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Bresser K, Nicolet BP, Jeko A, Wu W, Loayza-Puch F, Agami R, Heck AJR, Wolkers MC, Schumacher TN. Gene and protein sequence features augment HLA class I ligand predictions. Cell Rep 2024; 43:114325. [PMID: 38870014 DOI: 10.1016/j.celrep.2024.114325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 04/22/2024] [Accepted: 05/22/2024] [Indexed: 06/15/2024] Open
Abstract
The sensitivity of malignant tissues to T cell-based immunotherapies depends on the presence of targetable human leukocyte antigen (HLA) class I ligands. Peptide-intrinsic factors, such as HLA class I affinity and proteasomal processing, have been established as determinants of HLA ligand presentation. However, the role of gene and protein sequence features as determinants of epitope presentation has not been systematically evaluated. We perform HLA ligandome mass spectrometry to evaluate the contribution of 7,135 gene and protein sequence features to HLA sampling. This analysis reveals that a number of predicted modifiers of mRNA and protein abundance and turnover, including predicted mRNA methylation and protein ubiquitination sites, inform on the presence of HLA ligands. Importantly, integration of such "hard-coded" sequence features into a machine learning approach augments HLA ligand predictions to a comparable degree as experimental measures of gene expression. Our study highlights the value of gene and protein features for HLA ligand predictions.
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Affiliation(s)
- Kaspar Bresser
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Oncode Institute, Amsterdam, the Netherlands; Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands
| | - Benoit P Nicolet
- Sanquin Blood Supply Foundation, Department of Research, T cell differentiation lab, Amsterdam, The Netherlands; Amsterdam UMC, University of Amsterdam, Landsteiner Laboratory, Amsterdam, The Netherlands; Oncode Institute, Utrecht, The Netherlands
| | - Anita Jeko
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, the Netherlands
| | - Wei Wu
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, the Netherlands
| | - Fabricio Loayza-Puch
- Translational Control and Metabolism, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Reuven Agami
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, the Netherlands
| | - Monika C Wolkers
- Sanquin Blood Supply Foundation, Department of Research, T cell differentiation lab, Amsterdam, The Netherlands; Amsterdam UMC, University of Amsterdam, Landsteiner Laboratory, Amsterdam, The Netherlands; Oncode Institute, Utrecht, The Netherlands
| | - Ton N Schumacher
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Oncode Institute, Amsterdam, the Netherlands; Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands.
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2
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Xie M, Zhou L, Li T, Lin Y, Zhang R, Zheng X, Zeng C, Zheng L, Zhong L, Huang X, Zou Y, Kang T, Wu Y. Targeting the KAT8/YEATS4 Axis Represses Tumor Growth and Increases Cisplatin Sensitivity in Bladder Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2310146. [PMID: 38526153 PMCID: PMC11165526 DOI: 10.1002/advs.202310146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 02/13/2024] [Indexed: 03/26/2024]
Abstract
Bladder cancer (BC) is one of the most common tumors characterized by a high rate of relapse and a lack of targeted therapy. Here, YEATS domain-containing protein 4 (YEATS4) is an essential gene for BC cell viability using CRISPR-Cas9 library screening is reported, and that HUWE1 is an E3 ligase responsible for YEATS4 ubiquitination and proteasomal degradation by the Protein Stability Regulators Screening Assay. KAT8-mediated acetylation of YEATS4 impaired its interaction with HUWE1 and consequently prevented its ubiquitination and degradation. The protein levels of YEATS4 and KAT8 are positively correlated and high levels of these two proteins are associated with poor overall survival in BC patients. Importantly, suppression of YEATS4 acetylation with the KAT8 inhibitor MG149 decreased YEATS4 acetylation, reduced cell viability, and sensitized BC cells to cisplatin treatment. The findings reveal a critical role of the KAT8/YEATS4 axis in both tumor growth and cisplatin sensitivity in BC cells, potentially generating a novel therapeutic strategy for BC patients.
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Affiliation(s)
- Miner Xie
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
- Department of HematologyGuangzhou First People's HospitalSouth China University of TechnologyGuangzhou510060P. R. China
| | - Liwen Zhou
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Ting Li
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Yujie Lin
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Ruhua Zhang
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Xianchong Zheng
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Cuiling Zeng
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Lisi Zheng
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Li Zhong
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
- Center of Digestive DiseaseScientific Research CenterThe Seventh Affiliated HospitalSun Yat‐sen UniversityShenzhen518107P. R. China
| | - Xiaodan Huang
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Yezi Zou
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
- School of MedicineShenzhen Campus of Sun Yat‐Sen UniversityShenzhen518107P. R. China
| | - Tiebang Kang
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Yuanzhong Wu
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
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Li P, Feng X, Ma Z, Yuan Y, Jiang H, Xu G, Zhu Y, Yang X, Wang Y, Zhu C, Wang S, Gao P, Jiang Q, Shu G. Microbiota-derived 3-phenylpropionic acid promotes myotube hypertrophy by Foxo3/NAD + signaling pathway. Cell Biosci 2024; 14:62. [PMID: 38750565 PMCID: PMC11097579 DOI: 10.1186/s13578-024-01244-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 05/03/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND Gut microbiota and their metabolites play a regulatory role in skeletal muscle growth and development, which be known as gut-muscle axis. 3-phenylpropionic acid (3-PPA), a metabolite produced by colonic microorganisms from phenylalanine in the gut, presents in large quantities in the blood circulation. But few study revealed its function in skeletal muscle development. RESULTS Here, we demonstrated the beneficial effects of 3-PPA on muscle mass increase and myotubes hypertrophy both in vivo and vitro. Further, we discovered the 3-PPA effectively inhibited protein degradation and promoted protein acetylation in C2C12 and chick embryo primary skeletal muscle myotubes. Mechanistically, we supported that 3-PPA reduced NAD+ synthesis and subsequently suppressed tricarboxylic acid cycle and the mRNA expression of SIRT1/3, thus promoting the acetylation of total protein and Foxo3. Moreover, 3-PPA may inhibit Foxo3 activity by directly binding. CONCLUSIONS This study firstly revealed the effect of 3-PPA on skeletal muscle growth and development, and newly discovered the interaction between 3-PPA and Foxo3/NAD+ which mechanically promote myotubes hypertrophy. These results expand new understanding for the regulation of gut microbiota metabolites on skeletal muscle growth and development.
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Affiliation(s)
- Penglin Li
- State Key Laboratory of Swine and Poultry Breeding Industry, Tianhe District, 483 Wushan Road, Guangzhou, 510642, Guangdong, China
| | - Xiaohua Feng
- State Key Laboratory of Swine and Poultry Breeding Industry, Tianhe District, 483 Wushan Road, Guangzhou, 510642, Guangdong, China
| | - Zewei Ma
- State Key Laboratory of Swine and Poultry Breeding Industry, Tianhe District, 483 Wushan Road, Guangzhou, 510642, Guangdong, China
| | - Yexian Yuan
- State Key Laboratory of Swine and Poultry Breeding Industry, Tianhe District, 483 Wushan Road, Guangzhou, 510642, Guangdong, China
| | - Hongfeng Jiang
- State Key Laboratory of Swine and Poultry Breeding Industry, Tianhe District, 483 Wushan Road, Guangzhou, 510642, Guangdong, China
| | - Guli Xu
- State Key Laboratory of Swine and Poultry Breeding Industry, Tianhe District, 483 Wushan Road, Guangzhou, 510642, Guangdong, China
| | - Yunlong Zhu
- State Key Laboratory of Swine and Poultry Breeding Industry, Tianhe District, 483 Wushan Road, Guangzhou, 510642, Guangdong, China
| | - Xue Yang
- State Key Laboratory of Swine and Poultry Breeding Industry, Tianhe District, 483 Wushan Road, Guangzhou, 510642, Guangdong, China
| | - Yujun Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, Tianhe District, 483 Wushan Road, Guangzhou, 510642, Guangdong, China
| | - Canjun Zhu
- State Key Laboratory of Swine and Poultry Breeding Industry, Tianhe District, 483 Wushan Road, Guangzhou, 510642, Guangdong, China
| | - Songbo Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, Tianhe District, 483 Wushan Road, Guangzhou, 510642, Guangdong, China
| | - Ping Gao
- State Key Laboratory of Swine and Poultry Breeding Industry, Tianhe District, 483 Wushan Road, Guangzhou, 510642, Guangdong, China
| | - Qingyan Jiang
- State Key Laboratory of Swine and Poultry Breeding Industry, Tianhe District, 483 Wushan Road, Guangzhou, 510642, Guangdong, China.
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Tianhe District, 483 Wushan Road, Guangzhou, 510642, Guangdong, China.
- Key Laboratory of Animal Nutritional Regulation, College of Animal Science, South China Agricultural University, Tianhe District, 483 Wushan Road, Guangzhou, 510642, Guangdong, China.
| | - Gang Shu
- State Key Laboratory of Swine and Poultry Breeding Industry, Tianhe District, 483 Wushan Road, Guangzhou, 510642, Guangdong, China.
- Guangdong Laboratory for Lingnan Modern Agricultural and Guangdong Province, Tianhe District, 483 Wushan Road, Guangzhou, 510642, Guangdong, China.
- Key Laboratory of Animal Nutritional Regulation, College of Animal Science, South China Agricultural University, Tianhe District, 483 Wushan Road, Guangzhou, 510642, Guangdong, China.
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Xie Q, Hu B, Li H. Acetylation- and ubiquitination-regulated SFMBT2 acts as a tumor suppressor in clear cell renal cell carcinoma. Biol Direct 2024; 19:37. [PMID: 38734627 PMCID: PMC11088781 DOI: 10.1186/s13062-024-00480-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 05/02/2024] [Indexed: 05/13/2024] Open
Abstract
BACKGROUND Clear cell renal cell carcinoma (RCC) is the most common kidney tumor. The analysis from medical database showed that Scm-like with four MBT domains protein 2 (SFMBT2) was decreased in advanced clear cell RCC cases, and its downregulation was associated with the poor prognosis. This study aims to investigate the role of SFMBT2 in clear cell RCC. METHODS The expression of SFMBT2 in clear cell RCC specimens were determined by immunohistochemistry staining and western blot. The overexpression and knockdown of SFMBT2 was realized by infection of lentivirus loaded with SFMBT2 coding sequence or silencing fragment in 786-O and 769-P cells, and its effects on proliferation and metastasis were assessed by MTT, colony formation, flow cytometry, wound healing, transwell assay, xenograft and metastasis experiments in nude mice. The interaction of SFMBT2 with histone deacetylase 3 (HDAC3) and seven in absentia homolog 1 (SIAH1) was confirmed by co-immunoprecipitation. RESULTS In our study, SFMBT2 exhibited lower expression in clear cell RCC specimens with advanced stages than those with early stages. Overexpression of SFMBT2 inhibited the growth and metastasis of clear cell RCC cells, 786-O and 769-P, in vitro and in vivo, and its silencing displayed opposites effects. HDAC3 led to deacetylation of SFMBT2, and the HDAC3 inhibitor-induced acetylation prevented SFMBT2 from SIAH1-mediated ubiquitination modification and proteasome degradation. K687 in SFMBT2 protein molecule may be the key site for acetylation and ubiquitination. CONCLUSIONS SFMBT2 exerted an anti-tumor role in clear cell RCC cells, and HDAC3-mediated deacetylation promoted SIAH1-controlled ubiquitination of SFMBT2. SFMBT2 may be considered as a novel clinical diagnostic marker and/or therapeutic target of clear cell RCC, and crosstalk between its post-translational modifications may provide novel insights for agent development.
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Affiliation(s)
- Qingpeng Xie
- Department of Urology, Liaoning Cancer Hospital and Institute, Cancer Hospital of China Medical University, No. 44 Xiaoheyan Road, Dadong District, Shenyang, 110042, Liaoning, China
| | - Bin Hu
- Department of Urology, Liaoning Cancer Hospital and Institute, Cancer Hospital of China Medical University, No. 44 Xiaoheyan Road, Dadong District, Shenyang, 110042, Liaoning, China.
| | - Haosong Li
- Department of Pediatrics, Central Hospital Affiliated to Shenyang Medical College, Shenyang, Liaoning, China
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Zheng B, Jiang X, Liu Y, Cheng F, Zhang Y, Niu C, Cong Z, Niu Z, He W. Elevated histone deacetylase 10 expression promotes the progression of clear cell renal cell carcinoma by Notch-1-PTEN signaling axis. Discov Oncol 2024; 15:156. [PMID: 38733531 PMCID: PMC11088579 DOI: 10.1007/s12672-024-01018-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 05/07/2024] [Indexed: 05/13/2024] Open
Abstract
BACKGROUND Clear cell renal cell carcinoma (ccRCC), the most common pathological subtype of kidney cancer, accounts for approximately 70% to 80% of all cases. Histone deacetylase 10 (HDAC10) belongs to the HDAC class IIb subgroup, one of the histone deacetylases (HDAC) family. Previous studies suggest that HDAC10 may regulate the development of multiple tumor types. The specific molecular mechanisms employed by HDAC10 in the etiology of ccRCC still need to be discovered. METHODS The analysis included examining HDAC10 expression levels and their clinical importance within a cohort of inpatients and ccRCC patients documented in the Tumor Genome Atlas (TCGA). Moreover, the biological functions and underlying molecular mechanisms of HDAC10 were investigated. RESULTS HDAC10 showed increased expression in ccRCC tumor tissues. Subsequent analysis revealed overexpression of HDAC10 was associated with advanced clinical phenotype and unfavorable prognosis. The absence of HDAC10 significantly decreased ccRCC cell proliferation and migration capabilities. Mechanistic research suggests that HDAC10 may promote RCC development by activating the Notch-1 pathway and downregulating PTEN expression levels. CONCLUSION In summary, HDAC10 can modulate critical biological processes in ccRCC, including proliferation, migration, and apoptosis. Notably, the Notch-1 pathway and PTEN serve as crucial signaling pathways and target genes through which HDAC10 regulates the progression of ccRCC. These findings offer a novel outlook for ccRCC treatment.
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Affiliation(s)
- Bin Zheng
- Department of Urology, Shandong Provincial Hospital, Shandong University, Jinan, 250021, Shandong, China
| | - Xue Jiang
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China
| | - Yaqing Liu
- Department of Nephrology, Shandong Provincial Hospital, Shandong University, Jinan, 250021, Shandong, China
| | - Fajuan Cheng
- Department of Nephrology, Shandong Provincial Hospital, Shandong University, Jinan, 250021, Shandong, China
| | - Yiming Zhang
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China
| | - Chengtao Niu
- Department of Urology, Shandong Provincial Hospital, Shandong University, Jinan, 250021, Shandong, China
| | - Zixiang Cong
- Department of Urology, Shandong Provincial Hospital, Shandong University, Jinan, 250021, Shandong, China
| | - Zhihong Niu
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China
| | - Wei He
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China.
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Yang Z, Du J, Tan X, Zhang H, Li L, Li Y, Wei Z, Xu Z, Lu Y, Chen J, Sun Z. Histone deacetylase OsHDA706 orchestrates rice broad-spectrum antiviral immunity and is impeded by a viral effector. Cell Rep 2024; 43:113838. [PMID: 38386554 DOI: 10.1016/j.celrep.2024.113838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/18/2023] [Accepted: 02/05/2024] [Indexed: 02/24/2024] Open
Abstract
Lysine acetylation is a dynamic post-translational modification of proteins. Extensive studies have revealed that the acetylation modulated by histone acetyltransferases and histone deacetylases (HDACs) plays a crucial role in regulating protein function. However, there has been limited focus on how HDACs regulate jasmonic acid (JA) biosynthesis in plants. Here, we uncover that the protein stability of OsLOX14, a critical enzyme involved in JA biosynthesis, is regulated by a histone deacetylase, OsHDA706, and is hindered by a viral protein. Our results show that OsHDA706 deacetylates OsLOX14 and enhances the stability of OsLOX14, leading to JA accumulation and an improved broad-spectrum rice antiviral defense. Furthermore, we found that the viral protein P2, encoded by the destructive rice stripe virus, disrupts the association of OsHDA706-OsLOX14, promoting viral infection. Overall, our findings reveal how HDAC manipulates the interplay of deacetylation and protein stability of a JA biosynthetic enzyme to enhance plant antiviral responses.
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Affiliation(s)
- Zihang Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; College of Plant Protection, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Juan Du
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Xiaoxiang Tan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Hehong Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Lulu Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Yanjun Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Zhongyan Wei
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Zhongtian Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Yuwen Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; College of Plant Protection, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Zongtao Sun
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China.
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Kim Y, Jung KY, Kim YH, Xu P, Kang BE, Jo Y, Pandit N, Kwon J, Gariani K, Gariani J, Lee J, Verbeek J, Nam S, Bae SJ, Ha KT, Yi HS, Shong M, Kim KH, Kim D, Jung HJ, Lee CW, Kim KR, Schoonjans K, Auwerx J, Ryu D. Inhibition of SIRT7 overcomes sorafenib acquired resistance by suppressing ERK1/2 phosphorylation via the DDX3X-mediated NLRP3 inflammasome in hepatocellular carcinoma. Drug Resist Updat 2024; 73:101054. [PMID: 38277756 PMCID: PMC10935544 DOI: 10.1016/j.drup.2024.101054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/10/2023] [Accepted: 01/11/2024] [Indexed: 01/28/2024]
Abstract
AIMS Sirtuin 7 (SIRT7) plays an important role in tumor development, and has been characterized as a potent regulator of cellular stress. However, the effect of SIRT7 on sorafenib acquired resistance remains unclear and a possible anti-tumor mechanism beyond this process in HCC has not been clarified. We examined the therapeutic potential of SIRT7 and determined whether it functions synergistically with sorafenib to overcome chemoresistance. METHODS Cancer Genome Atlas-liver HCC data and unbiased gene set enrichment analyses were used to identify SIRT7 as a potential effector molecule in sorafenib acquired resistance. Two types of SIRT7 chemical inhibitors were developed to evaluate its therapeutic properties when synergized with sorafenib. Mass spectrometry was performed to discover a direct target of SIRT7, DDX3X, and DDX3X deacetylation levels and protein stability were explored. Moreover, an in vivo xenograft model was used to confirm anti-tumor effect of SIRT7 and DDX3X chemical inhibitors combined with sorafenib. RESULTS SIRT7 inhibition mediated DDX3X depletion can re-sensitize acquired sorafenib resistance by disrupting NLRP3 inflammasome assembly, finally suppressing hyperactive ERK1/2 signaling in response to NLRP3 inflammasome-mediated IL-1β inhibition. CONCLUSIONS SIRT7 is responsible for sorafenib acquired resistance, and its inhibition would be beneficial when combined with sorafenib by suppressing hyperactive pro-cell survival ERK1/2 signaling.
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Affiliation(s)
- Yuna Kim
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea.
| | - Kwan-Young Jung
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Yun Hak Kim
- Department of Anatomy, School of Medicine, Pusan National University, Yangsan, Republic of Korea; Department of Biomedical Informatics, School of Medicine, Pusan National University, Yangsan, Republic of Korea
| | - Pan Xu
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Baeki E Kang
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Yunju Jo
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
| | - Navin Pandit
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Jeongho Kwon
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Karim Gariani
- Service of Endocrinology, Diabetes, Nutrition and Therapeutic Patient Education, Geneva University Hospitals, Geneva, Switzerland
| | - Joanna Gariani
- Department of radiology, Hirslanden Grangettes Clinic, Geneva, Switzerland
| | - Junguee Lee
- Department of Pathology, Daejeon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Daejeon, Republic of Korea
| | - Jef Verbeek
- Laboratory of Hepatology, Department of Chronic Diseases and Metabolism (CHROMETA), KU Leuven, Belgium; Department of Gastroenterology and Hepatology, University Hospitals KU Leuven, Leuven, Belgium
| | - Seungyoon Nam
- Department of Genome Medicine and Science, AI Convergence Center for Medical Science, Gachon Institute of Genome Medicine and Science, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon, Republic of Korea; Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences and Technology (GAIHST), Republic of Korea
| | - Sung-Jin Bae
- Department of Molecular Biology and Immunology, Kosin University College of Medicine, Busan, Republic of Korea
| | - Ki-Tae Ha
- Department of Korean Medical Science, Pusan National University School of Korean Medicine, Yangsan, Republic of Korea
| | - Hyon-Seung Yi
- Laboratory of Endocrinology and Immune System, Chungnam National University School of Medicine, Daejeon, Republic of Korea
| | - Minho Shong
- Research Center for Endocrine and Metabolic Diseases, Chungnam National University School of Medicine, Daejeon, Republic of Korea
| | - Kyun-Hwan Kim
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Doyoun Kim
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Hee Jung Jung
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Chang-Woo Lee
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Kwang Rok Kim
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea.
| | - Kristina Schoonjans
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland.
| | - Johan Auwerx
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland.
| | - Dongryeol Ryu
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea; Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea.
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Russo S, Kwiatkowski M, Wolters JC, Gerding A, Hermans J, Govorukhina N, Bischoff R, Melgert BN. Effects of lysine deacetylase inhibitor treatment on LPS responses of alveolar-like macrophages. J Leukoc Biol 2024; 115:435-449. [PMID: 37811856 DOI: 10.1093/jleuko/qiad121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/14/2023] [Accepted: 09/18/2023] [Indexed: 10/10/2023] Open
Abstract
Macrophages are key immune cells that can adapt their metabolic phenotype in response to different stimuli. Lysine deacetylases are important enzymes regulating inflammatory gene expression and lysine deacetylase inhibitors have been shown to exert anti-inflammatory effects in models of chronic obstructive pulmonary disease. We hypothesized that these anti-inflammatory effects may be associated with metabolic changes in macrophages. To validate this hypothesis, we used an unbiased and a targeted proteomic approach to investigate metabolic enzymes, as well as liquid chromatography-mass spectrometry and gas chromatography-mass spectrometry, to quantify metabolites in combination with the measurement of functional parameters in primary murine alveolar-like macrophages after lipopolysaccharide-induced activation in the presence or absence of lysine deacetylase inhibition. We found that lysine deacetylase inhibition resulted in reduced production of inflammatory mediators such as tumor necrosis factor α and interleukin 1β. However, only minor changes in macrophage metabolism were observed, as only one of the lysine deacetylase inhibitors slightly increased mitochondrial respiration while no changes in metabolite levels were seen. However, lysine deacetylase inhibition specifically enhanced expression of proteins involved in ubiquitination, which may be a driver of the anti-inflammatory effects of lysine deacetylase inhibitors. Our data illustrate that a multiomics approach provides novel insights into how macrophages interact with cues from their environment. More detailed studies investigating ubiquitination as a potential driver of lysine deacetylase inhibition will help developing novel anti-inflammatory drugs for difficult-to-treat diseases such as chronic obstructive pulmonary disease.
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Affiliation(s)
- Sara Russo
- Department of Analytical Biochemistry, University of Groningen, Antonius Deusinglaan 1, Groningen 9713 AV, The Netherlands
| | - Marcel Kwiatkowski
- Functional Proteo-Metabolomics, Department of Biochemistry, University of Innsbruck, Innrain 80-82, Innsbruck 6020, Austria
| | - Justina C Wolters
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Hanzeplein 1, Groningen 9713 GZ, The Netherlands
| | - Albert Gerding
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Hanzeplein 1, Groningen 9713 GZ, The Netherlands
| | - Jos Hermans
- Department of Analytical Biochemistry, University of Groningen, Antonius Deusinglaan 1, Groningen 9713 AV, The Netherlands
| | - Natalia Govorukhina
- Department of Analytical Biochemistry, University of Groningen, Antonius Deusinglaan 1, Groningen 9713 AV, The Netherlands
| | - Rainer Bischoff
- Department of Analytical Biochemistry, University of Groningen, Antonius Deusinglaan 1, Groningen 9713 AV, The Netherlands
| | - Barbro N Melgert
- Department of Molecular Pharmacology, University of Groningen, Antonius Deusinglaan 1, Groningen 9713 AV, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Center Groningen, Hanzeplein 1, Groningen 9713 GZ, The Netherlands
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9
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Zhou HJ, Wang XY, Wang LQ, Zheng JS, Zhan RY, Pan JW. Interfering TRIB3 protects the blood brain barrier through PI3K/Akt pathway to alleviate cerebral ischemia-reperfusion injury in diabetes mellitus mice. Chem Biol Interact 2024; 387:110807. [PMID: 37980971 DOI: 10.1016/j.cbi.2023.110807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/24/2023] [Accepted: 11/13/2023] [Indexed: 11/21/2023]
Abstract
This study aimed to treat diabetic cerebral ischemia-reperfusion injury (CI/RI) by affecting blood brain barrier (BBB) permeability and integrity. The CI/RI model in DM mice and a high glucose (HG) treated oxygen and glucose deprivation/reoxygenation (OGD/R) brain endothelial cell model were established for the study. Evans blue (EB) staining was used to evaluate the permeability of BBB in vivo. TTC staining was used to analyze cerebral infarction. The location and expression of tribbles homolog 3 (TRIB3) in endothelial cells were detected by immunofluorescence. Western blotting was used to detect the protein expressions of TRIB3, tight junction molecules, adhesion molecules, phosphorylated protein kinase B (p-AKT) and AKT. The levels of pro-inflammatory cytokines were detected by qRT-PCR. Trans-epithelial electrical resistance (TEER) and fluorescein isothiocyanate (FITC)-dextran were used to measure vascular permeability in vitro. TRIB3 ubiquitination and acetylation levels were detected. Acetyltransferase bound to TRIB3 were identified by immunoprecipitation. TRIB3 was localized in cerebral endothelial cells and was highly expressed in diabetic CI/R mice. The BBB permeability in diabetic CI/R mice and HG-treated OGD/R cells was increased, while the junction integrity was decreased. Interference with TRIB3 in vitro reduces BBB permeability and increases junction integrity. In vivo interfering with TRIB3 reduced cerebral infarction volume, BBB permeability and inflammation levels, and upregulated p-AKT levels. The phosphatidylinositol 3-kinase (PI3K) inhibitor wortmannin reversed the effects of TRIB3-interfering plasmid. In vitro HG treatment induced TRIB3 acetylation through acetyltransferase p300, which in turn reduced ubiquitination and stabilized TRIB3. Interfering TRIB3 protects BBB by activating PI3K/AKT pathway and alleviates brain injury, which provides a new target for diabetic CI/RI.
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Affiliation(s)
- Heng-Jun Zhou
- Department of Neurosurgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Xiao-Yi Wang
- Department of Neurosurgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Li-Qing Wang
- Department of Anesthesiology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, China.
| | - Jie-Sheng Zheng
- Department of Neurosurgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Ren-Ya Zhan
- Department of Neurosurgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Jian-Wei Pan
- Department of Neurosurgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, China.
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10
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Hughes DC, Goodman CA, Baehr LM, Gregorevic P, Bodine SC. A critical discussion on the relationship between E3 ubiquitin ligases, protein degradation, and skeletal muscle wasting: it's not that simple. Am J Physiol Cell Physiol 2023; 325:C1567-C1582. [PMID: 37955121 PMCID: PMC10861180 DOI: 10.1152/ajpcell.00457.2023] [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: 09/18/2023] [Revised: 11/07/2023] [Accepted: 11/07/2023] [Indexed: 11/14/2023]
Abstract
Ubiquitination is an important post-translational modification (PTM) for protein substrates, whereby ubiquitin is added to proteins through the coordinated activity of activating (E1), ubiquitin-conjugating (E2), and ubiquitin ligase (E3) enzymes. The E3s provide key functions in the recognition of specific protein substrates to be ubiquitinated and aid in determining their proteolytic or nonproteolytic fates, which has led to their study as indicators of altered cellular processes. MuRF1 and MAFbx/Atrogin-1 were two of the first E3 ubiquitin ligases identified as being upregulated in a range of different skeletal muscle atrophy models. Since their discovery, the expression of these E3 ubiquitin ligases has often been studied as a surrogate measure of changes to bulk protein degradation rates. However, emerging evidence has highlighted the dynamic and complex regulation of the ubiquitin proteasome system (UPS) in skeletal muscle and demonstrated that protein ubiquitination is not necessarily equivalent to protein degradation. These observations highlight the potential challenges of quantifying E3 ubiquitin ligases as markers of protein degradation rates or ubiquitin proteasome system (UPS) activation. This perspective examines the usefulness of monitoring E3 ubiquitin ligases for determining specific or bulk protein degradation rates in the settings of skeletal muscle atrophy. Specific questions that remain unanswered within the skeletal muscle atrophy field are also identified, to encourage the pursuit of new research that will be critical in moving forward our understanding of the molecular mechanisms that govern protein function and degradation in muscle.
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Affiliation(s)
- David C Hughes
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States
| | - Craig A Goodman
- Centre for Muscle Research (CMR), Department of Anatomy and Physiology, The University of Melbourne, Parkville, Victoria, Australia
| | - Leslie M Baehr
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States
| | - Paul Gregorevic
- Centre for Muscle Research (CMR), Department of Anatomy and Physiology, The University of Melbourne, Parkville, Victoria, Australia
- Department of Neurology, The University of Washington School of Medicine, Seattle, Washington, United States
| | - Sue C Bodine
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States
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11
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Dale AL, Man L, Cordwell SJ. Global Acetylomics of Campylobacter jejuni Shows Lysine Acetylation Regulates CadF Adhesin Processing and Human Fibronectin Binding. J Proteome Res 2023; 22:3519-3533. [PMID: 37830485 DOI: 10.1021/acs.jproteome.3c00391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
Lysine acetylation (KAc) is a reversible post-translational modification (PTM) that can alter protein structure and function; however, specific roles for KAc are largely undefined in bacteria. Acetyl-lysine immunoprecipitation and LC-MS/MS identified 5567 acetylated lysines on 1026 proteins from the gastrointestinal pathogen Campylobacter jejuni (∼63% of the predicted proteome). KAc was identified on proteins from all subcellular locations, including the outer membrane (OM) and extracellular proteins. Label-based LC-MS/MS identified proteins and KAc sites during growth in 0.1% sodium deoxycholate (DOC, a component of gut bile salts). 3410 acetylated peptides were quantified, and 784 (from 409 proteins) were differentially abundant in DOC growth. Changes in KAc involved multiple pathways, suggesting a dynamic role for this PTM in bile resistance. As observed elsewhere, we show KAc is primarily nonenzymatically mediated via acetyl-phosphate; however, the deacetylase CobB also contributes to a global elevation of this modification in DOC. We observed several multiply acetylated OM proteins and altered DOC abundance of acetylated peptides in the fibronectin (Fn)-binding adhesin CadF. We show KAc reduces CadF Fn binding and prevalence of lower mass variants. This study provides the first system-wide lysine acetylome of C. jejuni and contributes to our understanding of KAc as an emerging PTM in bacteria.
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Affiliation(s)
- Ashleigh L Dale
- School of Life and Environmental Sciences, The University of Sydney, New South Wales 2006, Australia
- Charles Perkins Centre, The University of Sydney, New South Wales 2006, Australia
| | - Lok Man
- School of Life and Environmental Sciences, The University of Sydney, New South Wales 2006, Australia
- Charles Perkins Centre, The University of Sydney, New South Wales 2006, Australia
| | - Stuart J Cordwell
- School of Life and Environmental Sciences, The University of Sydney, New South Wales 2006, Australia
- Charles Perkins Centre, The University of Sydney, New South Wales 2006, Australia
- Sydney Mass Spectrometry, The University of Sydney, New South Wales 2006, Australia
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12
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Pi Y, Feng Q, Sun F, Wang Z, Zhao Y, Chen D, Liu Y, Lou G. Loss of SMURF2 expression enhances RACK1 stability and promotes ovarian cancer progression. Cell Death Differ 2023; 30:2382-2392. [PMID: 37828084 PMCID: PMC10657365 DOI: 10.1038/s41418-023-01226-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 09/09/2023] [Accepted: 09/19/2023] [Indexed: 10/14/2023] Open
Abstract
Receptor for activated C kinase 1 (RACK1) has been confirmed to take part in multiple biological events and the mechanism supporting abnormal RACK1 expression in ovarian cancer (OC) remains to be characterized. Here, we identified Smad ubiquitin regulatory factor 2 (SMURF2) as a bona fide E3 ligase of RACK1 in OC. SMURF2 effectively added the K6, K33 and K48 ubiquitin chains to the RACK1, resulting in polyubiquitination and instability of RACK1. PCAF promoted acetylation of RACK1 at K130, leading to SMURF2-mediated RACK1 ubiquitination inhibited and promote OC progression. The expression levels of SMURF2 and RACK1 were negatively correlated. SMURF2 was abnormal low expression in human ovarian cancer, resulting in decreased ubiquitination of RACK1 and increased stability, which promoted OC progression, and strongly associated with poor patients' prognosis. In general, our results demonstrated that SMURF2 plays a pivotal role in stabilizing RACK1, which in turn facilitates tumorigenesis in OC, suggesting that SMURF2-RACK1 axis may prove to be potential targets for the treatment of OC.
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Affiliation(s)
- Yanan Pi
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin, 150086, P. R. China
| | - Qiushi Feng
- Heilongjiang Academy of Chinese Medical Sciences, Harbin, 150036, P. R. China
| | - Fusheng Sun
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin, 150086, P. R. China
| | - Zhiqiang Wang
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin, 150086, P. R. China
| | - Yue Zhao
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin, 150086, P. R. China
| | - Dejia Chen
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin, 150086, P. R. China
| | - Yiming Liu
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin, 150086, P. R. China
| | - Ge Lou
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin, 150086, P. R. China.
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13
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Zhou Z, Zhong L, Chu X, Wan P, Dan W, Shao X, Chen S, Zhang Z, Lu Y, Liu B. HDAC11 mediates the ubiquitin-dependent degradation of p53 and inhibits the anti-leukemia effect of PD0166285. Med Oncol 2023; 40:325. [PMID: 37805625 DOI: 10.1007/s12032-023-02196-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 09/12/2023] [Indexed: 10/09/2023]
Abstract
Cytarabine-resistant acute myeloid leukemia (AML) is a common phenomenon, necessitating the search for new chemotherapeutics. WEE1 participates in cell cycle checkpoint signaling and inhibitors targeting WEE1 (WEE1i) constitute a potential novel strategy for AML treatment. HDAC (histone deacetylase) inhibitors have been shown to enhance the anti-tumor effects of WEE1i but molecular mechanisms of HDAC remain poorly characterized. In this study, the WEE1 inhibitor PD0166285 showed a relatively good anti-leukemia effect. Notably, PD0166285 can arise the expression of HDAC11 which was negatively correlated with survival of AML patients. Moreover, HDAC11 can reduced the anti-tumor effect of PD0166285 through an effect on p53 stability and the changes in phosphorylation levels of MAPK pathways. Overall, the cell cycle inhibitor, PD0166285, is a potential chemotherapeutic drug for AML. These fundings contribute to a functional understanding of HDAC11 in AML.
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Affiliation(s)
- Ziwei Zhou
- Central Laboratory of Yongchuan Hospital, Chongqing Medical University, Chongqing, 402160, China
| | - Liang Zhong
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Xuan Chu
- Central Laboratory of Yongchuan Hospital, Chongqing Medical University, Chongqing, 402160, China
| | - Peng Wan
- Central Laboratory of Yongchuan Hospital, Chongqing Medical University, Chongqing, 402160, China
| | - Wenran Dan
- Central Laboratory of Yongchuan Hospital, Chongqing Medical University, Chongqing, 402160, China
| | - Xin Shao
- Central Laboratory of Yongchuan Hospital, Chongqing Medical University, Chongqing, 402160, China
| | - Shuyu Chen
- Central Laboratory of Yongchuan Hospital, Chongqing Medical University, Chongqing, 402160, China
| | - Zhonghui Zhang
- Central Laboratory of Yongchuan Hospital, Chongqing Medical University, Chongqing, 402160, China
| | - Yang Lu
- Central Laboratory of Yongchuan Hospital, Chongqing Medical University, Chongqing, 402160, China
| | - Beizhong Liu
- Central Laboratory of Yongchuan Hospital, Chongqing Medical University, Chongqing, 402160, China.
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China.
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14
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Yang S, Yang G, Wang X, Xiang J, Kang L, Liang Z. SIRT2 alleviated renal fibrosis by deacetylating SMAD2 and SMAD3 in renal tubular epithelial cells. Cell Death Dis 2023; 14:646. [PMID: 37777567 PMCID: PMC10542381 DOI: 10.1038/s41419-023-06169-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 09/06/2023] [Accepted: 09/21/2023] [Indexed: 10/02/2023]
Abstract
Transforming growth factor-β (TGF-β) is the primary factor that drives fibrosis in most, if not all, forms of chronic kidney disease. In kidneys that are obstructed, specific deletion of Sirt2 in renal tubule epithelial cells (TEC) has been shown to aggravate renal fibrosis, while renal tubule specific overexpression of Sirt2 has been shown to ameliorate renal fibrosis. Similarly, specific deletion of Sirt2 in hepatocyte aggravated CCl4-induced hepatic fibrosis. In addition, we have demonstrated that SIRT2 overexpression and knockdown restrain and enhance TGF-β-induced fibrotic gene expression, respectively, in TEC. Mechanistically, SIRT2 reduced the phosphorylation, acetylation, and nuclear localization levels of SMAD2 and SMAD3, leading to inhibition of the TGF-β signaling pathway. Further studies have revealed that that SIRT2 was able to directly interact with and deacetylate SMAD2 at lysine 451, promoting its ubiquitination and degradation. Notably, loss of SMAD specific E3 ubiquitin protein ligase 2 abolishes the ubiquitination and degradation of SMAD2 induced by SIRT2 in SMAD2. Regarding SMAD3, we have found that SIRT2 interact with and deacetylates SMAD3 at lysine 341 and 378 only in the presence of TGF-β, thereby reducing its activation. This study provides initial indication of the anti-fibrotic role of SIRT2 in renal tubules and hepatocytes, suggesting its therapeutic potential for fibrosis.
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Affiliation(s)
- Shu Yang
- Department of Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College of Jinan University & The First Affiliated Hospital of Southern University of Science and Technology), Shenzhen, China.
- Guangdong Provincial Clinical Research Center for Geriatrics, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, Guangdong, China.
| | - Guangyan Yang
- Department of Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College of Jinan University & The First Affiliated Hospital of Southern University of Science and Technology), Shenzhen, China
| | - Xinyu Wang
- Department of Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College of Jinan University & The First Affiliated Hospital of Southern University of Science and Technology), Shenzhen, China
| | - Jiaqing Xiang
- Department of Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College of Jinan University & The First Affiliated Hospital of Southern University of Science and Technology), Shenzhen, China
| | - Lin Kang
- Department of Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College of Jinan University & The First Affiliated Hospital of Southern University of Science and Technology), Shenzhen, China.
- Guangdong Provincial Clinical Research Center for Geriatrics, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, Guangdong, China.
- The Biobank of National Innovation Center for Advanced Medical Devices, Shenzhen People's Hospital, Southern University of Science and Technology, Shenzhen, China.
| | - Zhen Liang
- Department of Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College of Jinan University & The First Affiliated Hospital of Southern University of Science and Technology), Shenzhen, China.
- Guangdong Provincial Clinical Research Center for Geriatrics, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, Guangdong, China.
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15
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Aleksandrova Y, Neganova M. Deciphering the Mysterious Relationship between the Cross-Pathogenetic Mechanisms of Neurodegenerative and Oncological Diseases. Int J Mol Sci 2023; 24:14766. [PMID: 37834214 PMCID: PMC10573395 DOI: 10.3390/ijms241914766] [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: 08/10/2023] [Revised: 09/22/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
The relationship between oncological pathologies and neurodegenerative disorders is extremely complex and is a topic of concern among a growing number of researchers around the world. In recent years, convincing scientific evidence has accumulated that indicates the contribution of a number of etiological factors and pathophysiological processes to the pathogenesis of these two fundamentally different diseases, thus demonstrating an intriguing relationship between oncology and neurodegeneration. In this review, we establish the general links between three intersecting aspects of oncological pathologies and neurodegenerative disorders, i.e., oxidative stress, epigenetic dysregulation, and metabolic dysfunction, examining each process in detail to establish an unusual epidemiological relationship. We also focus on reviewing the current trends in the research and the clinical application of the most promising chemical structures and therapeutic platforms that have a modulating effect on the above processes. Thus, our comprehensive analysis of the set of molecular determinants that have obvious cross-functional pathways in the pathogenesis of oncological and neurodegenerative diseases can help in the creation of advanced diagnostic tools and in the development of innovative pharmacological strategies.
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Affiliation(s)
- Yulia Aleksandrova
- Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry, Russian Academy of Sciences, 142432 Chernogolovka, Russia;
| | - Margarita Neganova
- Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry, Russian Academy of Sciences, 142432 Chernogolovka, Russia;
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, 420088 Kazan, Russia
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16
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Hsu YH, Chao CN, Huang HY, Zhao PW, Hsu PH, Shen CH, Chen SY, Fang CY. Histone deacetylase III interactions with BK polyomavirus large tumor antigen may affect protein stability. Virol J 2023; 20:155. [PMID: 37464367 DOI: 10.1186/s12985-023-02128-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 07/12/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND Human polyomavirus BK (BKPyV) causes associated nephropathy and contributes to urinary tract cancer development in renal transplant recipients. Large tumor antigen (LT) is an early protein essential in the polyomavirus life cycle. Protein acetylation plays a critical role in regulating protein stability, so this study investigated the acetylation of the BKPyV LT protein. METHODS The BKPyV LT nucleotide was synthesized, and the protein was expressed by transfection into permissive cells. The BKPyV LT protein was immunoprecipitated and subjected to LC-MS/MS analysis to determine the acetylation residues. The relative lysine was then mutated to arginine in the LT nucleotide and BKPyV genome to analyze the role of LT lysine acetylation in the BKPyV life cycle. RESULTS BKPyV LT acetylation sites were identified at Lys3 and Lys230 by mass spectrometry. HDAC3 and HDAC8 and their deacetylation activity are required for BKPyV LT expression. In addition, mutations of Lys3 and Lys230 to arginine increased LT expression, and the interaction of HDAC3 and LT was confirmed by coimmunoprecipitation. CONCLUSIONS HDAC3 is a newly identified protein that interacts with BKPyV LT, and LT acetylation plays a vital role in the BKPyV life cycle.
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Affiliation(s)
- Yueh-Han Hsu
- Division of Nephrology, Department of Internal Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan
- Department of Nursing, Min-Hwei Junior College of Health Care Management, Tainan, Taiwan
| | - Chun-Nun Chao
- Department of Pediatrics, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan
- Department of Biomedical Sciences, National Chung Cheng University, Chia-Yi, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung, Taiwan
| | - Hsin-Yi Huang
- Department of Medical Research, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan
| | - Pei-Wen Zhao
- Department of Medical Research, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan
| | - Pang-Hung Hsu
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Cheng-Huang Shen
- Department of Urology, Ditmanson Medical Foundation Chiayi Christian Hospital, Chia-Yi, Taiwan
| | - San-Yuan Chen
- Department of Chinese Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan.
- Department of Sports Management, Chia Nan University of Pharmacy & Science, Tainan City, Taiwan.
| | - Chiung-Yao Fang
- Department of Medical Research, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan.
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17
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Couto-Rodríguez RL, Koh J, Chen S, Maupin-Furlow JA. Insights into the Lysine Acetylome of the Haloarchaeon Haloferax volcanii during Oxidative Stress by Quantitative SILAC-Based Proteomics. Antioxidants (Basel) 2023; 12:1203. [PMID: 37371933 PMCID: PMC10294847 DOI: 10.3390/antiox12061203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/23/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Oxidative stress adaptation strategies are important to cell function and are linked to cardiac, neurodegenerative disease, and cancer. Representatives of the Archaea domain are used as model organisms based on their extreme tolerance to oxidants and close evolutionary relationship with eukaryotes. A study of the halophilic archaeon Haloferax volcanii reveals lysine acetylation to be associated with oxidative stress responses. The strong oxidant hypochlorite: (i) stimulates an increase in lysine acetyltransferase HvPat2 to HvPat1 abundance ratios and (ii) selects for lysine deacetylase sir2 mutants. Here we report the dynamic occupancy of the lysine acetylome of glycerol-grown H. volcanii as it shifts in profile in response to hypochlorite. These findings are revealed by the: (1) quantitative multiplex proteomics of the SILAC-compatible parent and Δsir2 mutant strains and (2) label-free proteomics of H26 'wild type' cells. The results show that lysine acetylation is associated with key biological processes including DNA topology, central metabolism, cobalamin biosynthesis, and translation. Lysine acetylation targets are found conserved across species. Moreover, lysine residues modified by acetylation and ubiquitin-like sampylation are identified suggesting post-translational modification (PTM) crosstalk. Overall, the results of this study expand the current knowledge of lysine acetylation in Archaea, with the long-term goal to provide a balanced evolutionary perspective of PTM systems in living organisms.
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Affiliation(s)
- Ricardo L. Couto-Rodríguez
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA;
| | - Jin Koh
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610, USA; (J.K.); (S.C.)
| | - Sixue Chen
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610, USA; (J.K.); (S.C.)
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
- Department of Biology, The University of Mississippi, Oxford, MS 38677, USA
| | - Julie A. Maupin-Furlow
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA;
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
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He Q, Yu C, Li Y, Hao P, Mai H, Guo R, Zhong G, Zhang K, Wong C, Chen Q, Chen Y. ERRα contributes to HDAC6-induced chemoresistance of osteosarcoma cells. Cell Biol Toxicol 2023; 39:813-825. [PMID: 34524571 DOI: 10.1007/s10565-021-09651-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 09/03/2021] [Indexed: 10/20/2022]
Abstract
Chemotherapy resistance is an important problem for clinical therapy of osteosarcoma (OS). The potential effects of histone deacetylases (HDACs) on OS chemoresistance are studied. The expression of HDACs in OS cells resistance to doxorubicin (Dox) and cisplatin (CDDP) is checked. Among 11 members of HDACs, levels of HDAC6 are significantly upregulated in OS cells resistance to Dox and CDDP. Inhibition of HDAC6 via its specific inhibitor ACY1215 restores chemosensitivity of OS-resistant cells. Further, HDAC6 directly binds with estrogen-related receptors alpha (ERRα) to regulate its acetylation and protein stability. Inhibition of ERRα further strengthens ACY1215-increased chemosensitivity of OS-resistant cells. Mechanistically, K129 acetylation is the key residue for HDAC6-regulated protein levels of ERRα. Collectively, we find that ERRα contributes to HDAC6-induced chemoresistance of OS cells. Inhibition of HDAC6/ERRα axis might be a potential approach to overcome chemoresistance and improve therapy efficiency for OS treatment. 1. HDAC6 was significantly upregulated in Dox and CDDP resistant OS cells; 2. Inhibition of HDAC6 can restore chemosensitivity of OS cells; 3. HDAC6 binds with ERRα at K129 to decrease its acetylation and increase protein stability; 4. ERRα contributes to HDAC6-induced chemoresistance of OS cells.
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Affiliation(s)
- Qing He
- Department of Surgical Intensive Care Unit, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Changzhi Yu
- Department of Chinese Traditional Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yang Li
- Pediatric Hematology and Oncology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Peng Hao
- Department of Surgical Intensive Care Unit, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Hantao Mai
- Department of Surgical Intensive Care Unit, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Ruilian Guo
- Department of Surgical Intensive Care Unit, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Guifang Zhong
- Department of Surgical Intensive Care Unit, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Kelin Zhang
- Department of Surgical Intensive Care Unit, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Chipiu Wong
- Department of Orthopedics, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, No.107, Yanjiang West Road, Yuexiu District, Guangzhou, 510120, China
| | - Qian Chen
- Department of Orthopedics, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, No.107, Yanjiang West Road, Yuexiu District, Guangzhou, 510120, China
| | - Yantao Chen
- Department of Orthopedics, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, No.107, Yanjiang West Road, Yuexiu District, Guangzhou, 510120, China.
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Bhattacharya A, Amin SA, Kumar P, Jha T, Gayen S. Exploring structural requirements of HDAC10 inhibitors through comparative machine learning approaches. J Mol Graph Model 2023; 123:108510. [PMID: 37216830 DOI: 10.1016/j.jmgm.2023.108510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/26/2023] [Accepted: 05/04/2023] [Indexed: 05/24/2023]
Abstract
Histone deacetylase (HDAC) inhibitors are in the limelight of anticancer drug development and research. HDAC10 is one of the class-IIb HDACs, responsible for cancer progression. The search for potent and effective HDAC10 selective inhibitors is going on. However, the absence of human HDAC10 crystal/NMR structure hampers the structure-based drug design of HDAC10 inhibitors. Different ligand-based modeling techniques are the only hope to speed up the inhibitor design. In this study, we applied different ligand-based modeling techniques on a diverse set of HDAC10 inhibitors (n = 484). Machine learning (ML) models were developed that could be used to screen unknown compounds as HDAC10 inhibitors from a large chemical database. Moreover, Bayesian classification and Recursive partitioning models were used to identify the structural fingerprints regulating the HDAC10 inhibitory activity. Additionally, a molecular docking study was performed to understand the binding pattern of the identified structural fingerprints towards the active site of HDAC10. Overall, the modeling insight might offer helpful information for medicinal chemists to design and develop efficient HDAC10 inhibitors.
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Affiliation(s)
- Arijit Bhattacharya
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India
| | - Sk Abdul Amin
- Department of Pharmaceutical Technology, JIS University, 81, Nilgunj Road, Agarpara, Kolkata, West Bengal, India; Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India
| | - Prabhat Kumar
- Department of Computer Science, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India.
| | - Shovanlal Gayen
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India.
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20
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Wu T, Zhao B, Cai C, Chen Y, Miao Y, Chu J, Sui Y, Li F, Chen W, Cai Y, Wang F, Jin J. The Males Absent on the First (MOF) Mediated Acetylation Alters the Protein Stability and Transcriptional Activity of YY1 in HCT116 Cells. Int J Mol Sci 2023; 24:ijms24108719. [PMID: 37240065 DOI: 10.3390/ijms24108719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 05/09/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
Yin Yang 1 (YY1) is a well-known transcription factor that controls the expression of many genes and plays an important role in the occurrence and development of various cancers. We previously found that the human males absent on the first (MOF)-containing histone acetyltransferase (HAT) complex may be involved in regulating YY1 transcriptional activity; however, the precise interaction between MOF-HAT and YY1, as well as whether the acetylation activity of MOF impacts the function of YY1, has not been reported. Here, we present evidence that the MOF-containing male-specific lethal (MSL) HAT complex regulates YY1 stability and transcriptional activity in an acetylation-dependent manner. First, the MOF/MSL HAT complex was bound to and acetylated YY1, and this acetylation further promoted the ubiquitin-proteasome degradation pathway of YY1. The MOF-mediated degradation of YY1 was mainly related to the 146-270 amino acid residues of YY1. Further research clarified that acetylation-mediated ubiquitin degradation of YY1 mainly occurred through lysine 183. A mutation at the YY1K183 site was sufficient to alter the expression level of p53-mediated downstream target genes, such as CDKN1A (encoding p21), and it also suppressed the transactivation of YY1 on CDC6. Furthermore, a YY1K183R mutant and MOF remarkably antagonized the clone-forming ability of HCT116 and SW480 cells facilitated by YY1, suggesting that the acetylation-ubiquitin mode of YY1 plays an important role in tumor cell proliferation. These data may provide new strategies for the development of therapeutic drugs for tumors with high expression of YY1.
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Affiliation(s)
- Tingting Wu
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Bingxin Zhao
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Chengyu Cai
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Yuyang Chen
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Yujuan Miao
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Jinmeng Chu
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Yi Sui
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Fuqiang Li
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Wenqi Chen
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Yong Cai
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Fei Wang
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Jingji Jin
- School of Life Sciences, Jilin University, Changchun 130012, China
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21
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Yang Y, Bhargava D, Chen X, Zhou T, Dursuk G, Jiang W, Wang J, Zong Z, Katz SI, Lomberk GA, Urrutia RA, Katz JP. KLF5 and p53 comprise an incoherent feed-forward loop directing cell-fate decisions following stress. Cell Death Dis 2023; 14:299. [PMID: 37130837 PMCID: PMC10154356 DOI: 10.1038/s41419-023-05731-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 03/01/2023] [Accepted: 03/13/2023] [Indexed: 05/04/2023]
Abstract
In response to stress, cells make a critical decision to arrest or undergo apoptosis, mediated in large part by the tumor suppressor p53. Yet the mechanisms of these cell fate decisions remain largely unknown, particularly in normal cells. Here, we define an incoherent feed-forward loop in non-transformed human squamous epithelial cells involving p53 and the zinc-finger transcription factor KLF5 that dictates responses to differing levels of cellular stress from UV irradiation or oxidative stress. In normal unstressed human squamous epithelial cells, KLF5 complexes with SIN3A and HDAC2 repress TP53, allowing cells to proliferate. With moderate stress, this complex is disrupted, and TP53 is induced; KLF5 then acts as a molecular switch for p53 function by transactivating AKT1 and AKT3, which direct cells toward survival. By contrast, severe stress results in KLF5 loss, such that AKT1 and AKT3 are not induced, and cells preferentially undergo apoptosis. Thus, in human squamous epithelial cells, KLF5 gates the response to UV or oxidative stress to determine the p53 output of growth arrest or apoptosis.
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Affiliation(s)
- Yizeng Yang
- Division of Gastroenterology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Dharmendra Bhargava
- Division of Gastroenterology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Xiao Chen
- Department of Radiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Taicheng Zhou
- Division of Gastroenterology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Gizem Dursuk
- Division of Gastroenterology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Wenpeng Jiang
- Division of Gastroenterology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Jinshen Wang
- Division of Gastroenterology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Zhen Zong
- Division of Gastroenterology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Sharyn I Katz
- Department of Radiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Gwen A Lomberk
- Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Raul A Urrutia
- Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Jonathan P Katz
- Division of Gastroenterology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
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22
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Yu Q, Zhao G, Liu J, Peng Y, Xu X, Zhao F, Shi Y, Jin C, Zhang J, Wei B. The role of histone deacetylases in cardiac energy metabolism in heart diseases. Metabolism 2023; 142:155532. [PMID: 36889378 DOI: 10.1016/j.metabol.2023.155532] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/08/2023]
Abstract
Heart diseases are associated with substantial morbidity and mortality worldwide. The underlying mechanisms and pathological changes associated with cardiac diseases are exceptionally complex. Highly active cardiomyocytes require sufficient energy metabolism to maintain their function. Under physiological conditions, the choice of fuel is a delicate process that depends on the whole body and organs to support the normal function of heart tissues. However, disordered cardiac metabolism has been discovered to play a key role in many forms of heart diseases, including ischemic heart disease, cardiac hypertrophy, heart failure, and cardiac injury induced by diabetes or sepsis. Regulation of cardiac metabolism has recently emerged as a novel approach to treat heart diseases. However, little is known about cardiac energy metabolic regulators. Histone deacetylases (HDACs), a class of epigenetic regulatory enzymes, are involved in the pathogenesis of heart diseases, as reported in previous studies. Notably, the effects of HDACs on cardiac energy metabolism are gradually being explored. Our knowledge in this respect would facilitate the development of novel therapeutic strategies for heart diseases. The present review is based on the synthesis of our current knowledge concerning the role of HDAC regulation in cardiac energy metabolism in heart diseases. In addition, the role of HDACs in different models is discussed through the examples of myocardial ischemia, ischemia/reperfusion, cardiac hypertrophy, heart failure, diabetic cardiomyopathy, and diabetes- or sepsis-induced cardiac injury. Finally, we discuss the application of HDAC inhibitors in heart diseases and further prospects, thus providing insights into new treatment possibilities for different heart diseases.
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Affiliation(s)
- Qingwen Yu
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, School of Pharmaceutical Sciences, Zhengzhou University, No. 100 Kexue Avenue, Zhengzhou, Henan 450001, PR China
| | - Guangyuan Zhao
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, School of Pharmaceutical Sciences, Zhengzhou University, No. 100 Kexue Avenue, Zhengzhou, Henan 450001, PR China
| | - Jingjing Liu
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, School of Pharmaceutical Sciences, Zhengzhou University, No. 100 Kexue Avenue, Zhengzhou, Henan 450001, PR China
| | - Yajie Peng
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, School of Pharmaceutical Sciences, Zhengzhou University, No. 100 Kexue Avenue, Zhengzhou, Henan 450001, PR China
| | - Xueli Xu
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, School of Pharmaceutical Sciences, Zhengzhou University, No. 100 Kexue Avenue, Zhengzhou, Henan 450001, PR China
| | - Fei Zhao
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, School of Pharmaceutical Sciences, Zhengzhou University, No. 100 Kexue Avenue, Zhengzhou, Henan 450001, PR China
| | - Yangyang Shi
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, School of Pharmaceutical Sciences, Zhengzhou University, No. 100 Kexue Avenue, Zhengzhou, Henan 450001, PR China
| | - Chengyun Jin
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, School of Pharmaceutical Sciences, Zhengzhou University, No. 100 Kexue Avenue, Zhengzhou, Henan 450001, PR China
| | - Ji Zhang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, PR China.
| | - Bo Wei
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, School of Pharmaceutical Sciences, Zhengzhou University, No. 100 Kexue Avenue, Zhengzhou, Henan 450001, PR China.
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23
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Luo G, Liu B, Fu T, Liu Y, Li B, Li N, Geng Q. The Role of Histone Deacetylases in Acute Lung Injury-Friend or Foe. Int J Mol Sci 2023; 24:ijms24097876. [PMID: 37175583 PMCID: PMC10178380 DOI: 10.3390/ijms24097876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/04/2023] [Accepted: 04/14/2023] [Indexed: 05/15/2023] Open
Abstract
Acute lung injury (ALI), caused by intrapulmonary or extrapulmonary factors such as pneumonia, shock, and sepsis, eventually disrupts the alveolar-capillary barrier, resulting in diffuse pulmonary oedema and microatasis, manifested by refractory hypoxemia, and respiratory distress. Not only is ALI highly lethal, but even if a patient survives, there are also multiple sequelae. Currently, there is no better treatment than supportive care, and we urgently need to find new targets to improve ALI. Histone deacetylases (HDACs) are epigenetically important enzymes that, together with histone acetylases (HATs), regulate the acetylation levels of histones and non-histones. While HDAC inhibitors (HDACis) play a therapeutic role in cancer, inflammatory, and neurodegenerative diseases, there is also a large body of evidence suggesting the potential of HDACs as therapeutic targets in ALI. This review explores the unique mechanisms of HDACs in different cell types of ALI, including macrophages, pulmonary vascular endothelial cells (VECs), alveolar epithelial cells (AECs), and neutrophils.
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Affiliation(s)
- Guoqing Luo
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Bohao Liu
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Tinglv Fu
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Yi Liu
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Boyang Li
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Ning Li
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Qing Geng
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
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24
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N 6-methyladenosine of Spi2a attenuates inflammation and sepsis-associated myocardial dysfunction in mice. Nat Commun 2023; 14:1185. [PMID: 36864027 PMCID: PMC9979126 DOI: 10.1038/s41467-023-36865-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 02/17/2023] [Indexed: 03/04/2023] Open
Abstract
Bacteria-triggered sepsis is characterized by systemic, uncontrolled inflammation in affected individuals. Controlling the excessive production of pro-inflammatory cytokines and subsequent organ dysfunction in sepsis remains challenging. Here, we demonstrate that Spi2a upregulation in lipopolysaccharide (LPS)-stimulated bone marrow-derived macrophages reduces the production of pro-inflammatory cytokines and myocardial impairment. In addition, exposure to LPS upregulates the lysine acetyltransferase, KAT2B, to promote METTL14 protein stability through acetylation at K398, leading to the increased m6A methylation of Spi2a in macrophages. m6A-methylated Spi2a directly binds to IKKβ to impair IKK complex formation and inactivate the NF-κB pathway. The loss of m6A methylation in macrophages aggravates cytokine production and myocardial damage in mice under septic conditions, whereas forced expression of Spi2a reverses this phenotype. In septic patients, the mRNA expression levels of the human orthologue SERPINA3 negatively correlates with those of the cytokines, TNF, IL-6, IL-1β and IFNγ. Altogether, these findings suggest that m6A methylation of Spi2a negatively regulates macrophage activation in the context of sepsis.
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25
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Histone acetyltransferase 1 (HAT1) acetylates hypoxia-inducible factor 2 alpha (HIF2A) to execute hypoxia response. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194900. [PMID: 36410688 DOI: 10.1016/j.bbagrm.2022.194900] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 11/15/2022] [Accepted: 11/15/2022] [Indexed: 11/20/2022]
Abstract
Hypoxic response to low oxygen levels is characteristic of most solid cancers. Hypoxia-inducible factors (HIFs) regulate cellular metabolism, survival, proliferation, and cancer stem cell growth during hypoxia. The genome-wide analysis identified HAT1, a type B histone acetyltransferase, as an upregulated and essential gene in glioblastoma (GBM). GSEA analysis of differentially regulated genes in HAT1 silenced cells identified significant depletion of "hypoxia" gene sets. Hypoxia conditions induced HIF2A, not HIF1A protein levels in glioma cells in a HAT1-dependent manner. HAT1 and HIF2A interacted with each other and occupied the promoter of VEGFA, a bonafide HIF1A/HIF2A target. Acetylation of K512 and K596 residues by HAT1 is essential for HIF2A stabilization under normoxia and hypoxia as HIF2A carrying acetylation mimic mutations at either of these residues (H512Q or K596Q) showed stable expression in HAT1 silenced cells under normoxia and hypoxia conditions. Finally, we demonstrate that the HAT1-HIF2A axis is essential for hypoxia-promoted cancer stem cell maintenance and reprogramming. Thus, our study identifies that the HAT1-dependent acetylation of HIF2A is vital to executing the hypoxia-induced cell survival and cancer stem cell growth, therefore proposing the HAT1-HIF2A axis as a potential therapeutic target.
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26
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Zou L, Yang Y, Wang Z, Fu X, He X, Song J, Li T, Ma H, Yu T. Lysine Malonylation and Its Links to Metabolism and Diseases. Aging Dis 2023; 14:84-98. [PMID: 36818560 PMCID: PMC9937698 DOI: 10.14336/ad.2022.0711] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 07/11/2022] [Indexed: 11/18/2022] Open
Abstract
Malonylation is a recently identified post-translational modification with malonyl-coenzyme A as the donor. It conserved both in prokaryotes and eukaryotes. Recent advances in the identification and quantification of lysine malonylation by bioinformatic analysis have improved our understanding of its role in the regulation of protein activity, interaction, and localization and have elucidated its involvement in many biological processes. Malonylation has been linked to diverse physiological processes, including metabolic disorders, inflammation, and immune regulation. This review discusses malonylation in theory, describes the underlying mechanism, and summarizes the recent progress in malonylation research. The latest findings point to novel functions of malonylation and highlight the mechanisms by which malonylation regulates a variety of cellular processes. Our review also marks the association between lysine malonylation, the enzymes involved, and various diseases, and discusses promising diagnostic and therapeutic biomolecular targets for future clinical applications.
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Affiliation(s)
- Lu Zou
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao, China.
| | - Yanyan Yang
- Department of Immunology, Basic Medicine School, Qingdao University, Qingdao, China.
| | - Zhibin Wang
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Qingdao, China.
| | - Xiuxiu Fu
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Qingdao, China.
| | - Xiangqin He
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Qingdao, China.
| | - Jiayi Song
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao, China.
| | - Tianxiang Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao, China.
| | - Huibo Ma
- Department of Vascular Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China.
| | - Tao Yu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao, China.,Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Qingdao, China.,Correspondence should be addressed to: Dr. Tao Yu, Center for Regenerative Medicine, Institute for Translational Medicine, the Affiliated Hospital of Qingdao University, Qingdao, China.
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27
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Targeting histone deacetylases for cancer therapy: Trends and challenges. Acta Pharm Sin B 2023. [DOI: 10.1016/j.apsb.2023.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023] Open
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28
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Garza-Domínguez R, Torres-Quiroz F. Evolutionary Signals in Coronaviral Structural Proteins Suggest Possible Complex Mechanisms of Post-Translational Regulation in SARS-CoV-2 Virus. Viruses 2022; 14:v14112469. [PMID: 36366566 PMCID: PMC9696223 DOI: 10.3390/v14112469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 10/18/2022] [Accepted: 10/31/2022] [Indexed: 11/11/2022] Open
Abstract
Post-translational regulation of proteins has emerged as a central topic of research in the field of functional proteomics. Post-translational modifications (PTMs) dynamically control the activities of proteins and are involved in a wide range of biological processes. Crosstalk between different types of PTMs represents a key mechanism of regulation and signaling. Due to the current pandemic of the novel and dangerous SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) virus, here we present an in silico analysis of different types of PTMs in structural proteins of coronaviruses. A dataset of PTM sites was studied at three levels: conservation analysis, mutational analysis and crosstalk analysis. We identified two sets of PTMs which could have important functional roles in the regulation of the structural proteins of coronaviruses. Additionally, we found seven interesting signals of potential crosstalk events. These results reveal a higher level of complexity in the mechanisms of post-translational regulation of coronaviral proteins and provide new insights into the adaptation process of the SARS-CoV-2 virus.
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29
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Kaur S, Rajoria P, Chopra M. HDAC6: A unique HDAC family member as a cancer target. Cell Oncol (Dordr) 2022; 45:779-829. [PMID: 36036883 DOI: 10.1007/s13402-022-00704-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/10/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND HDAC6, a structurally and functionally distinct member of the HDAC family, is an integral part of multiple cellular functions such as cell proliferation, apoptosis, senescence, DNA damage and genomic stability, all of which when deregulated contribute to carcinogenesis. Among several HDAC family members known so far, HDAC6 holds a unique position. It differs from the other HDAC family members not only in terms of its subcellular localization, but also in terms of its substrate repertoire and hence cellular functions. Recent findings have considerably expanded the research related to the substrate pool, biological functions and regulation of HDAC6. Studies in HDAC6 knockout mice highlighted the importance of HDAC6 as a cell survival player in stressful situations, making it an important anticancer target. There is ample evidence stressing the importance of HDAC6 as an anti-cancer synergistic partner of many chemotherapeutic drugs. HDAC6 inhibitors have been found to enhance the effectiveness of conventional chemotherapeutic drugs such as DNA damaging agents, proteasome inhibitors and microtubule inhibitors, thereby highlighting the importance of combination therapies involving HDAC6 inhibitors and other anti-cancer agents. CONCLUSIONS Here, we present a review on HDAC6 with emphasis on its role as a critical regulator of specific physiological cellular pathways which when deregulated contribute to tumorigenesis, thereby highlighting the importance of HDAC6 inhibitors as important anticancer agents alone and in combination with other chemotherapeutic drugs. We also discuss the synergistic anticancer effect of combination therapies of HDAC6 inhibitors with conventional chemotherapeutic drugs.
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Affiliation(s)
- Sumeet Kaur
- Laboratory of Molecular Modeling and Anticancer Drug Development, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, 110007, India
| | - Prerna Rajoria
- Laboratory of Molecular Modeling and Anticancer Drug Development, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, 110007, India
| | - Madhu Chopra
- Laboratory of Molecular Modeling and Anticancer Drug Development, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, 110007, India.
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30
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Deng Y, Gao J, Xu G, Yao Y, Sun Y, Shi Y, Hao X, Niu L, Li H. HDAC6-dependent deacetylation of AKAP12 dictates its ubiquitination and promotes colon cancer metastasis. Cancer Lett 2022; 549:215911. [PMID: 36122629 DOI: 10.1016/j.canlet.2022.215911] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/26/2022] [Accepted: 09/06/2022] [Indexed: 11/02/2022]
Abstract
Aberrant expression of histone deacetylase 6 (HDAC6) is greatly involved in neoplasm metastasis, which is a leading cause of colon cancer related death. Thus, deep understanding of the regulatory mechanisms of HDAC6 in the metastasis of colon cancer is warranted. In this study, we firstly found that HDAC6 expression was highly expressed in metastatic colon cancer tissues and inhibition or knockdown of HDAC6 suppressed colon cancer metastasis. Next, based on proteomic analysis we uncovered A-kinase anchoring protein 12 (AKAP12) was a novel substrate of HDAC6. HDAC6 interacted with AKAP12 and deacetylated the K526/K531 residues of AKAP12. Moreover, deacetylation of AKAP12 at K531 by HDAC6 increased its ubiquitination level, which facilitated AKAP12 proteasome-dependent degradation. Importantly, we observed an inverse correlation between AKAP12 and HDAC6 protein levels with human colon cancer specimens. Further deletion of AKAP12 in HDAC6 knockdown cells restored the cell motility defects and reactivated the protein kinase C isoforms, repression of which were responsible for the inhibition of cancer metastasis of AKAP12. Our study identified AKAP12 was a new interactor and substrate of HDAC6 and uncovered a novel mechanism through which HDAC6-dependent AKAP12 deacetylation led to its ubiquitination mediated degradation and promoted colon cancer metastasis.
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Affiliation(s)
- Yilin Deng
- Department of Gastrointestinal Cancer Biology, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China; Phase I Clinical Trial Ward, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China; Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Jinjin Gao
- Department of Gastrointestinal Cancer Biology, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China; Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Guangying Xu
- Department of Gastrointestinal Cancer Biology, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China; Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Yuan Yao
- Department of Gastrointestinal Cancer Biology, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China; Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Yan Sun
- Department of Pathology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Yehui Shi
- Phase I Clinical Trial Ward, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China; Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Xishan Hao
- Department of Gastrointestinal Cancer Biology, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China; Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Liling Niu
- Department of Gastrointestinal Cancer Biology, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China; Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China.
| | - Hui Li
- Department of Gastrointestinal Cancer Biology, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China; Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China.
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31
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Zhu Y, Lin X, Zhou X, Prochownik EV, Wang F, Li Y. Posttranslational control of lipogenesis in the tumor microenvironment. J Hematol Oncol 2022; 15:120. [PMID: 36038892 PMCID: PMC9422141 DOI: 10.1186/s13045-022-01340-1] [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: 04/13/2022] [Accepted: 08/11/2022] [Indexed: 11/30/2022] Open
Abstract
Metabolic reprogramming of cancer cells within the tumor microenvironment typically occurs in response to increased nutritional, translation and proliferative demands. Altered lipid metabolism is a marker of tumor progression that is frequently observed in aggressive tumors with poor prognosis. Underlying these abnormal metabolic behaviors are posttranslational modifications (PTMs) of lipid metabolism-related enzymes and other factors that can impact their activity and/or subcellular localization. This review focuses on the roles of these PTMs and specifically on how they permit the re-wiring of cancer lipid metabolism, particularly within the context of the tumor microenvironment.
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Affiliation(s)
- Yahui Zhu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China.,Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, 430071, China.,School of Medicine, Chongqing University, Chongqing, 400030, China
| | - Xingrong Lin
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China.,Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, 430071, China
| | - Xiaojun Zhou
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China.,Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, 430071, China
| | - Edward V Prochownik
- Division of Hematology/Oncology, Children's Hospital of Pittsburgh of UPMC, The Department of Microbiology and Molecular Genetics, The Pittsburgh Liver Research Center and The Hillman Cancer Center of UPMC, The University of Pittsburgh Medical Center, Pittsburgh, PA, 15224, USA
| | - Fubing Wang
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430072, China.
| | - Youjun Li
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China. .,Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, 430071, China.
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32
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Chen Z, Liu X, Li F, Li C, Marquez-Lago T, Leier A, Webb GI, Xu D, Akutsu T, Song J. Systematic Characterization of Lysine Post-translational Modification Sites Using MUscADEL. Methods Mol Biol 2022; 2499:205-219. [PMID: 35696083 DOI: 10.1007/978-1-0716-2317-6_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Among various types of protein post-translational modifications (PTMs), lysine PTMs play an important role in regulating a wide range of functions and biological processes. Due to the generation and accumulation of enormous amount of protein sequence data by ongoing whole-genome sequencing projects, systematic identification of different types of lysine PTM substrates and their specific PTM sites in the entire proteome is increasingly important and has therefore received much attention. Accordingly, a variety of computational methods for lysine PTM identification have been developed based on the combination of various handcrafted sequence features and machine-learning techniques. In this chapter, we first briefly review existing computational methods for lysine PTM identification and then introduce a recently developed deep learning-based method, termed MUscADEL (Multiple Scalable Accurate Deep Learner for lysine PTMs). Specifically, MUscADEL employs bidirectional long short-term memory (BiLSTM) recurrent neural networks and is capable of predicting eight major types of lysine PTMs in both the human and mouse proteomes. The web server of MUscADEL is publicly available at http://muscadel.erc.monash.edu/ for the research community to use.
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Affiliation(s)
- Zhen Chen
- Key Laboratory of Rice Biology in Henan Province, Henan Agricultural University, Zhengzhou, China
| | - Xuhan Liu
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Fuyi Li
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Chen Li
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, Australia
| | - Tatiana Marquez-Lago
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Cell, Developmental and Integrative Biology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - André Leier
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Cell, Developmental and Integrative Biology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Geoffrey I Webb
- Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC, Australia
| | - Dakang Xu
- Faculty of Medical Laboratory Science, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Department of Molecular and Translational Science, Faculty of Medicine, Hudson Institute of Medical Research, Monash University, Melbourne, VIC, Australia
| | - Tatsuya Akutsu
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, Japan.
| | - Jiangning Song
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, Australia.
- Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC, Australia.
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33
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Yin BK, Wang ZQ. Beyond HAT Adaptor: TRRAP Liaisons with Sp1-Mediated Transcription. Int J Mol Sci 2021; 22:12445. [PMID: 34830324 PMCID: PMC8625110 DOI: 10.3390/ijms222212445] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/09/2021] [Accepted: 11/15/2021] [Indexed: 12/19/2022] Open
Abstract
The members of the phosphatidylinositol 3-kinase-related kinase (PIKK) family play vital roles in multiple biological processes, including DNA damage response, metabolism, cell growth, mRNA decay, and transcription. TRRAP, as the only member lacking the enzymatic activity in this family, is an adaptor protein for several histone acetyltransferase (HAT) complexes and a scaffold protein for multiple transcription factors. TRRAP has been demonstrated to regulate various cellular functions in cell cycle progression, cell stemness maintenance and differentiation, as well as neural homeostasis. TRRAP is known to be an important orchestrator of many molecular machineries in gene transcription by modulating the activity of some key transcription factors, including E2F1, c-Myc, p53, and recently, Sp1. This review summarizes the biological and biochemical studies on the action mode of TRRAP together with the transcription factors, focusing on how TRRAP-HAT mediates the transactivation of Sp1-governing biological processes, including neurodegeneration.
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Affiliation(s)
- Bo-Kun Yin
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), 07745 Jena, Germany;
| | - Zhao-Qi Wang
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), 07745 Jena, Germany;
- Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany
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34
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Li W, Feng W, Su X, Luo D, Li Z, Zhou Y, Zhu Y, Zhang M, Chen J, Liu B, Huang H. SIRT6 protects vascular smooth muscle cell from osteogenic transdifferentiation via Runx2 in chronic kidney disease. J Clin Invest 2021; 132:150051. [PMID: 34793336 PMCID: PMC8718147 DOI: 10.1172/jci150051] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 11/12/2021] [Indexed: 12/03/2022] Open
Abstract
Vascular calcification (VC) is regarded as an important pathological change lacking effective treatment and associated with high mortality. Sirtuin 6 (SIRT6) is a member of the Sirtuin family, a class III histone deacetylase and a key epigenetic regulator. SIRT6 has a protective role in patients with chronic kidney disease (CKD). However, the exact role and molecular mechanism of SIRT6 in VC in patients with CKD remain unclear. Here, we demonstrated that SIRT6 was markedly downregulated in peripheral blood mononuclear cells (PBMCs) and in the radial artery tissue of patients with CKD with VC. SIRT6-transgenic (SIRT6-Tg) mice showed alleviated VC, while vascular smooth muscle cell–specific (VSMC-specific) SIRT6 knocked-down mice showed severe VC in CKD. SIRT6 suppressed the osteogenic transdifferentiation of VSMCs via regulation of runt-related transcription factor 2 (Runx2). Coimmunoprecipitation (co-IP) and immunoprecipitation (IP) assays confirmed that SIRT6 bound to Runx2. Moreover, Runx2 was deacetylated by SIRT6 and further promoted nuclear export via exportin 1 (XPO1), which in turn caused degradation of Runx2 through the ubiquitin-proteasome system. These results demonstrated that SIRT6 prevented VC by suppressing the osteogenic transdifferentiation of VSMCs, and as such targeting SIRT6 may be an appealing therapeutic target for VC in CKD.
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Affiliation(s)
- Wenxin Li
- Department of Cardiology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Weijing Feng
- Department of Cardiology, Nanfang Hospital, Southern Medical University, Shenzhen, China
| | - Xiaoyan Su
- Department of Nephropathy, Tungwah Hospital of Sun Yat-Sen University, Dongguan, China
| | - Dongling Luo
- Department of Cardiology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Zhibing Li
- Department of Cardiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yongqiao Zhou
- Department of Cardiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yongjun Zhu
- Department of Cardiology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Mengbi Zhang
- Department of Nephropathy, Tungwah Hospital of Sun Yat-Sen University, Dongguan, China
| | - Jie Chen
- Department of Radiation Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Baohua Liu
- Shenzhen University Health Science Center, ShenZhen University, Shenzhen, China
| | - Hui Huang
- Department of Cardiology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
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35
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Kats I, Reinbold C, Kschonsak M, Khmelinskii A, Armbruster L, Ruppert T, Knop M. Up-regulation of ubiquitin-proteasome activity upon loss of NatA-dependent N-terminal acetylation. Life Sci Alliance 2021; 5:5/2/e202000730. [PMID: 34764209 PMCID: PMC8605321 DOI: 10.26508/lsa.202000730] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 11/26/2022] Open
Abstract
Inactivation of N-terminal acetyltransferase A is found to alter Rpn4 as well as E3 ligase abundance, causing up-regulation of Ubiquitin–proteasome activity. In this context, Tom1 is also identified as a novel chain-elongating enzyme of the UFD-pathway. N-terminal acetylation is a prominent protein modification, and inactivation of N-terminal acetyltransferases (NATs) cause protein homeostasis stress. Using multiplexed protein stability profiling with linear ubiquitin fusions as reporters for the activity of the ubiquitin proteasome system, we observed increased ubiquitin proteasome system activity in NatA, but not NatB or NatC mutants. We find several mechanisms contributing to this behavior. First, NatA-mediated acetylation of the N-terminal ubiquitin–independent degron regulates the abundance of Rpn4, the master regulator of the expression of proteasomal genes. Second, the abundance of several E3 ligases involved in degradation of UFD substrates is increased in cells lacking NatA. Finally, we identify the E3 ligase Tom1 as a novel chain-elongating enzyme (E4) involved in the degradation of linear ubiquitin fusions via the formation of branched K11, K29, and K48 ubiquitin chains, independently of the known E4 ligases involved in UFD, leading to enhanced ubiquitination of the UFD substrates.
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Affiliation(s)
- Ilia Kats
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Christian Reinbold
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Marc Kschonsak
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | | | - Laura Armbruster
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Thomas Ruppert
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Michael Knop
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany .,Deutsches Krebsforschungszentrum (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
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36
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Shimizu K, Gi M, Suzuki S, North BJ, Watahiki A, Fukumoto S, Asara JM, Tokunaga F, Wei W, Inuzuka H. Interplay between protein acetylation and ubiquitination controls MCL1 protein stability. Cell Rep 2021; 37:109988. [PMID: 34758305 PMCID: PMC8621139 DOI: 10.1016/j.celrep.2021.109988] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 06/02/2021] [Accepted: 10/21/2021] [Indexed: 01/29/2023] Open
Abstract
The anti-apoptotic myeloid cell leukemia 1 (MCL1) protein belongs to the pro-survival BCL2 family and is frequently amplified or elevated in human cancers. MCL1 is highly unstable, with its stability being regulated by phosphorylation and ubiquitination. Here, we identify acetylation as another critical post-translational modification regulating MCL1 protein stability. We demonstrate that the lysine acetyltransferase p300 targets MCL1 at K40 for acetylation, which is counteracted by the deacetylase sirtuin 3 (SIRT3). Mechanistically, acetylation enhances MCL1 interaction with USP9X, resulting in deubiquitination and subsequent MCL1 stabilization. Therefore, ectopic expression of acetylation-mimetic MCL1 promotes apoptosis evasion of cancer cells, enhances colony formation potential, and facilitates xenografted tumor progression. We further demonstrate that elevated MCL1 acetylation sensitizes multiple cancer cells to pharmacological inhibition of USP9X. These findings reveal that acetylation of MCL1 is a critical post-translational modification enhancing its oncogenic function and provide a rationale for developing innovative therapeutic strategies for MCL1-dependent tumors. MCL1, an anti-apoptotic BCL2 family protein, is frequently overexpressed in a variety of cancers, and its oncogenic function is finely regulated by post-translational modifications such as phosphorylation and ubiquitination. Shimizu et al. dissect the molecular mechanism of acetylation-mediated MCL1 stability control, providing insights into potential therapeutic intervention targeting the MCL1 protein.
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Affiliation(s)
- Kouhei Shimizu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; Center for Advanced Stem Cell and Regenerative Research, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan; Department of Pathobiochemistry, Graduate School of Medicine, Osaka City University, Osaka 545-8585, Japan.
| | - Min Gi
- Department of Molecular Pathology, Graduate School of Medicine, Osaka City University, Osaka 545-8585, Japan; Department of Environmental Risk Assessment, Graduate School of Medicine, Osaka City University, Osaka 545-8585, Japan
| | - Shugo Suzuki
- Department of Molecular Pathology, Graduate School of Medicine, Osaka City University, Osaka 545-8585, Japan
| | - Brian J North
- Department of Biomedical Sciences, Creighton University, Omaha, NE 68178, USA
| | - Asami Watahiki
- Center for Advanced Stem Cell and Regenerative Research, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan
| | - Satoshi Fukumoto
- Center for Advanced Stem Cell and Regenerative Research, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan; Division of Pediatric Dentistry, Department of Oral Health and Development Sciences, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan; Section of Pediatric Dentistry, Division of Oral Health, Growth and Development, Kyushu University Faculty of Dental Science, Fukuoka 812-8582, Japan
| | - John M Asara
- Division of Signal Transduction, Beth Israel Deaconess Medical Center and Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
| | - Fuminori Tokunaga
- Department of Pathobiochemistry, Graduate School of Medicine, Osaka City University, Osaka 545-8585, Japan
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.
| | - Hiroyuki Inuzuka
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.
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37
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Peoples JN, Ghazal N, Duong DM, Hardin KR, Manning JR, Seyfried NT, Faundez V, Kwong JQ. Loss of the mitochondrial phosphate carrier SLC25A3 induces remodeling of the cardiac mitochondrial protein acylome. Am J Physiol Cell Physiol 2021; 321:C519-C534. [PMID: 34319827 DOI: 10.1152/ajpcell.00156.2021] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Mitochondria are recognized as signaling organelles because, under stress, mitochondria can trigger various signaling pathways to coordinate the cell's response. The specific pathway(s) engaged by mitochondria in response to mitochondrial energy defects in vivo and in high-energy tissues like the heart are not fully understood. Here, we investigated cardiac pathways activated in response to mitochondrial energy dysfunction by studying mice with cardiomyocyte-specific loss of the mitochondrial phosphate carrier (SLC25A3), an established model that develops cardiomyopathy as a result of defective mitochondrial ATP synthesis. Mitochondrial energy dysfunction induced a striking pattern of acylome remodeling, with significantly increased post-translational acetylation and malonylation. Mass spectrometry-based proteomics further revealed that energy dysfunction-induced remodeling of the acetylome and malonylome preferentially impacts mitochondrial proteins. Acetylation and malonylation modified a highly interconnected interactome of mitochondrial proteins, and both modifications were present on the enzyme isocitrate dehydrogenase 2 (IDH2). Intriguingly, IDH2 activity was enhanced in SLC25A3-deleted mitochondria, and further study of IDH2 sites targeted by both acetylation and malonylation revealed that these modifications can have site-specific and distinct functional effects. Finally, we uncovered a novel crosstalk between the two modifications, whereby mitochondrial energy dysfunction-induced acetylation of sirtuin 5 (SIRT5), inhibited its function. Because SIRT5 is a mitochondrial deacylase with demalonylase activity, this finding suggests that acetylation can modulate the malonylome. Together, our results position acylations as an arm of the mitochondrial response to energy dysfunction and suggest a mechanism by which focal disruption to the energy production machinery can have an expanded impact on global mitochondrial function.
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Affiliation(s)
- Jessica N Peoples
- Division of Pediatric Cardiology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, United States
| | - Nasab Ghazal
- Division of Pediatric Cardiology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, United States
| | - Duc M Duong
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, United States
| | - Katherine R Hardin
- Graduate Program in Biochemistry, Cell and Developmental Biology, Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA, United States
| | - Janet R Manning
- Division of Cardiology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, United States
| | - Victor Faundez
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, United States
| | - Jennifer Q Kwong
- Division of Pediatric Cardiology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, United States.,Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, United States
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38
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Kervin TA, Wiseman BC, Overduin M. Phosphoinositide Recognition Sites Are Blocked by Metabolite Attachment. Front Cell Dev Biol 2021; 9:690461. [PMID: 34368138 PMCID: PMC8340361 DOI: 10.3389/fcell.2021.690461] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/18/2021] [Indexed: 12/16/2022] Open
Abstract
Membrane readers take part in trafficking and signaling processes by localizing proteins to organelle surfaces and transducing molecular information. They accomplish this by engaging phosphoinositides (PIs), a class of lipid molecules which are found in different proportions in various cellular membranes. The prototypes are the PX domains, which exhibit a range of specificities for PIs. Our meta-analysis indicates that recognition of membranes by PX domains is specifically controlled by modification of lysine and arginine residues including acetylation, hydroxyisobutyrylation, glycation, malonylation, methylation and succinylation of sidechains that normally bind headgroups of phospholipids including organelle-specific PI signals. Such metabolite-modulated residues in lipid binding elements are named MET-stops here to highlight their roles as erasers of membrane reader functions. These modifications are concentrated in the membrane binding sites of half of all 49 PX domains in the human proteome and correlate with phosphoregulatory sites, as mapped using the Membrane Optimal Docking Area (MODA) algorithm. As these motifs are mutated and modified in various cancers and the responsible enzymes serve as potential drug targets, the discovery of MET-stops as a widespread inhibitory mechanism may aid in the development of diagnostics and therapeutics aimed at the readers, writers and erasers of the PI code.
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Affiliation(s)
- Troy A Kervin
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Brittany C Wiseman
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.,Molecular and Cellular Biology, MacEwan University, Edmonton, AB, Canada.,SMALP Network, Edmonton, AB, Canada
| | - Michael Overduin
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.,SMALP Network, Edmonton, AB, Canada
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39
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Xu Q, Liu Q, Chen Z, Yue Y, Liu Y, Zhao Y, Zhou DX. Histone deacetylases control lysine acetylation of ribosomal proteins in rice. Nucleic Acids Res 2021; 49:4613-4628. [PMID: 33836077 PMCID: PMC8096213 DOI: 10.1093/nar/gkab244] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 03/21/2021] [Accepted: 04/08/2021] [Indexed: 01/04/2023] Open
Abstract
Lysine acetylation (Kac) is well known to occur in histones for chromatin function and epigenetic regulation. In addition to histones, Kac is also detected in a large number of proteins with diverse biological functions. However, Kac function and regulatory mechanism for most proteins are unclear. In this work, we studied mutation effects of rice genes encoding cytoplasm-localized histone deacetylases (HDAC) on protein acetylome and found that the HDAC protein HDA714 was a major deacetylase of the rice non-histone proteins including many ribosomal proteins (r-proteins) and translation factors that were extensively acetylated. HDA714 loss-of-function mutations increased Kac levels but reduced abundance of r-proteins. In vitro and in vivo experiments showed that HDA714 interacted with r-proteins and reduced their Kac. Substitutions of lysine by arginine (depleting Kac) in several r-proteins enhance, while mutations of lysine to glutamine (mimicking Kac) decrease their stability in transient expression system. Ribo-seq analysis revealed that the hda714 mutations resulted in increased ribosome stalling frequency. Collectively, the results uncover Kac as a functional posttranslational modification of r-proteins which is controlled by histone deacetylases, extending the role of Kac in gene expression to protein translational regulation.
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Affiliation(s)
- Qiutao Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Qian Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Zhengting Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Yaping Yue
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Yuan Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Yu Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Dao-Xiu Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China.,Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, University Paris-Saclay, 91405 Orsay, France
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40
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Histone deacetylase 10, a potential epigenetic target for therapy. Biosci Rep 2021; 41:228655. [PMID: 33997894 PMCID: PMC8182986 DOI: 10.1042/bsr20210462] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 11/17/2022] Open
Abstract
Histone deacetylase (HDAC) 10, a class II family, has been implicated in various tumors and non-tumor diseases, which makes the discovery of biological functions and novel inhibitors a fundamental endeavor. In cancers, HDAC10 plays crucial roles in regulating various cellular processes through its epigenetic functions or targeting some decisive molecular or signaling pathways. It also has potential clinical utility for targeting tumors and non-tumor diseases, such as renal cell carcinoma, prostate cancer, immunoglobulin A nephropathy (IgAN), intracerebral hemorrhage, human immunodeficiency virus (HIV) infection and schizophrenia. To date, relatively few studies have investigated HDAC10-specific inhibitors. Therefore, it is important to study the biological functions of HDAC10 for the future development of specific HDAC10 inhibitors. In this review, we analyzed the biological functions, mechanisms and inhibitors of HDAC10, which makes HDAC10 an appealing therapeutic target.
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41
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Wang N, Peng YJ, Su X, Prabhakar NR, Nanduri J. Histone Deacetylase 5 Is an Early Epigenetic Regulator of Intermittent Hypoxia Induced Sympathetic Nerve Activation and Blood Pressure. Front Physiol 2021; 12:688322. [PMID: 34079475 PMCID: PMC8165245 DOI: 10.3389/fphys.2021.688322] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 04/26/2021] [Indexed: 12/29/2022] Open
Abstract
Intermittent hypoxia (IH) is a hallmark manifestation of obstructive sleep apnea (OSA). Long term IH (LT-IH) triggers epigenetic reprogramming of the redox state involving DNA hypermethylation in the carotid body chemo reflex pathway resulting in persistent sympathetic activation and hypertension. Present study examined whether IH also activates epigenetic mechanism(s) other than DNA methylation. Histone modification by lysine acetylation is another major epigenetic mechanism associated with gene regulation. Equilibrium between the activities of histone acetyltransferases (HATs) and histone deacetylases (HDACs) determine the level of lysine acetylation. Here we report that exposure of rat pheochromocytoma (PC)-12 cells to IH in vitro exhibited reduced HDAC enzyme activity due to proteasomal degradation of HDAC3 and HDAC5 proteins. Mechanistic investigations showed that IH-evoked decrease in HDAC activity increases lysine acetylation of α subunit of hypoxia inducible factor (HIF)-1α as well as Histone (H3) protein resulting in increased HIF-1 transcriptional activity. Trichostatin A (TSA), an inhibitor of HDACs, mimicked the effects of IH. Studies on rats treated with 10 days of IH or TSA showed reduced HDAC activity, HDAC5 protein, and increased HIF-1 dependent NADPH oxidase (NOX)-4 transcription in adrenal medullae (AM) resulting in elevated plasma catecholamines and blood pressure. Likewise, heme oxygenase (HO)-2 null mice, which exhibit IH because of high incidence of spontaneous apneas (apnea index 72 ± 1.2 apnea/h), also showed decreased HDAC activity and HDAC5 protein in the AM along with elevated circulating norepinephrine levels. These findings demonstrate that lysine acetylation of histone and non-histone proteins is an early epigenetic mechanism associated with sympathetic nerve activation and hypertension in rodent models of IH.
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Affiliation(s)
- Ning Wang
- Institute for Integrative Physiology, Center for Systems Biology of O2 Sensing, The University of Chicago, Chicago, IL, United States
| | - Ying-Jie Peng
- Institute for Integrative Physiology, Center for Systems Biology of O2 Sensing, The University of Chicago, Chicago, IL, United States
| | - Xiaoyu Su
- Institute for Integrative Physiology, Center for Systems Biology of O2 Sensing, The University of Chicago, Chicago, IL, United States
| | - Nanduri R Prabhakar
- Institute for Integrative Physiology, Center for Systems Biology of O2 Sensing, The University of Chicago, Chicago, IL, United States
| | - Jayasri Nanduri
- Institute for Integrative Physiology, Center for Systems Biology of O2 Sensing, The University of Chicago, Chicago, IL, United States
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42
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Baldensperger T, Glomb MA. Pathways of Non-enzymatic Lysine Acylation. Front Cell Dev Biol 2021; 9:664553. [PMID: 33996820 PMCID: PMC8116961 DOI: 10.3389/fcell.2021.664553] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/07/2021] [Indexed: 12/18/2022] Open
Abstract
Posttranslational protein modification by lysine acylation is an emerging mechanism of cellular regulation and fine-tunes metabolic processes to environmental changes. In this review we focus on recently discovered pathways of non-enzymatic lysine acylation by reactive acyl-CoA species, acyl phosphates, and α-dicarbonyls. We summarize the metabolic sources of these highly reactive intermediates, demonstrate their reaction mechanisms, give an overview of the resulting acyl lysine modifications, and evaluate the consequences for cellular regulatory processes. Finally, we discuss interferences between lysine acylation and lysine ubiquitylation as a potential molecular mechanism of dysregulated protein homeostasis in aging and related diseases.
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Affiliation(s)
- Tim Baldensperger
- Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Nuthetal, Germany
| | - Marcus A Glomb
- Institute of Chemistry, Food Chemistry, Martin-Luther-University Halle-Wittenberg, Halle, Germany
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43
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Shmueli MD, Sheban D, Eisenberg-Lerner A, Merbl Y. Histone degradation by the proteasome regulates chromatin and cellular plasticity. FEBS J 2021; 289:3304-3316. [PMID: 33914417 PMCID: PMC9292675 DOI: 10.1111/febs.15903] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 04/07/2021] [Accepted: 04/26/2021] [Indexed: 11/27/2022]
Abstract
Histones constitute the primary protein building blocks of the chromatin and play key roles in the dynamic control of chromatin compaction and epigenetic regulation. Histones are regulated by intricate mechanisms that alter their functionality and stability, thereby expanding the regulation of chromatin‐transacting processes. As such, histone degradation is tightly regulated to provide spatiotemporal control of cellular histone abundance. While several mechanisms have been implicated in controlling histone stability, here, we discuss proteasome‐dependent degradation of histones and the protein modifications that are associated with it. We then highlight specific cellular and physiological states that are associated with altered histone degradation by cellular proteasomes.
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Affiliation(s)
- Merav D Shmueli
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Daoud Sheban
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Yifat Merbl
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
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44
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Identification of epigenetic factor KAT2B gene variants for possible roles in congenital heart diseases. Biosci Rep 2021; 40:222531. [PMID: 32239175 PMCID: PMC7160239 DOI: 10.1042/bsr20191779] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 03/23/2020] [Accepted: 03/31/2020] [Indexed: 02/06/2023] Open
Abstract
Congenital heart disease (CHD) is a group of anatomic malformations in the heart with high morbidity and mortality. The mammalian heart is a complex organ, the formation and development of which are strictly regulated and controlled by gene regulatory networks of many signaling pathways such as TGF-β. KAT2B is an important histone acetyltransferase epigenetic factor in the TGF-β signaling pathway, and alteration in the gene is associated with the etiology of cardiovascular diseases. The aim of this work was to validate whether KAT2B variations might be associated with CHD. We sequenced the KAT2B gene for 400 Chinese Han CHD patients and evaluated SNPs rs3021408 and rs17006625. The statistical analyses and Hardy-Weinberg equilibrium tests of the CHD and control populations were conducted by the software SPSS (version 19.0) and PLINK. The experiment-wide significance threshold matrix of LD correlation for the markers and haplotype diagram of LD structure were calculated using the online software SNPSpD and Haploview software. We analyzed the heterozygous variants within the CDS region of the KAT2B genes and found that rs3021408 and rs17006625 were associated with the risk of CHD.
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Shi YH, Zhang XL, Ying PJ, Wu ZQ, Lin LL, Chen W, Zheng GQ, Zhu WZ. Neuroprotective Effect of Astragaloside IV on Cerebral Ischemia/Reperfusion Injury Rats Through Sirt1/Mapt Pathway. Front Pharmacol 2021; 12:639898. [PMID: 33841157 PMCID: PMC8033022 DOI: 10.3389/fphar.2021.639898] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 02/17/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Ischemic stroke is a common disease with poor prognosis, which has become one of the leading causes of morbidity and mortality worldwide. Astragaloside IV (AS-IV) is the main bioactive ingredient of Astragali Radix (which has been used for ischemic stroke for thousands of years) and has been found to have multiple bioactivities in the nervous system. In the present study, we aimed to explore the neuroprotective effects of AS-IV in rats with cerebral ischemia/reperfusion (CIR) injury targeting the Sirt1/Mapt pathway. Methods: Sprague-Dawley rats (male, 250-280 g) were randomly divided into the Sham group, middle cerebral artery occlusion/reperfusion (MCAO/R) group, AS-IV group, MCAO/R + EX527 (SIRT1-specific inhibitor) group, and AS-IV + EX527 group. Each group was further assigned into several subgroups according to ischemic time (6 h, 1 d, 3 d, and 7 days). The CIR injury was induced in MCAO/R group, AS-IV group, MCAO/R + EX527 group, and AS-IV + EX527 group by MCAO surgery in accordance with the modified Zea Longa criteria. Modified Neurological Severity Scores (mNSS) were used to evaluate the neurological deficits; TTC (2,3,5-triphenyltetrazolium chloride) staining was used to detect cerebral infarction area; Western Blot was used to assess the protein levels of SIRT1, acetylated MAPT (ac-MAPT), phosphorylated MAPT (p-MAPT), and total MAPT (t-MAPT); Real-time Quantitative Polymerase Chain Reaction (qRT-PCR) was used in the detection of Sirt1 and Mapt transcriptions. Results: Compared with the MCAO/R group, AS-IV can significantly improve the neurological dysfunction (p < 0.05), reduce the infarction area (p < 0.05), raise the expression of SIRT1 (p < 0.05), and alleviate the abnormal hyperacetylation and hyperphosphorylation of MAPT (p < 0.05). While compared with the AS-IV group, AS-IV + EX527 group showed higher mNSS scores (p < 0.05), more severe cerebral infarction (p < 0.05), lower SIRT1 expression (p < 0.01), and higher ac-MAPT and p-MAPT levels (p < 0.05). Conclusion: AS-IV can improve the neurological deficit after CIR injury in rats and reduce the cerebral infarction area, which exerts neuroprotective effects probably through the Sirt1/Mapt pathway.
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Affiliation(s)
- Yi-Hua Shi
- Department of Neurology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xi-Le Zhang
- Department of Neurology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Peng-Jie Ying
- Department of Neurology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Zi-Qian Wu
- Department of Neurology, Wenzhou Hospital of Traditional Chinese Medicine Affiliated toZhejiang Chinese Medical University, Wenzhou, China
| | - Le-Le Lin
- Department of Neurology, Wenzhou Hospital of Traditional Chinese Medicine Affiliated toZhejiang Chinese Medical University, Wenzhou, China
| | - Wei Chen
- Department of Radiology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Guo-Qing Zheng
- Department of Neurology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Wen-Zong Zhu
- Department of Neurology, Wenzhou Hospital of Traditional Chinese Medicine Affiliated toZhejiang Chinese Medical University, Wenzhou, China
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Kumar M, Joshi G, Chatterjee J, Kumar R. Epidermal Growth Factor Receptor and its Trafficking Regulation by Acetylation: Implication in Resistance and Exploring the Newer Therapeutic Avenues in Cancer. Curr Top Med Chem 2021; 20:1105-1123. [PMID: 32031073 DOI: 10.2174/1568026620666200207100227] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 01/17/2020] [Accepted: 01/24/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND The EGFR is overexpressed in numerous cancers. So, it becomes one of the most favorable drug targets. Single-acting EGFR inhibitors on prolong use induce resistance and side effects. Inhibition of EGFR and/or its interacting proteins by dual/combined/multitargeted therapies can deliver more efficacious drugs with less or no resistance. OBJECTIVE The review delves deeper to cover the aspects of EGFR mediated endocytosis, leading to its trafficking, internalization, and crosstalk(s) with HDACs. METHODS AND RESULTS This review is put forth to congregate relevant literature evidenced on EGFR, its impact on cancer prognosis, inhibitors, and its trafficking regulation by acetylation along with the current strategies involved in targeting these proteins (EGFR and HDACs) successfully by involving dual/hybrid/combination chemotherapy. CONCLUSION The current information on cross-talk of EGFR and HDACs would likely assist researchers in designing and developing dual or multitargeted inhibitors through combining the required pharmacophores.
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Affiliation(s)
- Manvendra Kumar
- Laboratory for Drug Design and Synthesis, Department of Pharmaceutical Sciences and Natural Products, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, 151001, India
| | - Gaurav Joshi
- Laboratory for Drug Design and Synthesis, Department of Pharmaceutical Sciences and Natural Products, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, 151001, India
| | - Joydeep Chatterjee
- Laboratory for Drug Design and Synthesis, Department of Pharmaceutical Sciences and Natural Products, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, 151001, India
| | - Raj Kumar
- Laboratory for Drug Design and Synthesis, Department of Pharmaceutical Sciences and Natural Products, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, 151001, India
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Wen S, Li J, Yang J, Li B, Li N, Zhan X. Quantitative Acetylomics Revealed Acetylation-Mediated Molecular Pathway Network Changes in Human Nonfunctional Pituitary Neuroendocrine Tumors. Front Endocrinol (Lausanne) 2021; 12:753606. [PMID: 34712204 PMCID: PMC8546192 DOI: 10.3389/fendo.2021.753606] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 09/27/2021] [Indexed: 12/11/2022] Open
Abstract
Acetylation at lysine residue in a protein mediates multiple cellular biological processes, including tumorigenesis. This study aimed to investigate the acetylated protein profile alterations and acetylation-mediated molecular pathway changes in human nonfunctional pituitary neuroendocrine tumors (NF-PitNETs). The anti-acetyl antibody-based label-free quantitative proteomics was used to analyze the acetylomes between NF-PitNETs (n = 4) and control pituitaries (n = 4). A total of 296 acetylated proteins with 517 acetylation sites was identified, and the majority of which were significantly down-acetylated in NF-PitNETs (p<0.05 or only be quantified in NF-PitNETs/controls). These acetylated proteins widely functioned in cellular biological processes and signaling pathways, including metabolism, translation, cell adhesion, and oxidative stress. The randomly selected acetylated phosphoglycerate kinase 1 (PGK1), which is involved in glycolysis and amino acid biosynthesis, was further confirmed with immunoprecipitation and western blot in NF-PitNETs and control pituitaries. Among these acetylated proteins, 15 lysine residues within 14 proteins were down-acetylated and simultaneously up-ubiquitinated in NF-PitNETs to demonstrate a direct competition relationship between acetylation and ubiquitination. Moreover, the potential effect of protein acetylation alterations on NF-PitNETs invasiveness was investigated. Overlapping analysis between acetylomics data in NF-PitNETs and transcriptomics data in invasive NF-PitNETs identified 26 overlapped molecules. These overlapped molecules were mainly involved in metabolism-associated pathways, which means that acetylation-mediated metabolic reprogramming might be the molecular mechanism to affect NF-PitNET invasiveness. This study provided the first acetylomic profiling and acetylation-mediated molecular pathways in human NF-PitNETs, and offered new clues to elucidate the biological functions of protein acetylation in NF-PitNETs and discover novel biomarkers for early diagnosis and targeted therapy of NF-PitNETs.
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Affiliation(s)
- Siqi Wen
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Central South University, Changsha, China
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
| | - Jiajia Li
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Central South University, Changsha, China
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
| | - Jingru Yang
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
| | - Biao Li
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Central South University, Changsha, China
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
| | - Na Li
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
- Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, Jinan, China
| | - Xianquan Zhan
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
- Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, Jinan, China
- Gastroenterology Research Institute and Clinical Center, Shandong First Medical University, Jinan, China
- *Correspondence: Xianquan Zhan,
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Arias-Alvarado A, Aghayev M, Ilchenko S, Rachdaoui N, Lepp J, Tsai TH, Zhang GF, Previs S, Kasumov T. Measuring acetyl-CoA and acetylated histone turnover in vivo: Effect of a high fat diet. Anal Biochem 2020; 615:114067. [PMID: 33340539 DOI: 10.1016/j.ab.2020.114067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 12/08/2020] [Accepted: 12/13/2020] [Indexed: 11/24/2022]
Abstract
Cellular availability of acetyl-CoA, a central intermediate of metabolism, regulates histone acetylation. The impact of a high-fat diet (HFD) on the turnover rates of acetyl-CoA and acetylated histones is unknown. We developed a method for simultaneous measurement of acetyl-CoA and acetylated histones kinetics using a single 2H2O tracer, and used it to examine effect of HFD-induced perturbations on hepatic histone acetylation in LDLR-/- mice, a mouse model of non-alcoholic fatty liver disease (NAFLD). Mice were given 2H2O in the drinking water and the kinetics of hepatic acetyl-CoA, histones, and acetylated histones were quantified based on their 2H-labeling. Consumption of a high fat Western-diet (WD) for twelve weeks led to decreased acetylation of hepatic histones (p< 0.05), as compared to a control diet. These changes were associated with 1.5-3-fold increased turnover rates of histones without any change in acetyl-CoA flux. Acetylation significantly reduced the stability of histones and the turnover rates of acetylated peptides were correlated with the number of acetyl groups in neighboring lysine sites. We conclude that 2H2O-method can be used to study metabolically controlled histone acetylation and acetylated histone turnover in vivo.
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Affiliation(s)
- Andrea Arias-Alvarado
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH, 44272, USA
| | - Mirjavid Aghayev
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH, 44272, USA
| | - Serguei Ilchenko
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH, 44272, USA
| | - Nadia Rachdaoui
- Department of Animal Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Josephine Lepp
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH, 44272, USA
| | - Tsung-Heng Tsai
- Department of Mathematical Sciences, Kent State University, Kent, OH, 44242, USA
| | - Guo-Fang Zhang
- Division of Division of Endocrinology, Metabolism and Nutrition, Duke Molecular Physiology Institute, And Department of Medicine, Duke University, Durham, NC, 27701, USA
| | - Stephen Previs
- Merck & Co., Inc, 2000 Galloping Hill Rd, Kenilworth, NJ, 07033, USA
| | - Takhar Kasumov
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH, 44272, USA; Departments of Gastroenterology, Hepatology and Nutrition, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA.
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Abstract
The current TB treatment regimen involves a combination of drugs administered for an extended duration that could last for 6 months to 2 years. This could lead to noncompliance and the emergence of newer drug resistance strains. The worldwide increase in the frequency of multidrug-resistant and extensively drug-resistant cases of tuberculosis is mainly due to therapeutic noncompliance associated with a lengthy treatment regimen. Depending on the drug susceptibility profile, the treatment duration can extend from 6 months to 2 years. This protracted regimen is attributed to a supposedly nonreplicating and metabolically inert subset of the Mycobacterium tuberculosis population, called “persisters.” The mechanism underlying stochastic generation and enrichment of persisters is not fully known. We have previously reported that the utilization of host cholesterol is essential for mycobacterial persistence. In this study, we have demonstrated that cholesterol-induced activation of a RNase toxin (VapC12) inhibits translation by targeting proT tRNA in M. tuberculosis. This results in cholesterol-specific growth modulation that increases the frequency of generation of the persisters in a heterogeneous M. tuberculosis population. Also, a null mutant strain of this toxin (ΔvapC12) demonstrated an enhanced growth phenotype in a guinea pig model of M. tuberculosis infection, depicting its role in disease persistence. Thus, we have identified a novel strategy through which cholesterol-specific activation of a toxin-antitoxin module in M. tuberculosis enhances persister formation during infection. The current findings provide an opportunity to target persisters, a new paradigm facilitating tuberculosis drug development. IMPORTANCE The current TB treatment regimen involves a combination of drugs administered for an extended duration that could last for 6 months to 2 years. This could lead to noncompliance and the emergence of newer drug resistance strains. It is widely perceived that the major culprits are the so-called nonreplicating and metabolically inactive “persister” bacteria. The importance of cholesterol utilization during the persistence stage of M. tuberculosis infection and its potential role in the generation of persisters is very intriguing. We explored the mechanism involved in the cholesterol-mediated generation of persisters in mycobacteria. In this study, we have identified a toxin-antitoxin (TA) system essential for the generation of persisters during M. tuberculosis infection. This study verified that M. tuberculosis strain devoid of the VapBC12 TA system failed to persist and showed a hypervirulent phenotype in a guinea pig infection model. Our studies indicate that the M. tuberculosis VapBC12 TA system acts as a molecular switch regulating persister generation during infection. VapBC12 TA system as a drug target offers opportunities to develop shorter and more effective treatment regimens against tuberculosis.
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50
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Wang H, Liu YC, Zhu CY, Yan F, Wang MZ, Chen XS, Wang XK, Pang BX, Li YH, Liu DH, Gao CJ, Liu SJ, Dou LP. Chidamide increases the sensitivity of refractory or relapsed acute myeloid leukemia cells to anthracyclines via regulation of the HDAC3 -AKT-P21-CDK2 signaling pathway. J Exp Clin Cancer Res 2020; 39:278. [PMID: 33298132 PMCID: PMC7724824 DOI: 10.1186/s13046-020-01792-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 11/26/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Induction therapy for acute myeloid leukemia (AML) is an anthracycline-based chemotherapy regimen. However, many patients experience a relapse or exhibit refractory disease (R/R). There is an urgent need for more effective regimens to reverse anthracycline resistance in these patients. METHODS In this paper, Twenty-seven R/R AML patients with anthracycline resistance consecutively received chidamide in combination with anthracycline-based regimen as salvage therapy at the Chinese PLA General Hospital. RESULTS Of the 27 patients who had received one course of salvage therapy, 13 achieved a complete response and 1 achieved a partial response. We found that the HDAC3-AKT-P21-CDK2 signaling pathway was significantly upregulated in anthracycline-resistant AML cells compared to non-resistant cells. AML patients with higher levels of HDAC3 had lower event-free survival (EFS) and overall survival (OS) rates. Moreover, anthracycline-resistant AML cells are susceptible to chidamide, a histone deacetylase inhibitor which can inhibit cell proliferation, increase cell apoptosis and induce cell-cycle arrest in a time- and dose-dependent manner. Chidamide increases the sensitivity of anthracycline-resistant cells to anthracycline drugs, and these effects are associated with the inhibition of the HDAC3-AKT-P21-CDK2 signaling pathway. CONCLUSION Chidamide can increase anthracycline drug sensitivity by inhibiting HDAC3-AKT-P21-CDK2 signaling pathway, thus demonstrating the potential for application.
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MESH Headings
- Adolescent
- Adult
- Aged
- Aminopyridines/administration & dosage
- Animals
- Anthracyclines/administration & dosage
- Antineoplastic Combined Chemotherapy Protocols/pharmacology
- Apoptosis
- Benzamides/administration & dosage
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Cell Cycle
- Cell Proliferation
- Child
- Cyclin-Dependent Kinase 2/genetics
- Cyclin-Dependent Kinase 2/metabolism
- Cyclin-Dependent Kinase Inhibitor p21/genetics
- Cyclin-Dependent Kinase Inhibitor p21/metabolism
- Drug Resistance, Neoplasm
- Female
- Gene Expression Regulation, Neoplastic/drug effects
- Histone Deacetylases/genetics
- Histone Deacetylases/metabolism
- Humans
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Male
- Mice
- Mice, Inbred NOD
- Mice, SCID
- Middle Aged
- Neoplasm Recurrence, Local/drug therapy
- Neoplasm Recurrence, Local/genetics
- Neoplasm Recurrence, Local/metabolism
- Neoplasm Recurrence, Local/pathology
- Prognosis
- Proto-Oncogene Proteins c-akt/genetics
- Proto-Oncogene Proteins c-akt/metabolism
- Salvage Therapy
- Survival Rate
- Tumor Cells, Cultured
- Xenograft Model Antitumor Assays
- Young Adult
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Affiliation(s)
- Hao Wang
- Department of Hematology, Chinese People's Liberation Army (PLA) General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Yu-Chen Liu
- Department of Hematology, Chinese People's Liberation Army (PLA) General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Cheng-Ying Zhu
- Department of Hematology, Chinese People's Liberation Army (PLA) General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Fei Yan
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry (NMAC), International Research Center for Chemistry-Medicine Joint Innovation, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
| | - Meng-Zhen Wang
- Department of Hematology, Chinese People's Liberation Army (PLA) General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Xiao-Su Chen
- School of Medicine, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Xiao-Kai Wang
- Department of Orthopedics, Xiqing Hospital, 403 Xiqing Road, Yangliuqing, Tianjin, 300000, China
| | - Bao-Xu Pang
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Yong-Hui Li
- Department of Hematology, Chinese People's Liberation Army (PLA) General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Dai-Hong Liu
- Department of Hematology, Chinese People's Liberation Army (PLA) General Hospital, 28 Fuxing Road, Beijing, 100853, China.
| | - Chun-Ji Gao
- Department of Hematology, Chinese People's Liberation Army (PLA) General Hospital, 28 Fuxing Road, Beijing, 100853, China.
| | - Shu-Jun Liu
- The Hormel Institute, University of Minnesota, 801 16th Avenue NE, Austin, MN, 55912, USA.
| | - Li-Ping Dou
- Department of Hematology, Chinese People's Liberation Army (PLA) General Hospital, 28 Fuxing Road, Beijing, 100853, China.
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