
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Spain
| | - Marta Martín
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, Spain
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Pilot Study Showing Feasibility of Phosphoproteomic Profiling of Pathway-Level Molecular Alterations in Barrett’s Esophagus. Genes (Basel) 2022; 13:genes13071215. [PMID: 35885999 PMCID: PMC9325186 DOI: 10.3390/genes13071215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/25/2022] [Accepted: 07/05/2022] [Indexed: 11/17/2022] Open
Abstract
(1) Background: Barrett’s esophagus is a major risk factor for esophageal adenocarcinoma. In this pilot study, we employed precision mass spectrometry to map global (phospho)protein perturbations in Barrett’s esophagus lesions and adjacent normal tissue to glean insights into disease progression. (2) Methods: Biopsies were collected from two small but independent cohorts. Comparative analyses were performed between Barrett’s esophagus samples and adjacent matched (normal) tissues from patients with known pathology, while specimens from healthy patients served as additional controls. (3) Results: We identified and quantified 6810 proteins and 6395 phosphosites in the discovery cohort, revealing hundreds of statistically significant differences in protein abundances and phosphorylation states. We identified a robust proteomic signature that accurately classified the disease status of samples from the independent patient cohorts. Pathway-level analysis of the phosphoproteomic profiles revealed the dysregulation of specific cellular processes, including DNA repair, in Barrett’s esophagus relative to paired controls. Comparative analysis with previously published transcriptomic profiles provided independent evidence in support of these preliminary findings. (4) Conclusions: This pilot study establishes the feasibility of using unbiased quantitative phosphoproteomics to identify molecular perturbations associated with disease progression in Barrett’s esophagus to define potentially clinically actionable targets warranting further assessment.
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Bisht P, Kumar VU, Pandey R, Velayutham R, Kumar N. Role of PARP Inhibitors in Glioblastoma and Perceiving Challenges as Well as Strategies for Successful Clinical Development. Front Pharmacol 2022; 13:939570. [PMID: 35873570 PMCID: PMC9297740 DOI: 10.3389/fphar.2022.939570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/10/2022] [Indexed: 11/13/2022] Open
Abstract
Glioblastoma multiform is the most aggressive primary type of brain tumor, representing 54% of all gliomas. The average life span for glioblastoma multiform is around 14-15 months instead of treatment. The current treatment for glioblastoma multiform includes surgical removal of the tumor followed by radiation therapy and temozolomide chemotherapy for 6.5 months, followed by another 6 months of maintenance therapy with temozolomide chemotherapy (5 days every month). However, resistance to temozolomide is frequently one of the limiting factors in effective treatment. Poly (ADP-ribose) polymerase (PARP) inhibitors have recently been investigated as sensitizing drugs to enhance temozolomide potency. However, clinical use of PARP inhibitors in glioblastoma multiform is difficult due to a number of factors such as limited blood-brain barrier penetration of PARP inhibitors, inducing resistance due to frequent use of PARP inhibitors, and overlapping hematologic toxicities of PARP inhibitors when co-administered with glioblastoma multiform standard treatment (radiation therapy and temozolomide). This review elucidates the role of PARP inhibitors in temozolomide resistance, multiple factors that make development of these PARP inhibitor drugs challenging, and the strategies such as the development of targeted drug therapies and combination therapy to combat the resistance of PARP inhibitors that can be adopted to overcome these challenges.
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Affiliation(s)
- Priya Bisht
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER-Hajipur), Hajipur, India
| | - V. Udaya Kumar
- Department of Pharmacy Practice, National Institute of Pharmaceutical Education and Research (NIPER-Hajipur), Hajipur, India
| | - Ruchi Pandey
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER-Hajipur), Hajipur, India
| | - Ravichandiran Velayutham
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER-Hajipur), Hajipur, India
| | - Nitesh Kumar
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER-Hajipur), Hajipur, India
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Shams F, Bayat H, Mohammadian O, Mahboudi S, Vahidnezhad H, Soosanabadi M, Rahimpour A. Advance trends in targeting homology-directed repair for accurate gene editing: An inclusive review of small molecules and modified CRISPR-Cas9 systems. BIOIMPACTS 2022; 12:371-391. [PMID: 35975201 PMCID: PMC9376165 DOI: 10.34172/bi.2022.23871] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 11/21/2021] [Accepted: 11/21/2021] [Indexed: 11/25/2022]
Abstract
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Introduction: Clustered regularly interspaced short palindromic repeat and its associated protein (CRISPR-Cas)-based technologies generate targeted modifications in host genome by inducing site-specific double-strand breaks (DSBs) that can serve as a substrate for homology-directed repair (HDR) in both in vitro and in vivo models. HDR pathway could enhance incorporation of exogenous DNA templates into the CRISPR-Cas9-mediated DSB site. Owing to low rate of HDR pathway, the efficiency of accurate genome editing is diminished. Enhancing the efficiency of HDR can provide fast, easy, and accurate technologies based on CRISPR-Cas9 technologies.
Methods: The current study presents an overview of attempts conducted on the precise genome editing strategies based on small molecules and modified CRISPR-Cas9 systems.
Results: In order to increase HDR rate in targeted cells, several logical strategies have been introduced such as generating CRISPR effector chimeric proteins, anti-CRISPR proteins, modified Cas9 with donor template, and using validated synthetic or natural small molecules for either inhibiting non-homologous end joining (NHEJ), stimulating HDR, or synchronizing cell cycle. Recently, high-throughput screening methods have been applied for identification of small molecules which along with the CRISPR system can regulate precise genome editing through HDR.
Conclusion: The stimulation of HDR components or inhibiting NHEJ can increase the accuracy of CRISPR-Cas-mediated engineering systems. Generating chimeric programmable endonucleases provide this opportunity to direct DNA template close proximity of CRISPR-Cas-mediated DSB. Small molecules and their derivatives can also proficiently block or activate certain DNA repair pathways and bring up novel perspectives for increasing HDR efficiency, especially in human cells. Further, high throughput screening of small molecule libraries could result in more discoveries of promising chemicals that improve HDR efficiency and CRISPR-Cas9 systems.
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Affiliation(s)
- Forough Shams
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hadi Bayat
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Omid Mohammadian
- Medical Nano-Technology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Somayeh Mahboudi
- Department of Food Science and Technology, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Hassan Vahidnezhad
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
- Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, USA
| | - Mohsen Soosanabadi
- Department of Medical Genetics, Semnan University of Medical Sciences, Semnan, Iran
| | - Azam Rahimpour
- Medical Nano-Technology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Lei T, Du S, Peng Z, Chen L. Multifaceted regulation and functions of 53BP1 in NHEJ‑mediated DSB repair (Review). Int J Mol Med 2022; 50:90. [PMID: 35583003 PMCID: PMC9162042 DOI: 10.3892/ijmm.2022.5145] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/29/2022] [Indexed: 12/02/2022] Open
Abstract
The repair of DNA double-strand breaks (DSBs) is crucial for the preservation of genomic integrity and the maintenance of cellular homeostasis. Non-homologous DNA end joining (NHEJ) is the predominant repair mechanism for any type of DNA DSB during the majority of the cell cycle. NHEJ defects regulate tumor sensitivity to ionizing radiation and anti-neoplastic agents, resulting in immunodeficiencies and developmental abnormalities in malignant cells. p53-binding protein 1 (53BP1) is a key mediator involved in DSB repair, which functions to maintain a balance in the repair pathway choices and in preserving genomic stability. 53BP1 promotes DSB repair via NHEJ and antagonizes DNA end overhang resection. At present, novel lines of evidence have revealed the molecular mechanisms underlying the recruitment of 53BP1 and DNA break-responsive effectors to DSB sites, and the promotion of NHEJ-mediated DSB repair via 53BP1, while preventing homologous recombination. In the present review article, recent advances made in the elucidation of the structural and functional characteristics of 53BP1, the mechanisms of 53BP1 recruitment and interaction with the reshaping of the chromatin architecture around DSB sites, the post-transcriptional modifications of 53BP1, and the up- and downstream pathways of 53BP1 are discussed. The present review article also focuses on the application perspectives, current challenges and future directions of 53BP1 research.
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Affiliation(s)
- Tiantian Lei
- Department of Pharmacy, Women and Children's Hospital of Chongqing Medical University, Chongqing 401147, P.R. China
| | - Suya Du
- Department of Clinical Pharmacy, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan 610041, P.R. China
| | - Zhe Peng
- Department of Pharmacy, Women and Children's Hospital of Chongqing Medical University, Chongqing 401147, P.R. China
| | - Lin Chen
- Department of Pharmacy, Women and Children's Hospital of Chongqing Medical University, Chongqing 401147, P.R. China
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Lee D, Apelt K, Lee SO, Chan HR, Luijsterburg MS, Leung JWC, Miller K. ZMYM2 restricts 53BP1 at DNA double-strand breaks to favor BRCA1 loading and homologous recombination. Nucleic Acids Res 2022; 50:3922-3943. [PMID: 35253893 PMCID: PMC9023290 DOI: 10.1093/nar/gkac160] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 02/11/2022] [Accepted: 02/22/2022] [Indexed: 12/14/2022] Open
Abstract
An inability to repair DNA double-strand breaks (DSBs) threatens genome integrity and can contribute to human diseases, including cancer. Mammalian cells repair DSBs mainly through homologous recombination (HR) and nonhomologous end-joining (NHEJ). The choice between these pathways is regulated by the interplay between 53BP1 and BRCA1, whereby BRCA1 excludes 53BP1 to promote HR and 53BP1 limits BRCA1 to facilitate NHEJ. Here, we identify the zinc-finger proteins (ZnF), ZMYM2 and ZMYM3, as antagonizers of 53BP1 recruitment that facilitate HR protein recruitment and function at DNA breaks. Mechanistically, we show that ZMYM2 recruitment to DSBs and suppression of break-associated 53BP1 requires the SUMO E3 ligase PIAS4, as well as SUMO binding by ZMYM2. Cells deficient for ZMYM2/3 display genome instability, PARP inhibitor and ionizing radiation sensitivity and reduced HR repair. Importantly, depletion of 53BP1 in ZMYM2/3-deficient cells rescues BRCA1 recruitment to and HR repair of DSBs, suggesting that ZMYM2 and ZMYM3 primarily function to restrict 53BP1 engagement at breaks to favor BRCA1 loading that functions to channel breaks to HR repair. Identification of DNA repair functions for these poorly characterized ZnF proteins may shed light on their unknown contributions to human diseases, where they have been reported to be highly dysregulated, including in several cancers.
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Affiliation(s)
- Doohyung Lee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Katja Apelt
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Seong-Ok Lee
- Department of Radiation Oncology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Hsin-Ru Chan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Justin W C Leung
- Department of Radiation Oncology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Kyle M Miller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
- Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA
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Ding X, Yuan W, Yang H, Liu C, Li S, Zhu L. β-Catenin-Specific Inhibitor, iCRT14, Promotes BoHV-1 Infection-Induced DNA Damage in Human A549 Lung Adenocarcinoma Cells by Enhancing Viral Protein Expression. Int J Mol Sci 2022; 23:ijms23042328. [PMID: 35216447 PMCID: PMC8878024 DOI: 10.3390/ijms23042328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 12/12/2022] Open
Abstract
Oncolytic bovine herpesvirus type 1 (BoHV-1) infection induces DNA damage in human lung adenocarcinoma cell line A549. However, the underlying mechanisms are not fully understood. We found that BoHV-1 infection decreased the steady-state protein levels of p53-binding protein 1 (53BP1), which plays a central role in dictating DNA damage repair and maintaining genomic stability. Furthermore, BoHV-1 impaired the formation of 53BP1 foci, suggesting that BoHV-1 inhibits 53BP1-mediated DNA damage repair. Interestingly, BoHV-1 infection redistributed intracellular β-catenin, and iCRT14 (5-[[2,5-Dimethyl-1-(3-pyridinyl)-1H-pyrrol-3-yl]methylene]-3-phenyl-2,4-thiazolidinedione), a β-catenin-specific inhibitor, enhanced certain viral protein expression, such as the envelope glycoproteins gC and gD, and enhanced virus infection-induced DNA damage. Therefore, for the first time, we provide evidence showing that BoHV-1 infection disrupts 53BP1-mediated DNA damage repair and suggest β-catenin as a potential host factor restricting both virus replication and DNA damage in A549 cells.
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Affiliation(s)
- Xiuyan Ding
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (X.D.); (H.Y.); (C.L.)
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
| | - Weifeng Yuan
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
| | - Hao Yang
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (X.D.); (H.Y.); (C.L.)
| | - Chang Liu
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (X.D.); (H.Y.); (C.L.)
| | - Shitao Li
- Department of Microbiology and Immunology, Tulane University, New Orleans, LA 70118, USA;
| | - Liqian Zhu
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (X.D.); (H.Y.); (C.L.)
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, College of Life Science, Hebei University, Baoding 071002, China
- Correspondence:
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Zheng Z, Hua R, Xu G, Yang H, Shi P. Gene losses may contribute to subterranean adaptations in naked mole-rat and blind mole-rat. BMC Biol 2022; 20:44. [PMID: 35172813 PMCID: PMC8851862 DOI: 10.1186/s12915-022-01243-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 01/28/2022] [Indexed: 01/18/2023] Open
Abstract
Background Naked mole-rats (Heterocephalus glaber, NMRs) and blind mole-rats (Spalax galili, BMRs) are representative subterranean rodents that have evolved many extraordinary traits, including hypoxia tolerance, longevity, and cancer resistance. Although multiple candidate loci responsible for these traits have been uncovered by genomic studies, many of them are limited to functional changes to amino acid sequence and little is known about the contributions of other genetic events. To address this issue, we focused on gene losses (unitary pseudogenes) and systematically analyzed gene losses in NMRs and BMRs, aiming to elucidate the potential roles of pseudogenes in their adaptation to subterranean lifestyle. Results We obtained the pseudogene repertoires in NMRs and BMRs, as well as their respective aboveground relatives, guinea pigs and rats, on a genome-wide scale. As a result, 167, 139, 341, and 112 pseudogenes were identified in NMRs, BMRs, guinea pigs, and rats, respectively. Functional enrichment analysis identified 4 shared and 2 species-specific enriched functional groups (EFGs) in subterranean lineages. Notably, the pseudogenes in these EFGs might be associated with either regressive (e.g., visual system) or adaptive (e.g., altered DNA damage response) traits. In addition, several pseudogenes including TNNI3K and PDE5A might be associated with specific cardiac features observed in subterranean lineages. Interestingly, we observed 20 convergent gene losses in NMRs and BMRs. Given that the functional investigations of these genes are generally scarce, we provided functional evidence that independent loss of TRIM17 in NMRs and BMRs might be beneficial for neuronal survival under hypoxia, supporting the positive role of eliminating TRIM17 function in hypoxia adaptation. Our results also suggested that pseudogenes, together with positively selected genes, reinforced subterranean adaptations cooperatively. Conclusions Our study provides new insights into the molecular underpinnings of subterranean adaptations and highlights the importance of gene losses in mammalian evolution. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01243-0.
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Affiliation(s)
- Zhizhong Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Rong Hua
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China.,Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Guoqiang Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China.,Joint Laboratory of Animal Models for Human Diseases and Drug Development, Soochow University and Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Hui Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China.
| | - Peng Shi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China. .,Joint Laboratory of Animal Models for Human Diseases and Drug Development, Soochow University and Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China. .,School of Future Technology, University of Chinese Academy of Sciences, Beijing, 101408, China.
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Bieńkowski M, Tomasik B, Braun M, Jassem J. PARP inhibitors for metastatic castration-resistant prostate cancer: Biological rationale and current evidence. Cancer Treat Rev 2022; 104:102359. [DOI: 10.1016/j.ctrv.2022.102359] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 02/06/2022] [Accepted: 02/07/2022] [Indexed: 12/27/2022]
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Kieffer SR, Lowndes NF. Immediate-Early, Early, and Late Responses to DNA Double Stranded Breaks. Front Genet 2022; 13:793884. [PMID: 35173769 PMCID: PMC8841529 DOI: 10.3389/fgene.2022.793884] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/10/2022] [Indexed: 12/18/2022] Open
Abstract
Loss or rearrangement of genetic information can result from incorrect responses to DNA double strand breaks (DSBs). The cellular responses to DSBs encompass a range of highly coordinated events designed to detect and respond appropriately to the damage, thereby preserving genomic integrity. In analogy with events occurring during viral infection, we appropriate the terms Immediate-Early, Early, and Late to describe the pre-repair responses to DSBs. A distinguishing feature of the Immediate-Early response is that the large protein condensates that form during the Early and Late response and are resolved upon repair, termed foci, are not visible. The Immediate-Early response encompasses initial lesion sensing, involving poly (ADP-ribose) polymerases (PARPs), KU70/80, and MRN, as well as rapid repair by so-called ‘fast-kinetic’ canonical non-homologous end joining (cNHEJ). Initial binding of PARPs and the KU70/80 complex to breaks appears to be mutually exclusive at easily ligatable DSBs that are repaired efficiently by fast-kinetic cNHEJ; a process that is PARP-, ATM-, 53BP1-, Artemis-, and resection-independent. However, at more complex breaks requiring processing, the Immediate-Early response involving PARPs and the ensuing highly dynamic PARylation (polyADP ribosylation) of many substrates may aid recruitment of both KU70/80 and MRN to DSBs. Complex DSBs rely upon the Early response, largely defined by ATM-dependent focal recruitment of many signalling molecules into large condensates, and regulated by complex chromatin dynamics. Finally, the Late response integrates information from cell cycle phase, chromatin context, and type of DSB to determine appropriate pathway choice. Critical to pathway choice is the recruitment of p53 binding protein 1 (53BP1) and breast cancer associated 1 (BRCA1). However, additional factors recruited throughout the DSB response also impact upon pathway choice, although these remain to be fully characterised. The Late response somehow channels DSBs into the appropriate high-fidelity repair pathway, typically either ‘slow-kinetic’ cNHEJ or homologous recombination (HR). Loss of specific components of the DSB repair machinery results in cells utilising remaining factors to effect repair, but often at the cost of increased mutagenesis. Here we discuss the complex regulation of the Immediate-Early, Early, and Late responses to DSBs proceeding repair itself.
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Understanding and overcoming resistance to PARP inhibitors in cancer therapy. Nat Rev Clin Oncol 2021; 18:773-791. [PMID: 34285417 DOI: 10.1038/s41571-021-00532-x] [Citation(s) in RCA: 214] [Impact Index Per Article: 71.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2021] [Indexed: 02/07/2023]
Abstract
Developing novel targeted anticancer therapies is a major goal of current research. The use of poly(ADP-ribose) polymerase (PARP) inhibitors in patients with homologous recombination-deficient tumours provides one of the best examples of a targeted therapy that has been successfully translated into the clinic. The success of this approach has so far led to the approval of four different PARP inhibitors for the treatment of several types of cancers and a total of seven different compounds are currently under clinical investigation for various indications. Clinical trials have demonstrated promising response rates among patients receiving PARP inhibitors, although the majority will inevitably develop resistance. Preclinical and clinical data have revealed multiple mechanisms of resistance and current efforts are focused on developing strategies to address this challenge. In this Review, we summarize the diverse processes underlying resistance to PARP inhibitors and discuss the potential strategies that might overcome these mechanisms such as combinations with chemotherapies, targeting the acquired vulnerabilities associated with resistance to PARP inhibitors or suppressing genomic instability.
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Blasiak J, Szczepańska J, Sobczuk A, Fila M, Pawlowska E. RIF1 Links Replication Timing with Fork Reactivation and DNA Double-Strand Break Repair. Int J Mol Sci 2021; 22:11440. [PMID: 34768871 PMCID: PMC8583789 DOI: 10.3390/ijms222111440] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 11/16/2022] Open
Abstract
Replication timing (RT) is a cellular program to coordinate initiation of DNA replication in all origins within the genome. RIF1 (replication timing regulatory factor 1) is a master regulator of RT in human cells. This role of RIF1 is associated with binding G4-quadruplexes and changes in 3D chromatin that may suppress origin activation over a long distance. Many effects of RIF1 in fork reactivation and DNA double-strand (DSB) repair (DSBR) are underlined by its interaction with TP53BP1 (tumor protein p53 binding protein). In G1, RIF1 acts antagonistically to BRCA1 (BRCA1 DNA repair associated), suppressing end resection and homologous recombination repair (HRR) and promoting non-homologous end joining (NHEJ), contributing to DSBR pathway choice. RIF1 is an important element of intra-S-checkpoints to recover damaged replication fork with the involvement of HRR. High-resolution microscopic studies show that RIF1 cooperates with TP53BP1 to preserve 3D structure and epigenetic markers of genomic loci disrupted by DSBs. Apart from TP53BP1, RIF1 interact with many other proteins, including proteins involved in DNA damage response, cell cycle regulation, and chromatin remodeling. As impaired RT, DSBR and fork reactivation are associated with genomic instability, a hallmark of malignant transformation, RIF1 has a diagnostic, prognostic, and therapeutic potential in cancer. Further studies may reveal other aspects of common regulation of RT, DSBR, and fork reactivation by RIF1.
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Affiliation(s)
- Janusz Blasiak
- Department of Molecular Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland
| | - Joanna Szczepańska
- Department of Pediatric Dentistry, Medical University of Lodz, 92-216 Lodz, Poland;
| | - Anna Sobczuk
- Department of Gynaecology and Obstetrics, Medical University of Lodz, 93-338 Lodz, Poland;
| | - Michal Fila
- Department of Developmental Neurology and Epileptology, Polish Mother’s Memorial Hospital Research Institute, 93-338 Lodz, Poland;
| | - Elzbieta Pawlowska
- Department of Orthodontics, Medical University of Lodz, 92-217 Lodz, Poland;
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Etourneaud L, Moussa A, Rass E, Genet D, Willaume S, Chabance-Okumura C, Wanschoor P, Picotto J, Thézé B, Dépagne J, Veaute X, Dizet E, Busso D, Barascu A, Irbah L, Kortulewski T, Campalans A, Le Chalony C, Zinn-Justin S, Scully R, Pennarun G, Bertrand P. Lamin B1 sequesters 53BP1 to control its recruitment to DNA damage. SCIENCE ADVANCES 2021; 7:eabb3799. [PMID: 34452908 PMCID: PMC8397269 DOI: 10.1126/sciadv.abb3799] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 07/07/2021] [Indexed: 05/09/2023]
Abstract
Double-strand breaks (DSBs) are harmful lesions and a major cause of genome instability. Studies have suggested a link between the nuclear envelope and the DNA damage response. Here, we show that lamin B1, a major component of the nuclear envelope, interacts directly with 53BP1 protein, which plays a pivotal role in the DSB repair. This interaction is dissociated after DNA damage. Lamin B1 overexpression impedes 53BP1 recruitment to DNA damage sites and leads to a persistence of DNA damage, a defect in nonhomologous end joining and an increased sensitivity to DSBs. The identification of interactions domains between lamin B1 and 53BP1 allows us to demonstrate that the defect of 53BP1 recruitment and the DSB persistence upon lamin B1 overexpression are due to sequestration of 53BP1 by lamin B1. This study highlights lamin B1 as a factor controlling the recruitment of 53BP1 to DNA damage sites upon injury.
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Affiliation(s)
- Laure Etourneaud
- Université de Paris and Université Paris Saclay, INSERM, iRCM/IBFJ, CEA, UMR Stabilité Génétique, Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- "DNA Repair and Ageing" Team, iRCM/IBFJ, DRF, CEA, France
| | - Angela Moussa
- Université de Paris and Université Paris Saclay, INSERM, iRCM/IBFJ, CEA, UMR Stabilité Génétique, Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- "DNA Repair and Ageing" Team, iRCM/IBFJ, DRF, CEA, France
| | - Emilie Rass
- Université de Paris and Université Paris Saclay, INSERM, iRCM/IBFJ, CEA, UMR Stabilité Génétique, Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- "DNA Repair and Ageing" Team, iRCM/IBFJ, DRF, CEA, France
| | - Diane Genet
- Université de Paris and Université Paris Saclay, INSERM, iRCM/IBFJ, CEA, UMR Stabilité Génétique, Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- "DNA Repair and Ageing" Team, iRCM/IBFJ, DRF, CEA, France
| | - Simon Willaume
- Université de Paris and Université Paris Saclay, INSERM, iRCM/IBFJ, CEA, UMR Stabilité Génétique, Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- "DNA Repair and Ageing" Team, iRCM/IBFJ, DRF, CEA, France
| | - Caroline Chabance-Okumura
- Université de Paris and Université Paris Saclay, INSERM, iRCM/IBFJ, CEA, UMR Stabilité Génétique, Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- "DNA Repair and Ageing" Team, iRCM/IBFJ, DRF, CEA, France
| | - Paul Wanschoor
- Université de Paris and Université Paris Saclay, INSERM, iRCM/IBFJ, CEA, UMR Stabilité Génétique, Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- "DNA Repair and Ageing" Team, iRCM/IBFJ, DRF, CEA, France
| | - Julien Picotto
- Université de Paris and Université Paris Saclay, INSERM, iRCM/IBFJ, CEA, UMR Stabilité Génétique, Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- "DNA Repair and Ageing" Team, iRCM/IBFJ, DRF, CEA, France
| | - Benoît Thézé
- Université de Paris and Université Paris Saclay, INSERM, iRCM/IBFJ, CEA, UMR Stabilité Génétique, Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- "DNA Repair and Ageing" Team, iRCM/IBFJ, DRF, CEA, France
| | - Jordane Dépagne
- Genetic Engineering and Expression Platform (CIGEX), iRCM, DRF, CEA, Fontenay-aux-Roses, France
| | - Xavier Veaute
- Genetic Engineering and Expression Platform (CIGEX), iRCM, DRF, CEA, Fontenay-aux-Roses, France
| | - Eléa Dizet
- Genetic Engineering and Expression Platform (CIGEX), iRCM, DRF, CEA, Fontenay-aux-Roses, France
| | - Didier Busso
- Genetic Engineering and Expression Platform (CIGEX), iRCM, DRF, CEA, Fontenay-aux-Roses, France
| | - Aurélia Barascu
- Université de Paris and Université Paris Saclay, INSERM, iRCM/IBFJ, CEA, UMR Stabilité Génétique, Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- "DNA Repair and Ageing" Team, iRCM/IBFJ, DRF, CEA, France
| | - Lamya Irbah
- Université de Paris and Université Paris Saclay, INSERM, iRCM/IBFJ, CEA, UMR Stabilité Génétique, Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- Imaging platform, iRCM, DRF, CEA, F-92265 Fontenay-aux-Roses, France
| | - Thierry Kortulewski
- Université de Paris and Université Paris Saclay, INSERM, iRCM/IBFJ, CEA, UMR Stabilité Génétique, Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- "Radiopathology" Team, iRCM/IBFJ, DRF, CEA, France
| | - Anna Campalans
- Université de Paris and Université Paris Saclay, iRCM/IBFJ, CEA, UMR Stabilité Génétique Cellules Souches et Radiations, "Genetic Instability Research" Team, F-92265 Fontenay-aux-Roses, France
| | - Catherine Le Chalony
- Université de Paris and Université Paris Saclay, INSERM, iRCM/IBFJ, CEA, UMR Stabilité Génétique, Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- "DNA Repair and Ageing" Team, iRCM/IBFJ, DRF, CEA, France
| | - Sophie Zinn-Justin
- Laboratory of Structural Biology and Radiobiology, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, F-91190 Gif-sur-Yvette, France
| | - Ralph Scully
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Gaëlle Pennarun
- Université de Paris and Université Paris Saclay, INSERM, iRCM/IBFJ, CEA, UMR Stabilité Génétique, Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- "DNA Repair and Ageing" Team, iRCM/IBFJ, DRF, CEA, France
| | - Pascale Bertrand
- Université de Paris and Université Paris Saclay, INSERM, iRCM/IBFJ, CEA, UMR Stabilité Génétique, Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France.
- "DNA Repair and Ageing" Team, iRCM/IBFJ, DRF, CEA, France
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Audoynaud C, Vagner S, Lambert S. Non-homologous end-joining at challenged replication forks: an RNA connection? Trends Genet 2021; 37:973-985. [PMID: 34238592 DOI: 10.1016/j.tig.2021.06.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/20/2021] [Accepted: 06/11/2021] [Indexed: 12/29/2022]
Abstract
Defective DNA replication, known as 'replication stress', is a source of DNA damage, a hallmark of numerous human diseases, including cancer, developmental defect, neurological disorders, and premature aging. Recent work indicates that non-homologous end-joining (NHEJ) is unexpectedly active during DNA replication to repair replication-born DNA lesions and to safeguard replication fork integrity. However, erroneous NHEJ events are deleterious to genome stability. RNAs are novel regulators of NHEJ activity through their ability to modulate the assembly of repair complexes in trans. At DNA damage sites, RNAs and DNA-embedded ribonucleotides modulate repair efficiency and fidelity. We discuss here how RNAs and associated proteins, including RNA binding proteins, may regulate NHEJ to sustain genome stability during DNA replication.
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Affiliation(s)
- Charlotte Audoynaud
- Institut Curie, Université PSL, CNRS UMR3348, INSERM U1278, 91400 Orsay, France; Université Paris-Saclay, CNRS UMR3348, INSERM U1278, 91400 Orsay, France; Equipes Labélisées Ligue Nationale Contre Le Cancer, 91400 Orsay, France
| | - Stéphan Vagner
- Institut Curie, Université PSL, CNRS UMR3348, INSERM U1278, 91400 Orsay, France; Université Paris-Saclay, CNRS UMR3348, INSERM U1278, 91400 Orsay, France; Equipes Labélisées Ligue Nationale Contre Le Cancer, 91400 Orsay, France
| | - Sarah Lambert
- Institut Curie, Université PSL, CNRS UMR3348, INSERM U1278, 91400 Orsay, France; Université Paris-Saclay, CNRS UMR3348, INSERM U1278, 91400 Orsay, France; Equipes Labélisées Ligue Nationale Contre Le Cancer, 91400 Orsay, France.
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40
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The nuclear kinesin KIF18B promotes 53BP1-mediated DNA double-strand break repair. Cell Rep 2021; 35:109306. [PMID: 34192545 DOI: 10.1016/j.celrep.2021.109306] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 04/29/2021] [Accepted: 06/03/2021] [Indexed: 12/13/2022] Open
Abstract
53BP1 is recruited to chromatin in the vicinity of DNA double-strand breaks (DSBs). We identify the nuclear kinesin, KIF18B, as a 53BP1-interacting protein and define its role in 53BP1-mediated DSB repair. KIF18B is a molecular motor protein involved in destabilizing astral microtubules during mitosis. It is primarily nuclear throughout the interphase and is constitutively chromatin bound. Our observations indicate a nuclear function during the interphase for a kinesin previously implicated in mitosis. We identify a central motif in KIF18B, which we term the Tudor-interacting motif (TIM), because of its interaction with the Tudor domain of 53BP1. TIM enhances the interaction between the 53BP1 Tudor domain and dimethylated lysine 20 of histone H4. TIM and the motor function of KIF18B are both required for efficient 53BP1 focal recruitment in response to damage and for fusion of dysfunctional telomeres. Our data suggest a role for KIF18B in efficient 53BP1-mediated end-joining of DSBs.
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Wang D, Ma J, Botuyan MV, Cui G, Yan Y, Ding D, Zhou Y, Krueger EW, Pei J, Wu X, Wang L, Pei H, McNiven MA, Ye D, Mer G, Huang H. ATM-phosphorylated SPOP contributes to 53BP1 exclusion from chromatin during DNA replication. SCIENCE ADVANCES 2021; 7:eabd9208. [PMID: 34144977 PMCID: PMC8213225 DOI: 10.1126/sciadv.abd9208] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 05/04/2021] [Indexed: 05/25/2023]
Abstract
53BP1 activates nonhomologous end joining (NHEJ) and inhibits homologous recombination (HR) repair of DNA double-strand breaks (DSBs). Dissociation of 53BP1 from DSBs and consequent activation of HR, a less error-prone pathway than NHEJ, helps maintain genome integrity during DNA replication; however, the underlying mechanisms are not fully understood. Here, we demonstrate that E3 ubiquitin ligase SPOP promotes HR during S phase of the cell cycle by excluding 53BP1 from DSBs. In response to DNA damage, ATM kinase-catalyzed phosphorylation of SPOP causes a conformational change in SPOP, revealed by x-ray crystal structures, that stabilizes its interaction with 53BP1. 53BP1-bound SPOP induces polyubiquitination of 53BP1, eliciting 53BP1 extraction from chromatin by a valosin-containing protein/p97 segregase complex. Our work shows that SPOP facilitates HR repair over NHEJ during DNA replication by contributing to 53BP1 removal from chromatin. Cancer-derived SPOP mutations block SPOP interaction with 53BP1, inducing HR defects and chromosomal instability.
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Affiliation(s)
- Dejie Wang
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
- Department of Gastroenterology, Collaborative Innovation Center of Gastroenterology, Angiocardiopathy and Neurosciences, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
| | - Jian Ma
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Maria Victoria Botuyan
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Gaofeng Cui
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Yuqian Yan
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Donglin Ding
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Yingke Zhou
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Eugene W Krueger
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Jiang Pei
- State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Xiaosheng Wu
- Division of Hematology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Liguo Wang
- Division of Computational Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Huadong Pei
- George Washington University Cancer Center, Washington, DC 20037, USA
- Department of Biochemistry and Molecular Medicine, George Washington University School of Medicine and Health Science, Washington, DC 20037, USA
| | - Mark A McNiven
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
- Mayo Clinic Cancer Center, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Dingwei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai 200032, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Georges Mer
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA.
- Mayo Clinic Cancer Center, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
- Department of Cancer Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Haojie Huang
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA.
- Mayo Clinic Cancer Center, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
- Department of Urology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
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42
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Parnandi N, Rendo V, Cui G, Botuyan MV, Remisova M, Nguyen H, Drané P, Beroukhim R, Altmeyer M, Mer G, Chowdhury D. TIRR inhibits the 53BP1-p53 complex to alter cell-fate programs. Mol Cell 2021; 81:2583-2595.e6. [PMID: 33961797 DOI: 10.1016/j.molcel.2021.03.039] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 01/19/2021] [Accepted: 03/24/2021] [Indexed: 12/13/2022]
Abstract
53BP1 influences genome stability via two independent mechanisms: (1) regulating DNA double-strand break (DSB) repair and (2) enhancing p53 activity. We discovered a protein, Tudor-interacting repair regulator (TIRR), that associates with the 53BP1 Tudor domain and prevents its recruitment to DSBs. Here, we elucidate how TIRR affects 53BP1 function beyond its recruitment to DSBs and biochemically links the two distinct roles of 53BP1. Loss of TIRR causes an aberrant increase in the gene transactivation function of p53, affecting several p53-mediated cell-fate programs. TIRR inhibits the complex formation between the Tudor domain of 53BP1 and a dimethylated form of p53 (K382me2) that is poised for transcriptional activation of its target genes. TIRR mRNA expression levels negatively correlate with the expression of key p53 target genes in breast and prostate cancers. Further, TIRR loss is selectively not tolerated in p53-proficient tumors. Therefore, we establish that TIRR is an important inhibitor of the 53BP1-p53 complex.
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Affiliation(s)
- Nishita Parnandi
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Veronica Rendo
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Cancer Program, Broad Institute, 415 Main Street, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Gaofeng Cui
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Michaela Remisova
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Huy Nguyen
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Pascal Drané
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Rameen Beroukhim
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Cancer Program, Broad Institute, 415 Main Street, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Georges Mer
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Dipanjan Chowdhury
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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Discovery of a novel 53BP1 inhibitor through AlphaScreen-based high-throughput screening. Bioorg Med Chem 2021; 34:116054. [PMID: 33571875 DOI: 10.1016/j.bmc.2021.116054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 01/18/2021] [Accepted: 01/26/2021] [Indexed: 11/23/2022]
Abstract
Tumor suppressor p53-binding protein 1 (53BP1), a tantem tudor domain (TTD) protein, takes part in DNA Damage Repair (DDR) pathways through the specific recognition of lysine methylation on histones. The dysregulation of 53BP1 is closely related to the development of many diseases including cancer. Moreover, recent studies found that deficiency of 53BP1 could increase the efficiency of precise CRISPR/Cas9 genome editing. Thus, discovery of inhibitor is beneficial to the study of biological functions of 53BP1 and the application of CRISPR/Cas9 genome editing. UNC2170 and its derivatives have been reported as 53BP1 targeted small molecular inhibitors with modest activities. Hence, to discover better 53BP1 inhibitors, we conducted an AlphaScreen assay based high-throughput screening (HTS) and identified a novel and effective 53BP1-TTD inhibitor DP308 which disrupts the binding between 53BP1 and H4K20me2 peptide with an IC50 value of 1.69 ± 0.73 μM. Both Microscale Themophoresis (MST) and Surface Plasmon Resonance (SPR) assays confirmed the direct binding between DP308 and 53BP1-TTD protein with binding affinity (Kd) of about 2.7 μM. Molecular docking studies further suggested that DP308 possibly occupies the H4K20me2 binding pocket of the 53BP1-TTD aromatic cage. These results demonstrated that DP308 is a promising small molecule inhibitor for further optimization towards a more potent chemical probe of 53BP1. Additionally, it could be a potential valuable tool for applying to gene editing therapy by increasing the efficiency of CRISPR/Cas9 genome editing.
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44
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Zhang F, Gong Z. Regulation of DNA double-strand break repair pathway choice: a new focus on 53BP1. J Zhejiang Univ Sci B 2021; 22:38-46. [PMID: 33448186 DOI: 10.1631/jzus.b2000306] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Maintenance of cellular homeostasis and genome integrity is a critical responsibility of DNA double-strand break (DSB) signaling. P53-binding protein 1 (53BP1) plays a critical role in coordinating the DSB repair pathway choice and promotes the non-homologous end-joining (NHEJ)-mediated DSB repair pathway that rejoins DSB ends. New insights have been gained into a basic molecular mechanism that is involved in 53BP1 recruitment to the DNA lesion and how 53BP1 then recruits the DNA break-responsive effectors that promote NHEJ-mediated DSB repair while inhibiting homologous recombination (HR) signaling. This review focuses on the up- and downstream pathways of 53BP1 and how 53BP1 promotes NHEJ-mediated DSB repair, which in turn promotes the sensitivity of poly(ADP-ribose) polymerase inhibitor (PARPi) in BRCA1-deficient cancers and consequently provides an avenue for improving cancer therapy strategies.
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Affiliation(s)
- Fan Zhang
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Zihua Gong
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA.
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45
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Chen Z, Chen J. Mass spectrometry-based protein‒protein interaction techniques and their applications in studies of DNA damage repair. J Zhejiang Univ Sci B 2021; 22:1-20. [PMID: 33448183 PMCID: PMC7818012 DOI: 10.1631/jzus.b2000356] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/08/2020] [Indexed: 02/06/2023]
Abstract
Proteins are major functional units that are tightly connected to form complex and dynamic networks. These networks enable cells and organisms to operate properly and respond efficiently to environmental cues. Over the past decades, many biochemical methods have been developed to search for protein-binding partners in order to understand how protein networks are constructed and connected. At the same time, rapid development in proteomics and mass spectrometry (MS) techniques makes it possible to identify interacting proteins and build comprehensive protein‒protein interaction networks. The resulting interactomes and networks have proven informative in the investigation of biological functions, such as in the field of DNA damage repair. In recent years, a number of proteins involved in DNA damage response and DNA repair pathways have been uncovered with MS-based protein‒protein interaction studies. As the technologies for enriching associated proteins and MS become more sophisticated, the studies of protein‒protein interactions are entering a new era. In this review, we summarize the strategies and recent developments for exploring protein‒protein interaction. In addition, we discuss the application of these tools in the investigation of protein‒protein interaction networks involved in DNA damage response and DNA repair.
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Affiliation(s)
- Zhen Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Junjie Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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46
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Regulation of DNA break repair by RNA. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 163:23-33. [PMID: 33385412 DOI: 10.1016/j.pbiomolbio.2020.12.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/25/2020] [Accepted: 12/17/2020] [Indexed: 12/19/2022]
Abstract
Genomic stability is critical for cell survival and its effective repair when damaged is a vital process for preserving genetic information. Failure to correctly repair the genome can lead to the accumulation of mutations that ultimately drives carcinogenesis. Life has evolved sophisticated surveillance, repair pathways, and mechanisms to recognize and mend genomic lesions to preserve its integrity. Many of these pathways involve a cascade of protein effectors that act to identify the type of damage, such as double-strand (ds) DNA breaks, propagate the damage signal, and recruit an array of other protein factors to resolve the damage without loss of genetic information. It is now becoming increasingly clear that there are a number of RNA processing factors, such as the transcriptional machinery, and microRNA biogenesis components, as well as RNA itself, that facilitate the repair of DNA damage. Here, some of the recent work unravelling the role of RNA in the DNA Damage Response (DDR), in particular the dsDNA break repair pathway, will be reviewed.
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Zhang J, Yan Z, Wang Y, Wang Y, Guo X, Jing J, Dong X, Dong S, Liu X, Yu X, Wu C. Cancer-associated 53BP1 mutations induce DNA damage repair defects. Cancer Lett 2020; 501:43-54. [PMID: 33359708 DOI: 10.1016/j.canlet.2020.12.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 12/18/2020] [Accepted: 12/21/2020] [Indexed: 12/29/2022]
Abstract
TP53 binding protein 1 (53BP1) plays an important role in DNA damage repair and maintaining genomic stability. However, the mutations of 53BP1 in human cancers have not been systematically examined. Here, we have analyzed 541 somatic mutations of 53BP1 across 34 types of human cancer from databases of The Cancer Genome Atlas, International Cancer Genome Consortium and Catalogue of Somatic Mutations in Cancer. Among these cancer-associated 53BP1 mutations, truncation mutations disrupt the nuclear localization of 53BP1 thus abolish its biological functions in DNA damage repair. Moreover, with biochemical analyses and structural modeling, we have examined the detailed molecular mechanism by which missense mutations in the key domains causes the DNA damage repair defects. Taken together, our results reveal the functional defects of a set of cancer-associated 53BP1 mutations.
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Affiliation(s)
- Jiajia Zhang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, Hebei, China
| | - Zhenzhen Yan
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, Hebei, China
| | - Yukun Wang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, Hebei, China
| | - Yaguang Wang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, Hebei, China
| | - Xin Guo
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, Hebei, China
| | - Ju Jing
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, Hebei, China
| | - Xiangnan Dong
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, Hebei, China
| | - Shasha Dong
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, Hebei, China
| | - Xiuhua Liu
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, Hebei, China.
| | - Xiaochun Yu
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China.
| | - Chen Wu
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, Hebei, China.
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Sundaravinayagam D, Rahjouei A, Andreani M, Tupiņa D, Balasubramanian S, Saha T, Delgado-Benito V, Coralluzzo V, Daumke O, Di Virgilio M. 53BP1 Supports Immunoglobulin Class Switch Recombination Independently of Its DNA Double-Strand Break End Protection Function. Cell Rep 2020; 28:1389-1399.e6. [PMID: 31390554 PMCID: PMC6693562 DOI: 10.1016/j.celrep.2019.06.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 05/16/2019] [Accepted: 06/07/2019] [Indexed: 01/29/2023] Open
Abstract
Class switch recombination (CSR) is a DNA recombination reaction that diversifies the effector functions of antibodies. CSR occurs via the formation and non-homologous end joining (NHEJ) repair of programmed DNA double-strand breaks (DSBs) at the immunoglobulin heavy chain locus. The DNA repair factors 53BP1 and Rif1 promote NHEJ and CSR by protecting DSBs against resection. However, to what extent repression of DNA end resection contributes to CSR is unknown. Here, we show that B lymphocytes devoid of 53BP1-Rif1-dependent DSB end protection activity undergo robust CSR. Inactivation of specific sets of phospho-sites within 53BP1 N-terminal SQ/TQ motifs abrogates Rif1 recruitment and inhibition of resection but only mildly reduces CSR. Furthermore, mutations within 53BP1 oligomerization domain abolish CSR without substantially affecting DNA end processing. Thus, inhibition of DNA end resection does not correlate with CSR efficiency, indicating that regulation of DSB processing is not a key determinant step in CSR. 53BP1 oligomerization is largely dispensable for inhibition of DSB resection 53BP1 higher order oligomerization is a pre-requisite for CSR B lymphocytes devoid of 53BP1-Rif1 DSB end protection activity undergo robust CSR 53BP1-mediated DSB end mobility is dispensable for CSR
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Affiliation(s)
- Devakumar Sundaravinayagam
- Laboratory of DNA Repair and Maintenance of Genome Stability, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Ali Rahjouei
- Laboratory of DNA Repair and Maintenance of Genome Stability, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Matteo Andreani
- Laboratory of DNA Repair and Maintenance of Genome Stability, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Dagnija Tupiņa
- Laboratory of Structural Biology of Membrane-Associated Processes, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Sandhya Balasubramanian
- Laboratory of DNA Repair and Maintenance of Genome Stability, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Tannishtha Saha
- Laboratory of DNA Repair and Maintenance of Genome Stability, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Verónica Delgado-Benito
- Laboratory of DNA Repair and Maintenance of Genome Stability, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Violeta Coralluzzo
- Laboratory of DNA Repair and Maintenance of Genome Stability, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Oliver Daumke
- Laboratory of Structural Biology of Membrane-Associated Processes, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Michela Di Virgilio
- Laboratory of DNA Repair and Maintenance of Genome Stability, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany.
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49
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Tang M, Feng X, Pei G, Srivastava M, Wang C, Chen Z, Li S, Zhang H, Zhao Z, Li X, Chen J. FOXK1 Participates in DNA Damage Response by Controlling 53BP1 Function. Cell Rep 2020; 32:108018. [PMID: 32783940 PMCID: PMC7458625 DOI: 10.1016/j.celrep.2020.108018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 06/09/2020] [Accepted: 07/17/2020] [Indexed: 01/28/2023] Open
Abstract
53BP1 plays a central role in dictating DNA repair choice between non-homologous end joining (NHEJ) and homologous recombination (HR), which is important for the sensitivity to poly(ADP-ribose) polymerase inhibitors (PARPis) of BRCA1-deficient cancers. In this study, we show that FOXK1 associates with 53BP1 and regulates 53BP1-dependent functions. FOXK1-53BP1 interaction is significantly enhanced upon DNA damage during the S phase in an ATM/CHK2-dependent manner, which reduces the association of 53BP1 with its downstream factors RIF1 and PTIP. Depletion of FOXK1 impairs DNA repair and induces compromised cell survival upon DNA damage. Overexpression of FOXK1 diminishes 53BP1 foci formation, which leads to resistance to PARPis and elevation of HR in BRCA1-deficient cells and decreased telomere fusion in TRF2-depleted cells. Collectively, our findings demonstrate that FOXK1 negatively regulates 53BP1 function by inhibiting 53BP1 localization to sites of DNA damage, which alters the DSB-induced protein complexes centering on 53BP1 and thus influences DNA repair choice.
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Affiliation(s)
- Mengfan Tang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xu Feng
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Guangsheng Pei
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Mrinal Srivastava
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chao Wang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhen Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Siting Li
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Huimin Zhang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Xu Li
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Junjie Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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50
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Aleksandrov R, Hristova R, Stoynov S, Gospodinov A. The Chromatin Response to Double-Strand DNA Breaks and Their Repair. Cells 2020; 9:cells9081853. [PMID: 32784607 PMCID: PMC7464352 DOI: 10.3390/cells9081853] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/03/2020] [Accepted: 08/04/2020] [Indexed: 02/07/2023] Open
Abstract
Cellular DNA is constantly being damaged by numerous internal and external mutagenic factors. Probably the most severe type of insults DNA could suffer are the double-strand DNA breaks (DSBs). They sever both DNA strands and compromise genomic stability, causing deleterious chromosomal aberrations that are implicated in numerous maladies, including cancer. Not surprisingly, cells have evolved several DSB repair pathways encompassing hundreds of different DNA repair proteins to cope with this challenge. In eukaryotic cells, DSB repair is fulfilled in the immensely complex environment of the chromatin. The chromatin is not just a passive background that accommodates the multitude of DNA repair proteins, but it is a highly dynamic and active participant in the repair process. Chromatin alterations, such as changing patterns of histone modifications shaped by numerous histone-modifying enzymes and chromatin remodeling, are pivotal for proficient DSB repair. Dynamic chromatin changes ensure accessibility to the damaged region, recruit DNA repair proteins, and regulate their association and activity, contributing to DSB repair pathway choice and coordination. Given the paramount importance of DSB repair in tumorigenesis and cancer progression, DSB repair has turned into an attractive target for the development of novel anticancer therapies, some of which have already entered the clinic.
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