1
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Abhishek S, Deeksha W, Rajakumara E. Mechanistic insights into allosteric regulation of methylated DNA and histone H3 recognition by SRA and SET domains of SUVH5 and the basis for di-methylation of lysine residue. FEBS J 2023; 290:1060-1077. [PMID: 36128736 DOI: 10.1111/febs.16633] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 08/22/2022] [Accepted: 09/20/2022] [Indexed: 12/01/2022]
Abstract
Su-(var)3-9 homologue 5 (SUVH5), a member of SUVH family of histone lysine methyltransferase (HKMT) in Arabidopsis, is involved in epigenetic regulation of chromatin by recognizing 5-methyl-cytosine (5mC), in both CpG and non-CpG DNA context, through SRA domain and simultaneously performing the di-methylation of lysine 9 of histone H3 (H3K9) through SET domain. Here, we establish that the SET domain of SUVH5 allosterically restricts the SRA domain to the 5mC containing strand(s) of fully methylated CpG, hemi-methylated CpG and methylated CpHpH DNA. In addition, SET domain enhances the binding affinity of the SRA-SET dual domains to fully-mCpG but not to hemi-mCpG. Also, the recognition of methylated DNA by the SRA positively influences the recognition of H3K9 by the SET domain. Our further studies revealed that the SET domain recognizes the "A(R/K)KST" motif present in H3K9 and in other histone H2A variants. Further, computational analyses and quantum mechanics/molecular mechanics calculations explain the bases for robust mono-MTase but weak di-MTase activities of SUVH5. Given that the majority of eukaryotic proteins, including those involved in epigenetic gene regulation, contain more than one domain, our study suggests that understanding the allosteric regulation among multiple domains of proteins is relevant for unravelling biological outcomes.
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Affiliation(s)
- Suman Abhishek
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Sangareddy, India
| | - Waghela Deeksha
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Sangareddy, India
| | - Eerappa Rajakumara
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Sangareddy, India
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2
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Pelicci S, Furia L, Pelicci PG, Faretta M. Correlative Multi-Modal Microscopy: A Novel Pipeline for Optimizing Fluorescence Microscopy Resolutions in Biological Applications. Cells 2023; 12:cells12030354. [PMID: 36766696 PMCID: PMC9913119 DOI: 10.3390/cells12030354] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/05/2023] [Accepted: 01/16/2023] [Indexed: 01/20/2023] Open
Abstract
The modern fluorescence microscope is the convergence point of technologies with different performances in terms of statistical sampling, number of simultaneously analyzed signals, and spatial resolution. However, the best results are usually obtained by maximizing only one of these parameters and finding a compromise for the others, a limitation that can become particularly significant when applied to cell biology and that can reduce the spreading of novel optical microscopy tools among research laboratories. Super resolution microscopy and, in particular, molecular localization-based approaches provide a spatial resolution and a molecular localization precision able to explore the scale of macromolecular complexes in situ. However, its use is limited to restricted regions, and consequently few cells, and frequently no more than one or two parameters. Correlative microscopy, obtained by the fusion of different optical technologies, can consequently surpass this barrier by merging results from different spatial scales. We discuss here the use of an acquisition and analysis correlative microscopy pipeline to obtain high statistical sampling, high content, and maximum spatial resolution by combining widefield, confocal, and molecular localization microscopy.
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Affiliation(s)
- Simone Pelicci
- Department of Experimental Oncology, European Institute of Oncology IRCCS, 20139 Milan, Italy
| | - Laura Furia
- Department of Experimental Oncology, European Institute of Oncology IRCCS, 20139 Milan, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, European Institute of Oncology IRCCS, 20139 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Mario Faretta
- Department of Experimental Oncology, European Institute of Oncology IRCCS, 20139 Milan, Italy
- Correspondence:
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3
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Furia L, Pelicci S, Scanarini M, Pelicci PG, Faretta M. From Double-Strand Break Recognition to Cell-Cycle Checkpoint Activation: High Content and Resolution Image Cytometry Unmasks 53BP1 Multiple Roles in DNA Damage Response and p53 Action. Int J Mol Sci 2022; 23:10193. [PMID: 36077590 PMCID: PMC9456172 DOI: 10.3390/ijms231710193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/25/2022] [Accepted: 09/02/2022] [Indexed: 11/29/2022] Open
Abstract
53BP1 protein has been isolated in-vitro as a putative p53 interactor. From the discovery of its engagement in the DNA-Damage Response (DDR), its role in sustaining the activity of the p53-regulated transcriptional program has been frequently under-evaluated, even in the case of a specific response to numerous DNA Double-Strand Breaks (DSBs), i.e., exposure to ionizing radiation. The localization of 53BP1 protein constitutes a key to decipher the network of activities exerted in response to stress. We present here an automated-microscopy for image cytometry protocol to analyze the evolution of the DDR, and to demonstrate how 53BP1 moved from damaged sites, where the well-known interaction with the DSB marker γH2A.X takes place, to nucleoplasm, interacting with p53, and enhancing the transcriptional regulation of the guardian of the genome protein. Molecular interactions have been quantitatively described and spatiotemporally localized at the highest spatial resolution by a simultaneous analysis of the impairment of the cell-cycle progression. Thanks to the high statistical sampling of the presented protocol, we provide a detailed quantitative description of the molecular events following the DSBs formation. Single-Molecule Localization Microscopy (SMLM) Analysis finally confirmed the p53-53BP1 interaction on the tens of nanometers scale during the distinct phases of the response.
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Affiliation(s)
- Laura Furia
- Department of Experimental Oncology, European Institute of Oncology IRCCS, 20139 Milan, Italy
| | - Simone Pelicci
- Department of Experimental Oncology, European Institute of Oncology IRCCS, 20139 Milan, Italy
| | - Mirco Scanarini
- Department of Experimental Oncology, European Institute of Oncology IRCCS, 20139 Milan, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, European Institute of Oncology IRCCS, 20139 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Mario Faretta
- Department of Experimental Oncology, European Institute of Oncology IRCCS, 20139 Milan, Italy
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4
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Yao Y, Gu X, Xu X, Ge S, Jia R. Novel insights into RB1 mutation. Cancer Lett 2022; 547:215870. [PMID: 35964818 DOI: 10.1016/j.canlet.2022.215870] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 08/05/2022] [Accepted: 08/05/2022] [Indexed: 01/09/2023]
Abstract
Since the discovery of the retinoblastoma susceptibility gene (RB1) decades ago, RB1 has been regarded as a prototype tumor suppressor gene providing a paradigm for tumor genetic research. Constant research has updated the understanding of RB1-related pathways and their impact on tumor and nontumor diseases. Mutation of RB1 gene has been observed in multiple types of malignant tumors including prostate cancer, lung cancer, breast cancer, and almost every familial and sporadic case of retinoblastoma. Even if well-known and long-investigated, the application potential of RB1 mutation has not been fully tapped. In this review, we focus on the mechanism underlying RB1 mutation during oncogenesis. Therapeutically, we have further discussed potential clinical strategies by targeting RB1-mutated cancers. The unsolved problems and prospects of RB1 mutation are also discussed.
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Affiliation(s)
- Yiran Yao
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China.
| | - Xiang Gu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China.
| | - Xiaofang Xu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China.
| | - Shengfang Ge
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China.
| | - Renbing Jia
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China.
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5
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Zhou L, Ng DSC, Yam JC, Chen LJ, Tham CC, Pang CP, Chu WK. Post-translational modifications on the retinoblastoma protein. J Biomed Sci 2022; 29:33. [PMID: 35650644 PMCID: PMC9161509 DOI: 10.1186/s12929-022-00818-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 05/26/2022] [Indexed: 11/21/2022] Open
Abstract
The retinoblastoma protein (pRb) functions as a cell cycle regulator controlling G1 to S phase transition and plays critical roles in tumour suppression. It is frequently inactivated in various tumours. The functions of pRb are tightly regulated, where post-translational modifications (PTMs) play crucial roles, including phosphorylation, ubiquitination, SUMOylation, acetylation and methylation. Most PTMs on pRb are reversible and can be detected in non-cancerous cells, playing an important role in cell cycle regulation, cell survival and differentiation. Conversely, altered PTMs on pRb can give rise to anomalies in cell proliferation and tumourigenesis. In this review, we first summarize recent findings pertinent to how individual PTMs impinge on pRb functions. As many of these PTMs on pRb were published as individual articles, we also provide insights on the coordination, either collaborations and/or competitions, of the same or different types of PTMs on pRb. Having a better understanding of how pRb is post-translationally modulated should pave the way for developing novel and specific therapeutic strategies to treat various human diseases.
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Affiliation(s)
- Linbin Zhou
- Department of Ophthalmology & Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Danny Siu-Chun Ng
- Department of Ophthalmology & Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Jason C Yam
- Department of Ophthalmology & Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China
| | - Li Jia Chen
- Department of Ophthalmology & Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China
| | - Clement C Tham
- Department of Ophthalmology & Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China
| | - Chi Pui Pang
- Department of Ophthalmology & Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China
| | - Wai Kit Chu
- Department of Ophthalmology & Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China.
- Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China.
- Department of Ophthalmology & Visual Sciences, The Chinese University of Hong Kong, Hong Kong Eye Hospital, 147K Argyle Street, Kowloon, Hong Kong, China.
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6
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Janostiak R, Torres-Sanchez A, Posas F, de Nadal E. Understanding Retinoblastoma Post-Translational Regulation for the Design of Targeted Cancer Therapies. Cancers (Basel) 2022; 14:cancers14051265. [PMID: 35267571 PMCID: PMC8909233 DOI: 10.3390/cancers14051265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/22/2022] [Accepted: 02/25/2022] [Indexed: 01/05/2023] Open
Abstract
Simple Summary Rb1 is a regulator of cell cycle progression and genomic stability. This review focuses on post-translational modifications, their effect on Rb1 interactors, and their role in intracellular signaling in the context of cancer development. Finally, we highlight potential approaches to harness these post-translational modifications to design novel effective anticancer therapies. Abstract The retinoblastoma protein (Rb1) is a prototypical tumor suppressor protein whose role was described more than 40 years ago. Together with p107 (also known as RBL1) and p130 (also known as RBL2), the Rb1 belongs to a family of structurally and functionally similar proteins that inhibits cell cycle progression. Given the central role of Rb1 in regulating proliferation, its expression or function is altered in most types of cancer. One of the mechanisms underlying Rb-mediated cell cycle inhibition is the binding and repression of E2F transcription factors, and these processes are dependent on Rb1 phosphorylation status. However, recent work shows that Rb1 is a convergent point of many pathways and thus the regulation of its function through post-translational modifications is more complex than initially expected. Moreover, depending on the context, downstream signaling can be both E2F-dependent and -independent. This review seeks to summarize the most recent research on Rb1 function and regulation and discuss potential avenues for the design of novel cancer therapies.
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Affiliation(s)
- Radoslav Janostiak
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain; (R.J.); (A.T.-S.)
- Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Ariadna Torres-Sanchez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain; (R.J.); (A.T.-S.)
- Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Francesc Posas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain; (R.J.); (A.T.-S.)
- Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Correspondence: (F.P.); (E.d.N.); Tel.: +34-93-403-4810 (F.P.); +34-93-403-9895 (E.d.N.)
| | - Eulàlia de Nadal
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain; (R.J.); (A.T.-S.)
- Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Correspondence: (F.P.); (E.d.N.); Tel.: +34-93-403-4810 (F.P.); +34-93-403-9895 (E.d.N.)
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7
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Spiotto MT, Taniguchi CM, Klopp AH, Colbert LE, Lin SH, Wang L, Frederick MJ, Osman AA, Pickering CR, Frank SJ. Biology of the Radio- and Chemo-Responsiveness in HPV Malignancies. Semin Radiat Oncol 2021; 31:274-285. [PMID: 34455983 DOI: 10.1016/j.semradonc.2021.02.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In multiple anatomic sites, patients with cancers associated with the Human Papillomavirus (HPV) experience better locoregional control and overall survival after radiotherapy and/or chemoradiotherapy than patients with HPV-negative cancers. These improved outcomes suggest that relatively unique biological features in HPV-positive cancers may increase sensitivity to DNA damaging agents as well as an impaired DNA damage response. This review will address potential biological mechanisms driving this increased sensitivity of HPV-positive cancer to radiation and/or chemotherapy. This review will discuss the clinical and preclinical observations that support the intrinsic radiosensitivity and/or chemosensitivity of HPV-positive cancers. Furthermore, this review will highlight the molecular mechanisms for increased radiation sensitivity using the classical "4 Rs" of radiobiology: repair, reassortment, repopulation, and reoxygenation. First, HPV-positive cancers have increased DNA damage due to increased oxidative stress and impaired DNA damage repair due to the altered activity TP53, p16, TIP60, and other repair proteins. Second, irradiated HPV-positive cancer cells display increased G2/M arrest leading to reassortment of cancer cells in more radiosensitive phases of the cell cycle. In addition, HPV-positive cancers have less radioresistant cancer stem cell subpopulations that may limit their repopulation during radiotherapy. Finally, HPV-positive cancers may also have less hypoxic tumor microenvironments that make these cancers more sensitive to radiation than HPV-negative cells. We will also discuss extrinsic immune and microenvironmental factors enriched in HPV-positive cancers that facilities responses to radiation. Therefore, these potential biological mechanisms may underpin the improved clinical outcomes often observed in these virally induced cancers.
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Affiliation(s)
- Michael T Spiotto
- Department of Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX.
| | - Cullen M Taniguchi
- Department of Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX
| | - Ann H Klopp
- Department of Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX
| | - Lauren E Colbert
- Department of Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX
| | - Steven H Lin
- Department of Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX
| | - Li Wang
- Department of Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX
| | | | - Abdullah A Osman
- Department of Head and Neck Surgery, The University of Texas M.D. Anderson Cancer Center, Houston, TX
| | - Curtis R Pickering
- Department of Head and Neck Surgery, The University of Texas M.D. Anderson Cancer Center, Houston, TX
| | - Steven J Frank
- Department of Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX
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8
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Urulangodi M, Mohanty A. DNA damage response and repair pathway modulation by non-histone protein methylation: implications in neurodegeneration. J Cell Commun Signal 2020; 14:31-45. [PMID: 31749026 PMCID: PMC7176765 DOI: 10.1007/s12079-019-00538-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/14/2019] [Indexed: 12/11/2022] Open
Abstract
Protein post-translational modifications (PTMs) have emerged to be combinatorial, essential mechanisms used by eukaryotic cells to regulate local chromatin structure, diversify and extend their protein functions and dynamically coordinate complex intracellular signalling processes. Most common types of PTMs include enzymatic addition of small chemical groups resulting in phosphorylation, glycosylation, poly(ADP-ribosyl)ation, nitrosylation, methylation, acetylation or covalent attachment of complete proteins such as ubiquitin and SUMO. Protein arginine methyltransferases (PRMTs) and protein lysine methyltransferases (PKMTs) enzymes catalyse the methylation of arginine and lysine residues in target proteins, respectively. Rapid progress in quantitative proteomic analysis and functional assays have not only documented the methylation of histone proteins post-translationally but also identified their occurrence in non-histone proteins which dynamically regulate a plethora of cellular functions including DNA damage response and repair. Emerging advances have now revealed the role of both histone and non-histone methylations in the regulating the DNA damage response (DDR) proteins, thereby modulating the DNA repair pathways both in proliferating and post-mitotic neuronal cells. Defects in many cellular DNA repair processes have been found primarily manifested in neuronal tissues. Moreover, fine tuning of the dynamicity of methylation of non-histone proteins as well as the perturbations in this dynamic methylation processes have recently been implicated in neuronal genomic stability maintenance. Considering the impact of methylation on chromatin associated pathways, in this review we attempt to link the evidences in non-histone protein methylation and DDR with neurodegenerative research.
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Affiliation(s)
- Madhusoodanan Urulangodi
- Department of Biochemistry, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala, PIN-695011, India.
| | - Abhishek Mohanty
- Rajiv Gandhi Cancer Institute and Research Centre, New Delhi, PIN-110085, India.
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9
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Wang H, Wang B, Wei J, Meng L, Zhang Q, Qu C, Xin Y, Jiang X. Molecular mechanisms underlying increased radiosensitivity in human papillomavirus-associated oropharyngeal squamous cell carcinoma. Int J Biol Sci 2020; 16:1035-1043. [PMID: 32140071 PMCID: PMC7053336 DOI: 10.7150/ijbs.40880] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 12/26/2019] [Indexed: 01/30/2023] Open
Abstract
Oropharyngeal squamous cell carcinoma (OPSCC) is an important type of head and neck squamous cell carcinoma (HNSCC). The traditional risk factors for OPSCC include carcinogen intake, smoking, alcohol consumption, and lifestyle. In recent years, cases of human papillomavirus (HPV)-related OPSCC have gradually increased. At present, HPV-related OPSCC in developed Western countries comprise up to 90% of all OPSCC cases, while in other developing countries, the proportion of HPV-related OPSCC cases is also gradually increasing. Compared with HPV-negative OPSCC, HPV-positive OPSCC patients have better overall survival rates and local control rates and this improved prognosis may be related to the increased radiosensitivity of HPV-positive tumors. Due to this more favorable prognosis, many downgraded treatment schemes are gradually emerging, including simple radiotherapy instead of concurrent radiotherapy or reduced radiotherapy dose. However, there is insufficient theoretical basis for such schemes. Some studies have shown that delayed repair of DNA damage after radiation, G2/M arrest, increased hypoxia, and decreased proliferation capacity are the main reasons for the increased radiosensitivity of HPV-positive tumor cells. In this review, we discuss the four principles of tumor cell damage caused by radiation, including repair, reoxygenation, redistribution, and regeneration in order to reveal the mechanism whereby HPV increases the radiosensitivity of tumor cells. An attempt was made to provide sufficient information to facilitate more individualized treatment for HPV-positive OPSCC patients, under the premise of good tumor control.
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Affiliation(s)
- Huanhuan Wang
- Department of Radiation Oncology, The First Hospital of Jilin University, Changchun 130021, China
| | - Bin Wang
- Department of Radiation Oncology, The First Hospital of Jilin University, Changchun 130021, China
| | - Jinlong Wei
- Department of Radiation Oncology, The First Hospital of Jilin University, Changchun 130021, China
| | - Lingbin Meng
- Department of Internal Medicine, Florida Hospital, Orlando, FL 32803, USA
| | - Qihe Zhang
- Department of Radiation Oncology, The First Hospital of Jilin University, Changchun 130021, China.,Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Chao Qu
- Department of Radiation Oncology, The First Hospital of Jilin University, Changchun 130021, China
| | - Ying Xin
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Xin Jiang
- Department of Radiation Oncology, The First Hospital of Jilin University, Changchun 130021, China
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10
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Zhang J, Lee YR, Dang F, Gan W, Menon AV, Katon JM, Hsu CH, Asara JM, Tibarewal P, Leslie NR, Shi Y, Pandolfi PP, Wei W. PTEN Methylation by NSD2 Controls Cellular Sensitivity to DNA Damage. Cancer Discov 2019; 9:1306-1323. [PMID: 31217297 DOI: 10.1158/2159-8290.cd-18-0083] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 04/05/2019] [Accepted: 06/14/2019] [Indexed: 12/13/2022]
Abstract
The function of PTEN in the cytoplasm largely depends on its lipid-phosphatase activity, though which it antagonizes the PI3K-AKT oncogenic pathway. However, molecular mechanisms underlying the role of PTEN in the nucleus remain largely elusive. Here, we report that DNA double-strand breaks (DSB) promote PTEN interaction with MDC1 upon ATM-dependent phosphorylation of T/S398-PTEN. Importantly, DNA DSBs enhance NSD2 (MMSET/WHSC1)-mediated dimethylation of PTEN at K349, which is recognized by the tudor domain of 53BP1 to recruit PTEN to DNA-damage sites, governing efficient repair of DSBs partly through dephosphorylation of γH2AX. Of note, inhibiting NSD2-mediated methylation of PTEN, either through expressing methylation-deficient PTEN mutants or through inhibiting NSD2, sensitizes cancer cells to combinatorial treatment with a PI3K inhibitor and DNA-damaging agents in both cell culture and in vivo xenograft models. Therefore, our study provides a novel molecular mechanism for PTEN regulation of DSB repair in a methylation- and protein phosphatase-dependent manner. SIGNIFICANCE: NSD2-mediated dimethylation of PTEN is recognized by the 53BP1 tudor domain to facilitate PTEN recruitment into DNA-damage sites, governing efficient repair of DNA DSBs. Importantly, inhibiting PTEN methylation sensitizes cancer cells to combinatorial treatment with a PI3K inhibitor combined with DNA-damaging agents in both cell culture and in vivo xenograft models.This article is highlighted in the In This Issue feature, p. 1143.
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Affiliation(s)
- Jinfang Zhang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, P.R. China.,Medical Research Institute, Wuhan University, Wuhan, P.R. China.,Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Yu-Ru Lee
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Boston, Massachusetts.,Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Fabin Dang
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Wenjian Gan
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts.,Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina
| | - Archita Venugopal Menon
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Boston, Massachusetts.,Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Jesse M Katon
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts.,Cancer Research Institute, Beth Israel Deaconess Cancer Center, Boston, Massachusetts
| | - Chih-Hung Hsu
- Department of Public Health, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R. China.,Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, Massachusetts.,Department of Cell Biology, Harvard Medical School, Boston, Massachusetts
| | - John M Asara
- Division of Signal Transduction, Beth Israel Deaconess Medical Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Priyanka Tibarewal
- Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot Watt University, Edinburgh, United Kingdom.,UCL Cancer Institute, University College London, London, United Kingdom
| | - Nicholas R Leslie
- Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot Watt University, Edinburgh, United Kingdom
| | - Yang Shi
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, Massachusetts.,Department of Cell Biology, Harvard Medical School, Boston, Massachusetts
| | - Pier Paolo Pandolfi
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Boston, Massachusetts. .,Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts.
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11
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Kori S, Ferry L, Matano S, Jimenji T, Kodera N, Tsusaka T, Matsumura R, Oda T, Sato M, Dohmae N, Ando T, Shinkai Y, Defossez PA, Arita K. Structure of the UHRF1 Tandem Tudor Domain Bound to a Methylated Non-histone Protein, LIG1, Reveals Rules for Binding and Regulation. Structure 2019; 27:485-496.e7. [PMID: 30639225 DOI: 10.1016/j.str.2018.11.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 10/19/2018] [Accepted: 11/28/2018] [Indexed: 12/21/2022]
Abstract
The protein UHRF1 is crucial for DNA methylation maintenance. The tandem Tudor domain (TTD) of UHRF1 binds histone H3K9me2/3 with micromolar affinity, as well as unmethylated linker regions within UHRF1 itself, causing auto-inhibition. Recently, we showed that a methylated histone-like region of DNA ligase 1 (LIG1K126me2/me3) binds the UHRF1 TTD with nanomolar affinity, permitting UHRF1 recruitment to chromatin. Here we report the crystal structure of the UHRF1 TTD bound to a LIG1K126me3 peptide. The data explain the basis for the high TTD-binding affinity of LIG1K126me3 and reveal that the interaction may be regulated by phosphorylation. Binding of LIG1K126me3 switches the overall structure of UHRF1 from a closed to a flexible conformation, suggesting that auto-inhibition is relieved. Our results provide structural insight into how UHRF1 performs its key function in epigenetic maintenance.
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Affiliation(s)
- Satomi Kori
- Graduate School of Medical Life Science, Yokohama City University, Yokohama 230-0045, Japan
| | - Laure Ferry
- University of Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR 7216 CNRS, 75013 Paris, France
| | - Shohei Matano
- Graduate School of Medical Life Science, Yokohama City University, Yokohama 230-0045, Japan
| | - Tomohiro Jimenji
- Graduate School of Medical Life Science, Yokohama City University, Yokohama 230-0045, Japan
| | - Noriyuki Kodera
- Bio-AFM Frontier Research Center, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan; WPI Nano Life Science Institute, Kakuma-machi, Kanazawa 920-1192, Japan; JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Takeshi Tsusaka
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Rumie Matsumura
- Graduate School of Medical Life Science, Yokohama City University, Yokohama 230-0045, Japan
| | - Takashi Oda
- Graduate School of Medical Life Science, Yokohama City University, Yokohama 230-0045, Japan
| | - Mamoru Sato
- Graduate School of Medical Life Science, Yokohama City University, Yokohama 230-0045, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Toshio Ando
- Bio-AFM Frontier Research Center, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan; WPI Nano Life Science Institute, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Yoichi Shinkai
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Pierre-Antoine Defossez
- University of Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR 7216 CNRS, 75013 Paris, France.
| | - Kyohei Arita
- Graduate School of Medical Life Science, Yokohama City University, Yokohama 230-0045, Japan; JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
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12
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Gu Y, Wang X, Liu H, Li G, Yu W, Ma Q. SET7/9 promotes hepatocellular carcinoma progression through regulation of E2F1. Oncol Rep 2018; 40:1863-1874. [PMID: 30106440 PMCID: PMC6111541 DOI: 10.3892/or.2018.6621] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 07/06/2018] [Indexed: 01/28/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most prevalent malignancies worldwide. Histone‑lysine N‑methyltransferase SET7/9 is a protein lysine monomethylase that methylates histone H3K4 as well as various non‑histone proteins. Deregulation of SET7/9 is frequently detected in human cancers. However, the role of SET7/9 in HCC development remains unclear. In the present study, upregulation of SET7/9 and E2F transcription factor 1 (E2F1) expression was detected in 68 samples of HCC tissues compared with these levels noted in the paired healthy liver samples. The expression levels of SET7/9 and E2F1 were significantly correlated with pathological stage and tumor size. Subcellular fractionation and co‑immunoprecipitation analyses revealed protein‑protein interaction between SET7/9 and E2F1 in the cytoplasm of HCC cells. Silencing of SET7/9, as well as treatment with 5'‑deoxy‑5'‑methylthioadenosine (MTA), a protein methylation inhibitor, led to reduced E2F1 protein abundance in HCC cells. Using Cell Counting Kit‑8 (CCK‑8) assay, Transwell migration assay and wound healing assay, significantly decreased cell proliferation, migration and invasion were observed in cells exhibiting downregulation of SET7/9 and E2F1 expression, as well as in wild‑type HCC cells treated with MTA. Furthermore, SET7/9 downregulation and MTA treatment resulted in reduced expression of downstream targets of E2F1, including cyclin A2, cyclin E1 and CDK2. In conclusion, the present study revealed an oncogenic function of SET7/9 in HCC and demonstrated that SET7/9 may be responsible for alterations in the proliferative ability, aggressiveness and invasive/metastatic potential of HCC cells through post‑translational regulation of E2F1.
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Affiliation(s)
- Ye Gu
- Department of Pathophysiology, Medical School of Southeast University, Nanjing, Jiangsu, 210009, P.R. China
| | - Xinling Wang
- Department of Pathology, No. 81 Hospital of PLA, Nanjing, Jiangsu 210002, P.R. China
| | - Hong Liu
- Department of Pathophysiology, Medical School of Southeast University, Nanjing, Jiangsu, 210009, P.R. China
| | - Guimei Li
- Department of Pathology, No. 81 Hospital of PLA, Nanjing, Jiangsu 210002, P.R. China
| | - Weiping Yu
- Department of Pathophysiology, Medical School of Southeast University, Nanjing, Jiangsu, 210009, P.R. China
| | - Qing Ma
- College of Biological and Environmental Engineering, Zhejiang Shuren University, Hangzhou, Zhejiang 310015, P.R. China
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13
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Wang J, Yuan Z, Cui Y, Xie R, Yang G, Kassab MA, Wang M, Ma Y, Wu C, Yu X, Liu X. Molecular basis for the inhibition of the methyl-lysine binding function of 53BP1 by TIRR. Nat Commun 2018; 9:2689. [PMID: 30002377 PMCID: PMC6043480 DOI: 10.1038/s41467-018-05174-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 06/14/2018] [Indexed: 11/09/2022] Open
Abstract
53BP1 performs essential functions in DNA double-strand break (DSB) repair and it was recently reported that Tudor interacting repair regulator (TIRR) negatively regulates 53BP1 during DSB repair. Here, we present the crystal structure of the 53BP1 tandem Tudor domain (TTD) in complex with TIRR. Our results show that three loops from TIRR interact with 53BP1 TTD and mask the methylated lysine-binding pocket in TTD. Thus, TIRR competes with histone H4K20 methylation for 53BP1 binding. We map key interaction residues in 53BP1 TTD and TIRR, whose mutation abolishes complex formation. Moreover, TIRR suppresses the relocation of 53BP1 to DNA lesions and 53BP1-dependent DNA damage repair. Finally, despite the high-sequence homology between TIRR and NUDT16, NUDT16 does not directly interact with 53BP1 due to the absence of key residues required for binding. Taken together, our study provides insights into the molecular mechanism underlying TIRR-mediated suppression of 53BP1-dependent DNA damage repair.
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Affiliation(s)
- Jiaxu Wang
- College of Life Sciences, Hebei University, Baoding, 071000, Hebei, China
| | - Zenglin Yuan
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, Shandong, China
| | - Yaqi Cui
- College of Life Sciences, Hebei University, Baoding, 071000, Hebei, China
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Rong Xie
- College of Life Sciences, Hebei University, Baoding, 071000, Hebei, China
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Guang Yang
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Muzaffer A Kassab
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Mengxi Wang
- College of Life Sciences, Hebei University, Baoding, 071000, Hebei, China
| | - Yinliang Ma
- College of Life Sciences, Hebei University, Baoding, 071000, Hebei, China
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Chen Wu
- College of Life Sciences, Hebei University, Baoding, 071000, Hebei, China
| | - Xiaochun Yu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA.
| | - Xiuhua Liu
- College of Life Sciences, Hebei University, Baoding, 071000, Hebei, China.
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Li S, Wang C, Wang W, Liu W, Zhang G. Abnormally high expression of POLD1, MCM2, and PLK4 promotes relapse of acute lymphoblastic leukemia. Medicine (Baltimore) 2018; 97:e10734. [PMID: 29768346 PMCID: PMC5976347 DOI: 10.1097/md.0000000000010734] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
This study aimed to explore the underlying mechanism of relapsed acute lymphoblastic leukemia (ALL).Datasets of GSE28460 and GSE18497 were downloaded from Gene Expression Omnibus (GEO). Differentially expressed genes (DEGs) between diagnostic and relapsed ALL samples were identified using Limma package in R, and a Venn diagram was drawn. Next, functional enrichment analyses of co-regulated DEGs were performed. Based on the String database, protein-protein interaction network and module analyses were also conducted. Moreover, transcription factors and miRNAs targeting co-regulated DEGs were predicted using the WebGestalt online tool.A total of 71 co-regulated DEGs were identified, including 56 co-upregulated genes and 15 co-downregulated genes. Functional enrichment analyses showed that upregulated DEGs were significantly enriched in the cell cycle, and DNA replication, and repair related pathways. POLD1, MCM2, and PLK4 were hub proteins in both protein-protein interaction network and module, and might be potential targets of E2F. Additionally, POLD1 and MCM2 were found to be regulated by miR-520H via E2F1.High expression of POLD1, MCM2, and PLK4 might play positive roles in the recurrence of ALL, and could serve as potential therapeutic targets for the treatment of relapsed ALL.
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Abhishek S, Nivya MA, Nakarakanti NK, Deeksha W, Khosla S, Rajakumara E. Biochemical and dynamic basis for combinatorial recognition of H3R2K9me2 by dual domains of UHRF1. Biochimie 2018; 149:105-114. [PMID: 29656054 DOI: 10.1016/j.biochi.2018.04.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 04/10/2018] [Indexed: 01/10/2023]
Abstract
UHRF1 is a multi-domain protein comprising of a tandem tudor (UHRF1 TTD), a PHD finger, and a SET and RING-associated domain. It is required for the maintenance of CG methylation, heterochromatin formation and DNA repair. Isothermal titration calorimetry binding studies of unmodified and methylated lysine histone peptides establish that the UHRF1 TTD binds dimethylated Lys9 on histone H3 (H3K9me2). Further, MD simulation and binding studies reveal that TTD-PHD of UHRF1 (UHRF1 TTD-PHD) preferentially recognizes dimethyl-lysine status. Importantly, we show that Asp145 in the binding pocket determines the preferential recognition of the dimethyl-ammonium group of H3K9me2. Interestingly, PHD finger of the UHRF1 TTD-PHD has a negligible contribution to the binding affinity for recognition of K9me2 by the UHRF1 TTD. Surprisingly, Lys4 methylation on H3 peptide has an insignificant effect on combinatorial recognition of R2 and K9me2 on H3 by the UHRF1 TTD-PHD. We propose that subtle variations of key residues at the binding pocket determine status specific recognition of histone methyl-lysines by the reader domains.
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Affiliation(s)
- Suman Abhishek
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, 502285, Telangana, India
| | - M Angel Nivya
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, 502285, Telangana, India
| | - Naveen Kumar Nakarakanti
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, 502285, Telangana, India
| | - Waghela Deeksha
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, 502285, Telangana, India
| | - Sanjeev Khosla
- Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, 500001, India.
| | - Eerappa Rajakumara
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, 502285, Telangana, India.
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16
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Martín-Morales L, Feldman M, Vershinin Z, Garre P, Caldés T, Levy D. SETD6 dominant negative mutation in familial colorectal cancer type X. Hum Mol Genet 2018; 26:4481-4493. [PMID: 28973356 DOI: 10.1093/hmg/ddx336] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 08/15/2017] [Indexed: 01/01/2023] Open
Abstract
Familiar colorectal cancer type X (FCCTX) comprises families that fulfill the Amsterdam criteria for hereditary non-polyposis colorectal cancer, but that lack the mismatch repair deficiency that defines the Lynch syndrome. Thus, the genetic cause that increases the predisposition to colorectal and other related cancers in families with FCCTX remains to be elucidated. Using whole-exome sequencing, we have identified a truncating mutation in the SETD6 gene (c.791_792insA, p.Met264IlefsTer3) in all the affected members of a FCCTX family. SETD6 is a mono-methyltransferase previously shown to modulate the NF-κB and Wnt signaling pathways, among other. In the present study, we characterized the truncated version of SETD6, providing evidence that this SETD6 mutation may play a role in the cancer inheritance in this family. Here we demonstrate that the truncated SETD6 lacks its enzymatic activity as a methyltransferase, while maintaining other properties such as its expression, localization and substrate-binding ability. In addition, we show that the mutant allele is expressed and that the resulting protein competes with the wild type for their substrates, pointing to a dominant negative nature. These findings suggest that the identified mutation impairs the normal function of SETD6, which may result in the deregulation of the different pathways in which it is involved, contributing to the increased susceptibility to cancer in this FCCTX family.
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Affiliation(s)
- Lorena Martín-Morales
- Molecular Oncology Laboratory, Department of Medical Oncology, Hospital Clínico San Carlos, IdISSC, CIBERONC, 28040 Madrid, Spain
| | - Michal Feldman
- The Shraga Segal Department of Microbiology, Immunology and Genetics.,National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er-Sheva 84105, Israel
| | - Zlata Vershinin
- The Shraga Segal Department of Microbiology, Immunology and Genetics.,National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er-Sheva 84105, Israel
| | - Pilar Garre
- Molecular Oncology Laboratory, Department of Medical Oncology, Hospital Clínico San Carlos, IdISSC, CIBERONC, 28040 Madrid, Spain
| | - Trinidad Caldés
- Molecular Oncology Laboratory, Department of Medical Oncology, Hospital Clínico San Carlos, IdISSC, CIBERONC, 28040 Madrid, Spain
| | - Dan Levy
- The Shraga Segal Department of Microbiology, Immunology and Genetics.,National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er-Sheva 84105, Israel
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17
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Huang A, Yao J, Liu T, Lin Z, Zhang S, Zhang T, Ma H. 53BP1 loss suppresses the radiosensitizing effect of icotinib hydrochloride in colorectal cancer cells. Int J Radiat Biol 2018; 94:327-334. [PMID: 29388453 DOI: 10.1080/09553002.2018.1434322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND This study aimed to investigate the influence of the expression of P53-binding protein 1 (53BP1), a key component in DNA damage repair pathways, on the radiosensitizing effect of icotinib hydrochloride in colorectal cancer and to elucidate the mechanisms underlying this influence. MATERIALS AND METHODS Real-time RT-PCR and Western blotting were performed to verify the gene-knockout effect of 53BP1 small hairpin RNA (ShRNA), and colony formation assay was employed to investigate the influence of 53BP1 downregulation on the radiosensitizing effect of icotinib hydrochloride in HCT116 cells. Cell apoptosis, cell cycle distributions, and histone H2AX (γ-H2AX) fluorescence foci after 53BP1 knockdown were evaluated. Relative protein expression in the ataxia telangiectasia mutated kinase (ATM)-checkpoint kinase-2 (CHK2)-P53 pathway was measured by Western blot analysis to unravel the molecular mechanisms linking the pathway to the above phenomena. RESULTS Icotinib hydrochloride increased the radiosensitivity of HCT116 cells; however, this effect was suppressed by the downregulation of 53BP1 expression, a change that inhibited cell apoptosis, increased the percentage of HCT116 cells arrested in S-phase and inhibited the protein expression of key molecules in the ATM-CHK2-P53 apoptotic pathway. CONCLUSION Our studies confirmed that the loss of 53BP1 serves as a negative regulator of the radiosensitizing effect of icotinib in part by suppressing the ATM-CHK2-P53 apoptotic pathway.
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Affiliation(s)
- Ai Huang
- a Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , China
| | - Jing Yao
- a Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , China
| | - Tao Liu
- a Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , China
| | - Zhenyu Lin
- a Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , China
| | - Sheng Zhang
- a Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , China
| | - Tao Zhang
- a Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , China
| | - Hong Ma
- a Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , China
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18
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Palopoli N, González Foutel NS, Gibson TJ, Chemes LB. Short linear motif core and flanking regions modulate retinoblastoma protein binding affinity and specificity. Protein Eng Des Sel 2018; 31:69-77. [DOI: 10.1093/protein/gzx068] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Accepted: 01/10/2018] [Indexed: 12/11/2022] Open
Affiliation(s)
- Nicolás Palopoli
- Department of Science and Technology, Universidad Nacional de Quilmes, CONICET. Roque Sáenz Peña 352. CP (B1876BXD), Bernal, Buenos Aires, Argentina
- Structural Bioinformatics Unit, Fundación Instituto Leloir and IIBBA-CONICET. Av. Patricias Argentinas 435 CP 1405, Buenos Aires, Argentina
| | - Nicolás S González Foutel
- Protein Structure Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET. Av. Patricias Argentinas 435 CP 1405, Buenos Aires, Argentina
| | - Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Lucía B Chemes
- Protein Structure Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET. Av. Patricias Argentinas 435 CP 1405, Buenos Aires, Argentina
- Instituto de Investigaciones Biotecnológicas IIB-INTECH, Universidad Nacional de San Martín. Av. 25 de Mayo y Francia CP 1650, San Martín, Buenos Aires, Argentina
- Departamento de Fisiología y Biología Molecular y Celular (DFBMC), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Intendente Güiraldes 2160, Ciudad Universitaria, C1428EGA, Argentina
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Carr SM, Munro S, Sagum CA, Fedorov O, Bedford MT, La Thangue NB. Tudor-domain protein PHF20L1 reads lysine methylated retinoblastoma tumour suppressor protein. Cell Death Differ 2017; 24:2139-2149. [PMID: 28841214 PMCID: PMC5686351 DOI: 10.1038/cdd.2017.135] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 07/12/2017] [Accepted: 07/14/2017] [Indexed: 12/30/2022] Open
Abstract
The retinoblastoma tumour suppressor protein (pRb) classically functions to regulate early cell cycle progression where it acts to enforce a number of checkpoints in response to cellular stress and DNA damage. Methylation at lysine (K) 810, which occurs within a critical CDK phosphorylation site and antagonises a CDK-dependent phosphorylation event at the neighbouring S807 residue, acts to hold pRb in the hypo-phosphorylated growth-suppressing state. This is mediated in part by the recruitment of the reader protein 53BP1 to di-methylated K810, which allows pRb activity to be effectively integrated with the DNA damage response. Here, we report the surprising observation that an additional methylation-dependent interaction occurs at K810, but rather than the di-methyl mark, it is selective for the mono-methyl K810 mark. Binding of the mono-methyl PHF20L1 reader to methylated pRb occurs on E2F target genes, where it acts to mediate an additional level of control by recruiting the MOF acetyltransferase complex to E2F target genes. Significantly, we find that the interplay between PHF20L1 and mono-methyl pRb is important for maintaining the integrity of a pRb-dependent G1-S-phase checkpoint. Our results highlight the distinct roles that methyl-lysine readers have in regulating the biological activity of pRb.
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Affiliation(s)
- Simon M Carr
- Department of Oncology, University of Oxford, Old Road Campus Research Building, Old Road Campus, Roosevelt Drive, Headington, Oxford OX3 7DQ, UK
| | - Shonagh Munro
- Department of Oncology, University of Oxford, Old Road Campus Research Building, Old Road Campus, Roosevelt Drive, Headington, Oxford OX3 7DQ, UK
| | - Cari A Sagum
- Department of Molecular Carcinogenesis, The University of Texas, MD Anderson Cancer Center, Smithville, TX 77030, USA
| | - Oleg Fedorov
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium Oxford, University of Oxford, Old Road Campus Research Building, Old Road Campus, Roosevelt Drive, Headington, Oxford OX3 7DQ, UK
| | - Mark T Bedford
- Department of Molecular Carcinogenesis, The University of Texas, MD Anderson Cancer Center, Smithville, TX 77030, USA
| | - Nicholas B La Thangue
- Department of Oncology, University of Oxford, Old Road Campus Research Building, Old Road Campus, Roosevelt Drive, Headington, Oxford OX3 7DQ, UK
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20
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Vélez-Cruz R, Johnson DG. The Retinoblastoma (RB) Tumor Suppressor: Pushing Back against Genome Instability on Multiple Fronts. Int J Mol Sci 2017; 18:ijms18081776. [PMID: 28812991 PMCID: PMC5578165 DOI: 10.3390/ijms18081776] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 08/13/2017] [Accepted: 08/13/2017] [Indexed: 12/13/2022] Open
Abstract
The retinoblastoma (RB) tumor suppressor is known as a master regulator of the cell cycle. RB is mutated or functionally inactivated in the majority of human cancers. This transcriptional regulator exerts its function in cell cycle control through its interaction with the E2F family of transcription factors and with chromatin remodelers and modifiers that contribute to the repression of genes important for cell cycle progression. Over the years, studies have shown that RB participates in multiple processes in addition to cell cycle control. Indeed, RB is known to interact with over 200 different proteins and likely exists in multiple complexes. RB, in some cases, acts through its interaction with E2F1, other members of the pocket protein family (p107 and p130), and/or chromatin remodelers and modifiers. RB is a tumor suppressor with important chromatin regulatory functions that affect genomic stability. These functions include the role of RB in DNA repair, telomere maintenance, chromosome condensation and cohesion, and silencing of repetitive regions. In this review we will discuss recent advances in RB biology related to RB, partner proteins, and their non-transcriptional functions fighting back against genomic instability.
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Affiliation(s)
- Renier Vélez-Cruz
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, 1808 Park Road 1C, P.O. Box 389, Smithville, TX 78957, USA.
- Department of Biochemistry, Midwestern University, Chicago College of Osteopathic Medicine, 555 31st Street, Downers Grove, IL 60515, USA.
| | - David G Johnson
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, 1808 Park Road 1C, P.O. Box 389, Smithville, TX 78957, USA.
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21
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Teske KA, Hadden MK. Methyllysine binding domains: Structural insight and small molecule probe development. Eur J Med Chem 2017; 136:14-35. [DOI: 10.1016/j.ejmech.2017.04.047] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 04/14/2017] [Accepted: 04/19/2017] [Indexed: 12/19/2022]
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22
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Abstract
In this review, Dyson summarizes some recent developments in pRB research and focuses on progress toward answers for the three fundamental questions that sit at the heart of the pRB literature: What does pRB do? How does the inactivation of RB change the cell? How can our knowledge of RB function be exploited to provide better treatment for cancer patients? The retinoblastoma susceptibility gene (RB1) was the first tumor suppressor gene to be molecularly defined. RB1 mutations occur in almost all familial and sporadic forms of retinoblastoma, and this gene is mutated at variable frequencies in a variety of other human cancers. Because of its early discovery, the recessive nature of RB1 mutations, and its frequency of inactivation, RB1 is often described as a prototype for the class of tumor suppressor genes. Its gene product (pRB) regulates transcription and is a negative regulator of cell proliferation. Although these general features are well established, a precise description of pRB's mechanism of action has remained elusive. Indeed, in many regards, pRB remains an enigma. This review summarizes some recent developments in pRB research and focuses on progress toward answers for the three fundamental questions that sit at the heart of the pRB literature: What does pRB do? How does the inactivation of RB change the cell? How can our knowledge of RB function be exploited to provide better treatment for cancer patients?
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23
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Yao J, Huang A, Zheng X, Liu T, Lin Z, Zhang S, Yang Q, Zhang T, Ma H. 53BP1 loss induces chemoresistance of colorectal cancer cells to 5-fluorouracil by inhibiting the ATM-CHK2-P53 pathway. J Cancer Res Clin Oncol 2016; 143:419-431. [PMID: 27838786 DOI: 10.1007/s00432-016-2302-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 11/05/2016] [Indexed: 01/23/2023]
Abstract
PURPOSE Loss of P53 binding protein 1 (53BP1) is considered a poor prognostic factor for colorectal cancer. However, its effect on chemosensitivity of colorectal cancer to 5-fluorouracil (5-FU) remains elusive. This study aimed to examine the association of 53BP1 expression with chemosensitivity of colorectal cancer cells to 5-FU. METHODS Immunohistochemistry was performed on 30 metastatic colorectal cancer samples to assess the associations of 53BP1 levels with clinical therapeutic effects. In vitro, IC50 values for 5-FU and 53BP1 levels were determined by MTT assay and Western blot in 5 colorectal cancer cell lines. Then, 53BP1 was silenced in HCT116 and HT29 cells, and cell proliferation, apoptosis and cell cycle distribution were evaluated. Relative protein levels of ATM-CHK2-P53 pathway effectors and Bcl-2 family members were measured by Western blot. Finally, the effects of 53BP1 knockdown on tumor growth and 5-FU chemoresistance were investigated in vivo. RESULTS 53BP1 expression was closely related to time to progression (TTP) after first-line chemotherapy. Namely, 53BP1 downregulation resulted in reduced TTP. In addition, 53BP1 silencing increased proliferation, inhibited apoptosis and induced S phase arrest in HCT116 and HT29 cells after 5-FU treatment. Moreover, 53BP1 knockdown also reduced the protein levels of ATM-CHK2-P53 apoptotic pathway effectors, caspase9 and caspase3, while increasing Bcl-2 expression. In vivo, 53BP1 silencing accelerated tumor proliferation in nude mice and enhanced resistance to 5-FU. CONCLUSIONS These findings confirmed that 53BP1 loss might be a negative factor for chemotherapy efficacy, promoting cell proliferation and inhibiting apoptosis by suppressing ATM-CHK2-P53 signaling, and finally inducing 5-FU resistance.
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Affiliation(s)
- Jing Yao
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 JieFang Avenue, Wuhan, 430022, Hubei, China
| | - Ai Huang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 JieFang Avenue, Wuhan, 430022, Hubei, China
| | - Xiumei Zheng
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 JieFang Avenue, Wuhan, 430022, Hubei, China
| | - Tao Liu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 JieFang Avenue, Wuhan, 430022, Hubei, China
| | - Zhenyu Lin
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 JieFang Avenue, Wuhan, 430022, Hubei, China
| | - Sheng Zhang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 JieFang Avenue, Wuhan, 430022, Hubei, China
| | - Qin Yang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 JieFang Avenue, Wuhan, 430022, Hubei, China
| | - Tao Zhang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 JieFang Avenue, Wuhan, 430022, Hubei, China
| | - Hong Ma
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 JieFang Avenue, Wuhan, 430022, Hubei, China.
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24
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Cuella-Martin R, Oliveira C, Lockstone HE, Snellenberg S, Grolmusova N, Chapman JR. 53BP1 Integrates DNA Repair and p53-Dependent Cell Fate Decisions via Distinct Mechanisms. Mol Cell 2016; 64:51-64. [PMID: 27546791 PMCID: PMC5065530 DOI: 10.1016/j.molcel.2016.08.002] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 07/08/2016] [Accepted: 07/29/2016] [Indexed: 12/28/2022]
Abstract
The tumor suppressor protein 53BP1, a pivotal regulator of DNA double-strand break (DSB) repair, was first identified as a p53-interacting protein over two decades ago. However, its direct contributions to p53-dependent cellular activities remain undefined. Here, we reveal that 53BP1 stimulates genome-wide p53-dependent gene transactivation and repression events in response to ionizing radiation (IR) and synthetic p53 activation. 53BP1-dependent p53 modulation requires both auto-oligomerization and tandem-BRCT domain-mediated bivalent interactions with p53 and the ubiquitin-specific protease USP28. Loss of these activities results in inefficient p53-dependent cell-cycle checkpoint and exit responses. Furthermore, we demonstrate 53BP1-USP28 cooperation to be essential for normal p53-promoter element interactions and gene transactivation-associated events, yet dispensable for 53BP1-dependent DSB repair regulation. Collectively, our data provide a mechanistic explanation for 53BP1-p53 cooperation in controlling anti-tumorigenic cell-fate decisions and reveal these activities to be distinct and separable from 53BP1's regulation of DNA double-strand break repair pathway choice.
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Affiliation(s)
- Raquel Cuella-Martin
- Chromatin and Genome Integrity Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Catarina Oliveira
- Chromatin and Genome Integrity Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Helen E Lockstone
- Bioinformatics and Statistical Genetics Core, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Suzanne Snellenberg
- Chromatin and Genome Integrity Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Natalia Grolmusova
- Chromatin and Genome Integrity Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - J Ross Chapman
- Chromatin and Genome Integrity Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.
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25
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Xiao Y, Zheng X, Huang A, Liu T, Zhang T, Ma H. Deficiency of 53BP1 inhibits the radiosensitivity of colorectal cancer. Int J Oncol 2016; 49:1600-8. [DOI: 10.3892/ijo.2016.3629] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 07/11/2016] [Indexed: 12/15/2022] Open
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26
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Chen Y, Zhu WG. Biological function and regulation of histone and non-histone lysine methylation in response to DNA damage. Acta Biochim Biophys Sin (Shanghai) 2016; 48:603-16. [PMID: 27217472 DOI: 10.1093/abbs/gmw050] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 04/21/2016] [Indexed: 02/07/2023] Open
Abstract
DNA damage response (DDR) signaling network is initiated to protect cells from various exogenous and endogenous damage resources. Timely and accurate regulation of DDR proteins is required for distinct DNA damage repair pathways. Post-translational modifications of histone and non-histone proteins play a vital role in the DDR factor foci formation and signaling pathway. Phosphorylation, ubiquitylation, SUMOylation, neddylation, poly(ADP-ribosyl)ation, acetylation, and methylation are all involved in the spatial-temporal regulation of DDR, among which phosphorylation and ubiquitylation are well studied. Studies in the past decade also revealed extensive roles of lysine methylation in response to DNA damage. Lysine methylation is finely regulated by plenty of lysine methyltransferases, lysine demethylases, and can be recognized by proteins with chromodomain, plant homeodomain, Tudor domain, malignant brain tumor domain, or proline-tryptophan-tryptophan-proline domain. In this review, we outline the dynamics and regulation of histone lysine methylation at canonical (H3K4, H3K9, H3K27, H3K36, H3K79, and H4K20) and non-canonical sites after DNA damage, and discuss their context-specific functions in DDR protein recruitment or extraction, chromatin environment establishment, and transcriptional regulation. We also present the emerging advances of lysine methylation in non-histone proteins during DDR.
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Affiliation(s)
- Yongcan Chen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing 100191, China Peking University-Tsinghua University Center for Life Sciences, Beijing 100191, China
| | - Wei-Guo Zhu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing 100191, China Peking University-Tsinghua University Center for Life Sciences, Beijing 100191, China School of Medicine, Shenzhen University, Shenzhen 518060, China
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27
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Loss of the N-terminal methyltransferase NRMT1 increases sensitivity to DNA damage and promotes mammary oncogenesis. Oncotarget 2016; 6:12248-63. [PMID: 25909287 PMCID: PMC4494936 DOI: 10.18632/oncotarget.3653] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 02/27/2015] [Indexed: 12/31/2022] Open
Abstract
Though discovered over four decades ago, the function of N-terminal methylation has mostly remained a mystery. Our discovery of the first mammalian N-terminal methyltransferase, NRMT1, has led to the discovery of many new functions for N-terminal methylation, including regulation of DNA/protein interactions, accurate mitotic division, and nucleotide excision repair (NER). Here we test whether NRMT1 is also important for DNA double-strand break (DSB) repair, and given its previously known roles in cell cycle regulation and the DNA damage response, assay if NRMT1 is acting as a tumor suppressor. We find that NRMT1 knockdown significantly enhances the sensitivity of breast cancer cell lines to both etoposide treatment and γ-irradiation, as well as, increases proliferation rate, invasive potential, anchorage-independent growth, xenograft tumor size, and tamoxifen sensitivity. Interestingly, this positions NRMT1 as a tumor suppressor protein involved in multiple DNA repair pathways, and indicates, similar to BRCA1 and BRCA2, its loss may result in tumors with enhanced sensitivity to diverse DNA damaging chemotherapeutics.
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28
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Cleary C, Leeman JE, Higginson DS, Katabi N, Sherman E, Morris L, McBride S, Lee N, Riaz N. Biological Features of Human Papillomavirus-related Head and Neck Cancers Contributing to Improved Response. Clin Oncol (R Coll Radiol) 2016; 28:467-74. [PMID: 27052795 DOI: 10.1016/j.clon.2016.03.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 02/29/2016] [Accepted: 03/01/2016] [Indexed: 01/08/2023]
Abstract
Head and neck squamous cell carcinomas (HNSCC) are the sixth most common malignancy globally, and an increasing proportion of oropharyngeal HNSCCs are associated with the human papillomavirus (HPV). Patients with HPV-associated tumours have markedly improved overall and disease-specific survival compared with their HPV-negative counterparts when treated with chemoradiation. Although the difference in outcomes between these two groups is clearly established, the mechanism underlying these differences remains an area of investigation. Data from preclinical, clinical and genomics studies have started to suggest that an increase in radio-sensitivity of HPV-positive HNSCC may be responsible for improved outcomes, the putative mechanisms of which we will review here. The Cancer Genome Atlas and others have recently documented a multitude of molecular differences between HPV-positive and HPV-negative tumours. Preclinical investigations by multiple groups have explored possible mechanisms of increased sensitivity to therapy, including examining differences in DNA repair, hypoxia and the immune response. In addition to differences in the response to therapy, some groups have started to investigate phenotypic differences between the two diseases, such as tumour invasiveness. Finally, we will conclude with a brief review of ongoing clinical trials that are attempting to de-escalate treatment to minimise long-term toxicity while maintaining cure rates. New insights from preclinical and genomic studies may eventually lead to personalised treatment paradigms for HPV-positive patients.
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Affiliation(s)
- C Cleary
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - J E Leeman
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - D S Higginson
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - N Katabi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - E Sherman
- Department of Medical Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - L Morris
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - S McBride
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - N Lee
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - N Riaz
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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29
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Huang PH, Cook R, Zoumpoulidou G, Luczynski MT, Mittnacht S. Retinoblastoma family proteins: New players in DNA repair by non-homologous end-joining. Mol Cell Oncol 2016; 3:e1053596. [PMID: 27308588 PMCID: PMC4905371 DOI: 10.1080/23723556.2015.1053596] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 05/17/2015] [Accepted: 05/18/2015] [Indexed: 10/23/2022]
Abstract
Loss of retinoblastoma protein (RB1) function is a major driver in cancer development. We have recently reported that, in addition to its well-documented functions in cell cycle and fate control, RB1 and its paralogs have a novel role in regulating DNA repair by non-homologous end joining (NHEJ). Here we summarize our findings and present mechanistic hypotheses on how RB1 may support the DNA repair process and the therapeutic implications for patients who harbor RB1-negative cancers.
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Affiliation(s)
- Paul H. Huang
- The Institute of Cancer Research, Division of Cancer Biology, Chester Beatty Laboratories, London, UK
| | - Rebecca Cook
- The Institute of Cancer Research, Division of Cancer Biology, Chester Beatty Laboratories, London, UK
- Cancer Cell Signalling, UCL Cancer Institute, University College London, London, UK
| | - Georgia Zoumpoulidou
- The Institute of Cancer Research, Division of Cancer Biology, Chester Beatty Laboratories, London, UK
| | - Maciej T. Luczynski
- The Institute of Cancer Research, Division of Cancer Biology, Chester Beatty Laboratories, London, UK
| | - Sibylle Mittnacht
- The Institute of Cancer Research, Division of Cancer Biology, Chester Beatty Laboratories, London, UK
- Cancer Cell Signalling, UCL Cancer Institute, University College London, London, UK
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30
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Brasil JN, Cabral LM, Eloy NB, Primo LMF, Barroso-Neto IL, Grangeiro LPP, Gonzalez N, Inzé D, Ferreira PCG, Hemerly AS. AIP1 is a novel Agenet/Tudor domain protein from Arabidopsis that interacts with regulators of DNA replication, transcription and chromatin remodeling. BMC PLANT BIOLOGY 2015; 15:270. [PMID: 26538092 PMCID: PMC4634149 DOI: 10.1186/s12870-015-0641-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 10/08/2015] [Indexed: 05/05/2023]
Abstract
BACKGROUND DNA replication and transcription are dynamic processes regulating plant development that are dependent on the chromatin accessibility. Proteins belonging to the Agenet/Tudor domain family are known as histone modification "readers" and classified as chromatin remodeling proteins. Histone modifications and chromatin remodeling have profound effects on gene expression as well as on DNA replication, but how these processes are integrated has not been completely elucidated. It is clear that members of the Agenet/Tudor family are important regulators of development playing roles not well known in plants. METHODS Bioinformatics and phylogenetic analyses of the Agenet/Tudor Family domain in the plant kingdom were carried out with sequences from available complete genomes databases. 3D structure predictions of Agenet/Tudor domains were calculated by I-TASSER server. Protein interactions were tested in two-hybrid, GST pulldown, semi-in vivo pulldown and Tandem Affinity Purification assays. Gene function was studied in a T-DNA insertion GABI-line. RESULTS In the present work we analyzed the family of Agenet/Tudor domain proteins in the plant kingdom and we mapped the organization of this family throughout plant evolution. Furthermore, we characterized a member from Arabidopsis thaliana named AIP1 that harbors Agenet/Tudor and DUF724 domains. AIP1 interacts with ABAP1, a plant regulator of DNA replication licensing and gene transcription, with a plant histone modification "reader" (LHP1) and with non modified histones. AIP1 is expressed in reproductive tissues and its down-regulation delays flower development timing. Also, expression of ABAP1 and LHP1 target genes were repressed in flower buds of plants with reduced levels of AIP1. CONCLUSIONS AIP1 is a novel Agenet/Tudor domain protein in plants that could act as a link between DNA replication, transcription and chromatin remodeling during flower development.
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Affiliation(s)
- Juliana Nogueira Brasil
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Luiz Mors Cabral
- Departamento de Biologia Celular e Molecular, Universidade Federal Fluminense, Niterói, Rio de Janeiro, Brazil.
| | - Nubia B Eloy
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), Ghent, Belgium.
| | - Luiza M F Primo
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
- Programa de Biologia Celular, Instituto Nacional de Câncer, Rio de Janeiro, Rio de Janeiro, Brazil.
| | | | - Letícia P Perdigão Grangeiro
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Nathalie Gonzalez
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), Ghent, Belgium.
| | - Dirk Inzé
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), Ghent, Belgium.
| | - Paulo C G Ferreira
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Adriana S Hemerly
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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31
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Carr SM, Poppy Roworth A, Chan C, La Thangue NB. Post-translational control of transcription factors: methylation ranks highly. FEBS J 2015; 282:4450-65. [PMID: 26402372 DOI: 10.1111/febs.13524] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 09/04/2015] [Accepted: 09/21/2015] [Indexed: 01/31/2023]
Abstract
Methylation of lysine and arginine residues on histones has long been known to determine both chromatin structure and gene expression. In recent years, the methylation of non-histone proteins has emerged as a prevalent modification which impacts on diverse processes such as cell cycle control, DNA repair, senescence, differentiation, apoptosis and tumourigenesis. Many of these non-histone targets represent transcription factors, cell signalling molecules and tumour suppressor proteins. Evidence now suggests that the dysregulation of methyltransferases, demethylases and reader proteins is involved in the development of many diseases, including cancer, and several of these proteins represent potential therapeutic targets for small molecule compounds, fuelling a recent surge in chemical inhibitor design. Such molecules will greatly help us to understand the role of methylation in both health and disease.
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Affiliation(s)
- Simon M Carr
- Laboratory of Cancer Biology, Department of Oncology, University of Oxford, UK
| | - A Poppy Roworth
- Laboratory of Cancer Biology, Department of Oncology, University of Oxford, UK
| | - Cheryl Chan
- Laboratory of Cancer Biology, Department of Oncology, University of Oxford, UK
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32
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Affiliation(s)
- Paul H Huang
- The Institute of Cancer Research, Division of Cancer Biology, Chester Beatty Laboratories, London, UK
| | - Rebecca Cook
- The Institute of Cancer Research, Division of Cancer Biology, Chester Beatty Laboratories, London, UK
- Cancer Cell Signalling, UCL Cancer Institute, University College London, London, UK
| | - Sibylle Mittnacht
- The Institute of Cancer Research, Division of Cancer Biology, Chester Beatty Laboratories, London, UK
- Cancer Cell Signalling, UCL Cancer Institute, University College London, London, UK
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33
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Bonsignore LA, Tooley JG, Van Hoose PM, Wang E, Cheng A, Cole MP, Schaner Tooley CE. NRMT1 knockout mice exhibit phenotypes associated with impaired DNA repair and premature aging. Mech Ageing Dev 2015; 146-148:42-52. [PMID: 25843235 DOI: 10.1016/j.mad.2015.03.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 03/17/2015] [Accepted: 03/30/2015] [Indexed: 12/11/2022]
Abstract
Though defective genome maintenance and DNA repair have long been known to promote phenotypes of premature aging, the role protein methylation plays in these processes is only now emerging. We have recently identified the first N-terminal methyltransferase, NRMT1, which regulates protein-DNA interactions and is necessary for both accurate mitotic division and nucleotide excision repair. To demonstrate if complete loss of NRMT1 subsequently resulted in developmental or aging phenotypes, we constructed the first NRMT1 knockout (Nrmt1(-/-)) mouse. The majority of these mice die shortly after birth. However, the ones that survive, exhibit decreased body size, female-specific infertility, kyphosis, decreased mitochondrial function, and early-onset liver degeneration; phenotypes characteristic of other mouse models deficient in DNA repair. The livers from Nrmt1(-/-) mice produce less reactive oxygen species (ROS) than wild type controls, and Nrmt1(-/-) mouse embryonic fibroblasts show a decreased capacity for handling oxidative damage. This indicates that decreased mitochondrial function may benefit Nrmt1(-/-) mice and protect them from excess internal ROS and subsequent DNA damage. These studies position the NRMT1 knockout mouse as a useful new system for studying the effects of genomic instability and defective DNA damage repair on organismal and tissue-specific aging.
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Affiliation(s)
- Lindsay A Bonsignore
- Department of Biochemistry & Molecular Genetics, Gheens Center on Aging, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - John G Tooley
- Department of Biochemistry & Molecular Genetics, Gheens Center on Aging, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Patrick M Van Hoose
- Department of Biochemistry & Molecular Genetics, Gheens Center on Aging, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Eugenia Wang
- Department of Biochemistry & Molecular Genetics, Gheens Center on Aging, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Alan Cheng
- Department of Biochemistry & Molecular Genetics, Gheens Center on Aging, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Marsha P Cole
- Department of Biochemistry & Molecular Genetics, Gheens Center on Aging, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Christine E Schaner Tooley
- Department of Biochemistry & Molecular Genetics, Gheens Center on Aging, University of Louisville School of Medicine, Louisville, KY 40202, USA.
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34
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Cook R, Zoumpoulidou G, Luczynski MT, Rieger S, Moquet J, Spanswick VJ, Hartley JA, Rothkamm K, Huang PH, Mittnacht S. Direct involvement of retinoblastoma family proteins in DNA repair by non-homologous end-joining. Cell Rep 2015; 10:2006-18. [PMID: 25818292 PMCID: PMC4386026 DOI: 10.1016/j.celrep.2015.02.059] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2014] [Revised: 01/02/2015] [Accepted: 02/24/2015] [Indexed: 12/31/2022] Open
Abstract
Deficiencies in DNA double-strand break (DSB) repair lead to genetic instability, a recognized cause of cancer initiation and evolution. We report that the retinoblastoma tumor suppressor protein (RB1) is required for DNA DSB repair by canonical non-homologous end-joining (cNHEJ). Support of cNHEJ involves a mechanism independent of RB1's cell-cycle function and depends on its amino terminal domain with which it binds to NHEJ components XRCC5 and XRCC6. Cells with engineered loss of RB family function as well as cancer-derived cells with mutational RB1 loss show substantially reduced levels of cNHEJ. RB1 variants disabled for the interaction with XRCC5 and XRCC6, including a cancer-associated variant, are unable to support cNHEJ despite being able to confer cell-cycle control. Our data identify RB1 loss as a candidate driver of structural genomic instability and a causative factor for cancer somatic heterogeneity and evolution.
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Affiliation(s)
- Rebecca Cook
- Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK; Cancer Cell Signalling, UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, UK
| | - Georgia Zoumpoulidou
- Cancer Cell Signalling, UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, UK
| | - Maciej T Luczynski
- Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Simone Rieger
- Cancer Cell Signalling, UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, UK
| | - Jayne Moquet
- Public Health England, Centre for Radiation, Chemical and Environmental Hazards, Chilton, Didcot OX11 0RQ, UK
| | - Victoria J Spanswick
- Cancer Research UK Drug-DNA Interactions Research Group, UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, UK
| | - John A Hartley
- Cancer Research UK Drug-DNA Interactions Research Group, UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, UK
| | - Kai Rothkamm
- Public Health England, Centre for Radiation, Chemical and Environmental Hazards, Chilton, Didcot OX11 0RQ, UK
| | - Paul H Huang
- Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK.
| | - Sibylle Mittnacht
- Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK; Cancer Cell Signalling, UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, UK.
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35
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Tong Q, Cui G, Botuyan MV, Rothbart SB, Hayashi R, Musselman CA, Singh N, Appella E, Strahl BD, Mer G, Kutateladze TG. Structural plasticity of methyllysine recognition by the tandem tudor domain of 53BP1. Structure 2015; 23:312-21. [PMID: 25579814 DOI: 10.1016/j.str.2014.11.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 11/11/2014] [Accepted: 11/13/2014] [Indexed: 11/29/2022]
Abstract
p53 is dynamically regulated through various posttranslational modifications (PTMs), which differentially modulate its function and stability. The dimethylated marks p53K370me2 and p53K382me2 are associated with p53 activation or stabilization and both are recognized by the tandem Tudor domain (TTD) of 53BP1, a p53 cofactor. Here we detail the molecular mechanisms for the recognition of p53K370me2 and p53K382me2 by 53BP1. The solution structures of TTD in complex with the p53K370me2 and p53K382me2 peptides show a remarkable plasticity of 53BP1 in accommodating these diverse dimethyllysine-containing sequences. We demonstrate that dimeric TTDs are capable of interacting with the two PTMs on a single p53K370me2K382me2 peptide, greatly strengthening the 53BP1-p53 interaction. Analysis of binding affinities of TTD toward methylated p53 and histones reveals strong preference of 53BP1 for p53K382me2, H4K20me2, and H3K36me2 and suggests a possible role of multivalent contacts of 53BP1 in p53 targeting to and accumulation at the sites of DNA damage.
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Affiliation(s)
- Qiong Tong
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Gaofeng Cui
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Scott B Rothbart
- Department of Biochemistry and Biophysics and the Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Ryo Hayashi
- Laboratory of Cell Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Catherine A Musselman
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Namit Singh
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Ettore Appella
- Laboratory of Cell Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Brian D Strahl
- Department of Biochemistry and Biophysics and the Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Georges Mer
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA.
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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36
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Zhu G, Liu L, She L, Tan H, Wei M, Chen C, Su Z, Huang D, Tian Y, Qiu Y, Liu Y, Zhang X. Elevated expression of histone demethylase PHF8 associates with adverse prognosis in patients of laryngeal and hypopharyngeal squamous cell carcinoma. Epigenomics 2014; 7:143-53. [PMID: 25496457 DOI: 10.2217/epi.14.82] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
AIM Overexpression of histone demethylase PHF8 has been reported to function as an oncoprotein in many cancers; however, the implications of PHF8 involvement in laryngeal and hypopharyngeal squamous cell carcinoma (LHSCC) remain unclear. This study aims to explore the expression of PHF8 and its clinical significance in LHSCC. MATERIALS & METHODS Western blotting and immunohistochemistry were performed to evaluate PHF8 protein expression in fresh and archived LHSCC samples. Global expressions of H3K27 and H3K9 methylation were analyzed in a cell line with PHF8 siRNA treatment. RESULTS & CONCLUSION In our study, PHF8 was upregulated in fresh LHSCC tissues. Immunohistochemical staining revealed that the expression of PHF8 was positively associated with T classification, clinical stage, primary tumor position and tumor relapse. Survival analysis demonstrated that high PHF8 expression was significantly associated with shorter overall survival and disease-free survival. Moreover, PHF8 regulates the levels of H3K9me2 and H3K27me2 in LHSCC. Taken together, PHF8 might be a novel prognostic marker for this disease.
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Affiliation(s)
- Gangcai Zhu
- Department of Otolaryngology Head & Neck Surgery, Xiangya Hospital, Central South University, Xiangya Road 87, Changsha 410008, Hunan, China
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37
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Winter DL, Erce MA, Wilkins MR. A Web of Possibilities: Network-Based Discovery of Protein Interaction Codes. J Proteome Res 2014; 13:5333-8. [DOI: 10.1021/pr500585p] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Daniel L. Winter
- Systems Biology Initiative,
School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Melissa A. Erce
- Systems Biology Initiative,
School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Marc R. Wilkins
- Systems Biology Initiative,
School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
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