1
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Hao B, Chen K, Zhai L, Liu M, Liu B, Tan M. Substrate and Functional Diversity of Protein Lysine Post-translational Modifications. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzae019. [PMID: 38862432 DOI: 10.1093/gpbjnl/qzae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 11/11/2023] [Accepted: 01/08/2024] [Indexed: 06/13/2024]
Abstract
Lysine post-translational modifications (PTMs) are widespread and versatile protein PTMs that are involved in diverse biological processes by regulating the fundamental functions of histone and non-histone proteins. Dysregulation of lysine PTMs is implicated in many diseases, and targeting lysine PTM regulatory factors, including writers, erasers, and readers, has become an effective strategy for disease therapy. The continuing development of mass spectrometry (MS) technologies coupled with antibody-based affinity enrichment technologies greatly promotes the discovery and decoding of PTMs. The global characterization of lysine PTMs is crucial for deciphering the regulatory networks, molecular functions, and mechanisms of action of lysine PTMs. In this review, we focus on lysine PTMs, and provide a summary of the regulatory enzymes of diverse lysine PTMs and the proteomics advances in lysine PTMs by MS technologies. We also discuss the types and biological functions of lysine PTM crosstalks on histone and non-histone proteins and current druggable targets of lysine PTM regulatory factors for disease therapy.
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Affiliation(s)
- Bingbing Hao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Tianjian Laboratory of Advanced Biomedical Sciences, Institute of Advanced Biomedical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Kaifeng Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Linhui Zhai
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
| | - Muyin Liu
- Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Bin Liu
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China
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2
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Liu R, Li Y, Zheng Q, Ding M, Zhou H, Li X. Epigenetic modification in liver fibrosis: Promising therapeutic direction with significant challenges ahead. Acta Pharm Sin B 2024; 14:1009-1029. [PMID: 38486982 PMCID: PMC10935124 DOI: 10.1016/j.apsb.2023.10.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 08/18/2023] [Accepted: 09/13/2023] [Indexed: 03/17/2024] Open
Abstract
Liver fibrosis, characterized by scar tissue formation, can ultimately result in liver failure. It's a major cause of morbidity and mortality globally, often associated with chronic liver diseases like hepatitis or alcoholic and non-alcoholic fatty liver diseases. However, current treatment options are limited, highlighting the urgent need for the development of new therapies. As a reversible regulatory mechanism, epigenetic modification is implicated in many biological processes, including liver fibrosis. Exploring the epigenetic mechanisms involved in liver fibrosis could provide valuable insights into developing new treatments for chronic liver diseases, although the current evidence is still controversial. This review provides a comprehensive summary of the regulatory mechanisms and critical targets of epigenetic modifications, including DNA methylation, histone modification, and RNA modification, in liver fibrotic diseases. The potential cooperation of different epigenetic modifications in promoting fibrogenesis was also highlighted. Finally, available agonists or inhibitors regulating these epigenetic mechanisms and their potential application in preventing liver fibrosis were discussed. In summary, elucidating specific druggable epigenetic targets and developing more selective and specific candidate medicines may represent a promising approach with bright prospects for the treatment of chronic liver diseases.
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Affiliation(s)
- Runping Liu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102400, China
| | - Yajing Li
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 102400, China
| | - Qi Zheng
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102400, China
| | - Mingning Ding
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 102400, China
| | - Huiping Zhou
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA 22460, USA
| | - Xiaojiaoyang Li
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 102400, China
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3
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Hu Y, Xu Y, Zhang T, Han Q, Li L, Liu M, Li N, Shao G. Cisplatin-activated ERβ/DCAF8 positive feedback loop induces chemoresistance in non-small cell lung cancer via PTEN/Akt axis. Drug Resist Updat 2023; 71:101014. [PMID: 37913652 DOI: 10.1016/j.drup.2023.101014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 10/20/2023] [Accepted: 10/20/2023] [Indexed: 11/03/2023]
Abstract
High levels of the estrogen receptor β (ERβ) predict poor prognosis following platinum-containing adjuvant chemotherapies in patients with non-small cell lung cancer (NSCLC). However, the precise role of ERβ remains elusive. In this study, we demonstrated that targeting ERβ could significantly increase the cytotoxicity of cisplatin both in vitro and in vivo. Mechanically, cisplatin directly binds to ERβ, which facilitates its homodimerization and nuclear translocation. ERβ activation transcriptionally represses the expression of DCAF8, an adaptor of CRL4 E3 ubiquitin ligase, which in turn attenuates the proteasomal degradation of ERβ, leading to ERβ accumulation; this positive feedback loop results in Akt activation and eventually cisplatin resistance in NSCLC through PTEN inhibition. Moreover, low expression of DCAF8 and high expression of ERβ are associated with treatment resistance in patients receiving cisplatin-containing adjuvant chemotherapy. The present results provide insights into the underlying mechanism of ERβ-induced cisplatin resistance and offer an alternative therapeutic strategy to improve the efficacy of platinum-based chemotherapy in patients with NSCLC.
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Affiliation(s)
- Yumeng Hu
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yongjie Xu
- Office of Cancer Screening, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Ting Zhang
- Department of Gynecology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
| | - Qianying Han
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Li Li
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Mingyang Liu
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China.
| | - Ni Li
- Office of Cancer Screening, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China.
| | - Genze Shao
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.
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4
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Chai X, Tao Q, Li L. The role of RING finger proteins in chromatin remodeling and biological functions. Epigenomics 2023; 15:1053-1068. [PMID: 37964749 DOI: 10.2217/epi-2023-0234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023] Open
Abstract
Mammalian DNA duplexes are highly condensed with different components, including histones, enabling chromatin formation. Chromatin remodeling is involved in multiple biological processes, including gene transcription regulation and DNA damage repair. Recent research has highlighted the significant involvement of really interesting new gene (RING) finger proteins in chromatin remodeling, primarily attributed to their E3 ubiquitin ligase activities. In this review, we highlight the pivotal role of RING finger proteins in chromatin remodeling and provide an overview of their capacity to ubiquitinate specific histones, modulate ATP-dependent chromatin remodeling complexes and interact with various histone post-translational modifications. We also discuss the diverse biological effects of RING finger protein-mediated chromatin remodeling and explore potential therapeutic strategies for targeting these proteins.
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Affiliation(s)
- Xiaoxue Chai
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, State Key Laboratory of Translational Oncology, Sir YK Pao Center for Cancer, The Chinese University of Hong Kong, Hong Kong
| | - Qian Tao
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, State Key Laboratory of Translational Oncology, Sir YK Pao Center for Cancer, The Chinese University of Hong Kong, Hong Kong
| | - Lili Li
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, State Key Laboratory of Translational Oncology, Sir YK Pao Center for Cancer, The Chinese University of Hong Kong, Hong Kong
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5
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Stier A, Gilberto S, Mohamed WI, Royall LN, Helenius J, Mikicic I, Sajic T, Beli P, Müller DJ, Jessberger S, Peter M. The CUL4B-based E3 ubiquitin ligase regulates mitosis and brain development by recruiting phospho-specific DCAFs. EMBO J 2023; 42:e112847. [PMID: 37365982 PMCID: PMC10476281 DOI: 10.15252/embj.2022112847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 05/31/2023] [Accepted: 06/13/2023] [Indexed: 06/28/2023] Open
Abstract
The paralogs CUL4A and CUL4B assemble cullin-RING E3 ubiquitin ligase (CRL) complexes regulating multiple chromatin-associated cellular functions. Although they are structurally similar, we found that the unique N-terminal extension of CUL4B is heavily phosphorylated during mitosis, and the phosphorylation pattern is perturbed in the CUL4B-P50L mutation causing X-linked intellectual disability (XLID). Phenotypic characterization and mutational analysis revealed that CUL4B phosphorylation is required for efficient progression through mitosis, controlling spindle positioning and cortical tension. While CUL4B phosphorylation triggers chromatin exclusion, it promotes binding to actin regulators and to two previously unrecognized CUL4B-specific substrate receptors (DCAFs), LIS1 and WDR1. Indeed, co-immunoprecipitation experiments and biochemical analysis revealed that LIS1 and WDR1 interact with DDB1, and their binding is enhanced by the phosphorylated N-terminal domain of CUL4B. Finally, a human forebrain organoid model demonstrated that CUL4B is required to develop stable ventricular structures that correlate with onset of forebrain differentiation. Together, our study uncovers previously unrecognized DCAFs relevant for mitosis and brain development that specifically bind CUL4B, but not the CUL4B-P50L patient mutant, by a phosphorylation-dependent mechanism.
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Affiliation(s)
- Anna Stier
- Institute of BiochemistryETH ZurichZurichSwitzerland
| | - Samuel Gilberto
- Institute of BiochemistryETH ZurichZurichSwitzerland
- Present address:
Monte Rosa TherapeuticsBaselSwitzerland
| | | | - Lars N Royall
- Brain Research InstituteUniversity of ZurichZurichSwitzerland
| | - Jonne Helenius
- Department of Biosystems Science and EngineeringETH ZurichBaselSwitzerland
| | | | - Tatjana Sajic
- Institute of Molecular Systems BiologyETH ZürichZürichSwitzerland
- Present address:
Faculty Unit of Toxicology, CURML, Faculty of Biology and MedicineUniversity of LausanneLausanneSwitzerland
| | - Petra Beli
- Institute of Molecular BiologyMainzGermany
- Institute of Developmental Biology and Neurobiology (IDN)Johannes Gutenberg UniversityMainzGermany
| | - Daniel J Müller
- Department of Biosystems Science and EngineeringETH ZurichBaselSwitzerland
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6
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Malaguarnera R, Gabriele C, Santamaria G, Giuliano M, Vella V, Massimino M, Vigneri P, Cuda G, Gaspari M, Belfiore A. Comparative proteomic analysis of insulin receptor isoform A and B signaling. Mol Cell Endocrinol 2022; 557:111739. [PMID: 35940390 DOI: 10.1016/j.mce.2022.111739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 07/17/2022] [Accepted: 07/28/2022] [Indexed: 11/30/2022]
Abstract
The insulin receptor (IR) gene undergoes differential splicing generating two IR isoforms, IR-A and IR-B. The roles of IR-A in cancer and of IR-B in metabolic regulation are well known but the molecular mechanisms responsible for their different biological effects are poorly understood. We aimed to identify different or similar protein substrates and signaling linked to each IR isoforms. We employed mouse fibroblasts lacking IGF1R gene and expressing exclusively either IR-A or IR-B. By proteomic analysis a total of 2530 proteins were identified and quantified. Proteins and pathways mostly associated with insulin-activated IR-A were involved in cancer, stemness and interferon signaling. Instead, proteins and pathways associated with insulin-stimulated IR-B-expressing cells were mostly involved in metabolic or tumor suppressive functions. These results show that IR-A and IR-B recruit partially different multiprotein complexes in response to insulin, suggesting partially different functions of IR isoforms in physiology and in disease.
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Affiliation(s)
| | - Caterina Gabriele
- Research Centre for Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, "Magna Græcia" University of Catanzaro, 88100, Catanzaro, Italy.
| | - Gianluca Santamaria
- Research Centre for Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, "Magna Græcia" University of Catanzaro, 88100, Catanzaro, Italy; Klinikum rechts der Isar, Department of Medicine and Molecular Cardiology, Technical University of Munich, Germany.
| | - Marika Giuliano
- Unit of Endocrinology, Department of Clinical and Experimental Medicine, University of Catania, Garibaldi-Nesima Hospital, 95122, Catania, Italy.
| | - Veronica Vella
- Unit of Endocrinology, Department of Clinical and Experimental Medicine, University of Catania, Garibaldi-Nesima Hospital, 95122, Catania, Italy.
| | - Michele Massimino
- Department of Clinical and Experimental Medicine, Oncology Unit, University of Catania, 95100, Catania, Italy.
| | - Paolo Vigneri
- Department of Clinical and Experimental Medicine, Oncology Unit, University of Catania, 95100, Catania, Italy.
| | - Giovanni Cuda
- Research Centre for Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, "Magna Græcia" University of Catanzaro, 88100, Catanzaro, Italy.
| | - Marco Gaspari
- Research Centre for Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, "Magna Græcia" University of Catanzaro, 88100, Catanzaro, Italy.
| | - Antonino Belfiore
- Unit of Endocrinology, Department of Clinical and Experimental Medicine, University of Catania, Garibaldi-Nesima Hospital, 95122, Catania, Italy.
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7
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Ai H, Sun M, Liu A, Sun Z, Liu T, Cao L, Liang L, Qu Q, Li Z, Deng Z, Tong Z, Chu G, Tian X, Deng H, Zhao S, Li JB, Lou Z, Liu L. H2B Lys34 Ubiquitination Induces Nucleosome Distortion to Stimulate Dot1L Activity. Nat Chem Biol 2022; 18:972-980. [PMID: 35739357 DOI: 10.1038/s41589-022-01067-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/19/2022] [Indexed: 11/09/2022]
Abstract
Ubiquitination-dependent histone crosstalk plays critical roles in chromatin-associated processes and is highly associated with human diseases. Mechanism studies of the crosstalk have been of the central focus. Here our study on the crosstalk between H2BK34ub and Dot1L-catalyzed H3K79me suggests a novel mechanism of ubiquitination-induced nucleosome distortion to stimulate the activity of an enzyme. We determined the cryo-electron microscopy structures of Dot1L-H2BK34ub nucleosome complex and the H2BK34ub nucleosome alone. The structures reveal that H2BK34ub induces an almost identical orientation and binding pattern of Dot1L on nucleosome as H2BK120ub, which positions Dot1L for the productive conformation through direct ubiquitin-enzyme contacts. However, H2BK34-anchored ubiquitin does not directly interact with Dot1L as occurs in the case of H2BK120ub, but rather induces DNA and histone distortion around the modified site. Our findings establish the structural framework for understanding the H2BK34ub-H3K79me trans-crosstalk and highlight the diversity of mechanisms for histone ubiquitination to activate chromatin-modifying enzymes.
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Affiliation(s)
- Huasong Ai
- Department of Chemistry, Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, China
| | - Maoshen Sun
- Department of Chemistry, Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, China
| | - Aijun Liu
- MOE Key Laboratory of Protein Science, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, China.,Kobilka Institute of Innovative Drug Discovery, School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Zixian Sun
- MOE Key Laboratory of Protein Science, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, China
| | - Tingting Liu
- iHuman Institute, ShanghaiTech University, Shanghai, China
| | - Lin Cao
- MOE Key Laboratory of Protein Science, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, China.,State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Response, College of Life Sciences, and College of Pharmacy, Nankai University, Tianjin, China
| | - Lujun Liang
- Department of Chemistry, Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, China
| | - Qian Qu
- Department of Chemistry, Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, China
| | - Zichen Li
- Department of Chemistry, Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, China
| | - Zhiheng Deng
- Department of Chemistry, Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, China
| | - Zebin Tong
- Department of Chemistry, Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, China
| | - Guochao Chu
- Department of Chemistry, Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, China
| | - Xiaolin Tian
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Suwen Zhao
- iHuman Institute, ShanghaiTech University, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jia-Bin Li
- College of Pharmaceutical Sciences, Soochow University, Suzhou, China.
| | - Zhiyong Lou
- MOE Key Laboratory of Protein Science, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, China.
| | - Lei Liu
- Department of Chemistry, Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, China.
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8
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Lv X, Chen J, He J, Hou L, Ren Y, Shen X, Wang Y, Ji T, Cai X. Gasdermin D-mediated pyroptosis suppresses liver regeneration after 70% partial hepatectomy. Hepatol Commun 2022; 6:2340-2353. [PMID: 35509206 PMCID: PMC9426395 DOI: 10.1002/hep4.1973] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 03/26/2022] [Accepted: 04/08/2022] [Indexed: 11/24/2022] Open
Abstract
Pyroptosis is a kind of programmed cell death primarily mediated by gasdermin D (GSDMD) and shown to regulate multiple diseases. However, its contribution to liver regeneration, a fine‐tuned tissue repair process mediated primarily by hepatocytes after mass loss, remains unclear. Herein, we found that caspase‐11/GSDMD‐mediated pyroptosis was activated in regenerating liver after 70% partial hepatectomy. Impeding pyroptosis by deleting GSDMD significantly reduced liver injury and accelerated liver regeneration. Mechanistically, GSDMD deficiency up‐regulates the activation of hepatocyte growth factor/c‐Met and epidermal growth factor receptor mitogenic pathways at the initiation phase. Moreover, activin A and glypican 3 (GPC3), two terminators of liver regeneration, were inhibited when GSDMD was absent. In vitro study suggested the expressions of activin A and GPC3 were induced by interleukin (IL)–1β and IL‐18, whose maturations were regulated by GSDMD‐mediated pyroptosis. Similarly, pharmacologically inhibiting GSDMD recapitulates these phenomena. Conclusion: This study characterizes the role of GSDMD‐mediated pyroptosis in liver regeneration and lays the foundation for enhancing liver restoration by targeting GSDMD in liver patients with impaired regenerative capacity.
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Affiliation(s)
- Xingyu Lv
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Laparoscopic Technology, Hangzhou, China
| | - Jiang Chen
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Laparoscopic Technology, Hangzhou, China
| | - Jiayan He
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Laparoscopic Technology, Hangzhou, China
| | - Lidan Hou
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Laparoscopic Technology, Hangzhou, China
| | - Yiyue Ren
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Laparoscopic Technology, Hangzhou, China
| | - Xiaoyun Shen
- Zhejiang Provincial Key Laboratory of Laparoscopic Technology, Hangzhou, China
| | - Yifan Wang
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Laparoscopic Technology, Hangzhou, China
| | - Tong Ji
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Laparoscopic Technology, Hangzhou, China
| | - Xiujun Cai
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Laparoscopic Technology, Hangzhou, China
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9
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Cai Q, Gan C, Tang C, Wu H, Gao J. Mechanism and Therapeutic Opportunities of Histone Modifications in Chronic Liver Disease. Front Pharmacol 2021; 12:784591. [PMID: 34887768 PMCID: PMC8650224 DOI: 10.3389/fphar.2021.784591] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/08/2021] [Indexed: 02/05/2023] Open
Abstract
Chronic liver disease (CLD) represents a global health problem, accounting for the heavy burden of disability and increased health care utilization. Epigenome alterations play an important role in the occurrence and progression of CLD. Histone modifications, which include acetylation, methylation, and phosphorylation, represent an essential part of epigenetic modifications that affect the transcriptional activity of genes. Different from genetic mutations, histone modifications are plastic and reversible. They can be modulated pharmacologically without changing the DNA sequence. Thus, there might be chances to establish interventional solutions by targeting histone modifications to reverse CLD. Here we summarized the roles of histone modifications in the context of alcoholic liver disease (ALD), metabolic associated fatty liver disease (MAFLD), viral hepatitis, autoimmune liver disease, drug-induced liver injury (DILI), and liver fibrosis or cirrhosis. The potential targets of histone modifications for translation into therapeutics were also investigated. In prospect, high efficacy and low toxicity drugs that are selectively targeting histone modifications are required to completely reverse CLD and prevent the development of liver cirrhosis and malignancy.
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Affiliation(s)
- Qiuyu Cai
- Laboratory of Gastroenterology and Hepatology, West China Hospital, Sichuan University, Chengdu, China.,Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
| | - Can Gan
- Laboratory of Gastroenterology and Hepatology, West China Hospital, Sichuan University, Chengdu, China.,Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
| | - Chengwei Tang
- Laboratory of Gastroenterology and Hepatology, West China Hospital, Sichuan University, Chengdu, China.,Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
| | - Hao Wu
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
| | - Jinhang Gao
- Laboratory of Gastroenterology and Hepatology, West China Hospital, Sichuan University, Chengdu, China.,Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
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10
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Bacheva AV, Gotmanova NN, Belogurov AA, Kudriaeva AA. Control of Genome through Variative Nature of Histone-Modifying Ubiquitin Ligases. BIOCHEMISTRY (MOSCOW) 2021; 86:S71-S95. [PMID: 33827401 DOI: 10.1134/s0006297921140066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Covalent attachment of ubiquitin residue is not only the proteasomal degradation signal, but also a widespread posttranslational modification of cellular proteins in eukaryotes. One of the most important targets of the regulatory ubiquitination are histones. Localization of ubiquitin residue in different regions of the nucleosome attracts a strictly determined set of cellular factors with varied functionality. Depending on the type of histone and the particular lysine residue undergoing modification, histone ubiquitination can lead both to transcription activation and to gene repression, as well as contribute to DNA repair via different mechanisms. An extremely interesting feature of the family of RING E3 ubiquitin ligases catalyzing histone ubiquitination is the striking structural diversity of the domains providing high specificity of modification very similar initial targets. It is obvious that further elucidation of peculiarities of the ubiquitination system involved in histone modification, as well as understanding of physiological role of this process in the maintenance of homeostasis of both single cells and the entire organism, will substantially expand the possibilities of treating a number of socially significant diseases.
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Affiliation(s)
- Anna V Bacheva
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | | | - Alexey A Belogurov
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Anna A Kudriaeva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
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11
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Zhang X, Xia Z, Lv X, Li D, Liu M, Zhang R, Ji T, Liu P, Ren R. DDB1- and CUL4-associated factor 8 plays a critical role in spermatogenesis. Front Med 2021; 15:302-312. [PMID: 33855678 DOI: 10.1007/s11684-021-0851-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 02/20/2021] [Indexed: 11/26/2022]
Abstract
Cullin-RING E3 ubiquitin ligase (CRL)-4 is a member of the large CRL family in eukaryotes. It plays important roles in a wide range of cellular processes, organismal development, and physiological and pathological conditions. DDB1- and CUL4-associated factor 8 (DCAF8) is a WD40 repeat-containing protein, which serves as a substrate receptor for CRL4. The physiological role of DCAF8 is unknown. In this study, we constructed Dcaf8 knockout mice. Homozygous mice were viable with no noticeable abnormalities. However, the fertility of Dcaf8-deficient male mice was markedly impaired, consistent with the high expression of DCAF8 in adult mouse testis. Sperm movement characteristics, including progressive motility, path velocity, progressive velocity, and track speed, were significantly lower in Dcaf8 knockout mice than in wild-type (WT) mice. However, the total motility was similar between WT and Dcaf8 knockout sperm. More than 40% of spermatids in Dcaf8 knockout mice showed pronounced morphological abnormalities with typical bent head malformation. The acrosome and nucleus of Dcaf8 knockout sperm looked similar to those of WT sperm. In vitro tests showed that the fertilization rate of Dcaf8 knockout mice was significantly reduced. The results demonstrated that DCAF8 plays a critical role in spermatogenesis, and DCAF8 is a key component of CRL4 function in the reproductive system.
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Affiliation(s)
- Xiuli Zhang
- Shanghai Institute of Hematology, State Key Laboratory for Medical Genomics, National Research Center for Translational Medicine at Shanghai, Collaborative Innovation Center of Hematology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zhizhou Xia
- Shanghai Institute of Hematology, State Key Laboratory for Medical Genomics, National Research Center for Translational Medicine at Shanghai, Collaborative Innovation Center of Hematology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xingyu Lv
- Key Laboratory of Laparoscopic Technology of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Donghe Li
- Shanghai Institute of Hematology, State Key Laboratory for Medical Genomics, National Research Center for Translational Medicine at Shanghai, Collaborative Innovation Center of Hematology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Mingzhu Liu
- Shanghai Institute of Hematology, State Key Laboratory for Medical Genomics, National Research Center for Translational Medicine at Shanghai, Collaborative Innovation Center of Hematology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ruihong Zhang
- Shanghai Institute of Hematology, State Key Laboratory for Medical Genomics, National Research Center for Translational Medicine at Shanghai, Collaborative Innovation Center of Hematology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Tong Ji
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.
| | - Ping Liu
- Shanghai Institute of Hematology, State Key Laboratory for Medical Genomics, National Research Center for Translational Medicine at Shanghai, Collaborative Innovation Center of Hematology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Ruibao Ren
- Shanghai Institute of Hematology, State Key Laboratory for Medical Genomics, National Research Center for Translational Medicine at Shanghai, Collaborative Innovation Center of Hematology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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12
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White SM, Bhoj E, Nellåker C, Lachmeijer AM, Marshall AE, Boycott KM, Li D, Smith W, Hartley T, McBride A, Ernst ME, May AS, Wieczorek D, Abou Jamra R, Koch-Hogrebe M, Õunap K, Pajusalu S, van Gassen K, Sadedin S, Ellingwood S, Tan TY, Christodoulou J, Barea J, Lockhart PJ, Nezarati MM, Kernohan KD, Kernohan KD. A DNA repair disorder caused by de novo monoallelic DDB1 variants is associated with a neurodevelopmental syndrome. Am J Hum Genet 2021; 108:749-756. [PMID: 33743206 DOI: 10.1016/j.ajhg.2021.03.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 03/02/2021] [Indexed: 12/27/2022] Open
Abstract
The DNA damage-binding protein 1 (DDB1) is part of the CUL4-DDB1 ubiquitin E3 ligase complex (CRL4), which is essential for DNA repair, chromatin remodeling, DNA replication, and signal transduction. Loss-of-function variants in genes encoding the complex components CUL4 and PHIP have been reported to cause syndromic intellectual disability with hypotonia and obesity, but no phenotype has been reported in association with DDB1 variants. Here, we report eight unrelated individuals, identified through Matchmaker Exchange, with de novo monoallelic variants in DDB1, including one recurrent variant in four individuals. The affected individuals have a consistent phenotype of hypotonia, mild to moderate intellectual disability, and similar facies, including horizontal or slightly bowed eyebrows, deep-set eyes, full cheeks, a short nose, and large, fleshy and forward-facing earlobes, demonstrated in the composite face generated from the cohort. Digital anomalies, including brachydactyly and syndactyly, were common. Three older individuals have obesity. We show that cells derived from affected individuals have altered DDB1 function resulting in abnormal DNA damage signatures and histone methylation following UV-induced DNA damage. Overall, our study adds to the growing family of neurodevelopmental phenotypes mediated by disruption of the CRL4 ubiquitin ligase pathway and begins to delineate the phenotypic and molecular effects of DDB1 misregulation.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Kristin D Kernohan
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada; Newborn Screening Ontario, Ottawa, ON K1H 8L1, Canada
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13
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Peris-Moreno D, Taillandier D, Polge C. MuRF1/TRIM63, Master Regulator of Muscle Mass. Int J Mol Sci 2020; 21:ijms21186663. [PMID: 32933049 PMCID: PMC7555135 DOI: 10.3390/ijms21186663] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/04/2020] [Accepted: 09/08/2020] [Indexed: 02/07/2023] Open
Abstract
The E3 ubiquitin ligase MuRF1/TRIM63 was identified 20 years ago and suspected to play important roles during skeletal muscle atrophy. Since then, numerous studies have been conducted to decipher the roles, molecular mechanisms and regulation of this enzyme. This revealed that MuRF1 is an important player in the skeletal muscle atrophy process occurring during catabolic states, making MuRF1 a prime candidate for pharmacological treatments against muscle wasting. Indeed, muscle wasting is an associated event of several diseases (e.g., cancer, sepsis, diabetes, renal failure, etc.) and negatively impacts the prognosis of patients, which has stimulated the search for MuRF1 inhibitory molecules. However, studies on MuRF1 cardiac functions revealed that MuRF1 is also cardioprotective, revealing a yin and yang role of MuRF1, being detrimental in skeletal muscle and beneficial in the heart. This review discusses data obtained on MuRF1, both in skeletal and cardiac muscles, over the past 20 years, regarding the structure, the regulation, the location and the different functions identified, and the first inhibitors reported, and aim to draw the picture of what is known about MuRF1. The review also discusses important MuRF1 characteristics to consider for the design of future drugs to maintain skeletal muscle mass in patients with different pathologies.
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14
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Huang D, Liu C, Sun X, Sun X, Qu Y, Tang Y, Li G, Tong T. CRL4 DCAF8 and USP11 oppositely regulate the stability of myeloid leukemia factors (MLFs). Biochem Biophys Res Commun 2020; 529:127-132. [PMID: 32703400 DOI: 10.1016/j.bbrc.2020.05.186] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 05/25/2020] [Indexed: 01/20/2023]
Abstract
Myeloid leukemia factors (MLF1 and MLF2) are proteins associated with leukemia and several other cancers. However, little is known about the regulatory mechanisms underlying the stability of these proteins. Here, we show that DDB1 and CUL4 associated factor 8 (DCAF8), which can form a functional E3 ligase complex (CRL4DCAF8), has a strong interaction with the MLF2 protein. DCAF8 could promote MLF2 degradation through the ubiquitin-proteasome pathway. In contrast, ubiquitin specific peptidase 11 (USP11) associates with MLF2, thereby increasing its stability. Since MLF1 is highly related to MLF2, we demonstrated that MLF1 also interacts with DCAF8 and USP11, suggesting that CRL4DCAF8 and USP11 may also regulate the expression of MLF1. TCGA analysis revealed that both the myeloid leukemia factors (MLF1 and MLF2) show significant differential expression in various tumors. The results of our study indicate that CRL4DCAF8 and USP11 play opposite roles in the regulation of MLF1 and MLF2, which may, in turn, affect their biological functions in various cancers.
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Affiliation(s)
- Daoyuan Huang
- Peking University Research Center on Aging, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing, 100191, China
| | - Cheng Liu
- Peking University Research Center on Aging, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing, 100191, China
| | - Xiwen Sun
- Peking University Research Center on Aging, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing, 100191, China
| | - Xinpei Sun
- Peking University Research Center on Aging, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing, 100191, China
| | - Yanan Qu
- Peking University Research Center on Aging, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing, 100191, China
| | - Yunyi Tang
- Peking University Research Center on Aging, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing, 100191, China
| | - Guodong Li
- Peking University Research Center on Aging, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing, 100191, China
| | - Tanjun Tong
- Peking University Research Center on Aging, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing, 100191, China.
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15
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Minor MM, Hollinger FB, McNees AL, Jung SY, Jain A, Hyser JM, Bissig KD, Slagle BL. Hepatitis B Virus HBx Protein Mediates the Degradation of Host Restriction Factors through the Cullin 4 DDB1 E3 Ubiquitin Ligase Complex. Cells 2020; 9:E834. [PMID: 32235678 PMCID: PMC7226812 DOI: 10.3390/cells9040834] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/24/2020] [Accepted: 03/25/2020] [Indexed: 02/06/2023] Open
Abstract
The hepatitis B virus (HBV) regulatory HBx protein is required for infection, and its binding to cellular damaged DNA binding protein 1 (DDB1) is critical for this function. DDB1 is an adaptor protein for the cullin 4A Really Interesting New Gene (RING) E3 ubiquitin ligase (CRL4) complex and functions by binding cellular DDB1 cullin associated factor (DCAF) receptor proteins that recruit substrates for ubiquitination and degradation. We compared the proteins found in the CRL4 complex immunoprecipitated from uninfected versus HBV-infected hepatocytes from human liver chimeric mice for insight into mechanisms by which HBV and the cell interact within the CRL4 complex. Consistent with its role as a viral DCAF, HBx was found in the HBV CRL4 complexes. In tissue culture transfection experiments, we showed that HBx expression led to decreased levels of known restriction factor structural maintenance of chromosomes protein 6 (SMC6) and putative restriction factors stromal interaction molecule 1 (STIM1, zinc finger E-box binding homeobox 2 (ZEB2), and proteasome activator subunit 4 (PSME4). Moreover, silencing of these proteins led to increased HBV replication in the HepG2-sodium taurocholate cotransporting polypeptide (NTCP) infection model. We also identified cellular DCAF receptors in CRL4 complexes from humanized mice. Increasing amounts of HBx did not reveal competitive DCAF binding to cullin4 (CUL4)-DDB1 in plasmid-transfected cells. Our results suggest a model in which HBx benefits virus replication by directly or indirectly degrading multiple cellular restriction factors.
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Affiliation(s)
- Marissa M. Minor
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (M.M.M.); (F.B.H.); (A.L.M.); (J.M.H.)
| | - F. Blaine Hollinger
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (M.M.M.); (F.B.H.); (A.L.M.); (J.M.H.)
| | - Adrienne L. McNees
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (M.M.M.); (F.B.H.); (A.L.M.); (J.M.H.)
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Sung Yun Jung
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA;
- Department of Biochemistry, Baylor College of Medicine, Houston, TX 77030, USA
| | - Antrix Jain
- Mass Spectrometry Proteomics Core, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Joseph M. Hyser
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (M.M.M.); (F.B.H.); (A.L.M.); (J.M.H.)
| | - Karl-Dimiter Bissig
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Betty L. Slagle
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (M.M.M.); (F.B.H.); (A.L.M.); (J.M.H.)
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA;
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16
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Xu L, Jiang H. Writing and Reading Histone H3 Lysine 9 Methylation in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2020; 11:452. [PMID: 32435252 PMCID: PMC7218100 DOI: 10.3389/fpls.2020.00452] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/27/2020] [Indexed: 05/05/2023]
Abstract
In eukaryotes, histone H3 lysine 9 methylation (H3K9me) mediates the silencing of invasive and repetitive sequences by preventing the expression of aberrant gene products and the activation of transposition. In Arabidopsis, while it is well known that dimethylation of histone H3 at lysine 9 (H3K9me2) is maintained through a feedback loop between H3K9me2 and DNA methylation, the details of the H3K9me2-dependent silencing pathway have not been fully elucidated. Recently, the regulation and the function of H3K9 methylation have been extensively characterized. In this review, we summarize work from the recent studies regarding the regulation of H3K9me2, emphasizing the process of deposition and reading and the biological significance of H3K9me2 in Arabidopsis.
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17
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Kim JE. Bookmarking by histone methylation ensures chromosomal integrity during mitosis. Arch Pharm Res 2019; 42:466-480. [PMID: 31020544 DOI: 10.1007/s12272-019-01156-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 04/19/2019] [Indexed: 12/22/2022]
Abstract
The cell cycle is an orchestrated process that replicates DNA and transmits genetic information to daughter cells. Cell cycle progression is governed by diverse histone modifications that control gene transcription in a timely fashion. Histone modifications also regulate cell cycle progression by marking specific chromatic regions. While many reviews have covered histone phosphorylation and acetylation as regulators of the cell cycle, little attention has been paid to the roles of histone methylation in the faithful progression of mitosis. Indeed, specific histone methylations occurring before, during, or after mitosis affect kinetochore assembly and chromosome condensation and segregation. In addition to timing, histone methylations specify the chromatin regions such as chromosome arms, pericentromere, and centromere. Therefore, spatiotemporal programming of histone methylations ensures epigenetic inheritance through mitosis. This review mainly discusses histone methylations and their relevance to mitotic progression.
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Affiliation(s)
- Ja-Eun Kim
- Department of Pharmacology, School of Medicine, Kyung Hee University, Seoul, 02447, Republic of Korea.
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18
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The Molecular Chaperone Heat Shock Protein 70 Controls Liver Cancer Initiation and Progression by Regulating Adaptive DNA Damage and Mitogen-Activated Protein Kinase/Extracellular Signal-Regulated Kinase Signaling Pathways. Mol Cell Biol 2019; 39:MCB.00391-18. [PMID: 30745413 DOI: 10.1128/mcb.00391-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 02/04/2019] [Indexed: 02/06/2023] Open
Abstract
Delineating the mechanisms that drive hepatic injury and hepatocellular carcinoma (HCC) progression is critical for development of novel treatments for recurrent and advanced HCC but also for the development of diagnostic and preventive strategies. Heat shock protein 70 (HSP70) acts in concert with several cochaperones and nucleotide exchange factors and plays an essential role in protein quality control that increases survival by protecting cells against environmental stressors. Specifically, the HSP70-mediated response has been implicated in the pathogenesis of cancer, but the specific mechanisms by which HSP70 may support malignant cell transformation remains to be fully elucidated. Here, we show that genetic ablation of HSP70 markedly impairs HCC initiation and progression by distinct but overlapping pathways. This includes the potentiation of the carcinogen-induced DNA damage response, at the tumor initiation stage, to increase the p53-dependent surveillance response leading to the cell cycle exit or death of genomically damaged differentiated pericentral hepatocytes, and this may also prevent their conversion into more proliferating HCC progenitor cells. Subsequently, activation of a mitogen-activated protein kinase/extracellular signal-regulated kinase (MAPK/ERK) negative feedback pathway diminishes oncogenic signals, thereby attenuating premalignant cell transformation and tumor progression. Modulation of HSP70 function may be a strategy for interfering with oncogenic signals driving liver cell transformation and tumor progression, thus providing an opportunity for human cancer control.
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19
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Nowak M, Suenkel B, Porras P, Migotti R, Schmidt F, Kny M, Zhu X, Wanker EE, Dittmar G, Fielitz J, Sommer T. DCAF8, a novel MuRF1 interaction partner, promotes muscle atrophy. J Cell Sci 2019; 132:jcs.233395. [DOI: 10.1242/jcs.233395] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 07/22/2019] [Indexed: 12/29/2022] Open
Abstract
The muscle-specific RING-finger protein MuRF1 constitutes a bona fide ubiquitin ligase that routes proteins like Myosin heavy chain (MyHC) to proteasomal degradation during muscle atrophy. In two unbiased screens we identified DCAF8 as a new MuRF1 binding partner. MuRF1 physically interacts with DCAF8 and both proteins localize to overlapping structures in muscle cells. Noteworthy, similar to MuRF1, DCAF8 levels increase during atrophy and the down-regulation of either protein substantially impedes muscle wasting and MyHC degradation in C2C12 myotubes, a model system for muscle differentiation and atrophy. DCAF proteins typically serve as substrate receptors in Cullin 4-type (Cul4) ubiquitin ligases (CRL) and we demonstrate that DCAF8 and MuRF1 associate with the subunits of such a protein complex. Because genetic downregulation of DCAF8 and inhibition of Cullin activity also impair myotube atrophy in C2C12 cells, our data imply that the DCAF8 promotes muscle wasting by targeting proteins like MyHC as an integral substrate receptor of a CRL4A ubiquitin ligase.
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Affiliation(s)
- Marcel Nowak
- Intracellular Proteolysis, Max Delbrück Center (MDC) for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125 Berlin-Buch, Germany
- Experimental and Clinical Research Center (ECRC), Charité - Universitätsmedizin Berlin, MDC, Lindenberger Weg 80, 13125 Berlin-Buch, Germany
- Present address: DUNN Labortechnik GmbH, Thelenberg 6, 53567, Asbach, Germany
| | - Benjamin Suenkel
- Intracellular Proteolysis, Max Delbrück Center (MDC) for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125 Berlin-Buch, Germany
| | - Pablo Porras
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, MDC, USA
- Present address: European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Rebekka Migotti
- Mass Spectrometric Core Unit, MDC, USA
- Present address: ProPharma Group, Siemensdamm 62, 13627 Berlin, Germany
| | - Franziska Schmidt
- Experimental and Clinical Research Center (ECRC), Charité - Universitätsmedizin Berlin, MDC, Lindenberger Weg 80, 13125 Berlin-Buch, Germany
- Present address: BCRT Flow and Mass Cytometry Lab, Charité – Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Melanie Kny
- Experimental and Clinical Research Center (ECRC), Charité - Universitätsmedizin Berlin, MDC, Lindenberger Weg 80, 13125 Berlin-Buch, Germany
| | - Xiaoxi Zhu
- Experimental and Clinical Research Center (ECRC), Charité - Universitätsmedizin Berlin, MDC, Lindenberger Weg 80, 13125 Berlin-Buch, Germany
| | - Erich E. Wanker
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, MDC, USA
| | - Gunnar Dittmar
- Mass Spectrometric Core Unit, MDC, USA
- Present address: Proteome and Genome Research Laboratory, Luxembourg Institute of Health, 1a Rue Thomas Edison, L-1445 Strassen, Luxembourg, Europe
| | - Jens Fielitz
- Experimental and Clinical Research Center (ECRC), Charité - Universitätsmedizin Berlin, MDC, Lindenberger Weg 80, 13125 Berlin-Buch, Germany
- Department of Internal Medicine B, Cardiology, University Medicine Greifswald, Germany
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Fleischmann Strasse 41, 17475 Greifswald, Germany
| | - Thomas Sommer
- Intracellular Proteolysis, Max Delbrück Center (MDC) for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125 Berlin-Buch, Germany
- Institute of Biology, Humboldt-University Berlin, Invalidenstrasse 43, 10115 Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Oudenarder Straße 16, 13347 Berlin, Germany
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20
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Cheng J, Guo J, North BJ, Tao K, Zhou P, Wei W. The emerging role for Cullin 4 family of E3 ligases in tumorigenesis. Biochim Biophys Acta Rev Cancer 2018; 1871:138-159. [PMID: 30602127 DOI: 10.1016/j.bbcan.2018.11.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 11/28/2018] [Accepted: 11/29/2018] [Indexed: 02/06/2023]
Abstract
As a member of the Cullin-RING ligase family, Cullin-RING ligase 4 (CRL4) has drawn much attention due to its broad regulatory roles under physiological and pathological conditions, especially in neoplastic events. Based on evidence from knockout and transgenic mouse models, human clinical data, and biochemical interactions, we summarize the distinct roles of the CRL4 E3 ligase complexes in tumorigenesis, which appears to be tissue- and context-dependent. Notably, targeting CRL4 has recently emerged as a noval anti-cancer strategy, including thalidomide and its derivatives that bind to the substrate recognition receptor cereblon (CRBN), and anticancer sulfonamides that target DCAF15 to suppress the neoplastic proliferation of multiple myeloma and colorectal cancers, respectively. To this end, PROTACs have been developed as a group of engineered bi-functional chemical glues that induce the ubiquitination-mediated degradation of substrates via recruiting E3 ligases, such as CRL4 (CRBN) and CRL2 (pVHL). We summarize the recent major advances in the CRL4 research field towards understanding its involvement in tumorigenesis and further discuss its clinical implications. The anti-tumor effects using the PROTAC approach to target the degradation of undruggable targets are also highlighted.
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Affiliation(s)
- Ji Cheng
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Jianping Guo
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Brian J North
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Kaixiong Tao
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Pengbo Zhou
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065, USA.
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.
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21
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Rawłuszko-Wieczorek AA, Knodel F, Tamas R, Dhayalan A, Jeltsch A. Identification of protein lysine methylation readers with a yeast three-hybrid approach. Epigenetics Chromatin 2018; 11:4. [PMID: 29370823 PMCID: PMC5784651 DOI: 10.1186/s13072-018-0175-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 01/15/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Protein posttranslational modifications (PTMs) occur broadly in the human proteome, and their biological outcome is often mediated indirectly by reader proteins that specifically bind to modified proteins and trigger downstream effects. Particularly, many lysine methylation sites among histone and nonhistone proteins have been characterized; however, the list of readers associated with them is incomplete. RESULTS This study introduces a modified yeast three-hybrid system (Y3H) to screen for methyllysine readers. A lysine methyltransferase is expressed together with its target protein or protein domain functioning as bait, and a human cDNA library serves as prey. Proof of principle was established using H3K9me3 as a bait and known H3K9me3 readers like the chromodomains of CBX1 or MPP8 as prey. We next conducted an unbiased screen using a library composed of human-specific open reading frames. It led to the identification of already known lysine methylation-dependent readers and of novel methyllysine reader candidates, which were further confirmed by co-localization with H3K9me3 in human cell nuclei. CONCLUSIONS Our approach introduces a cost-effective method for screening reading domains binding to histone and nonhistone proteins which is not limited by expression levels of the candidate reading proteins. Identification of already known and novel H3K9me3 readers proofs the power of the Y3H assay which will allow for proteome-wide screens of PTM readers.
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Affiliation(s)
- Agnieszka Anna Rawłuszko-Wieczorek
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany.,Department of Biochemistry and Molecular Biology, Poznań University of Medical Sciences, Święcickiego 6 St., 60-781, Poznan, Poland
| | - Franziska Knodel
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Raluca Tamas
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Arunkumar Dhayalan
- Department of Biotechnology, Pondicherry University, R.V. Nagar, Kalapet, Pondicherry, 605014, India
| | - Albert Jeltsch
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany.
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22
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Abstract
Human development requires intricate cell specification and communication pathways that allow an embryo to generate and appropriately connect more than 200 different cell types. Key to the successful completion of this differentiation programme is the quantitative and reversible regulation of core signalling networks, and post-translational modification with ubiquitin provides embryos with an essential tool to accomplish this task. Instigated by E3 ligases and reversed by deubiquitylases, ubiquitylation controls many processes that are fundamental for development, such as cell division, fate specification and migration. As aberrant function or regulation of ubiquitylation enzymes is at the roots of developmental disorders, cancer, and neurodegeneration, modulating the activity of ubiquitylation enzymes is likely to provide strategies for therapeutic intervention.
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