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Wang Q, Shi B, Yang G, Zhu X, Shao H, Qian K, Ye J, Qin A. Metabolomic profiling of Marek's disease virus infection in host cell based on untargeted LC-MS. Front Microbiol 2023; 14:1270762. [PMID: 38029131 PMCID: PMC10666056 DOI: 10.3389/fmicb.2023.1270762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023] Open
Abstract
Marek's disease (MD) caused by Marek's disease virus (MDV), poses a serious threat to the poultry industry by inducing neurological disease and malignant lymphoma in infected chickens. However, the underlying mechanisms how MDV disrupts host cells and causes damage still remain elusive. Recently, the application of metabolomics has shown great potential for uncovering the complex mechanisms during virus-host interactions. In this study, chicken embryo fibroblasts (CEFs) infected with MDV were subjected to ultrahigh-performance liquid chromatography-quadrupole time-of-flight tandem mass spectrometry (UHPLC-QTOF-MS) and multivariate statistical analysis. The results showed that 261 metabolites were significantly altered upon MDV infection, with most changes occurring in amino acid metabolism, energy metabolism, nucleotide metabolism, and lipid metabolism. Notably, MDV infection induces an up-regulation of amino acids in host cells during the early stages of infection to provide the energy and intermediary metabolites necessary for efficient multiplication of its own replication. Taken together, these data not only hold promise in identifying the biochemical molecules utilized by MDV replication in host cells, but also provides a new insight into understanding MDV-host interactions.
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Affiliation(s)
- Qingsen Wang
- The International Joint Laboratory for Cooperation in Agriculture and Agricultural Product Safety, Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou, Jiangsu, China
| | - Bin Shi
- The International Joint Laboratory for Cooperation in Agriculture and Agricultural Product Safety, Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou, Jiangsu, China
| | - Guifu Yang
- The International Joint Laboratory for Cooperation in Agriculture and Agricultural Product Safety, Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou, Jiangsu, China
| | - Xueying Zhu
- The International Joint Laboratory for Cooperation in Agriculture and Agricultural Product Safety, Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou, Jiangsu, China
| | - Hongxia Shao
- The International Joint Laboratory for Cooperation in Agriculture and Agricultural Product Safety, Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou, Jiangsu, China
| | - Kun Qian
- The International Joint Laboratory for Cooperation in Agriculture and Agricultural Product Safety, Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou, Jiangsu, China
| | - Jianqiang Ye
- The International Joint Laboratory for Cooperation in Agriculture and Agricultural Product Safety, Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou, Jiangsu, China
| | - Aijian Qin
- The International Joint Laboratory for Cooperation in Agriculture and Agricultural Product Safety, Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou, Jiangsu, China
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Du X, Zhou D, Zhou J, Xue J, Cheng Z. Marek's Disease Virus and Reticuloendotheliosis Virus Coinfection Enhances Viral Replication and Alters Cellular Protein Profiles. Front Vet Sci 2022; 9:854007. [PMID: 35392111 PMCID: PMC8981388 DOI: 10.3389/fvets.2022.854007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 02/08/2022] [Indexed: 12/12/2022] Open
Abstract
Coinfection with Marek's disease virus (MDV) and reticuloendotheliosis virus (REV) causes synergistic pathogenic effects and serious losses to the poultry industry. However, whether there is a synergism between the two viruses in viral replication and the roles of host factors in regulating MDV and REV coinfection remains elusive. In this study, we found that MDV and REV coinfection increased viral replication in coinfected cells as compared to a single infection in a limited period. Further, we explore the host cell responses to MDV and REV coinfection using tandem mass tag (TMT) peptide labeling coupled with liquid chromatography–tandem mass spectrometry (LC-MS/MS). Compared with MDV/REV-infected cells, 38 proteins increased (fold change > 1.2) and 60 decreased (fold change < 0.83) their abundance in MDV and REV coinfected cells. Differentially accumulated proteins (DAPs) were involved in important biological processes involved in the immune system process, cell adhesion and migration, cellular processes, and multicellular organismal systems. STRING analysis found that IRF7, MX1, TIMP3, and AKT1 may be associated with MDV and REV synergistic replication in chicken embryo fibroblasts (CEFs). Western blotting analysis showed that the selected DAPs were identical to the quantitative proteomics data. Taken together, we verified that MDV and REV can synergistically replicate in coinfected cells and revealed the host molecules involved in it. However, the synergistic pathogenesis of MDV and REV needs to be further studied.
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Hu F, Li Y, Yu K, Ma X, Liu C, Guo X, Song M, Wu J, Huang B. Proteome analysis of reticuloendotheliosis-virus-infected chicken embryo fibroblast cells through iTRAQ-based quantitative proteomics. Arch Virol 2019; 164:2995-3006. [PMID: 31576460 DOI: 10.1007/s00705-019-04409-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Accepted: 08/18/2019] [Indexed: 12/17/2022]
Abstract
Reticuloendotheliosis virus (REV) is an important representative avian retrovirus. To improve our understanding of the host cellular responses to virus infection and the pathogenesis of REV infection, we applied isobaric tags for relative and absolute quantification (iTRAQ) labeling coupled with multidimensional liquid chromatography-tandem mass spectrometry to detect changes in protein levels in chicken embryo fibroblast cells (CEFs) that were infected with REV or mock infected. In total, 605 cellular proteins were differentially expressed, among which 196, 345, and 286 were differentially expressed in REV-infected CEFs at 1, 3, and 5 days postinfection, respectively. Gene Ontology analysis indicated that the biological processes of the differentially expressed proteins were primarily related to cellular processes, metabolic processes, biological regulation, response to stimulus, and immune system processes and that the molecular functions in which the differentially expressed proteins were mainly involved were binding, catalytic activity, and enzyme regulator activity. Pathway analysis showed that a total of 143, 167, and 179 pathways, including protein digestion and absorption, focal adhesion, ECM-receptor interaction, cytokine-cytokine receptor interaction, Toll-like receptors, and JAK-STAT signaling, were enriched in REV-infected CEFs at 1, 3, and 5 days postinfection, respectively. In conclusion, this study is the first to analyze the protein profile of REV-infected CEFs using an iTRAQ approach. The results of this study provide valuable information for better understanding the host response to REV infection.
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Affiliation(s)
- Feng Hu
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences/Shandong Provincial Key Laboratory of Immunity and Diagnosis of Poultry Diseases, No. 1 Jiaoxiao road, Jinan, 250023, Shandong, China
| | - Yufeng Li
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences/Shandong Provincial Key Laboratory of Immunity and Diagnosis of Poultry Diseases, No. 1 Jiaoxiao road, Jinan, 250023, Shandong, China
| | - Kexiang Yu
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences/Shandong Provincial Key Laboratory of Immunity and Diagnosis of Poultry Diseases, No. 1 Jiaoxiao road, Jinan, 250023, Shandong, China
| | - Xiuli Ma
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences/Shandong Provincial Key Laboratory of Immunity and Diagnosis of Poultry Diseases, No. 1 Jiaoxiao road, Jinan, 250023, Shandong, China
| | - Cunxia Liu
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences/Shandong Provincial Key Laboratory of Immunity and Diagnosis of Poultry Diseases, No. 1 Jiaoxiao road, Jinan, 250023, Shandong, China
| | - Xiaozhen Guo
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences/Shandong Provincial Key Laboratory of Immunity and Diagnosis of Poultry Diseases, No. 1 Jiaoxiao road, Jinan, 250023, Shandong, China
| | - Minxun Song
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences/Shandong Provincial Key Laboratory of Immunity and Diagnosis of Poultry Diseases, No. 1 Jiaoxiao road, Jinan, 250023, Shandong, China.
| | - Jiaqiang Wu
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences/Shandong Provincial Key Laboratory of Immunity and Diagnosis of Poultry Diseases, No. 1 Jiaoxiao road, Jinan, 250023, Shandong, China. .,College of Life Sciences, Shandong Normal University, 88, East Culture Road, Jinan, 250014, Shandong, China.
| | - Bing Huang
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences/Shandong Provincial Key Laboratory of Immunity and Diagnosis of Poultry Diseases, No. 1 Jiaoxiao road, Jinan, 250023, Shandong, China.
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Tong M, Yi L, Sun N, Cheng Y, Cao Z, Wang J, Li S, Lin P, Sun Y, Cheng S. Quantitative Analysis of Cellular Proteome Alterations in CDV-Infected Mink Lung Epithelial Cells. Front Microbiol 2017; 8:2564. [PMID: 29312244 PMCID: PMC5743685 DOI: 10.3389/fmicb.2017.02564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Accepted: 12/11/2017] [Indexed: 12/14/2022] Open
Abstract
Canine distemper virus (CDV), a paramyxovirus, causes a severe highly contagious lethal disease in carnivores, such as mink. Mink lung epithelial cells (Mv.1.Lu cells) are sensitive to CDV infection and are homologous to the natural host system of mink. The current study analyzed the response of Mv.1.Lu cells to CDV infection by iTRAQ combined with LC-MS/MS. In total, 151 and 369 differentially expressed proteins (DEPs) were markedly up-regulated or down-regulated, respectively. Thirteen DEPs were validated via real-time RT-PCR or western blot analysis. Network and KEGG pathway analyses revealed several regulated proteins associated with the NF-κB signaling pathway. Further validation was performed by western blot analysis and immunofluorescence assay, which demonstrated that different CDV strains induced NF-κB P65 phosphorylation and nuclear translocation. Moreover, the results provided interesting information that some identified DEPs possibly associated with the pathogenesis and the immune response upon CDV infection. This study is the first overview of the responses to CDV infection in Mv.1.Lu cells, and the findings will help to analyze further aspects of the molecular mechanisms involved in viral pathogenesis and the immune responses upon CDV infection.
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Affiliation(s)
- Mingwei Tong
- State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Economic Animal and Plant Science, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Li Yi
- State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Economic Animal and Plant Science, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Na Sun
- State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Economic Animal and Plant Science, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Yuening Cheng
- State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Economic Animal and Plant Science, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Zhigang Cao
- State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Economic Animal and Plant Science, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Jianke Wang
- State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Economic Animal and Plant Science, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Shuang Li
- State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Economic Animal and Plant Science, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Peng Lin
- State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Economic Animal and Plant Science, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Yaru Sun
- State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Economic Animal and Plant Science, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Shipeng Cheng
- State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Economic Animal and Plant Science, Chinese Academy of Agricultural Sciences, Changchun, China
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Lin H, Li B, Chen L, Ma Z, He K, Fan H. Differential Protein Analysis of IPEC-J2 Cells Infected with Porcine Epidemic Diarrhea Virus Pandemic and Classical Strains Elucidates the Pathogenesis of Infection. J Proteome Res 2017; 16:2113-2120. [PMID: 28506058 DOI: 10.1021/acs.jproteome.6b00957] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Porcine epidemic diarrhea (PED) re-emerged in China in late 2010 and has now become widespread. Accumulated evidence indicates that this large-scale outbreak of diarrhea was caused by variants of the highly virulent porcine epidemic diarrhea virus (PEDV). A pandemic PEDV YC2014 strain (YC2014) was isolated from clinical samples. An iTRAQ-based comparative quantitative proteomic study of IPEC-J2 cells infected with YC2014 and a classical CV777 strain (CV777) was performed to determine the differences between pandemic and classical PEDV strain infection. Totals of 353 and 299 differentially expressed proteins were identified upon YC2014 and CV777 infection, respectively. The canonical pathways and functional networks involved in both PEDV infections were analyzed. The results indicated that the PEDV suppressed protein synthesis of IPEC-J2 cells through down-regulation of the PI3K-AKT/mTOR signaling pathways. Infection with YC2014 could activate the JAK-STAT signaling pathway and the NF-κB pathway more intensively than CV777. YC2014 could activate NF-κB pathway more intensively than CV777. On the basis of differentially expressed proteins, we propose that PEDV might disrupt apoptosis and may elicit stronger inflammatory cascades as well. This study might contribute to an understanding of the pathogenesis of PEDV infection and aid in the development of effective preventive and control vaccines.
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Affiliation(s)
- Huixing Lin
- College of Veterinary Medicine, Nanjing Agricultural University , Nanjing, Jiangsu 210095, China
| | - Bin Li
- Institute of Veterinary Medicine , Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Lei Chen
- College of Veterinary Medicine, Nanjing Agricultural University , Nanjing, Jiangsu 210095, China
| | - Zhe Ma
- College of Veterinary Medicine, Nanjing Agricultural University , Nanjing, Jiangsu 210095, China
| | - Kongwang He
- Institute of Veterinary Medicine , Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Hongjie Fan
- College of Veterinary Medicine, Nanjing Agricultural University , Nanjing, Jiangsu 210095, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses , Yangzhou, China
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Kong BW, Lassiter K, Piekarski-Welsher A, Dridi S, Reverter-Gomez A, Hudson NJ, Bottje WG. Proteomics of Breast Muscle Tissue Associated with the Phenotypic Expression of Feed Efficiency within a Pedigree Male Broiler Line: I. Highlight on Mitochondria. PLoS One 2016; 11:e0155679. [PMID: 27244447 PMCID: PMC4887024 DOI: 10.1371/journal.pone.0155679] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 05/03/2016] [Indexed: 02/07/2023] Open
Abstract
As feed represents 60 to 70% of the cost of raising an animal to market weight, feed efficiency (the amount of dry weight intake to amount of wet weight gain) remains an important genetic trait in animal agriculture. To gain greater understanding of cellular mechanisms of feed efficiency (FE), shotgun proteomics was conducted using in-gel trypsin digestion and tandem mass spectrometry on breast muscle samples obtained from pedigree male (PedM) broilers exhibiting high feed efficiency (FE) or low FE phenotypes (n = 4 per group). The high FE group had greater body weight gain (P = 0.004) but consumed the same amount of feed (P = 0.30) from 6 to 7 wk resulting in higher FE (P < 0.001). Over 1800 proteins were identified, of which 152 were different (P < 0.05) by at least 1.3 fold and ≤ 15 fold between the high and low FE phenotypes. Data were analyzed for a modified differential expression (DE) metric (Phenotypic Impact Factors or PIF) and interpretation of protein expression data facilitated using the Ingenuity Pathway Analysis (IPA) program. In the entire data set, 228 mitochondrial proteins were identified whose collective expression indicates a higher mitochondrial expression in the high FE phenotype (binomial probability P < 0.00001). Within the top up and down 5% PIF molecules in the dataset, there were 15 mitoproteome proteins up-regulated and only 5 down-regulated in the high FE phenotype. Pathway enrichment analysis also identified mitochondrial dysfunction and oxidative phosphorylation as the number 1 and 5 differentially expressed canonical pathways (up-regulated in high FE) in the proteomic dataset. Upstream analysis (based on DE of downstream molecules) predicted that insulin receptor, insulin like growth receptor 1, nuclear factor, erythroid 2-like 2, AMP activated protein kinase (α subunit), progesterone and triiodothyronine would be activated in the high FE phenotype whereas rapamycin independent companion of target of rapamycin, mitogen activated protein kinase 4, and serum response factor would be inhibited in the high FE phenotype. The results provide additional insight into the fundamental molecular landscape of feed efficiency in breast muscle of broilers as well as further support for a role of mitochondria in the phenotypic expression of FE. Funding provided by USDA-NIFA (#2013–01953), Arkansas Biosciences Institute (Little Rock, AR), McMaster Fellowship (AUS to WB) and the Agricultural Experiment Station (Univ. of Arkansas, Fayetteville).
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Affiliation(s)
- Byung-Whi Kong
- Department of Poultry Science, Center of Excellence for Poultry Science, University of Arkansas, Fayetteville AR 72701, United States of America
| | - Kentu Lassiter
- Department of Poultry Science, Center of Excellence for Poultry Science, University of Arkansas, Fayetteville AR 72701, United States of America
| | - Alissa Piekarski-Welsher
- Department of Poultry Science, Center of Excellence for Poultry Science, University of Arkansas, Fayetteville AR 72701, United States of America
| | - Sami Dridi
- Department of Poultry Science, Center of Excellence for Poultry Science, University of Arkansas, Fayetteville AR 72701, United States of America
| | - Antonio Reverter-Gomez
- CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Road, St. Lucia, QLD 4067, Australia
| | - Nicholas James Hudson
- CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Road, St. Lucia, QLD 4067, Australia
| | - Walter Gay Bottje
- Department of Poultry Science, Center of Excellence for Poultry Science, University of Arkansas, Fayetteville AR 72701, United States of America
- * E-mail:
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Guo X, Hu H, Chen F, Li Z, Ye S, Cheng S, Zhang M, He Q. iTRAQ-based comparative proteomic analysis of Vero cells infected with virulent and CV777 vaccine strain-like strains of porcine epidemic diarrhea virus. J Proteomics 2015; 130:65-75. [PMID: 26361011 PMCID: PMC7102838 DOI: 10.1016/j.jprot.2015.09.002] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Revised: 08/28/2015] [Accepted: 09/02/2015] [Indexed: 12/24/2022]
Abstract
The re-emerging porcine epidemic diarrhea virus (PEDV) variant related diarrhea has been documented in China since late 2010 and now with global distribution. Currently, a virulent PEDV CH/YNKM-8/2013 and a CV777 vaccine strain-like AH-M have been successfully isolated from the clinical samples. To dissect out the underlying pathogenic mechanism of virulent PEDV and clarify the differences between virulent and CV777 vaccine strain-like PEDV infections, we performed an iTRAQ-based comparative quantitative proteomic study of Vero cells infected with both PEDV strains. A total of 661 and 474 differentially expressed proteins were identified upon virulent and CV777 vaccine strain-like isolates infection, respectively. Ingenuity Pathway Analysis was employed to investigate the canonical pathways and functional networks involved in both PEDV infections. Comprehensive studies have revealed that the PEDV virulent strain suppressed protein synthesis of Vero cells through down-regulating mTOR as well as its downstream targets 4EBP1 and p70S6K activities, which were validated by immunoblotting. In addition, the virulent strain could activate NF-κB pathway more intensively than the CV777 vaccine strain-like isolate, and elicit stronger inflammatory cascades as well. These data might provide new insights for elucidating the specific pathogenesis of PEDV infection, and pave the way for the development of effective therapeutic strategies. Biological significance Porcine epidemic diarrhea is now worldwide distributed and causing huge economic losses to swine industry. The immunomodulation and pathogenesis between PEDV and host, as well as the difference between virulent and attenuated strains of PEDV infections are still largely unknown. In this study, we presented for the first application of proteomic analysis to compare whole cellular protein alterations induced by virulent and CV777 vaccine strain-like PEDV infections, which might contribute to understand the pathogenesis of PEDV and anti-viral strategy development. Vero cells proteome was individually analyzed upon virulent and attenuated PEDV infections. Many pathways and interactive networks were constructed based on differentially expressed proteins. Virulent PEDV strain suppressed mTOR as well as its downstream targets 4EBP1 and p70S6K activities. Virulent PEDV strain activated NF-κB pathway more intensively than the attenuated isolate.
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Affiliation(s)
- Xiaozhen Guo
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Han Hu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Fangzhou Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhonghua Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Shiyi Ye
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuang Cheng
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430070, China
| | - Mengjia Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Qigai He
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.
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Alpert AJ, Hudecz O, Mechtler K. Anion-exchange chromatography of phosphopeptides: weak anion exchange versus strong anion exchange and anion-exchange chromatography versus electrostatic repulsion-hydrophilic interaction chromatography. Anal Chem 2015; 87:4704-11. [PMID: 25827581 PMCID: PMC4423237 DOI: 10.1021/ac504420c] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 03/31/2015] [Indexed: 02/08/2023]
Abstract
Most phosphoproteomics experiments rely on prefractionation of tryptic digests before online liquid chromatography-mass spectrometry. This study compares the potential and limitations of electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) and anion-exchange chromatography (AEX). At a pH higher than 5, phosphopeptides have two negative charges per residue and are well-retained in AEX. However, peptides with one or two phosphate groups are not separated from peptides with multiple Asp or Glu residues, interfering with the identification of phosphopeptides. At a pH of 2, phosphate residues have just a single negative charge but Asp and Glu are uncharged. This facilitates the separation of phosphopeptides from unmodified acidic peptides. Singly phosphorylated peptides are retained weakly under these conditions, due to electrostatic repulsion, unless hydrophilic interaction is superimposed in the ERLIC mode. Weak anion-exchange (WAX) and strong anion-exchange (SAX) columns were compared, with both peptide standards and a HeLa cell tryptic digest. The SAX column exhibited greater retention at pH 6 than did the WAX column. However, only about 60% as many phosphopeptides were identified with SAX at pH 6 than via ERLIC at pH 2. In one ERLIC run, 12 467 phosphopeptides were identified, including 4233 with more than one phosphate. We conclude that chromatography of phosphopeptides is best performed at low pH in the ERLIC mode. Under those conditions, the performances of the SAX and WAX materials were comparable. The data have been deposited with the ProteomeXchange with identifier PXD001333.
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Affiliation(s)
- Andrew J. Alpert
- PolyLC
Inc., 9151 Rumsey Road,
Ste. 175, Columbia, Maryland 21045, United States
| | - Otto Hudecz
- Research
Institute of Molecular Pathology (IMP), Dr. Bohr-Gasse 7, 1030 Vienna, Austria
- Institute
of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Karl Mechtler
- Research
Institute of Molecular Pathology (IMP), Dr. Bohr-Gasse 7, 1030 Vienna, Austria
- Institute
of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
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Loroch S, Zahedi RP, Sickmann A. Highly Sensitive Phosphoproteomics by Tailoring Solid-Phase Extraction to Electrostatic Repulsion-Hydrophilic Interaction Chromatography. Anal Chem 2015; 87:1596-604. [DOI: 10.1021/ac502708m] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Stefan Loroch
- Leibniz-Institut für Analytische Wissenschaften−ISAS−e.V., Otto-Hahn-Straße 6b, 44227 Dortmund, Germany
| | - René Peiman Zahedi
- Leibniz-Institut für Analytische Wissenschaften−ISAS−e.V., Otto-Hahn-Straße 6b, 44227 Dortmund, Germany
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften−ISAS−e.V., Otto-Hahn-Straße 6b, 44227 Dortmund, Germany
- School of Natural & Computing Sciences, University of Aberdeen, Meston Building, Meston Walk, Old Aberdeen AB24 3UE, United Kingdom
- Medizinische
Fakultät, Ruhr-Universität Bochum, Universitätsstraße
150, 44801 Bochum, Germany
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10
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Biggar KK, Storey KB. New Approaches to Comparative and Animal Stress Biology Research in the Post-genomic Era: A Contextual Overview. Comput Struct Biotechnol J 2014; 11:138-46. [PMID: 25408848 PMCID: PMC4232569 DOI: 10.1016/j.csbj.2014.09.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 09/07/2014] [Accepted: 09/11/2014] [Indexed: 02/06/2023] Open
Abstract
Although much is known about the physiological responses of many environmental stresses in tolerant animals, studies evaluating the regulation of stress-induced mechanisms that regulate the transitions to and from this state are beginning to explore new and fascinating areas of molecular research. Current findings have developed a general, but refined, view of the important molecular pathways contributing to stress-survival. However, studies utilizing newly developed technologies that broadly focus on genomic and proteomic screening are beginning to identify many new targets for future study. This minireview will provide a contextual overview on the use of DNA/RNA sequencing, microRNA annotation and prediction software, protein structure and function prediction tools, as well as methods of high-throughput protein expression analysis. We will also use select examples to highlight the existing use of these technologies in stress biology research. Such tools can be used in comparative stress biology in the characterization of animal responses to environmental challenges. Although there are many areas of study left to be explored, research in comparative stress biology will always be continuing as new technologies allow the further analysis of cell function, and new paradigms in gene regulation and regulatory molecules (such as microRNAs) are continuing to be discovered. Building upon the findings of past research, while utilizing new technologies in the appropriate manner, future studies can be carried out in new and exciting areas still unexplored. Proper use of rapidly developing technologies will help to create a complete understanding of the animal stress response and survival mechanisms utilized by many diverse organisms.
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Affiliation(s)
| | - Kenneth B. Storey
- Institute of Biochemistry, Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada
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UPLC–MSE application in disease biomarker discovery: The discoveries in proteomics to metabolomics. Chem Biol Interact 2014; 215:7-16. [DOI: 10.1016/j.cbi.2014.02.014] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Revised: 02/14/2014] [Accepted: 02/28/2014] [Indexed: 01/05/2023]
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Alegre-Aguarón E, Sampat SR, Xiong JC, Colligan RM, Bulinski JC, Cook JL, Ateshian GA, Brown LM, Hung CT. Growth factor priming differentially modulates components of the extracellular matrix proteome in chondrocytes and synovium-derived stem cells. PLoS One 2014; 9:e88053. [PMID: 24516581 PMCID: PMC3917883 DOI: 10.1371/journal.pone.0088053] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 01/03/2014] [Indexed: 12/17/2022] Open
Abstract
To make progress in cartilage repair it is essential to optimize protocols for two-dimensional cell expansion. Chondrocytes and SDSCs are promising cell sources for cartilage repair. We previously observed that priming with a specific growth factor cocktail (1 ng/mL transforming growth factor-β1, 5 ng/mL basic fibroblast growth factor, and 10 ng/mL platelet-derived growth factor-BB) in two-dimensional culture, led to significant improvement in mechanical and biochemical properties of synovium-derived stem cell (SDSC)-seeded constructs. The current study assessed the effect of growth factor priming on the proteome of canine chondrocytes and SDSCs. In particular, growth factor priming modulated the proteins associated with the extracellular matrix in two-dimensional cultures of chondrocytes and SDSCs, inducing a partial dedifferentiation of chondrocytes (most proteins associated with cartilage were down-regulated in primed chondrocytes) and a partial differentiation of SDSCs (some collagen-related proteins were up-regulated in primed SDSCs). However, when chondrocytes and SDSCs were grown in pellet culture, growth factor-primed cells maintained their chondrogenic potential with respect to glycosaminoglycan and collagen production. In conclusion, the strength of the label-free proteomics technique is that it allows for the determination of changes in components of the extracellular matrix proteome in chondrocytes and SDSCs in response to growth factor priming, which could help in future tissue engineering strategies.
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Affiliation(s)
- Elena Alegre-Aguarón
- Department of Biomedical Engineering, Columbia University, New York, New York, United States of America
| | - Sonal R. Sampat
- Department of Biomedical Engineering, Columbia University, New York, New York, United States of America
| | - Jennifer C. Xiong
- Department of Biomedical Engineering, Columbia University, New York, New York, United States of America
| | - Ryan M. Colligan
- Quantitative Proteomics Center, Columbia University, New York, New York, United States of America
| | - J. Chloë Bulinski
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - James L. Cook
- Comparative Orthopaedic Laboratory, University of Missouri, Columbia, Missouri, United States of America
| | - Gerard A. Ateshian
- Department of Biomedical Engineering, Columbia University, New York, New York, United States of America
- Department of Mechanical Engineering, Columbia University, New York, New York, United States of America
| | - Lewis M. Brown
- Quantitative Proteomics Center, Columbia University, New York, New York, United States of America
- * E-mail: (LMB); (CTH)
| | - Clark T. Hung
- Department of Biomedical Engineering, Columbia University, New York, New York, United States of America
- * E-mail: (LMB); (CTH)
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