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Hong X, Cai Z, Zhou F, Jin X, Wang G, Ouyang B, Zhang J. Improved pharmacokinetics of tenofovir ester prodrugs strengthened the inhibition of HBV replication and the rebalance of hepatocellular metabolism in preclinical models. Front Pharmacol 2022; 13:932934. [PMID: 36105197 PMCID: PMC9465247 DOI: 10.3389/fphar.2022.932934] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
Tenofovir (TFV) ester prodrugs, a class of nucleotide analogs (NAs), are the first-line clinical anti-hepatitis B virus (HBV) drugs with potent antiviral efficacy, low resistance rate and high safety. In this work, three marketed TFV ester drugs, tenofovir disoproxil fumarate (TDF), tenofovir alafenamide fumarate (TAF) and tenofovir amibufenamide fumarate (TMF), were used as probes to investigate the relationships among prodrug structures, pharmacokinetic characteristics, metabolic activations, pharmacological responses and to reveal the key factors of TFV ester prodrug design. The results indicated that TMF and TAF exhibited significantly stronger inhibition of HBV DNA replication than did TDF in HBV-positive HepG2.2.15 cells. The anti-HBV activity of TMF was slightly stronger than TAF after 9 days of treatment (EC50 7.29 ± 0.71 nM vs. 12.17 ± 0.56 nM). Similar results were observed in the HBV decline period post drug administration to the HBV transgenic mouse model, although these three TFV prodrugs finally achieved the same anti-HBV effect after 42 days treatments. Furthermore, TFV ester prodrugs showed a correcting effect on disordered host hepatic biochemical metabolism, including TCA cycle, glycolysis, pentose phosphate pathway, purine/pyrimidine metabolism, amino acid metabolism, ketone body metabolism and phospholipid metabolism. The callback effects of the three TFV ester prodrugs were ranked as TMF > TAF > TDF. These advantages of TMF were believed to be attributed to its greater bioavailability in preclinical animals (SD rats, C57BL/6 mice and beagle dogs) and better target loading, especially in terms of the higher hepatic level of the pharmacologically active metabolite TFV-DP, which was tightly related to anti-HBV efficacy. Further analysis indicated that stability in intestinal fluid determined the actual amount of TFV prodrug at the absorption site, and hepatic/intestinal stability determined the maintenance amount of prodrug in circulation, both of which influenced the oral bioavailability of TFV prodrugs. In conclusion, our research revealed that improved pharmacokinetics of TFV ester prodrugs (especially intestinal stability) strengthened the inhibition of HBV replication and the rebalance of hepatocellular metabolism, which provides new insights and a basis for the design, modification and evaluation of new TFV prodrugs in the future.
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Affiliation(s)
- Xiaodan Hong
- Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Zuhuan Cai
- Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Fang Zhou
- Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Xiaoliang Jin
- Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Guangji Wang
- Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, China
- *Correspondence: Guangji Wang, ; Bingchen Ouyang, ; Jingwei Zhang,
| | - Bingchen Ouyang
- Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
- *Correspondence: Guangji Wang, ; Bingchen Ouyang, ; Jingwei Zhang,
| | - Jingwei Zhang
- Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, China
- *Correspondence: Guangji Wang, ; Bingchen Ouyang, ; Jingwei Zhang,
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2
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Boulahtouf Z, Virzì A, Baumert TF, Verrier ER, Lupberger J. Signaling Induced by Chronic Viral Hepatitis: Dependence and Consequences. Int J Mol Sci 2022; 23:ijms23052787. [PMID: 35269929 PMCID: PMC8911453 DOI: 10.3390/ijms23052787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/27/2022] [Accepted: 03/01/2022] [Indexed: 12/12/2022] Open
Abstract
Chronic viral hepatitis is a main cause of liver disease and hepatocellular carcinoma. There are striking similarities in the pathological impact of hepatitis B, C, and D, although these diseases are caused by very different viruses. Paired with the conventional study of protein-host interactions, the rapid technological development of -omics and bioinformatics has allowed highlighting the important role of signaling networks in viral pathogenesis. In this review, we provide an integrated look on the three major viruses associated with chronic viral hepatitis in patients, summarizing similarities and differences in virus-induced cellular signaling relevant to the viral life cycles and liver disease progression.
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Affiliation(s)
- Zakaria Boulahtouf
- Institut de Recherche sur les Maladies Virales et Hepatiques UMR_S1110, Université de Strasbourg, Inserm, F-67000 Strasbourg, France; (Z.B.); (A.V.); (T.F.B.); (E.R.V.)
| | - Alessia Virzì
- Institut de Recherche sur les Maladies Virales et Hepatiques UMR_S1110, Université de Strasbourg, Inserm, F-67000 Strasbourg, France; (Z.B.); (A.V.); (T.F.B.); (E.R.V.)
| | - Thomas F. Baumert
- Institut de Recherche sur les Maladies Virales et Hepatiques UMR_S1110, Université de Strasbourg, Inserm, F-67000 Strasbourg, France; (Z.B.); (A.V.); (T.F.B.); (E.R.V.)
- Service d’Hépato-Gastroentérologie, Hôpitaux Universitaires de Strasbourg, F-67000 Strasbourg, France
- Institut Universitaire de France (IUF), F-75005 Paris, France
| | - Eloi R. Verrier
- Institut de Recherche sur les Maladies Virales et Hepatiques UMR_S1110, Université de Strasbourg, Inserm, F-67000 Strasbourg, France; (Z.B.); (A.V.); (T.F.B.); (E.R.V.)
| | - Joachim Lupberger
- Institut de Recherche sur les Maladies Virales et Hepatiques UMR_S1110, Université de Strasbourg, Inserm, F-67000 Strasbourg, France; (Z.B.); (A.V.); (T.F.B.); (E.R.V.)
- Correspondence:
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Zhang H, Qin Z, Yue X, Liu Y, Sun X, Feng J, Xu Z, Zhao J, Li K, Qiu J, Yang W, He F, Ding C. Proteome-wide profiling of transcriptional machinery on accessible chromatin with biotinylated transposons. SCIENCE ADVANCES 2021; 7:eabh1022. [PMID: 34678055 PMCID: PMC10763760 DOI: 10.1126/sciadv.abh1022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 08/31/2021] [Indexed: 06/13/2023]
Abstract
To directly and quantitatively identify the transcriptional protein complexes assembled on accessible chromatin, we develop an assay for transposase-accessible chromatin using mass spectrum (ATAC-MS) based on direct transposition of biotinylated adaptors into open chromatin. Coupling with activated gene sequence information by ATAC-seq, ATAC-MS can profile the accessible chromatin-protein machinery. ATAC-MS, combined with fractionation strategies (fATAC-MS), can provide a high-resolution chromatin-transcriptional machinery atlas. ATAC-MS with a novel Tn5-dCas9 fusion protein [dCas9-targeted ATAC-MS (ctATAC-MS)] further facilitates systematic pinpointing of the transcriptional machinery at specific open chromatin regions. We used ATAC-MS and ATAC-seq to investigate transcriptional regulation during C2C12 cell differentiation and demonstrated the role of RFX1 in regulating the proliferation and differentiation of C2C12 cells. Our strategy provides a universal toolbox including ATAC-MS, fATAC-MS, and ctATAC-MS, which enables us to portray the transcriptional regulation machinery atlas in genome scale and investigate the protein-DNA complex at a specific genomic locus.
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Affiliation(s)
- Haizhu Zhang
- State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Zhaoyu Qin
- State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Xuetong Yue
- State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Yang Liu
- State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Xiaogang Sun
- State Key Laboratory Cell Differentiation and Regulation, Overseas Expertise Introduction Center for Discipline Innovation of Pulmonary Fibrosis, (111 Project), College of Life Science, Henan Normal University, Xinxiang, Henan 453007, China
| | - Jinwen Feng
- State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Ziyan Xu
- State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Jiangyan Zhao
- State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Kai Li
- State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Jiange Qiu
- Cell Signaling and Proteomics Research Center, Academy of Medical Science, Zhengzhou University, Zhengzhou 450000, China
| | - Wenjun Yang
- Department of Pediatric Orthopedics, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Fuchu He
- State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200433, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing 102206, China
| | - Chen Ding
- State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200433, China
- State Key Laboratory Cell Differentiation and Regulation, Overseas Expertise Introduction Center for Discipline Innovation of Pulmonary Fibrosis, (111 Project), College of Life Science, Henan Normal University, Xinxiang, Henan 453007, China
- Cell Signaling and Proteomics Research Center, Academy of Medical Science, Zhengzhou University, Zhengzhou 450000, China
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Peroxiredoxins-The Underrated Actors during Virus-Induced Oxidative Stress. Antioxidants (Basel) 2021; 10:antiox10060977. [PMID: 34207367 PMCID: PMC8234473 DOI: 10.3390/antiox10060977] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/09/2021] [Accepted: 06/15/2021] [Indexed: 12/19/2022] Open
Abstract
Enhanced production of reactive oxygen species (ROS) triggered by various stimuli, including viral infections, has attributed much attention in the past years. It has been shown that different viruses that cause acute or chronic diseases induce oxidative stress in infected cells and dysregulate antioxidant its antioxidant capacity. However, most studies focused on catalase and superoxide dismutases, whereas a family of peroxiredoxins (Prdx), the most effective peroxide scavengers, were given little or no attention. In the current review, we demonstrate that peroxiredoxins scavenge hydrogen and organic peroxides at their physiological concentrations at various cell compartments, unlike many other antioxidant enzymes, and discuss their recycling. We also provide data on the regulation of their expression by various transcription factors, as they can be compared with the imprint of viruses on transcriptional machinery. Next, we discuss the involvement of peroxiredoxins in transferring signals from ROS on specific proteins by promoting the oxidation of target cysteine groups, as well as briefly demonstrate evidence of nonenzymatic, chaperone, functions of Prdx. Finally, we give an account of the current state of research of peroxiredoxins for various viruses. These data clearly show that Prdx have not been given proper attention despite all the achievements in general redox biology.
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Vairetti M, Di Pasqua LG, Cagna M, Richelmi P, Ferrigno A, Berardo C. Changes in Glutathione Content in Liver Diseases: An Update. Antioxidants (Basel) 2021; 10:364. [PMID: 33670839 PMCID: PMC7997318 DOI: 10.3390/antiox10030364] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 02/07/2023] Open
Abstract
Glutathione (GSH), a tripeptide particularly concentrated in the liver, is the most important thiol reducing agent involved in the modulation of redox processes. It has also been demonstrated that GSH cannot be considered only as a mere free radical scavenger but that it takes part in the network governing the choice between survival, necrosis and apoptosis as well as in altering the function of signal transduction and transcription factor molecules. The purpose of the present review is to provide an overview on the molecular biology of the GSH system; therefore, GSH synthesis, metabolism and regulation will be reviewed. The multiple GSH functions will be described, as well as the importance of GSH compartmentalization into distinct subcellular pools and inter-organ transfer. Furthermore, we will highlight the close relationship existing between GSH content and the pathogenesis of liver disease, such as non-alcoholic fatty liver disease (NAFLD), alcoholic liver disease (ALD), chronic cholestatic injury, ischemia/reperfusion damage, hepatitis C virus (HCV), hepatitis B virus (HBV) and hepatocellular carcinoma. Finally, the potential therapeutic benefits of GSH and GSH-related medications, will be described for each liver disorder taken into account.
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Affiliation(s)
| | - Laura Giuseppina Di Pasqua
- Unit of Cellular and Molecular Pharmacology and Toxicology, Department of Internal Medicine and Therapeutics, University of Pavia, 27100 Pavia, Italy; (M.V.); (M.C.); (P.R.); (C.B.)
| | | | | | - Andrea Ferrigno
- Unit of Cellular and Molecular Pharmacology and Toxicology, Department of Internal Medicine and Therapeutics, University of Pavia, 27100 Pavia, Italy; (M.V.); (M.C.); (P.R.); (C.B.)
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Wang Y, Song L, Liu M, Ge R, Zhou Q, Liu W, Li R, Qie J, Zhen B, Wang Y, He F, Qin J, Ding C. A proteomics landscape of circadian clock in mouse liver. Nat Commun 2018; 9:1553. [PMID: 29674717 PMCID: PMC5908788 DOI: 10.1038/s41467-018-03898-2] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 03/20/2018] [Indexed: 01/07/2023] Open
Abstract
As a circadian organ, liver executes diverse functions in different phase of the circadian clock. This process is believed to be driven by a transcription program. Here, we present a transcription factor (TF) DNA-binding activity-centered multi-dimensional proteomics landscape of the mouse liver, which includes DNA-binding profiles of different TFs, phosphorylation, and ubiquitylation patterns, the nuclear sub-proteome, the whole proteome as well as the transcriptome, to portray the hierarchical circadian clock network of this tissue. The TF DNA-binding activity indicates diurnal oscillation in four major pathways, namely the immune response, glucose metabolism, fatty acid metabolism, and the cell cycle. We also isolate the mouse liver Kupffer cells and measure their proteomes during the circadian cycle to reveal a cell-type resolved circadian clock. These comprehensive data sets provide a rich data resource for the understanding of mouse hepatic physiology around the circadian clock. As a circadian organ, liver functions are regulated by circadian clock. Here, the authors present a comprehensive proteomics landscape of the mouse liver, including transcription factor binding profiles, phosphorylation and ubiquitylation patterns, nuclear and whole proteome, and the transcriptome.
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Affiliation(s)
- Yunzhi Wang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Institutes of Biomedical Sciences, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Lei Song
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Mingwei Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing, 102206, China
| | - Rui Ge
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Institutes of Biomedical Sciences, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Quan Zhou
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing, 102206, China
| | - Wanlin Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing, 102206, China
| | - Ruiyang Li
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Institutes of Biomedical Sciences, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Jingbo Qie
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Institutes of Biomedical Sciences, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Bei Zhen
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing, 102206, China
| | - Yi Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing, 102206, China.,Alkek Center for Molecular Discovery, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Fuchu He
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Institutes of Biomedical Sciences, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200032, China. .,School of Life Sciences, Tsinghua University, Beijing, 100084, China. .,State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing, 102206, China.
| | - Jun Qin
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Institutes of Biomedical Sciences, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200032, China. .,State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing, 102206, China. .,Alkek Center for Molecular Discovery, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Chen Ding
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Institutes of Biomedical Sciences, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
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Abstract
Even with an effective vaccine, an estimated 240 million people are chronically infected with hepatitis B virus (HBV) worldwide. Current antiviral therapies, including interferon and nucleot(s)ide analogues, rarely cure chronic hepatitis B. Animal models are very crucial for understanding the pathogenesis of chronic hepatitis B and developing new therapeutic drugs or strategies. HBV can only infect humans and chimpanzees, with the use of chimpanzees in HBV research strongly restricted. Thus, most advances in HBV research have been gained using mouse models with HBV replication or infection or models with HBV-related hepadnaviral infection. This review summarizes the animal models currently available for the study of HBV infection.
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Affiliation(s)
- Wei-Na Guo
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan Hubei 430022, China
| | - Bin Zhu
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan Hubei 430022, China
| | - Ling Ai
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan Hubei 430022, China
| | - Dong-Liang Yang
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan Hubei 430022, China
| | - Bao-Ju Wang
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan Hubei 430022, China.
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8
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Oxidative stress, a trigger of hepatitis C and B virus-induced liver carcinogenesis. Oncotarget 2018; 8:3895-3932. [PMID: 27965466 PMCID: PMC5354803 DOI: 10.18632/oncotarget.13904] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 12/05/2016] [Indexed: 12/11/2022] Open
Abstract
Virally induced liver cancer usually evolves over long periods of time in the context of a strongly oxidative microenvironment, characterized by chronic liver inflammation and regeneration processes. They ultimately lead to oncogenic mutations in many cellular signaling cascades that drive cell growth and proliferation. Oxidative stress, induced by hepatitis viruses, therefore is one of the factors that drives the neoplastic transformation process in the liver. This review summarizes current knowledge on oxidative stress and oxidative stress responses induced by human hepatitis B and C viruses. It focuses on the molecular mechanisms by which these viruses activate cellular enzymes/systems that generate or scavenge reactive oxygen species (ROS) and control cellular redox homeostasis. The impact of an altered cellular redox homeostasis on the initiation and establishment of chronic viral infection, as well as on the course and outcome of liver fibrosis and hepatocarcinogenesis will be discussed The review neither discusses reactive nitrogen species, although their metabolism is interferes with that of ROS, nor antioxidants as potential therapeutic remedies against viral infections, both subjects meriting an independent review.
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Kan F, Ye L, Yan T, Cao J, Zheng J, Li W. Proteomic and transcriptomic studies of HBV-associated liver fibrosis of an AAV-HBV-infected mouse model. BMC Genomics 2017; 18:641. [PMID: 28830339 PMCID: PMC5568174 DOI: 10.1186/s12864-017-3984-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 08/01/2017] [Indexed: 01/05/2023] Open
Abstract
Background Human hepatitis B virus (HBV) infection is an important public health issue in the Asia-Pacific region and is associated with chronic hepatitis, liver fibrosis, cirrhosis and even liver cancer. However, the underlying mechanisms of HBV-associated liver fibrosis remain incompletely understood. Results In the present study, proteomic and transcriptomic approaches as well as biological network analyses were performed to investigate the differentially expressed molecular signature and key regulatory networks that were associated with HBV-mediated liver fibrosis. RNA sequencing and 2DE-MALDI-TOF/TOF were performed on liver tissue samples obtained from HBV-infected C57BL/6 mouse generated via AAV8-HBV virus. The results showed that 322 genes and 173 proteins were differentially expressed, and 28 HBV-specific proteins were identified by comprehensive proteomic and transcriptomic analysis. GO analysis indicated that the differentially expressed proteins were predominantly involved in oxidative stress, which plays a key role in HBV-related liver fibrosis. Importantly, CAT, PRDX1, GSTP1, NXN and BLVRB were shown to be associated with oxidative stress among the differentially expressed proteins. The most striking results were validated by Western blot and RT-qPCR. The RIG-I like receptor signaling pathway was found to be the major signal pathway that changed during HBV-related fibrosis. Conclusions This study provides novel insights into HBV-associated liver fibrosis and reveals the significant role of oxidative stress in liver fibrosis. Furthermore, CAT, BLVRB, NXN, PRDX1, and IDH1 may be candidates for detection of liver fibrosis or therapeutic targets for the treatment of liver fibrosis. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3984-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fangming Kan
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Lei Ye
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Tao Yan
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jiaqi Cao
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jianhua Zheng
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| | - Wuping Li
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
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10
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Wan Q, Wang Y, Tang H. Quantitative 13C Traces of Glucose Fate in Hepatitis B Virus-Infected Hepatocytes. Anal Chem 2017; 89:3293-3299. [PMID: 28221022 DOI: 10.1021/acs.analchem.6b03200] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Quantitative characterization of 13C-labeled metabolites is an important part of the stable isotope tracing method widely used in metabolic flux analysis. Given the long relaxation time and low sensitivity of 13C nuclei, direct measurement of 13C-labeled metabolites using one-dimensional 13C NMR often fails to meet the demand of metabolomics studies, especially with large numbers of samples and metabolites having low abundance. Although HSQC-based 2D NMR methods have improved sensitivity with inversion detection, they are time-consuming and thus unsuitable for high-throughput absolute quantification of 13C-labeled metabolites. In this study, we developed a method for absolute quantification of 13C-labeled metabolites using naturally abundant TSP as a reference with the first increment of the HMQC pulse sequence, taking polarization transfer efficiencies into consideration. We validated this method using a mixture of 13C-labeled alanine, methionine, glucose, and formic acid together with a mixture of alanine, lactate, glycine, uridine, cytosine, and hypoxanthine, which have natural 13C abundance with known concentrations. We subsequently applied this method to analyze the flux of glucose in HepG2 cells infected with hepatitis B virus (HBV). The results showed that HBV infection increased the cellular uptake of glucose, stimulated glycolysis, and enhanced the pentose phosphate and hexosamine pathways for biosynthesis of RNA and DNA and nucleotide sugars to facilitate HBV replication. This method saves experimental time and provides a possibility for absolute quantitative tracking of the 13C-labeled metabolites for high-throughput studies.
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Affiliation(s)
- Qianfen Wan
- State Key Laboratory of Genetic Engineering, Zhongshan Hospital and School of Life Sciences, Fudan University , Shanghai International Centre for Molecular Phenomics, Collaborative Innovation Center for Genetics and Development, Shanghai 200438, China
| | - Yulan Wang
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences , Wuhan 430071, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310058, China
| | - Huiru Tang
- State Key Laboratory of Genetic Engineering, Zhongshan Hospital and School of Life Sciences, Fudan University , Shanghai International Centre for Molecular Phenomics, Collaborative Innovation Center for Genetics and Development, Shanghai 200438, China
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11
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Ding C, Li Y, Guo F, Jiang Y, Ying W, Li D, Yang D, Xia X, Liu W, Zhao Y, He Y, Li X, Sun W, Liu Q, Song L, Zhen B, Zhang P, Qian X, Qin J, He F. A Cell-type-resolved Liver Proteome. Mol Cell Proteomics 2016; 15:3190-3202. [PMID: 27562671 PMCID: PMC5054343 DOI: 10.1074/mcp.m116.060145] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Indexed: 01/16/2023] Open
Abstract
Parenchymatous organs consist of multiple cell types, primarily defined as parenchymal cells (PCs) and nonparenchymal cells (NPCs). The cellular characteristics of these organs are not well understood. Proteomic studies facilitate the resolution of the molecular details of different cell types in organs. These studies have significantly extended our knowledge about organogenesis and organ cellular composition. Here, we present an atlas of the cell-type-resolved liver proteome. In-depth proteomics identified 6000 to 8000 gene products (GPs) for each cell type and a total of 10,075 GPs for four cell types. This data set revealed features of the cellular composition of the liver: (1) hepatocytes (PCs) express the least GPs, have a unique but highly homogenous proteome pattern, and execute fundamental liver functions; (2) the division of labor among PCs and NPCs follows a model in which PCs make the main components of pathways, but NPCs trigger the pathways; and (3) crosstalk among NPCs and PCs maintains the PC phenotype. This study presents the liver proteome at cell resolution, serving as a research model for dissecting the cell type constitution and organ features at the molecular level.
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Affiliation(s)
- Chen Ding
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China; **State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Yanyan Li
- ¶School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Feifei Guo
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China
| | - Ying Jiang
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China
| | - Wantao Ying
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China
| | - Dong Li
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China
| | - Dong Yang
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China
| | - Xia Xia
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China
| | - Wanlin Liu
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China
| | - Yan Zhao
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China
| | - Yangzhige He
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China; ¶School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xianyu Li
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China
| | - Wei Sun
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China
| | - Qiongming Liu
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China
| | - Lei Song
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China
| | - Bei Zhen
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China
| | - Pumin Zhang
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China
| | - Xiaohong Qian
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China;
| | - Jun Qin
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China; ‖Alkek Center for Molecular Discovery, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030; **State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Fuchu He
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100039, China; §National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China; **State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China
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12
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Hou ZH, Han QJ, Zhang C, Tian ZG, Zhang J. miR146a impairs the IFN-induced anti-HBV immune response by downregulating STAT1 in hepatocytes. Liver Int 2014; 34:58-68. [PMID: 23890093 DOI: 10.1111/liv.12244] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Accepted: 06/09/2013] [Indexed: 12/15/2022]
Abstract
BACKGROUND & AIMS Previous studies have shown that hepatitis B virus (HBV) interferes with host antiviral immunity via multiple pathways. In clinical practice, interferon resistance is a serious issue for treatment of HBV infection. Now, miRNAs have been reported to be widely involved in antiviral immunity and have become a novel tool to study virus-host interaction. We question whether miRNAs play a role in HBV-induced interferon resistance in hepatocytes. METHODS MiRNAs levels in HepG2 and HepG2.2.15 cells were compared by qRT-PCR. The effects of miR146a on HBV infection were characterized by interference miR146a level, followed by the quantification of HBV mRNA, DNA and antigens. We employed qRT-PCR and western blot to study the effects of miR146a on the IFN-α signalling pathway. The miR146a promoter activity was validated by a luciferase reporter assay. RESULTS HBV infection impaired IFN-α signalling pathway in hepatocytes. MiR146a was upregulated in HBV+ HepG2.2.15 cells, and the transcriptional activity of miR146a in HepG2.2.15 cells was increased compared with HepG2 cells. HBV infection, especially the introduction of HBx, induced miR146a expression in vitro. Moreover, miR146a attenuated the production of type I interferon-induced antiviral factors. Low STAT1 levels were noticed in HBV+ HCC cells, and the luciferase reporter assay showed that STAT1 was post-transcriptionally downregulated by miR146a. Furthermore, the silencing of miR146a by antisense inhibitors enhanced IFN-α-mediated anti-HBV efficiency. CONCLUSIONS Our findings demonstrate that HBV infection promotes miR146a transcription, which represses STAT1 and results in interferon resistance. These observations reveal a novel role for miR146a in HBV immunopathogenesis, and provide a potential target for the therapeutic recovery of IFN-α-induced anti-HBV effects.
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Affiliation(s)
- Zhao H Hou
- Institute of Immunopharmacology & Immunotherapy, School of Pharmaceutical Sciences, Shandong University, Jinan, China
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13
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Zhang H, Li H, Yang Y, Li S, Ren H, Zhang D, Hu H. Differential regulation of host genes including hepatic fatty acid synthase in HBV-transgenic mice. J Proteome Res 2013; 12:2967-79. [PMID: 23675653 DOI: 10.1021/pr400247f] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Hepatitis B virus (HBV) is the most common of the hepatitis viruses that cause chronic liver infections in humans, and it is considered to be a major global health problem. To gain a better understanding of HBV pathogenesis, and identify novel putative targets for anti-HBV therapy, this study was designed to elucidate the differential expression of host proteins in liver tissue from HBV-transgenic mice. Liver samples from two groups, (1) HBV-transgenic (Tg) mice, (2) corresponding background normal mice, wild-type (WT) mice, were collected and subjected to iTRAQ and mass spectrometry analysis. In total, 1950 unique proteins were identified, and 68 proteins were found to be differentially expressed in HBV-Tg mice as compared with that in WT mice. Several differentially expressed proteins were further validated by real-time quantitative RT-PCR, Western blot and immunohistochemical analysis. Furthermore, the association of HBV replication with fatty acid synthase (FASN), one of the highly expressed proteins in HBV-Tg mice, was verified. Silencing of FASN expression in HepG2.2.15 cells suppressed viral replication through the IFN signaling pathway, and some downstream antiviral effectors. The implicated role of FASN in HBV replication provides an opportunity to test existing compounds against FASN for adjuvant therapy and/or treatment of HBV replication.
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Affiliation(s)
- Hongmin Zhang
- Department of Infectious Diseases, Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
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14
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Guo Y, Luan G, Shen G, Wu L, Jia H, Zhong Y, Li R, Li G, Shen Y, Sun J, Hu S, Xiao W. Production and characterization of recombinant 9 and 15 kDa granulysin by fed-batch fermentation in Pichia pastoris. Appl Microbiol Biotechnol 2012; 97:7669-77. [PMID: 23224405 DOI: 10.1007/s00253-012-4602-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2012] [Revised: 10/22/2012] [Accepted: 11/17/2012] [Indexed: 01/11/2023]
Abstract
Granulysin is a cytolytic, proinflammatory protein produced by human cytolytic T-lymphocytes and natural killer cells. Granulysin has two stable isoforms with molecular weight of 9 and 15 kDa; the 9-kDa form is a result of proteolytic maturation of the 15-kDa precursor. Recombinant 9-kDa granulysin exhibits cytolytic activity against a variety of microbes, such as bacteria, parasites, fungi, yeast and a variety of tumor cell lines. However, it is difficult to produce granulysin in large quantities by traditional methods. In this study, we developed a simple and robust fed-batch fermentation process for production and purification of recombinant 9- and 15-kDa granulysin using Pichia pastoris in a basal salt medium at high cell density. The granulysin yield reaches at least 100 mg/l in fermentation, and over 95 % purity was achieved with common His-select affinity and ion exchange chromatography. Functional analysis revealed that the yeast-expressed granulysin displayed dose-dependent target cytotoxicity. These results suggest that fermentation in P. pastoris provides a sound strategy for large-scale recombinant granulysin production that may be used in clinical applications and basic research.
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Affiliation(s)
- Yugang Guo
- Hefei National Laboratory for Physical Sciences at Microscale, Hefei, China
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15
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Affiliation(s)
| | - Sinéad M. Miggin
- Immune Signalling Group; Institute of Immunology; Department of Biology; National University of Ireland Maynooth; Co. Kildare Ireland
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16
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Zhong ZR, Zhou HB, Li XY, Luo QL, Song XR, Wang W, Wen HQ, Yu L, Wei W, Shen JL. Serological proteome-oriented screening and application of antigens for the diagnosis of Schistosomiasis japonica. Acta Trop 2010; 116:1-8. [PMID: 20451489 DOI: 10.1016/j.actatropica.2010.04.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2009] [Revised: 04/26/2010] [Accepted: 04/29/2010] [Indexed: 12/12/2022]
Abstract
Schistosomiasis remains a major parasitic disease, with 200 million people infected and 779 million people at risk worldwide. The lack of reliable diagnostic techniques makes this disease difficult to control. In an attempt to discover useful candidates for the diagnosis of schistosomiasis, proteomics in combination with western blotting were employed in this study. This serological proteome assay yielded more than 30 immunodominant spots. Ten of these spots were precisely matched with a homologous two-dimensional electrophoresis (2-DE) gel and successfully identified by LC/MS-MS as corresponding to four different proteins. Of these proteins, SjLAP and SjFBPA were successfully expressed, and their recombinant protein products were further applied in the diagnosis of human Schistosomiasis japonica using ELISA. The ELISA results revealed sensitivities of 98.1% and 87.8% for acute and chronic schistosomiasis with rSjLAP and 100% and 84.7% with rSjFBPA, whereas the assays showed a specificity of 96.7% with both recombinant proteins. After treatment with praziquantel, the titres of the antibodies against both antigens declined significantly (P<0.001). Our data therefore suggest that these antibody-oriented recombinant proteins had a high efficacy for the diagnosis of S. japonica, and 2-DE based screening followed by LC/MS-MS has promising potential in the screening of candidate antigens for the diagnosis of schistosomiasis.
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