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Hu Y, Liu C, Yang J, Zhong M, Qian B, Chen J, Zhang Y, Song J. HMGB1 is involved in viral replication and the inflammatory response in coxsackievirus A16-infected 16HBE cells via proteomic analysis and identification. Virol J 2023; 20:178. [PMID: 37559147 PMCID: PMC10410909 DOI: 10.1186/s12985-023-02150-8] [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: 04/18/2023] [Accepted: 08/02/2023] [Indexed: 08/11/2023] Open
Abstract
Coxsackievirus A16 (CV-A16) is still an important pathogen that causes hand, foot and mouth disease (HFMD) in young children and infants worldwide. Previous studies indicated that CV-A16 infection is usually mild or self-limiting, but it was also found that CV-A16 infection can trigger severe neurological complications and even death. However, there are currently no vaccines or antiviral compounds available to either prevent or treat CV-A16 infection. Therefore, investigation of the virus‒host interaction and identification of host proteins that play a crucial regulatory role in the pathogenesis of CV-A16 infection may provide a novel strategy to develop antiviral drugs. Here, to increase our understanding of the interaction of CV-A16 with the host cell, we analyzed changes in the proteome of 16HBE cells in response to CV-A16 using tandem mass tag (TMT) in combination with LC‒MS/MS. There were 6615 proteins quantified, and 172 proteins showed a significant alteration during CV-A16 infection. These differentially regulated proteins were involved in fundamental biological processes and signaling pathways, including metabolic processes, cytokine‒cytokine receptor interactions, B-cell receptor signaling pathways, and neuroactive ligand‒receptor interactions. Further bioinformatics analysis revealed the characteristics of the protein domains and subcellular localization of these differentially expressed proteins. Then, to validate the proteomics data, 3 randomly selected proteins exhibited consistent changes in protein expression with the TMT results using Western blotting and immunofluorescence methods. Finally, among these differentially regulated proteins, we primarily focused on HMGB1 based on its potential effects on viral replication and virus infection-induced inflammatory responses. It was demonstrated that overexpression of HMGB1 could decrease viral replication and upregulate the release of inflammatory cytokines, but deletion of HMGB1 increased viral replication and downregulated the release of inflammatory cytokines. In conclusion, the results from this study have helped further elucidate the potential molecular pathogenesis of CV-A16 based on numerous protein changes and the functions of HMGB1 Found to be involved in the processes of viral replication and inflammatory response, which may facilitate the development of new antiviral therapies as well as innovative diagnostic methods.
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Affiliation(s)
- Yajie Hu
- Department of Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province, Kunming, China
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Chen Liu
- Department of Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province, Kunming, China
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Jinghui Yang
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
- Department of Pediatrics, The First People's Hospital of Yunnan Province, Kunming, China
| | - Mingmei Zhong
- Department of Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province, Kunming, China
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Baojiang Qian
- Department of Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province, Kunming, China
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Juan Chen
- Department of Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province, Kunming, China
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Yunhui Zhang
- Department of Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province, Kunming, China.
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China.
| | - Jie Song
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, China.
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Sepasi A, Ghafourian M, Taghizadeh M, Mahdavi M. Formulation of Recombinant H1N1 Hemagglutinin in MF59 and Alum Adjuvants: A Comparison of the Vaccines Potency and Efficacy in BALB/C Mice. Viral Immunol 2023; 36:401-408. [PMID: 37504965 DOI: 10.1089/vim.2023.0003] [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: 07/29/2023] Open
Abstract
In this study, we reported the expression and potency of the recombinant H1N1 hemagglutinin (HA) vaccine as our in-house vaccine in a BALB/c mouse model. Recombinant H1N1 HA was produced in SF9 cell line, purified and formulated in MF59 adjuvant. Experimental mice were injected on days 0 and 14 with MF59-formulated vaccine, alum-based vaccine, and phosphate-buffered saline (PBS). Interleukin (IL)-2, IL-4, and interferon (IFN)-γ were assessed with commercial enzyme-linked immunosorbent assay (ELISA). Antibody responses and cytotoxic T lymphocyte (CTL) activity were assessed by hemagglutination inhibition and granzyme B ELISA, respectively. Moreover, the mice were challenged to show the vaccine efficacy. A considerable rise in IFN-γ and IL-4, as well as IFN-γ/IL-4 ratio, was observed in comparison with the alum-based vaccine and PBS group. Furthermore, our candidate vaccine showed superiority in humoral immune responses and CTL activity versus the alum-based vaccine and PBS group. The challenge showed that the survival rate in the vaccinated groups revealed a significant increase as compared with that in the PBS group. In conclusion, our candidate vaccine showed a robust Th1 response and CTL activity the alum-based vaccine. Moreover, a significant humoral immune response and a higher survival rate were detected in our vaccine as compared with the alum-based vaccine. It seems that the superiority of the MF59-based vaccine is due to the type of vaccine formulation in the candidate vaccine.
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Affiliation(s)
- Aref Sepasi
- Department of Immunology, School of Medicine; Medical Basic Sciences Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mehri Ghafourian
- Department of Immunology, School of Medicine; Medical Basic Sciences Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Cellular and Molecular Research Center, Medical Basic Sciences Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Morteza Taghizadeh
- Department of Medical Vaccine, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Mehdi Mahdavi
- Advanced Therapy Medicinal Product (ATMP) Department, Breast Cancer Research Center, Motamed Cancer Institute, Academic Center for Education, Culture and Research (ACECR), Tehran, Iran
- Recombinant Vaccine Research Center, Tehran University of Medical Sciences, Tehran, Iran
- Immunotherapy Group, The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
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Yajie H, Shenglan W, Wei Z, Rufang L, Tingting Y, Yunhui Z, Jie S. Global quantitative proteomic analysis profiles of host protein expression in response to Enterovirus A71 infection in bronchial epithelial cells based on tandem mass tag (TMT) peptide labeling coupled with LC-MS/MS uncovers the key role of proteasome in virus replication. Virus Res 2023; 330:199118. [PMID: 37072100 DOI: 10.1016/j.virusres.2023.199118] [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: 11/24/2022] [Revised: 03/30/2023] [Accepted: 04/15/2023] [Indexed: 04/20/2023]
Abstract
Enterovirus A71 (EV-A71) is a neurotropic human pathogen which mainly caused hand, foot and mouth disease (HFMD) mostly in children under 5 years-old. Generally, EV-A71-associated HFMD is a relatively self-limiting febrile disease, but there will still be a small percentage of patients with rapid disease progression and severe neurological complications. To date, the underlying mechanism of EV-A71 inducing pathological injury of central nervous system (CNS) remains largely unclear. It has been investigated and discussed the changes of mRNA, miRNA and circRNA expression profile during infection by EV-A71 in our previous studies. However, these studies were only analyzed at the RNA level, not at the protein level. It's the protein levels that ultimately do the work in the body. Here, to address this, we performed a tandem mass tag (TMT) peptide labeling coupled with LC-MS/MS approach to quantitatively identify cellular proteome changes at 24 h post-infection (hpi) in EV-A71-infected 16HBE cells. In total, 6615 proteins were identified by using TMT coupled with LC-MS/MS in this study. In the EV-A71- and mock-infected groups, 210 differentially expressed proteins were found, including 86 upregulated and 124 downregulated proteins, at 24 hpi. To ensure the validity and reliability of the proteomics data, 3 randomly selected proteins were verified by Western blot and Immunofluorescence analysis, and the results were consistent with the TMT results. Subsequently, functional enrichment analysis indicated that the up-regulated and down-regulated proteins were individually involved in various biological processes and signaling pathways, including metabolic process, AMPK signaling pathway, Neurotrophin signaling pathway, Viral myocarditis, GABAergic synapse, and so on. Moreover, among these enriched functional analysis, the "Proteasome" pathway was up-regulated, which has caught our attention. Inhibition of proteasome was found to obviously suppress the EV-A71 replication. Finally, further in-depth analysis revealed that these differentially expressed proteins contained distinct domains and localized in different subcellular components. Taken together, our data provided a comprehensive view of host cell response to EV-A71 and identified host proteins may lead to better understanding of the pathogenic mechanisms and host responses to EV-A71 infection, and also to the identification of new therapeutic targets for EV-A71 infection.
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Affiliation(s)
- Hu Yajie
- Department of Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province; The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China.; Yunnan Provincial Key Laboratory of Clinical Virology
| | - Wang Shenglan
- Department of Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province; The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Zhao Wei
- Department of Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province; The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Li Rufang
- Department of Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province; The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Yang Tingting
- Department of Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province; The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Zhang Yunhui
- Department of Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province; The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China..
| | - Song Jie
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, China.
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Host Molecule Incorporation into HIV Virions, Potential Influences in HIV Pathogenesis. Viruses 2022; 14:v14112523. [PMID: 36423132 PMCID: PMC9694329 DOI: 10.3390/v14112523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/08/2022] [Accepted: 11/12/2022] [Indexed: 11/16/2022] Open
Abstract
During the last phase of HIV viral production, nascent HIV virions acquire a fraction of the cellular lipid membrane to create the external lipid envelope, a process by which cellular proteins present on the surface of the infected cell can be incorporated along with Env trimers. Interestingly, several studies indicated that these incorporated host molecules could conserve their biological activity and consequently contribute to HIV pathogenesis either by enhancing the infectivity of HIV virions, their tissue tropism or by affecting immune cell functions. The following review will describe the main approaches used to characterize membrane bound host molecule incorporation into HIV virions, the proposed mechanisms involved, and the role of a non-exhaustive list of incorporated molecules.
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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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Wani SA, Sahu AR, Khan RIN, Praharaj MR, Saxena S, Rajak KK, Muthuchelvan D, Sahoo A, Mishra B, Singh RK, Mishra BP, Gandham RK. Proteome Modulation in Peripheral Blood Mononuclear Cells of Peste des Petits Ruminants Vaccinated Goats and Sheep. Front Vet Sci 2021; 8:670968. [PMID: 34631844 PMCID: PMC8493254 DOI: 10.3389/fvets.2021.670968] [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: 02/22/2021] [Accepted: 05/31/2021] [Indexed: 12/03/2022] Open
Abstract
In the present study, healthy goats and sheep (n = 5) that were confirmed negative for peste des petits ruminants virus (PPRV) antibodies by monoclonal antibody-based competitive ELISA and by serum neutralization test and for PPRV antigen by s-ELISA were vaccinated with Sungri/96. A quantitative study was carried out to compare the proteome of peripheral blood mononuclear cells (PBMCs) of vaccinated goat and sheep [5 days post-vaccination (dpv) and 14 dpv] vs. unvaccinated (0 day) to divulge the alteration in protein expression following vaccination. A total of 232 and 915 proteins were differentially expressed at 5 and 14 dpv, respectively, in goats. Similarly, 167 and 207 proteins were differentially expressed at 5 and 14 dpv, respectively, in sheep. Network generated by Ingenuity Pathway Analysis was “infectious diseases, antimicrobial response, and inflammatory response,” which includes the highest number of focus molecules. The bio functions, cell-mediated immune response, and humoral immune response were highly enriched in goats at 5 dpv and at 14 dpv. At the molecular level, the immune response produced by the PPRV vaccine virus in goats is effectively coordinated and stronger than that in sheep, though the vaccine provides protection from virulent virus challenge in both. The altered expression of certain PBMC proteins especially ISG15 and IRF7 induces marked changes in cellular signaling pathways to coordinate host immune responses.
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Affiliation(s)
- Sajad Ahmad Wani
- Division of Veterinary Biotechnology, Indian Council of Agricultural Research - Indian Veterinary Research Institute, Bareilly, India.,College of Pharmacy, Pharmaceutics and Pharmaceutical Chemistry, The Ohio State University, Columbus, OH, United States
| | - Amit Ranjan Sahu
- Division of Veterinary Biotechnology, Indian Council of Agricultural Research - Indian Veterinary Research Institute, Bareilly, India
| | - Raja Ishaq Nabi Khan
- Division of Veterinary Biotechnology, Indian Council of Agricultural Research - Indian Veterinary Research Institute, Bareilly, India
| | - Manas Ranjan Praharaj
- Systems Biology Lab, Department of Biotechnology -National Institute of Animal Biotechnology, Hyderabad, India
| | - Shikha Saxena
- Division of Veterinary Biotechnology, Indian Council of Agricultural Research - Indian Veterinary Research Institute, Bareilly, India
| | - Kaushal Kishor Rajak
- Division of Biological Products, Indian Council of Agricultural Research - Indian Veterinary Research Institute, Bareilly, India
| | - Dhanavelu Muthuchelvan
- Division of Virology, Indian Council of Agricultural Research - Indian Veterinary Research Institute, Mukteswar, India
| | - Aditya Sahoo
- Division of Veterinary Biotechnology, Indian Council of Agricultural Research - Indian Veterinary Research Institute, Bareilly, India
| | - Bina Mishra
- Division of Biological Products, Indian Council of Agricultural Research - Indian Veterinary Research Institute, Bareilly, India
| | - R K Singh
- Division of Veterinary Biotechnology, Indian Council of Agricultural Research - Indian Veterinary Research Institute, Bareilly, India
| | - Bishnu Prasad Mishra
- Division of Veterinary Biotechnology, Indian Council of Agricultural Research - Indian Veterinary Research Institute, Bareilly, India
| | - Ravi Kumar Gandham
- Division of Veterinary Biotechnology, Indian Council of Agricultural Research - Indian Veterinary Research Institute, Bareilly, India.,Systems Biology Lab, Department of Biotechnology -National Institute of Animal Biotechnology, Hyderabad, India
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Kaikai H, Zhao D, Liu Y, Liu Q, Huang X, Yang J, Zhang L, Li Y. The E3 Ubiquitin Ligase TRIM25 Inhibits Tembusu Virus Replication in vitro. Front Vet Sci 2021; 8:722113. [PMID: 34595229 PMCID: PMC8476877 DOI: 10.3389/fvets.2021.722113] [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: 06/08/2021] [Accepted: 08/19/2021] [Indexed: 12/03/2022] Open
Abstract
Duck Tembusu virus (DTMUV) is a newly emerging pathogenic flavivirus that has caused significant economic losses to the duck industry in China since 2010 due to egg production losses and neurological dysfunction. DTMUV is a public health concern because the infection spreads rapidly among birds. Retinoic acid-inducible gene-I (RIG-I)serves as an innate immune sensor and plays a key role in host antiviral defenses. Tripartite motif-containing protein 25 (TRIM25), an E3 ubiquitin ligase, is pivotal for RIG-I ubiquitination and activation. In addition, TRIM25 acts as an interferon-stimulated gene and mediates the antiviral activity. However, the effect of duck TRIM25 on DTMUV has not been assessed. Herein, we reportthe antiviral function of TRIM25 against DTMUV. First, we constructed the pcDNA3.1-c-myc-duTRIM25 plasmid. TRIM25 has a 2052 bp open reading frame that encodes a predicted 684 amino acid protein consisting of a RING finger domain, a B-box domain, a coiled-coil domain, and a PRY/SPRY domain. The protein sequence identity with chicken, mouse, and human TRIM25 is 69.7, 47.8, and 48.3%, respectively. TRIM25 was upregulated in BHK-21 cells, duck embryo fibroblasts, and 293T cellsupon DTMUV infection. The expression of viral RNA and proteins was significantly lower in cells over expressing TRIM25 than in control cells. Furthermore, siRNA-mediated silencing of TRIM25 increased the production of viral progeny. These results help elucidate the molecular mechanisms underlying the host response to DTMUV infection and suggest potential control measures for DTMUV outbreaks.
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Affiliation(s)
- Han Kaikai
- Key Laboratory of Veterinary Diagnosis, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,Institute of Life Sciences, Jiangsu University, Zhenjiang, China.,College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China
| | - Dongmin Zhao
- Key Laboratory of Veterinary Diagnosis, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,Institute of Life Sciences, Jiangsu University, Zhenjiang, China.,College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Yuzhuo Liu
- Key Laboratory of Veterinary Diagnosis, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Qingtao Liu
- Key Laboratory of Veterinary Diagnosis, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,Institute of Life Sciences, Jiangsu University, Zhenjiang, China.,College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Xinmei Huang
- Key Laboratory of Veterinary Diagnosis, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,Institute of Life Sciences, Jiangsu University, Zhenjiang, China.,College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Jing Yang
- Key Laboratory of Veterinary Diagnosis, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Lijiao Zhang
- Key Laboratory of Veterinary Diagnosis, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yin Li
- Key Laboratory of Veterinary Diagnosis, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,Institute of Life Sciences, Jiangsu University, Zhenjiang, China.,College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
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Lin Z, Zhao C, Lei Z, Zhang Y, Huang R, Lin B, Dong Y, Zhang H, Li J, Li X. Epidermal stem cells maintain stemness via a biomimetic micro/nanofiber scaffold that promotes wound healing by activating the Notch signaling pathway. Stem Cell Res Ther 2021; 12:341. [PMID: 34112252 PMCID: PMC8193873 DOI: 10.1186/s13287-021-02418-2] [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: 01/28/2021] [Accepted: 05/25/2021] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Epidermal stem cells (EpSCs) play a vital role in wound healing and skin renewal. Although biomaterial scaffolds have been used for transplantation of EpSCs in wound healing, the ex vivo differentiation of EpSCs limits their application. METHODS To inhibit the differentiation of EpSCs and maintain their stemness, we developed an electrospun polycaprolactone (PCL)+cellulose acetate (CA) micro/nanofiber for the culture and transplantation of EpSCs. The modulation effect on EpSCs of the scaffold and the underlying mechanism were explored. Liquid chromatography-tandem mass spectrometry for label-free quantitative proteomics was used to analyze proteomic changes in EpSCs cultured on scaffolds. In addition, the role of transplanted undifferentiated EpSCs in wound healing was also studied. RESULTS In this study, we found that the PCL+CA micro/nanofiber scaffold can inhibit the differentiation of EpSCs through YAP activation-mediated inhibition of the Notch signaling pathway. Significantly differentially expressed proteomics was observed in EpSCs cultured on scaffolds and IV collagen-coated culture dishes. Importantly, differential expression levels of ribosome-related proteins and metabolic pathway-related proteins were detected. Moreover, undifferentiated EpSCs transplanted with the PCL+CA scaffold can promote wound healing through the activation of the Notch signaling pathway in rat full-thickness skin defect models. CONCLUSIONS Overall, our study demonstrated the role of the PCL+CA micro-nanofiber scaffold in maintaining the stemness of EpSCs for wound healing, which can be helpful for the development of EpSCs maintaining scaffolds and exploration of interactions between biomaterials and EpSCs.
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Affiliation(s)
- Zhixiao Lin
- Department of Plastic Surgery, Tangdu Hospital, Airforce Military Medical University, Xi'an, 710038, China
| | - Congying Zhao
- Department of Plastic Surgery, Tangdu Hospital, Airforce Military Medical University, Xi'an, 710038, China
| | - Zhanjun Lei
- Department of Plastic Surgery, Tangdu Hospital, Airforce Military Medical University, Xi'an, 710038, China
| | - Yuheng Zhang
- Department of Plastic Surgery, Tangdu Hospital, Airforce Military Medical University, Xi'an, 710038, China
| | - Rong Huang
- Department of Plastic Surgery, Tangdu Hospital, Airforce Military Medical University, Xi'an, 710038, China
| | - Bin Lin
- Department of Plastic Surgery, Tangdu Hospital, Airforce Military Medical University, Xi'an, 710038, China
| | - Yuchen Dong
- Department of Plastic Surgery, Tangdu Hospital, Airforce Military Medical University, Xi'an, 710038, China
| | - Hao Zhang
- Department of Plastic Surgery, Tangdu Hospital, Airforce Military Medical University, Xi'an, 710038, China
| | - Jinqing Li
- Department of Plastic Surgery, Tangdu Hospital, Airforce Military Medical University, Xi'an, 710038, China.
| | - Xueyong Li
- Department of Plastic Surgery, Tangdu Hospital, Airforce Military Medical University, Xi'an, 710038, China.
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Luo R, Huan C, Gao Q, Pan H, Chen P, Liu X, Gao S. AlphaB-crystallin promotes porcine circovirus type 2 replication in a cell proliferation-dependent manner. Virus Res 2021; 301:198435. [PMID: 33961899 DOI: 10.1016/j.virusres.2021.198435] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 04/06/2021] [Accepted: 04/21/2021] [Indexed: 11/20/2022]
Abstract
Porcine circovirus type 2 (PCV2) is the primary causative agent of postweaning multisystemic wasting syndrome (PMWS) and causes heavy economic losses to the porcine industry worldwide. In this study, PK-15 cells were infected with PCV2 for 48 h, then harvested and subjected to label-free quantitative proteomic mass spectrometry. In total, 1212 proteins were differentially expressed in PCV2-infected cells compared with mock-infected cells, including 796 upregulated and 416 downregulated proteins. Gene ontology analysis showed that these differentially expressed proteins were involved in biological processes, cellular components and molecular functions, and these categories included cellular processes, environmental information processing, genetic information processing, disease, metabolism, and body systems. Enrichment analysis of the KEGG pathway showed that innate immune responses were significantly enriched. AlphaB-crystallin (CRYAB) interacts with desmin and cytoplasmic actin to prevent protein misfolding and aggregation, helping to maintain cytoskeletal integrity and promoting cell proliferation. In this study, CRYAB was found to effect the replication of PCV2, as verified by qRT-PCR, TCID50 determination and western blot analysis. Overexpression of CRYAB significantly upregulated PCV2 capsid protein and increased viral titers in both PK-15 cells and culture supernatants, whereas the opposite results were obtained in CRYAB knockdown cells. Furthermore, we revealed that the promotion of PCV2 replication by CRYAB was dependent on cell proliferation. To our knowledge, this is the first report of the effect of CRYAB on PCV2 replication and our findings contribute to a greater understanding of the mechanism of PCV2 replication and pathogenesis, as well as the host's response to PCV2 infection.
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Affiliation(s)
- Rongdi Luo
- Key Laboratory of Avian Bioproduct Development, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, Jiangsu, 225009, China; College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Changchao Huan
- Key Laboratory of Avian Bioproduct Development, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, Jiangsu, 225009, China; College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Qingqing Gao
- Key Laboratory of Avian Bioproduct Development, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, Jiangsu, 225009, China; College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Haochun Pan
- Key Laboratory of Avian Bioproduct Development, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, Jiangsu, 225009, China; College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Pengxiang Chen
- Key Laboratory of Avian Bioproduct Development, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, Jiangsu, 225009, China; College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Xiufan Liu
- Key Laboratory of Avian Bioproduct Development, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, Jiangsu, 225009, China; College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Song Gao
- Key Laboratory of Avian Bioproduct Development, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, Jiangsu, 225009, China; College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, China.
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10
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Han K, Zhao D, Liu Q, Liu Y, Huang X, Yang J, Zhang L, Li Y. Transcriptome analysis reveals new insight of duck Tembusu virus (DTMUV)-infected DF-1 cells. Res Vet Sci 2021; 137:150-158. [PMID: 33975194 DOI: 10.1016/j.rvsc.2021.04.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 04/20/2021] [Accepted: 04/22/2021] [Indexed: 11/16/2022]
Abstract
Duck Tembusu virus (DTMUV) is a newly emerging pathogenic flavivirus that has caused huge economic losses to the duck industry in China since 2010. Moreover, the infection has spread rapidly, resulted in a potential public health concern. To improve our understanding of the host cellular responses to virus infection and the pathogenesis of DTMUV infection, we used RNA-Seq to detect the gene changes in DF-1 cells infected and mock-infected with DTMUV. A total of 663 differentially-expressed genes (DEGs) were identified in DTMUV-infected compared with mock-infected DF-1 cells at 24 h post-infection (hpi), among which 590 were up regulated and 73 were down regulated. Gene Ontology analysis indicated that the DEGs were mainly involved in cellular process, immune system processes, metabolic processes, and signal-organism process. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the DEGs were mainly involved in several signaling pathways such as Toll-like receptor signaling, Jak-STAT signaling, RIG-I-like receptor signaling and AGE-RAGE signaling pathway. Moreover, some selected DEGs were further confirmed by real-time PCR and the results were consistent with the sequencing data. To our knowledge, this study is the first to analyze the transcriptomic change in DF-1 cells following DTMUV infection. We believe that our research provides useful information in better understanding the host response to DTMUV infection and the inherent mechanism of DTMUV replication and pathogenicity.
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Affiliation(s)
- Kaikai Han
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Diagnosis, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, 210014, China; Institute of life sciences, Jiangsu University, Zhenjiang 212013, China.
| | - Dongmin Zhao
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Diagnosis, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, 210014, China
| | - Qingtao Liu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Diagnosis, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, 210014, China
| | - Yuzhuo Liu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Diagnosis, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, 210014, China
| | - Xinmei Huang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Diagnosis, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, 210014, China
| | - Jing Yang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Diagnosis, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, 210014, China
| | - Lijiao Zhang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Diagnosis, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, 210014, China
| | - Yin Li
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Diagnosis, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, 210014, China
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11
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Zhong C, Li J, Mao L, Liu M, Zhu X, Li W, Sun M, Ji X, Xiao F, Yang L, Zhang W, Liao Z. Proteomics analysis reveals heat shock proteins involved in caprine parainfluenza virus type 3 infection. BMC Vet Res 2019; 15:151. [PMID: 31101113 PMCID: PMC6525452 DOI: 10.1186/s12917-019-1897-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 05/01/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Caprine parainfluenza virus type 3 (CPIV3) is major pathogen of goat herds causing serious respiratory tract disease and economic losses to the goat industry in China. We analyzed the differential proteomics of CPIV3-infected Madin-Darby bovine kidney (MDBK) cells using quantitative iTRAQ coupled LC-MS/MS. In addition, four DEPs were validated by qRT-PCR and western blot analysis. RESULTS Quantitative proteomics analysis revealed 163 differentially expressed proteins (DEPs) between CPIV3-infected and mock-infected groups (p-value < 0.05 and fold change > 1.2), among which 91 were down-regulated and 72 were up-regulated. Gene ontology (GO) analysis showed that these DEPs were involved in molecular functions, cellular components and biological processes. Biological functions in which the DEPs were involved in included diseases, genetic information processing, metabolism, environmental information processing, cellular processes, and organismal systems. STRING analysis revealed that four heat shock proteins (HSPs) included HSPA5, HSPA1B, HSP90B1 and HSPA6 may be associated with proliferation of CPIV3 in MDBK cells. qRT-PCR and western blot analysis showed that the selected HSPs were identical to the quantitative proteomics data. CONCLUSION To our knowledge, this is the first report of the proteomic changes in MDBK cells after CPIV3 infection.
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Affiliation(s)
- Chunyan Zhong
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, 210014, China.,College of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Jizong Li
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, 210014, China. .,School of Pharmacy, Linyi University, Linyi, 276000, China.
| | - Li Mao
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, 210014, China.,Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Nanjing, 210014, China
| | - Maojun Liu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, 210014, China
| | - Xing Zhu
- College of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Wenliang Li
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, 210014, China
| | - Min Sun
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, 210014, China
| | - Xinqin Ji
- College of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Fang Xiao
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, 210014, China.,College of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Leilei Yang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, 210014, China
| | - Wenwen Zhang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, 210014, China
| | - Zheng Liao
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, 210014, China.,College of Animal Science, Guizhou University, Guiyang, 550025, China
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12
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Zhang J, Sun L. Global profiling of megalocytivirus-induced proteins in tongue sole (Cynoglossus semilaevis) spleen identifies cellular processes essential to viral infection. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2019; 92:150-159. [PMID: 30428365 PMCID: PMC7102559 DOI: 10.1016/j.dci.2018.11.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 11/06/2018] [Accepted: 11/06/2018] [Indexed: 05/30/2023]
Abstract
Megalocytivirus is a DNA virus with a broad host range among farmed fish including tongue sole (Cynoglossus semilaevis). In this study, label-free proteomics was performed to examine protein expression in tongue sole spleen induced by megalocytivirus at 8 and 12 days post infection (dpi). Compared to uninfected control fish, virus-infected fish displayed 315 up-regulated proteins and 111 down-regulated proteins at 8 dpi, and 48 up-regulated proteins and 43 down-regulated proteins at 12 dpi. The expressions of five differentially expressed proteins were confirmed by Western blot. The differentially expressed proteins were enriched in the pathways and processes associated with innate immune response and viral infection. Interference with the expression of two up-regulated proteins of the ubiquitin proteasome system (UPS), i.e. proteasome assembly chaperone 2 and proteasome maturation protein, significantly reduced viral propagation in fish, whereas overexpression of these two proteins significantly enhanced viral propagation. Consistently, inhibition of the functioning of proteasome significantly impaired viral replication in vivo. This study provided the first global protein profile responsive to megalocytivirus in tongue sole, and revealed an essential role of UPS in viral infection.
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Affiliation(s)
- Jian Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China; Deep Sea Research Center, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Li Sun
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.
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13
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Burnie J, Guzzo C. The Incorporation of Host Proteins into the External HIV-1 Envelope. Viruses 2019; 11:v11010085. [PMID: 30669528 PMCID: PMC6356245 DOI: 10.3390/v11010085] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 01/15/2019] [Accepted: 01/16/2019] [Indexed: 02/07/2023] Open
Abstract
The incorporation of biologically active host proteins into HIV-1 is a well-established phenomenon, particularly due to the budding mechanism of viral egress in which viruses acquire their external lipid membrane directly from the host cell. While this mechanism might seemingly imply that host protein incorporation is a passive uptake of all cellular antigens associated with the plasma membrane at the site of budding, this is not the case. Herein, we review the evidence indicating that host protein incorporation can be a selective and conserved process. We discuss how HIV-1 virions displaying host proteins on their surface can exhibit a myriad of altered phenotypes, with notable impacts on infectivity, homing, neutralization, and pathogenesis. This review describes the canonical and emerging methods to detect host protein incorporation, highlights the well-established host proteins that have been identified on HIV-1 virions, and reflects on the role of these incorporated proteins in viral pathogenesis and therapeutic targeting. Despite many advances in HIV treatment and prevention, there remains a global effort to develop increasingly effective anti-HIV therapies. Given the broad range of biologically active host proteins acquired on the surface of HIV-1, additional studies on the mechanisms and impacts of these incorporated host proteins may inform the development of novel treatments and vaccine designs.
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Affiliation(s)
- Jonathan Burnie
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON M5S 3G5, Canada.
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada.
| | - Christina Guzzo
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON M5S 3G5, Canada.
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada.
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14
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Walper SA, Lasarte Aragonés G, Sapsford KE, Brown CW, Rowland CE, Breger JC, Medintz IL. Detecting Biothreat Agents: From Current Diagnostics to Developing Sensor Technologies. ACS Sens 2018; 3:1894-2024. [PMID: 30080029 DOI: 10.1021/acssensors.8b00420] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Although a fundamental understanding of the pathogenicity of most biothreat agents has been elucidated and available treatments have increased substantially over the past decades, they still represent a significant public health threat in this age of (bio)terrorism, indiscriminate warfare, pollution, climate change, unchecked population growth, and globalization. The key step to almost all prevention, protection, prophylaxis, post-exposure treatment, and mitigation of any bioagent is early detection. Here, we review available methods for detecting bioagents including pathogenic bacteria and viruses along with their toxins. An introduction placing this subject in the historical context of previous naturally occurring outbreaks and efforts to weaponize selected agents is first provided along with definitions and relevant considerations. An overview of the detection technologies that find use in this endeavor along with how they provide data or transduce signal within a sensing configuration follows. Current "gold" standards for biothreat detection/diagnostics along with a listing of relevant FDA approved in vitro diagnostic devices is then discussed to provide an overview of the current state of the art. Given the 2014 outbreak of Ebola virus in Western Africa and the recent 2016 spread of Zika virus in the Americas, discussion of what constitutes a public health emergency and how new in vitro diagnostic devices are authorized for emergency use in the U.S. are also included. The majority of the Review is then subdivided around the sensing of bacterial, viral, and toxin biothreats with each including an overview of the major agents in that class, a detailed cross-section of different sensing methods in development based on assay format or analytical technique, and some discussion of related microfluidic lab-on-a-chip/point-of-care devices. Finally, an outlook is given on how this field will develop from the perspective of the biosensing technology itself and the new emerging threats they may face.
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Affiliation(s)
- Scott A. Walper
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Guillermo Lasarte Aragonés
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University Fairfax, Virginia 22030, United States
| | - Kim E. Sapsford
- OMPT/CDRH/OIR/DMD Bacterial Respiratory and Medical Countermeasures Branch, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Carl W. Brown
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University Fairfax, Virginia 22030, United States
| | - Clare E. Rowland
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- National Research Council, Washington, D.C. 20036, United States
| | - Joyce C. Breger
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
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15
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Qu Z, Gao F, Li L, Zhang Y, Jiang Y, Yu L, Zhou Y, Zheng H, Tong W, Li G, Tong G. Label-Free Quantitative Proteomic Analysis of Differentially Expressed Membrane Proteins of Pulmonary Alveolar Macrophages Infected with Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Virus and Its Attenuated Strain. Proteomics 2017; 17. [PMID: 29052333 PMCID: PMC6084361 DOI: 10.1002/pmic.201700101] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 09/19/2017] [Indexed: 12/11/2022]
Abstract
Significant differences exist between the highly pathogenic (HP) porcine reproductive and respiratory syndrome virus (PRRSV) and its attenuated pathogenic (AP) strain in the ability to infect host cells. The mechanisms by which different virulent strains invade host cells remain relatively unknown. In this study, pulmonary alveolar macrophages (PAMs) are infected with HP‐PRRSV (HuN4) and AP‐PRRSV (HuN4‐F112) for 24 h, then harvested and subjected to label‐free quantitative MS. A total of 2849 proteins are identified, including 95 that are differentially expressed. Among them, 26 proteins are located on the membrane. The most differentially expressed proteins are involved in response to stimulus, metabolic process, and immune system process, which mainly have the function of binding and catalytic activity. Cluster of differentiation CD163, vimentin (VIM), and nmII as well as detected proteins are assessed together by string analysis, which elucidated a potentially different infection mechanism. According to the function annotations, PRRSV with different virulence may mainly differ in immunology, inflammation, immune evasion as well as cell apoptosis. This is the first attempt to explore the differential characteristics between HP‐PRRSV and its attenuated PRRSV infected PAMs focusing on membrane proteins which will be of great help to further understand the different infective mechanisms of HP‐PRRSV and AP‐PRRSV.
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Affiliation(s)
- Zehui Qu
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P. R. China
| | - Fei Gao
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P. R. China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, P. R. China
| | - Liwei Li
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P. R. China
| | - Yujiao Zhang
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P. R. China
| | - Yifeng Jiang
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P. R. China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, P. R. China
| | - Lingxue Yu
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P. R. China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, P. R. China
| | - Yanjun Zhou
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P. R. China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, P. R. China
| | - Hao Zheng
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P. R. China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, P. R. China
| | - Wu Tong
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P. R. China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, P. R. China
| | - Guoxin Li
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P. R. China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, P. R. China
| | - Guangzhi Tong
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P. R. China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, P. R. China
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16
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Zhang J, Xu R, Yu B, He Y, Li Y, Qin Z. Study on the properties of Pb–Co3O4–PbO2 composite inert anodes prepared by vacuum hot pressing technique. RSC Adv 2017. [DOI: 10.1039/c7ra07898f] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
In this research, the Pb–Co3O4–PbO2 composite inert anodes were prepared by vacuum hot pressing technique, which showed good electrochemical performance.
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Affiliation(s)
- Jingshi Zhang
- Faculty of Metallurgical and Energy Engineering
- Kunming University of Science and Technology
- Kunming 650093
- China
- State Key Laboratory of Complex Nonferrous Metal Resources Clean Utilization
| | - Ruidong Xu
- Faculty of Metallurgical and Energy Engineering
- Kunming University of Science and Technology
- Kunming 650093
- China
- State Key Laboratory of Complex Nonferrous Metal Resources Clean Utilization
| | - Bohao Yu
- Faculty of Metallurgical and Energy Engineering
- Kunming University of Science and Technology
- Kunming 650093
- China
| | - Yunlong He
- Faculty of Metallurgical and Energy Engineering
- Kunming University of Science and Technology
- Kunming 650093
- China
| | - Yiyang Li
- Faculty of Metallurgical and Energy Engineering
- Kunming University of Science and Technology
- Kunming 650093
- China
| | - Ziyang Qin
- Faculty of Metallurgical and Energy Engineering
- Kunming University of Science and Technology
- Kunming 650093
- China
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17
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Han K, Zhao D, Liu Y, Liu Q, Huang X, Yang J, An F, Li Y. Quantitative Proteomic Analysis of Duck Ovarian Follicles Infected with Duck Tembusu Virus by Label-Free LC-MS. Front Microbiol 2016; 7:463. [PMID: 27066001 PMCID: PMC4815560 DOI: 10.3389/fmicb.2016.00463] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 03/21/2016] [Indexed: 12/15/2022] Open
Abstract
Duck Tembusu virus (DTMUV) is a newly emerging pathogenic flavivirus that has caused massive economic losses to the duck industry in China. DTMUV infection mainly results in significant decreases in egg production in egg-laying ducks within 1–2 weeks post infection. However, information on the comparative protein expression of host tissues in response to DTMUV infection is limited. In the present study, the cellular protein response to DTMUV infection in duck ovarian follicles was analyzed using nano-flow high-performance liquid chromatography-electrospray tandem mass spectrometry. Quantitative proteomic analysis revealed 131 differentially expressed proteins, among which 53 were up regulated and 78 were down regulated. The identified proteins were involved in the regulation of essential processes such as cellular structure and integrity, RNA processing, protein biosynthesis and modification, vesicle transport, signal transduction, and mitochondrial pathway. Some selected proteins that were found to be regulated in DTMUV-infected tissues were screened by quantitative real-time PCR to examine their regulation at the transcriptional level, western blot analysis was used to validate the changes of some selected proteins on translational level. To our knowledge, this study is the first to analyze the proteomic changes in duck ovarian follicles following DTMUV infection. The protein-related information obtained in this study may be useful to understand the host response to DTMUV infection and the inherent mechanism of DTMUV replication and pathogenicity.
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Affiliation(s)
- Kaikai Han
- Key Laboratory of Veterinary Biological Engineering and Technology, National Center for Engineering Research of Veterinary Bio-products, Institute of Veterinary Medicine, Ministry of Agriculture, Jiangsu Academy of Agricultural SciencesNanjing, China; Jiangsu Key Lab of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and ZoonosesYangzhou, China
| | - Dongmin Zhao
- Key Laboratory of Veterinary Biological Engineering and Technology, National Center for Engineering Research of Veterinary Bio-products, Institute of Veterinary Medicine, Ministry of Agriculture, Jiangsu Academy of Agricultural SciencesNanjing, China; Jiangsu Key Lab of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and ZoonosesYangzhou, China
| | - Yuzhuo Liu
- Key Laboratory of Veterinary Biological Engineering and Technology, National Center for Engineering Research of Veterinary Bio-products, Institute of Veterinary Medicine, Ministry of Agriculture, Jiangsu Academy of Agricultural SciencesNanjing, China; Jiangsu Key Lab of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and ZoonosesYangzhou, China
| | - Qingtao Liu
- Key Laboratory of Veterinary Biological Engineering and Technology, National Center for Engineering Research of Veterinary Bio-products, Institute of Veterinary Medicine, Ministry of Agriculture, Jiangsu Academy of Agricultural SciencesNanjing, China; Jiangsu Key Lab of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and ZoonosesYangzhou, China
| | - Xinmei Huang
- Key Laboratory of Veterinary Biological Engineering and Technology, National Center for Engineering Research of Veterinary Bio-products, Institute of Veterinary Medicine, Ministry of Agriculture, Jiangsu Academy of Agricultural SciencesNanjing, China; Jiangsu Key Lab of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and ZoonosesYangzhou, China
| | - Jing Yang
- Key Laboratory of Veterinary Biological Engineering and Technology, National Center for Engineering Research of Veterinary Bio-products, Institute of Veterinary Medicine, Ministry of Agriculture, Jiangsu Academy of Agricultural SciencesNanjing, China; Jiangsu Key Lab of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and ZoonosesYangzhou, China
| | - Fengjiao An
- Key Laboratory of Veterinary Biological Engineering and Technology, National Center for Engineering Research of Veterinary Bio-products, Institute of Veterinary Medicine, Ministry of Agriculture, Jiangsu Academy of Agricultural SciencesNanjing, China; Jiangsu Key Lab of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and ZoonosesYangzhou, China
| | - Yin Li
- Key Laboratory of Veterinary Biological Engineering and Technology, National Center for Engineering Research of Veterinary Bio-products, Institute of Veterinary Medicine, Ministry of Agriculture, Jiangsu Academy of Agricultural SciencesNanjing, China; Jiangsu Key Lab of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and ZoonosesYangzhou, China
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18
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Huong TN, Tan BH, Sugrue RJ. A Proteomic-Based Workflow Using Purified Respiratory Syncytial Virus Particles to Identify Cellular Factors as Drug Targets. Methods Mol Biol 2016; 1442:175-194. [PMID: 27464695 DOI: 10.1007/978-1-4939-3687-8_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The identification of cellular factors that play a role in respiratory syncytial virus (RSV) replication is an alternative strategy in the identification of druggable cellular protein that are essential for RSV replication. In this regard experimental strategies that are able to screen relevant proteins from the vast array of proteins in the cellular milieu will facilitate the identification of potential drug targets. In this chapter we describe a procedure where RSV particles are purified from cells that are permissive for RSV infection, and the protein composition of the purified virus particles characterized using a proteomics-based strategy. This procedure revealed that actin, several actin-binding proteins, and the chaperones HSP70 and HSP90 also co-purified with the virus particles. The relevance of the HSP90 protein to virus replication was then further validated using imaging, gene silencing and by using an established small molecule HSP90 inhibitor.
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Affiliation(s)
- Tra Nguyen Huong
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Boon Huan Tan
- Detection and Diagnostics Laboratory, DSO National Laboratories, 27 Medical Drive, Singapore, 117510, Singapore
| | - Richard J Sugrue
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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Saxena R, Gupta S, Singh K, Mitra K, Tripathi AK, Tripathi RK. Proteomic profiling of SupT1 cells reveal modulation of host proteins by HIV-1 Nef variants. PLoS One 2015; 10:e0122994. [PMID: 25874870 PMCID: PMC4395413 DOI: 10.1371/journal.pone.0122994] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 02/26/2015] [Indexed: 01/14/2023] Open
Abstract
Nef is an accessory viral protein that promotes HIV-1 replication, facilitating alterations in cellular pathways via multiple protein-protein interactions. The advent of proteomics has expanded the focus on better identification of novel molecular pathways regulating disease progression. In this study, nef was sequenced from randomly selected patients, however, sequence variability identified did not elicited any specific mutation that could have segregated HIV-1 patients in different stages of disease progression. To explore the difference in Nef functionality based on sequence variability we used proteomics approach. Proteomic profiling was done to compare the effect of Nef variants in host cell protein expression. 2DGE in control and Nef transfected SupT1 cells demonstrated several differentially expressed proteins. Fourteen protein spots were detected with more than 1.5 fold difference. Significant down regulation was seen in six unique protein spots in the Nef treated cells. Proteins were identified as Cyclophilin A, EIF5A-1 isoform B, Rho GDI 1 isoform a, VDAC1, OTUB1 and α-enolase isoform 1 (ENO1) through LC-MS/MS. The differential expression of the 6 proteins was analyzed by Real time PCR, Western blotting and Immunofluorescence studies with two Nef variants (RP14 and RP01) in SupT1 cells. There was contrasting difference between the effect of these Nef variants upon the expression of these six proteins. Downregulation of α-enolase (ENO1), VDAC1 and OTUB1 was more significant by Nef RP01 whereas Cyclophilin A and RhoGDI were found to be more downregulated by Nef RP14. This difference in Nef variants upon host protein expression was also studied through a site directed mutant of Nef RP01 (55AAAAAAA61) and the effect was found to be reversed. Deciphering the role of these proteins mediated by Nef variants will open a new avenue of research in understanding Nef mediated pathogenesis. Overall study determines modulation of cellular protein expression in T cells by HIV-1 Nef variants.
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Affiliation(s)
- Reshu Saxena
- Toxicology division, CSIR-Central Drug Research Institute, Sector-10, Janakipuram Extension, Sitapur Road, Lucknow, India
| | - Sudipti Gupta
- Toxicology division, CSIR-Central Drug Research Institute, Sector-10, Janakipuram Extension, Sitapur Road, Lucknow, India
| | - Kavita Singh
- Electron Microscopy Lab, Sophisticated Analytical Instrument Facility, CSIR-Central Drug Research Institute, Sector-10, Janakipuram Extension, Sitapur Road, Lucknow, India
| | - Kalyan Mitra
- Electron Microscopy Lab, Sophisticated Analytical Instrument Facility, CSIR-Central Drug Research Institute, Sector-10, Janakipuram Extension, Sitapur Road, Lucknow, India
| | - Anil Kumar Tripathi
- Department of Medicine, King George’s Medical University, Chowk, Lucknow, India
| | - Raj Kamal Tripathi
- Toxicology division, CSIR-Central Drug Research Institute, Sector-10, Janakipuram Extension, Sitapur Road, Lucknow, India
- * E-mail:
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20
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Durmuş S, Çakır T, Özgür A, Guthke R. A review on computational systems biology of pathogen-host interactions. Front Microbiol 2015; 6:235. [PMID: 25914674 PMCID: PMC4391036 DOI: 10.3389/fmicb.2015.00235] [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: 12/01/2014] [Accepted: 03/10/2015] [Indexed: 12/27/2022] Open
Abstract
Pathogens manipulate the cellular mechanisms of host organisms via pathogen-host interactions (PHIs) in order to take advantage of the capabilities of host cells, leading to infections. The crucial role of these interspecies molecular interactions in initiating and sustaining infections necessitates a thorough understanding of the corresponding mechanisms. Unlike the traditional approach of considering the host or pathogen separately, a systems-level approach, considering the PHI system as a whole is indispensable to elucidate the mechanisms of infection. Following the technological advances in the post-genomic era, PHI data have been produced in large-scale within the last decade. Systems biology-based methods for the inference and analysis of PHI regulatory, metabolic, and protein-protein networks to shed light on infection mechanisms are gaining increasing demand thanks to the availability of omics data. The knowledge derived from the PHIs may largely contribute to the identification of new and more efficient therapeutics to prevent or cure infections. There are recent efforts for the detailed documentation of these experimentally verified PHI data through Web-based databases. Despite these advances in data archiving, there are still large amounts of PHI data in the biomedical literature yet to be discovered, and novel text mining methods are in development to unearth such hidden data. Here, we review a collection of recent studies on computational systems biology of PHIs with a special focus on the methods for the inference and analysis of PHI networks, covering also the Web-based databases and text-mining efforts to unravel the data hidden in the literature.
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Affiliation(s)
- Saliha Durmuş
- Computational Systems Biology Group, Department of Bioengineering, Gebze Technical University, KocaeliTurkey
| | - Tunahan Çakır
- Computational Systems Biology Group, Department of Bioengineering, Gebze Technical University, KocaeliTurkey
| | - Arzucan Özgür
- Department of Computer Engineering, Boǧaziçi University, IstanbulTurkey
| | - Reinhard Guthke
- Leibniz Institute for Natural Product Research and Infection Biology – Hans-Knoell-Institute, JenaGermany
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Croft NP, de Verteuil DA, Smith SA, Wong YC, Schittenhelm RB, Tscharke DC, Purcell AW. Simultaneous Quantification of Viral Antigen Expression Kinetics Using Data-Independent (DIA) Mass Spectrometry. Mol Cell Proteomics 2015; 14:1361-72. [PMID: 25755296 DOI: 10.1074/mcp.m114.047373] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Indexed: 11/06/2022] Open
Abstract
The generation of antigen-specific reagents is a significant bottleneck in the study of complex pathogens that express many hundreds to thousands of different proteins or to emerging or new strains of viruses that display potential pandemic qualities and therefore require rapid investigation. In these instances the development of antibodies for example can be prohibitively expensive to cover the full pathogen proteome, or the lead time may be unacceptably long in urgent cases where new highly pathogenic viral strains may emerge. Because genomic information on such pathogens can be rapidly acquired this opens up avenues using mass spectrometric approaches to study pathogen antigen expression, host responses and for screening the utility of therapeutics. In particular, data-independent acquisition (DIA) modalities on high-resolution mass spectrometers generate spectral information on all components of a complex sample providing depth of coverage hitherto only seen in genomic deep sequencing. The spectral information generated by DIA can be iteratively interrogated for potentially any protein of interest providing both evidence of protein expression and quantitation. Here we apply a solely DIA mass spectrometry based methodology to profile the viral antigen expression in cells infected with vaccinia virus up to 9 h post infection without the need for antigen specific antibodies or other reagents. We demonstrate deep coverage of the vaccinia virus proteome using a SWATH-MS acquisition approach, extracting quantitative kinetics of 100 virus proteins within a single experiment. The results highlight the complexity of vaccinia protein expression, complementing what is known at the transcriptomic level, and provide a valuable resource and technique for future studies of viral infection and replication kinetics. Furthermore, they highlight the utility of DIA and mass spectrometry in the dissection of host-pathogen interactions.
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Affiliation(s)
- Nathan P Croft
- From the ‡Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3141, Australia
| | - Danielle A de Verteuil
- From the ‡Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3141, Australia
| | - Stewart A Smith
- §Research School of Biology, The Australian National University, Canberra, ACT, 0200, Australia
| | - Yik Chun Wong
- §Research School of Biology, The Australian National University, Canberra, ACT, 0200, Australia
| | - Ralf B Schittenhelm
- From the ‡Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3141, Australia
| | - David C Tscharke
- §Research School of Biology, The Australian National University, Canberra, ACT, 0200, Australia
| | - Anthony W Purcell
- From the ‡Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3141, Australia;
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22
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Role of Analytics in Viral Safety. VACCINE ANALYSIS: STRATEGIES, PRINCIPLES, AND CONTROL 2015. [PMCID: PMC7122056 DOI: 10.1007/978-3-662-45024-6_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
In summary, this chapter reviews the principles of how the current and routine tests detect adventitious agents, and reviews how novel and emerging methods differ in their detection principles. These facets may permit novel methods to emerge to supplement, refine, or replace the routine methods. We have suggested a framework for risk assessment to assure biosafety in vaccines and suggested quantitative modeling to help crystallize thinking about the place of testing, either routine or novel, in this assurance. We assert that testing for adventitious agents should not be the sole basis on which product biosafety is assured. Appropriate sourcing and quality control of raw and starting materials, adherence to principles of Good Manufacturing Practices, including environmental and personnel monitoring and process validation, and finally, testing as verification are the package needed for maximal assurance of biosafety. Thus, a pathway forward to a new paradigm for adventitious agent testing exists in which detection of a broader array of potential adventitious agents might be included in the testing, with adequate sensitivity to provide the needed assurance of verification that there has been no catastrophic breach, in the context of the overall process, design, and adherence to cGMP. Furthermore, it is our hope that we may be able to implement the 3 Rs policy to reduce, replace, and/or refine the use of animals in product safety testing, at the same time that we provide greater assurance of the biosafety of vaccines.
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23
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Liu X, Yang Y, Zhao M, Bode L, Zhang L, Pan J, Lv L, Zhan Y, Liu S, Zhang L, Wang X, Huang R, Zhou J, Xie P. Proteomics reveal energy metabolism and mitogen-activated protein kinase signal transduction perturbation in human Borna disease virus Hu-H1-infected oligodendroglial cells. Neuroscience 2014; 268:284-96. [PMID: 24637096 PMCID: PMC7116963 DOI: 10.1016/j.neuroscience.2014.03.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 03/01/2014] [Accepted: 03/06/2014] [Indexed: 12/19/2022]
Abstract
A human strain of BDV (BDV Hu-H1) was used to infect human oligodendroglial cells (OL cells). Energy metabolism was the most significantly altered pathway in BDV Hu-H1-infected OL cells. The Raf/MEK/ERK signaling cascade was significantly perturbed in BDV Hu-H1-infected OL cells. BDV Hu-H1caused constitutive activation of the ERK1/2 pathway, but cell proliferation was down-regulated at the same time. BDV Hu-H1 manages to down-regulate cell proliferation, in the presence of activated but not translocated ERK–RSK complex.
Borna disease virus (BDV) is a neurotropic, non-cytolytic RNA virus which replicates in the cell nucleus targeting mainly hippocampal neurons, but also astroglial and oligodendroglial cells in the brain. BDV is associated with a large spectrum of neuropsychiatric pathologies in animals. Its relationship to human neuropsychiatric illness still remains controversial. We could recently demonstrate that human BDV strain Hu-H1 promoted apoptosis and inhibited cell proliferation in a human oligodendroglial cell line (OL cells) whereas laboratory BDV strain V acted contrariwise. Here, differential protein expression between BDV Hu-H1-infected OL cells and non-infected OL cells was assessed through a proteomics approach, using two-dimensional electrophoresis followed by matrix-assisted laser desorption ionization-time of flight tandem mass spectrometry. A total of 63 differential host proteins were identified in BDV Hu-H1-infected OL cells compared to non-infected OL cells. We found that most changes referred to alterations related to the pentose phosphate pathway, glyoxylate and dicarboxylate metabolism, the tricarboxylic acid (TCA) cycle, and glycolysis /gluconeogenesis. By manual querying, two differential proteins were found to be associated with mitogen-activated protein kinase (MAPK) signal transduction. Five key signaling proteins of this pathway (i.e., p-Raf, p-MEK, p-ERK1/2, p-RSK, and p-MSK) were selected for Western blotting validation. p-ERK1/2 and p-RSK were found to be significantly up-regulated, and p-MSK was found to be significantly down-regulated in BDV Hu-H1-infected OL cells compared to non-infected OL cell. Although BDV Hu-H1 constitutively activated the ERK–RSK pathway, host cell proliferation and nuclear translocation of activated pERK in BDV Hu-H1-infected OL cells were impaired. These findings indicate that BDV Hu-H1 infection of human oligodendroglial cells significantly perturbs host energy metabolism, activates the downstream ERK–RSK complex of the Raf/MEK/ERK signaling cascade, and disturbs host cell proliferation possibly through impaired nuclear translocation of pERK, a finding which warrants further research.
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Affiliation(s)
- X Liu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - Y Yang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - M Zhao
- Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - L Bode
- Bornavirus Research Group affiliated to the Free University of Berlin, Berlin, Germany
| | - L Zhang
- Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - J Pan
- Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - L Lv
- Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - Y Zhan
- Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - S Liu
- Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - L Zhang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - X Wang
- Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - R Huang
- Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, China; Department of Rehabilitation, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - J Zhou
- Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - P Xie
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, China.
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24
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Amaya M, Baer A, Voss K, Campbell C, Mueller C, Bailey C, Kehn-Hall K, Petricoin E, Narayanan A. Proteomic strategies for the discovery of novel diagnostic and therapeutic targets for infectious diseases. Pathog Dis 2014; 71:177-89. [PMID: 24488789 PMCID: PMC7108530 DOI: 10.1111/2049-632x.12150] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 01/18/2014] [Accepted: 01/23/2014] [Indexed: 12/14/2022] Open
Abstract
Viruses have developed numerous and elegant strategies to manipulate the host cell machinery to establish a productive infectious cycle. The interaction of viral proteins with host proteins plays an important role in infection and pathogenesis, often bypassing traditional host defenses such as the interferon response and apoptosis. Host–viral protein interactions can be studied using a variety of proteomic approaches ranging from genetic and biochemical to large‐scale high‐throughput technologies. Protein interactions between host and viral proteins are greatly influenced by host signal transduction pathways. In this review, we will focus on comparing proteomic information obtained through differing technologies and how their integration can be used to determine the functional aspect of the host response to infection. We will briefly review and evaluate techniques employed to elucidate viral–host interactions with a primary focus on Protein Microarrays (PMA) and Mass Spectrometry (MS) as potential tools in the discovery of novel therapeutic targets. As many potential molecular markers and targets are proteins, proteomic profiling is expected to yield both clearer and more direct answers to functional and pharmacologic questions.
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Affiliation(s)
- Moushimi Amaya
- National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, VA, USA
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25
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Zhao H, Yang J, Li K, Ding X, Lin R, Ma Y, Liu J, Zhong Z, Qian X, Bo X, Zhou Z, Wang S. Proteomic analysis at the subcellular level for host targets against influenza A virus (H1N1). Antiviral Res 2013; 100:673-87. [PMID: 24161511 DOI: 10.1016/j.antiviral.2013.10.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Revised: 10/10/2013] [Accepted: 10/14/2013] [Indexed: 01/28/2023]
Abstract
Influenza viruses (IVs) trigger a series of intracellular signaling events and induce complex cellular responses from the infected host cell. Accumulating evidence suggests that host cell proteins play an essential role in viral propagation and represent novel antiviral therapeutic targets. Subcellular proteomic technology provides a method for understanding regional differences at the protein level. The present study, which utilized subcellular proteomic technology, aimed to identify host cell proteins involved in influenza virus (HIN1) infection. Two-dimensional gel electrophoresis (2-DE) combined with mass spectrum (MS) was performed on protein extracts from the nuclei, cytoplasm, and mitochondria of infected and control human lung epithelial cells (A549). In total, 112 differentially expressed protein molecules were identified; 80 protein spots were successfully validated using MS. The differential expression of ISG15, MIF, PDCD5, and UCHL1 was confirmed by western blot. Furthermore, antisense oligodeoxyribonucleotide (ODN) targeting ISG15, MIF, PDCD5, and UCHL1 significantly mitigated HIN1 propagation, cytopathic effects, vRNA by RT-qPCR, and rescued cell viability in A549 cells. Taken together, the differentially expressed proteins identified in this study might provide novel targets for anti-influenza drug development.
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Affiliation(s)
- Haibao Zhao
- Beijing Institute of Radiation Medicine, Beijing 100850, PR China
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26
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Altered protein networks and cellular pathways in severe west nile disease in mice. PLoS One 2013; 8:e68318. [PMID: 23874584 PMCID: PMC3707916 DOI: 10.1371/journal.pone.0068318] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 05/28/2013] [Indexed: 01/25/2023] Open
Abstract
Background The recent West Nile virus (WNV) outbreaks in developed countries, including Europe and the United States, have been associated with significantly higher neuropathology incidence and mortality rate than previously documented. The changing epidemiology, the constant risk of (re-)emergence of more virulent WNV strains, and the lack of effective human antiviral therapy or vaccines makes understanding the pathogenesis of severe disease a priority. Thus, to gain insight into the pathophysiological processes in severe WNV infection, a kinetic analysis of protein expression profiles in the brain of WNV-infected mice was conducted using samples prior to and after the onset of clinical symptoms. Methodology/Principal Findings To this end, 2D-DIGE and gel-free iTRAQ labeling approaches were combined, followed by protein identification by mass spectrometry. Using these quantitative proteomic approaches, a set of 148 proteins with modified abundance was identified. The bioinformatics analysis (Ingenuity Pathway Analysis) of each protein dataset originating from the different time-point comparisons revealed that four major functions were altered during the course of WNV-infection in mouse brain tissue: i) modification of cytoskeleton maintenance associated with virus circulation; ii) deregulation of the protein ubiquitination pathway; iii) modulation of the inflammatory response; and iv) alteration of neurological development and neuronal cell death. The differential regulation of selected host protein candidates as being representative of these biological processes were validated by western blotting using an original fluorescence-based method. Conclusion/Significance This study provides novel insights into the in vivo kinetic host reactions against WNV infection and the pathophysiologic processes involved, according to clinical symptoms. This work offers useful clues for anti-viral research and further evaluation of early biomarkers for the diagnosis and prevention of severe neurological disease caused by WNV.
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27
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Zhang LK, Chai F, Li HY, Xiao G, Guo L. Identification of host proteins involved in Japanese encephalitis virus infection by quantitative proteomics analysis. J Proteome Res 2013; 12:2666-78. [PMID: 23647205 DOI: 10.1021/pr400011k] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Japanese encephalitis virus (JEV) enters host cells via receptor-mediated endocytosis and replicates in the cytoplasm of infected cells. To study virus-host cell interactions, we performed a SILAC-based quantitative proteomics study of JEV-infected HeLa cells using a subcellular fractionation strategy. We identified 158 host proteins as differentially regulated by JEV (defined as exhibiting a greater than 1.5-fold change in protein abundance upon JEV infection). The mass spectrometry quantitation data for selected proteins were validated by Western blot and immunofluorescence confocal microscopy. Bioinformatics analyses were used to generate JEV-regulated host response networks consisting of regulated proteins, which included 35 proteins that were newly added based on the results of this study. The JEV infection-induced host response was found to be coordinated primarily through the immune response process, the ubiquitin-proteasome system (UPS), the intracellular membrane system, and lipid metabolism-related proteins. Protein functional studies of selected host proteins using RNA interference-based techniques were carried out in HeLa cells infected with an attenuated or a highly virulent strain of JEV. We demonstrated that the knockdown of interferon-induced transmembrane protein 3 (IFITM3), Ran-binding protein 2 (RANBP2), sterile alpha motif domain-containing protein 9 (SAMD9) and vesicle-associated membrane protein 8 (VAMP8) significantly increased JEV replication. The results presented here not only promote a better understanding of the host response to JEV infection but also highlight multiple potential targets for the development of antiviral agents.
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Affiliation(s)
- Lei-Ke Zhang
- State Key Laboratory of Virology, Wuhan University, Wuhan, China
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28
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Kuzmanov U, Emili A. Protein-protein interaction networks: probing disease mechanisms using model systems. Genome Med 2013; 5:37. [PMID: 23635424 PMCID: PMC3706760 DOI: 10.1186/gm441] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Protein-protein interactions (PPIs) and multi-protein complexes perform central roles in the cellular systems of all living organisms. In humans, disruptions of the normal patterns of PPIs and protein complexes can be causative or indicative of a disease state. Recent developments in the biological applications of mass spectrometry (MS)-based proteomics have expanded the horizon for the application of systematic large-scale mapping of physical interactions to probe disease mechanisms. In this review, we examine the application of MS-based approaches for the experimental analysis of PPI networks and protein complexes, focusing on the different model systems (including human cells) used to study the molecular basis of common diseases such as cancer, cardiomyopathies, diabetes, microbial infections, and genetic and neurodegenerative disorders.
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Affiliation(s)
- Uros Kuzmanov
- Banting and Best Department of Medical Research and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Andrew Emili
- Banting and Best Department of Medical Research and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
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29
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Guthals A, Watrous JD, Dorrestein PC, Bandeira N. The spectral networks paradigm in high throughput mass spectrometry. MOLECULAR BIOSYSTEMS 2013; 8:2535-44. [PMID: 22610447 DOI: 10.1039/c2mb25085c] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
High-throughput proteomics is made possible by a combination of modern mass spectrometry instruments capable of generating many millions of tandem mass (MS(2)) spectra on a daily basis and the increasingly sophisticated associated software for their automated identification. Despite the growing accumulation of collections of identified spectra and the regular generation of MS(2) data from related peptides, the mainstream approach for peptide identification is still the nearly two decades old approach of matching one MS(2) spectrum at a time against a database of protein sequences. Moreover, database search tools overwhelmingly continue to require that users guess in advance a small set of 4-6 post-translational modifications that may be present in their data in order to avoid incurring substantial false positive and negative rates. The spectral networks paradigm for analysis of MS(2) spectra differs from the mainstream database search paradigm in three fundamental ways. First, spectral networks are based on matching spectra against other spectra instead of against protein sequences. Second, spectral networks find spectra from related peptides even before considering their possible identifications. Third, spectral networks determine consensus identifications from sets of spectra from related peptides instead of separately attempting to identify one spectrum at a time. Even though spectral networks algorithms are still in their infancy, they have already delivered the longest and most accurate de novo sequences to date, revealed a new route for the discovery of unexpected post-translational modifications and highly-modified peptides, enabled automated sequencing of cyclic non-ribosomal peptides with unknown amino acids and are now defining a novel approach for mapping the entire molecular output of biological systems that is suitable for analysis with tandem mass spectrometry. Here we review the current state of spectral networks algorithms and discuss possible future directions for automated interpretation of spectra from any class of molecules.
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Affiliation(s)
- Adrian Guthals
- Dept. Computer Science and Engineering, University of California, San Diego, USA
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30
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Zheng J, Tan BH, Sugrue R, Tang K. Current approaches on viral infection: proteomics and functional validations. Front Microbiol 2012; 3:393. [PMID: 23162545 PMCID: PMC3499792 DOI: 10.3389/fmicb.2012.00393] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 10/25/2012] [Indexed: 12/16/2022] Open
Abstract
Viruses could manipulate cellular machinery to ensure their continuous survival and thus become parasites of living organisms. Delineation of sophisticated host responses upon virus infection is a challenging task. It lies in identifying the repertoire of host factors actively involved in the viral infectious cycle and characterizing host responses qualitatively and quantitatively during viral pathogenesis. Mass spectrometry based proteomics could be used to efficiently study pathogen-host interactions and virus-hijacked cellular signaling pathways. Moreover, direct host and viral responses upon infection could be further investigated by activity-based functional validation studies. These approaches involve drug inhibition of secretory pathway, immunofluorescence staining, dominant negative mutant of protein target, real-time PCR, small interfering siRNA-mediated knockdown, and molecular cloning studies. In this way, functional validation could gain novel insights into the high-content proteomic dataset in an unbiased and comprehensive way.
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Affiliation(s)
- Jie Zheng
- Division of Chemical Biology and Biotechnology, School of Biological Sciences, Nanyang Technological University Singapore
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31
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Mancone C, Ciccosanti F, Montaldo C, Perdomo AB, Piacentini M, Alonzi T, Fimia GM, Tripodi M. Applying proteomic technology to clinical virology. Clin Microbiol Infect 2012; 19:23-28. [PMID: 23034105 PMCID: PMC7129767 DOI: 10.1111/1469-0691.12029] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Developing antiviral drugs, vaccines and diagnostic markers is still the most ambitious challenge in clinical virology. In the past few decades, data from high‐throughput technologies have allowed for the rapid development of new antiviral therapeutic strategies, thus making a profound impact on translational research. Most of the current preclinical studies in virology are aimed at evaluating the dynamic composition and localization of the protein platforms involved in various host–virus interactions. Among the different possible approaches, mass spectrometry‐based proteomics is increasingly being used to define the protein composition in subcellular compartments, quantify differential protein expression among samples, characterize protein complexes, and analyse protein post‐translational modifications. Here, we review the current knowledge of the most useful proteomic approaches in the study of viral persistence and pathogenicity, with a particular focus on recent advances in hepatitis C research.
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Affiliation(s)
- C Mancone
- 'Lazzaro Spallanzani' National Institute for Infectious Diseases I.R.C.C.S.; Department of Cellular Biotechnologies and Haematology, Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University of Rome.
| | - F Ciccosanti
- 'Lazzaro Spallanzani' National Institute for Infectious Diseases I.R.C.C.S
| | - C Montaldo
- 'Lazzaro Spallanzani' National Institute for Infectious Diseases I.R.C.C.S.; Department of Cellular Biotechnologies and Haematology, Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University of Rome
| | - A B Perdomo
- 'Lazzaro Spallanzani' National Institute for Infectious Diseases I.R.C.C.S
| | - M Piacentini
- 'Lazzaro Spallanzani' National Institute for Infectious Diseases I.R.C.C.S.; Department of Biology, University of Rome 'Tor Vergata', Rome, Italy
| | - T Alonzi
- 'Lazzaro Spallanzani' National Institute for Infectious Diseases I.R.C.C.S
| | - G M Fimia
- 'Lazzaro Spallanzani' National Institute for Infectious Diseases I.R.C.C.S
| | - M Tripodi
- 'Lazzaro Spallanzani' National Institute for Infectious Diseases I.R.C.C.S.; 'Lazzaro Spallanzani' National Institute for Infectious Diseases I.R.C.C.S
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Lippé R. Deciphering novel host-herpesvirus interactions by virion proteomics. Front Microbiol 2012; 3:181. [PMID: 22783234 PMCID: PMC3390586 DOI: 10.3389/fmicb.2012.00181] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 04/27/2012] [Indexed: 12/15/2022] Open
Abstract
Over the years, a vast array of information concerning the interactions of viruses with their hosts has been collected. However, recent advances in proteomics and other system biology techniques suggest these interactions are far more complex than anticipated. One particularly interesting and novel aspect is the analysis of cellular proteins incorporated into mature virions. Though sometimes considered purification contaminants in the past, their repeated detection by different laboratories suggests that a number of these proteins are bona fide viral components, some of which likely contribute to the viral life cycles. The present mini review focuses on cellular proteins detected in herpesviruses. It highlights the common cellular functions of these proteins, their potential implications for host–pathogen interactions, discusses technical limitations, the need for complementing methods and probes potential future research avenues.
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Affiliation(s)
- Roger Lippé
- Department of Pathology and Cell biology, University of Montreal Montreal, QC, Canada
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Proteomic technologies for the study of osteosarcoma. Sarcoma 2012; 2012:169416. [PMID: 22550414 PMCID: PMC3329661 DOI: 10.1155/2012/169416] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Accepted: 12/04/2011] [Indexed: 02/07/2023] Open
Abstract
Osteosarcoma is the most common primary bone cancer of children and is established during stages of rapid bone growth. The disease is a consequence of immature osteoblast differentiation, which gives way to a rapidly synthesized incompletely mineralized and disorganized bone matrix. The mechanism of osteosarcoma tumorogenesis is poorly understood, and few proteomic studies have been used to interrogate the disease thus far. Accordingly, these studies have identified proteins that have been known to be associated with other malignancies, rather than being osteosarcoma specific. In this paper, we focus on the growing list of available state-of-the-art proteomic technologies and their specific application to the discovery of novel osteosarcoma diagnostic and therapeutic targets. The current signaling markers/pathways associated with primary and metastatic osteosarcoma that have been identified by early-stage proteomic technologies thus far are also described.
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Munday DC, Surtees R, Emmott E, Dove BK, Digard P, Barr JN, Whitehouse A, Matthews D, Hiscox JA. Using SILAC and quantitative proteomics to investigate the interactions between viral and host proteomes. Proteomics 2012; 12:666-72. [PMID: 22246955 DOI: 10.1002/pmic.201100488] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 10/28/2011] [Accepted: 11/02/2011] [Indexed: 02/05/2023]
Abstract
Viruses continue to pose some of the greatest threats to human and animal health, and food security worldwide. Therefore, new approaches are required to increase our understanding of virus-host cell interactions and subsequently design more effective therapeutic countermeasures. Quantitative proteomics based on stable isotope labeling by amino acids in cell culture (SILAC), coupled to LC-MS/MS and bioinformatic analysis, is providing an excellent resource for studying host cell proteomes and can readily be applied for the study of virus infection. Here, we review this approach and discuss how virus-host cell interactions can best be studied, what is realistically feasible, and the potential limitations. For example, sub-cellular fractionation can reduce sample complexity for LC-MS/MS, increase data return and provide information regarding protein trafficking between different cellular compartments. The key to successful quantitative proteomics combines good experimental design and appropriate sample preparation with statistical analysis and validation of the MS data through the use of independent techniques and functional analysis. The annotation of the human genome and the increasing availability of biological reagents such as antibodies, provide the optimum parameters for studying viruses that infect humans, in human cell lines. SILAC-based quantitative proteomics can also be used to study the interactome of viral proteins with the host cell. Coupling proteomic studies with global transcriptomic and RNA depletion experiments will provide great insights into the complexity of the infection process, and potentially reveal new antiviral targets.
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Affiliation(s)
- Diane C Munday
- Faculty of Biological Sciences, and Astbury Centre for StructuralMolecular Biology, Institute of Molecular and Cellular Biology, University of Leeds, Leeds, UK.
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