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Li L, Jones K, Mei H. Doublecotin-Like Kinase 1 Increases Chemoresistance of Colorectal Cancer Cells through the Anti-Apoptosis Pathway. JOURNAL OF STEM CELL RESEARCH & THERAPY 2019; 9. [PMID: 31372308 DOI: 10.4172/2157-7633.1000447] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Background Colorectal Cancer (CRC) is the third most common cancer diagnosed and the second leading cause of cancer-related deaths in the United States. Cancer Stem Cells (CSCs) are believed to be the primary reason for the recurrence of CRC. Specific stem cell marker, doublecortin-like kinase 1 (DCLK1) plays critical roles in the tumorigenesis and progression of CRC. Up-regulation of DCLK1 is correlated with poor prognosis. Whether DCLK1 is correlated with enhanced chemoresistance of CRC cells is unclear. We aim to reveal the association of DCLK1 with chemoresistance of CRC cells and the underlying molecular mechanisms. Methods Stable DCLK1 over-expression cells (DCLK1+) were established using the HCT116 cells (WT). DCLK1+ and WT cells were treated with 5-Fluorouracil (5-Fu) at different doses for 24 or 48 hours. MTT assay was used to evaluate cell viability and IC50 of 5-Fu was determined. Quantitative real-time PCR was applied to determine the gene expression of caspase-3 (casp-3), casp-4, and casp-10. Cleaved casp-3 expression was investigated using Western blot and immunofluorescence. Results Our results demonstrated that IC50 of 5-Fu for the DCLK1+ cells was significantly higher than that of the WT cells for both 24 and 48-hour treatment (p=0.002 and 0.048 respectively), indicating increased chemoresistance of the DCLK1+ cells. Gene expression of casp-3, casp-4, and casp-10 were significantly inhibited in the DCLK1+ cells after 5-Fu treatment compared to the WT cells (p=7.616e-08, 1.575e-05 and 5.307e-08, respectively). Cleaved casp-3 amount and casp-3 positive cells were significantly decreased in the DCLK1+ cells after 5-Fu treatment compared to the WT cells (p=0.015). Conclusions In conclusion, our results demonstrated that DCLK1 overexpression enhanced the chemoresistance of CRC cells to 5-Fu treatment by suppressing gene expression of key caspases in the apoptosis pathway and activation of the apoptosis pathway. DCLK1 can be an intriguing therapeutic target for the effective treatment of CRC patients.
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Affiliation(s)
- Lianna Li
- Biology Department, Tougaloo College, Tougaloo, USA
| | - Kierra Jones
- Biology Department, Tougaloo College, Tougaloo, USA
| | - Hao Mei
- Department of Data Science, University of Mississippi Medical Center, USA
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Dulwich KL, Giotis ES, Gray A, Nair V, Skinner MA, Broadbent AJ. Differential gene expression in chicken primary B cells infected ex vivo with attenuated and very virulent strains of infectious bursal disease virus (IBDV). J Gen Virol 2017; 98:2918-2930. [PMID: 29154745 DOI: 10.1099/jgv.0.000979] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Infectious bursal disease virus (IBDV) belongs to the family Birnaviridae and is economically important to the poultry industry worldwide. IBDV infects B cells in the bursa of Fabricius (BF), causing immunosuppression and morbidity in young chickens. In addition to strains that cause classical Gumboro disease, the so-called 'very virulent' (vv) strain, also in circulation, causes more severe disease and increased mortality. IBDV has traditionally been controlled through the use of live attenuated vaccines, with attenuation resulting from serial passage in non-lymphoid cells. However, the factors that contribute to the vv or attenuated phenotypes are poorly understood. In order to address this, we aimed to investigate host cell-IBDV interactions using a recently described chicken primary B-cell model, where chicken B cells are harvested from the BF and cultured ex vivo in the presence of chicken CD40L. We demonstrated that these cells could support the replication of IBDV when infected ex vivo in the laboratory. Furthermore, we evaluated the gene expression profiles of B cells infected with an attenuated strain (D78) and a very virulent strain (UK661) by microarray. We found that key genes involved in B-cell activation and signalling (TNFSF13B, CD72 and GRAP) were down-regulated following infection relative to mock, which we speculate could contribute to IBDV-mediated immunosuppression. Moreover, cells responded to infection by expressing antiviral type I IFNs and IFN-stimulated genes, but the induction was far less pronounced upon infection with UK661, which we speculate could contribute to its virulence.
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Affiliation(s)
- Katherine L Dulwich
- The Pirbright Institute, Ash Road, Woking, GU24 0NF, UK
- Section of Virology, Faculty of Medicine, Imperial College London, St. Mary's Campus, Norfolk Place, London W2 1PG, UK
| | - Efstathios S Giotis
- Section of Virology, Faculty of Medicine, Imperial College London, St. Mary's Campus, Norfolk Place, London W2 1PG, UK
| | - Alice Gray
- The Pirbright Institute, Ash Road, Woking, GU24 0NF, UK
| | | | - Michael A Skinner
- Section of Virology, Faculty of Medicine, Imperial College London, St. Mary's Campus, Norfolk Place, London W2 1PG, UK
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Reshi L, Wu JL, Wang HV, Hong JR. Aquatic viruses induce host cell death pathways and its application. Virus Res 2015; 211:133-44. [PMID: 26494167 DOI: 10.1016/j.virusres.2015.10.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 10/07/2015] [Accepted: 10/14/2015] [Indexed: 11/15/2022]
Abstract
Virus infections of mammalian and animal cells consist of a series of events. As intracellular parasites, viruses rely on the use of host cellular machinery. Through the use of cell culture and molecular approaches over the past decade, our knowledge of the biology of aquatic viruses has grown exponentially. The increase in aquaculture operations worldwide has provided new approaches for the transmission of aquatic viruses that include RNA and DNA viruses. Therefore, the struggle between the virus and the host for control of the cell's death machinery is crucial for survival. Viruses are obligatory intracellular parasites and, as such, must modulate apoptotic pathways to control the lifespan of their host to complete their replication cycle. This paper updates the discussion on the detailed mechanisms of action that various aquatic viruses use to induce cell death pathways in the host, such as Bad-mediated, mitochondria-mediated, ROS-mediated and Fas-mediated cell death circuits. Understanding how viruses exploit the apoptotic pathways of their hosts may provide great opportunities for the development of future potential therapeutic strategies and pathogenic insights into different aquatic viral diseases.
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Affiliation(s)
- Latif Reshi
- Laboratory of Molecular Virology and Biotechnology, College of Bioscience and Biotechnology, Institute of Biotechnology, National Cheng Kung University, No 1. University Road, Tainan City 701, Taiwan, ROC; Department of Life Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, No. 1. University Road, Tainan City 701, Taiwan, ROC
| | - Jen-Leih Wu
- Laboratory of Marine Molecular Biology and Biotechnology, Institute of Cellular and Organismic Biology, Academia Sinica, Nankang, Taipei 115, Taiwan, ROC
| | - Hao-Ven Wang
- Department of Life Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, No. 1. University Road, Tainan City 701, Taiwan, ROC
| | - Jiann-Ruey Hong
- Laboratory of Molecular Virology and Biotechnology, College of Bioscience and Biotechnology, Institute of Biotechnology, National Cheng Kung University, No 1. University Road, Tainan City 701, Taiwan, ROC.
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Berard AR, Severini A, Coombs KM. Comparative proteomic analyses of two reovirus T3D subtypes and comparison to T1L identifies multiple novel proteins in key cellular pathogenic pathways. Proteomics 2015; 15:2113-35. [DOI: 10.1002/pmic.201400602] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 02/23/2015] [Accepted: 04/16/2015] [Indexed: 01/14/2023]
Affiliation(s)
- Alicia R. Berard
- Department of Medical Microbiology; Faculty of Medicine; University of Manitoba; Winnipeg Canada R3E 0J9
- Manitoba Center for Proteomics and Systems Biology; Room 799 John Buhler Research Centre University of Manitoba; Winnipeg Canada R3E 3P4
| | - Alberto Severini
- Department of Medical Microbiology; Faculty of Medicine; University of Manitoba; Winnipeg Canada R3E 0J9
- National Microbiology Laboratory; Public Health Agency of Canada; 1015 Arlington St. Winnipeg Canada R3E 3R2
| | - Kevin M. Coombs
- Department of Medical Microbiology; Faculty of Medicine; University of Manitoba; Winnipeg Canada R3E 0J9
- Manitoba Center for Proteomics and Systems Biology; Room 799 John Buhler Research Centre University of Manitoba; Winnipeg Canada R3E 3P4
- Manitoba Institute of Child Health; Room 641 John Buhler Research Center; University of Manitoba; Winnipeg Canada R3E 3P4
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Ezzati P, Komher K, Severini G, Coombs KM. Comparative proteomic analyses demonstrate enhanced interferon and STAT-1 activation in reovirus T3D-infected HeLa cells. Front Cell Infect Microbiol 2015; 5:30. [PMID: 25905045 PMCID: PMC4388007 DOI: 10.3389/fcimb.2015.00030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 03/18/2015] [Indexed: 12/28/2022] Open
Abstract
As obligate intracellular parasites, viruses are exclusively and intimately dependent upon their host cells for replication. During replication viruses induce profound changes within cells, including: induction of signaling pathways, morphological changes, and cell death. Many such cellular perturbations have been analyzed at the transcriptomic level by gene arrays and recent efforts have begun to analyze cellular proteomic responses. We recently described comparative stable isotopic (SILAC) analyses of reovirus, strain type 3 Dearing (T3D)-infected HeLa cells. For the present study we employed the complementary labeling strategy of iTRAQ (isobaric tags for relative and absolute quantitation) to examine HeLa cell changes induced by T3D, another reovirus strain, type 1 Lang, and UV-inactivated T3D (UV-T3D). Triplicate replicates of cytosolic and nuclear fractions identified a total of 2375 proteins, of which 50, 57, and 46 were significantly up-regulated, and 37, 26, and 44 were significantly down-regulated by T1L, T3D, and UV-T3D, respectively. Several pathways, most notably the Interferon signaling pathway and the EIF2 and ILK signaling pathways, were induced by virus infection. Western blots confirmed that cells were more strongly activated by live T3D as demonstrated by elevated levels of key proteins like STAT-1, ISG-15, IFIT-1, IFIT-3, and Mx1. This study expands our understanding of reovirus-induced host responses.
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Affiliation(s)
- Peyman Ezzati
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba Winnipeg, MB, Canada
| | - Krysten Komher
- Department of Medical Microbiology, Faculty of Medicine, University of Manitoba Winnipeg, MB, Canada
| | - Giulia Severini
- Department of Medical Microbiology, Faculty of Medicine, University of Manitoba Winnipeg, MB, Canada
| | - Kevin M Coombs
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba Winnipeg, MB, Canada ; Department of Medical Microbiology, Faculty of Medicine, University of Manitoba Winnipeg, MB, Canada ; Manitoba Institute of Child Health, John Buhler Research Centre Winnipeg, MB, Canada
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Kolliopoulou A, Van Nieuwerburgh F, Stravopodis DJ, Deforce D, Swevers L, Smagghe G. Transcriptome analysis of Bombyx mori larval midgut during persistent and pathogenic cytoplasmic polyhedrosis virus infection. PLoS One 2015; 10:e0121447. [PMID: 25816294 PMCID: PMC4376736 DOI: 10.1371/journal.pone.0121447] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 02/12/2015] [Indexed: 12/12/2022] Open
Abstract
Many insects can be persistently infected with viruses but do not show any obvious adverse effects with respect to physiology, development or reproduction. Here, Bombyx mori strain Daizo, persistently infected with cytoplasmic polyhedrosis virus (BmCPV), was used to study the host's transcriptional response after pathogenic infection with the same virus in midgut tissue of larvae persistently and pathogenically infected as 2nd and 4th instars. Next generation sequencing revealed that from 13,769 expressed genes, 167 were upregulated and 141 downregulated in both larval instars following pathogenic infection. Several genes that could possibly be involved in B. mori immune response against BmCPV or that may be induced by the virus in order to increase infectivity were identified, whereas classification of differentially expressed transcripts (confirmed by qRT-PCR) resulted in gene categories related to physical barriers, immune responses, proteolytic/metabolic enzymes, heat-shock proteins, hormonal signaling and uncharacterized proteins. Comparison of our data with the available literature (pathogenic infection of persistently vs. non-persistently infected larvae) unveiled various similarities of response in both cases, which suggests that pre-existing persistent infection does not affect in a major way the transcriptome response against pathogenic infection. To investigate the possible host's RNAi response against BmCPV challenge, the differential expression of RNAi-related genes and the accumulation of viral small RNAs (vsRNAs) were studied. During pathogenic infection, siRNA-like traces like the 2-fold up-regulation of the core RNAi genes Ago-2 and Dcr-2 as well as a peak of 20 nt small RNAs were observed. Interestingly, vsRNAs of the same size were detected at lower rates in persistently infected larvae. Collectively, our data provide an initial assessment of the relative significance of persistent infection of silkworm larvae on the host response following pathogenic infection with CPV, while they also highlight the relative importance of RNAi as an antiviral mechanism.
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Affiliation(s)
- Anna Kolliopoulou
- Insect Molecular Genetics and Biotechnology, Institute of Biosciences and Applications, National Centre for Scientific Research “Demokritos”, Aghia Paraskevi, Athens, Greece
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Dimitrios J. Stravopodis
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Athens, Greece
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Luc Swevers
- Insect Molecular Genetics and Biotechnology, Institute of Biosciences and Applications, National Centre for Scientific Research “Demokritos”, Aghia Paraskevi, Athens, Greece
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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Sherry B. Generating primary cultures of murine cardiac myocytes and cardiac fibroblasts to study viral myocarditis. Methods Mol Biol 2015; 1299:1-16. [PMID: 25836571 DOI: 10.1007/978-1-4939-2572-8_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Viruses can induce direct damage to cardiac myocytes and cardiac fibroblasts resulting in myocarditis and impaired cardiac function. Cardiac myocytes and cardiac fibroblasts display different capacities to support viral infection and generate a protective antiviral response. This chapter provides detailed protocols for generation and characterization of primary cultures of murine cardiac myocytes and cardiac fibroblasts, offering a powerful tool to probe cell type-specific responses that determine protection against viral myocarditis.
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Affiliation(s)
- Barbara Sherry
- College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA,
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Jia R, Cao LP, Du JL, Liu YJ, Wang JH, Jeney G, Yin GJ. Grass carp reovirus induces apoptosis and oxidative stress in grass carp (Ctenopharyngodon idellus) kidney cell line. Virus Res 2014; 185:77-81. [DOI: 10.1016/j.virusres.2014.03.021] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 03/17/2014] [Accepted: 03/17/2014] [Indexed: 10/25/2022]
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Kroeker AL, Coombs KM. Systems biology unravels interferon responses to respiratory virus infections. World J Biol Chem 2014; 5:12-25. [PMID: 24600511 PMCID: PMC3942539 DOI: 10.4331/wjbc.v5.i1.12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 12/11/2013] [Accepted: 01/06/2014] [Indexed: 02/05/2023] Open
Abstract
Interferon production is an important defence against viral replication and its activation is an attractive therapeutic target. However, it has long been known that viruses perpetually evolve a multitude of strategies to evade these host immune responses. In recent years there has been an explosion of information on virus-induced alterations of the host immune response that have resulted from data-rich omics technologies. Unravelling how these systems interact and determining the overall outcome of the host response to viral infection will play an important role in future treatment and vaccine development. In this review we focus primarily on the interferon pathway and its regulation as well as mechanisms by which respiratory RNA viruses interfere with its signalling capacity.
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Gao G, Xuan C, Yang Q, Liu XC, Liu ZG, He GW. Identification of altered plasma proteins by proteomic study in valvular heart diseases and the potential clinical significance. PLoS One 2013; 8:e72111. [PMID: 24015209 PMCID: PMC3754973 DOI: 10.1371/journal.pone.0072111] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 07/06/2013] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Little is known about genetic basis and proteomics in valvular heart disease (VHD) including rheumatic (RVD) and degenerative (DVD) valvular disease. The present proteomic study examined the hypothesis that certain proteins may be associated with the pathological changes in the plasma of VHD patients. METHODS AND RESULTS Differential protein analysis in the plasma identified 18 differentially expressed protein spots and 14 corresponding proteins or polypeptides by two-dimensional electrophoresis and mass spectrometry in 120 subjects. Two up-regulated (complement C4A and carbonic anhydrase 1) and three down-regulated proteins (serotransferrin, alpha-1-antichymotrypsin, and vitronectin) were validated by ELISA in enlarging samples. The plasma levels (n = 40 for each) of complement C4A in RVD (715.8±35.6 vs. 594.7±28.2 ng/ml, P = 0.009) and carbonic anhydrase 1 (237.70±15.7 vs. 184.7±10.8 U/L, P = 0.007) in DVD patients were significantly higher and that of serotransferrin (2.36±0.20 vs. 2.93±0.16 mg/ml, P = 0.025) and alpha-1-antichymotrypsin (370.0±13.7 vs. 413.0±11.6 µg/ml, P = 0.019) in RVD patients were significantly lower than those in controls. The plasma vitronectin level in both RVD (281.3±11.0 vs. 323.2±10.0 µg/ml, P = 0.006) and DVD (283.6±11.4 vs. 323.2±10.0 µg/ml, P = 0.011) was significantly lower than those in normal controls. CONCLUSIONS We have for the first time identified alterations of 14 differential proteins or polypeptides in the plasma of patients with various VHD. The elevation of plasma complement C4A in RVD and carbonic anhydrase 1 in DVD and the decrease of serotransferrin and alpha-1-antichymotrypsin in RVD patients may be useful biomarkers for these valvular diseases. The decreased plasma level of vitronectin - a protein related to the formation of valvular structure - in both RVD and DVD patients might indicate the possible genetic deficiency in these patients.
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Affiliation(s)
- Ge Gao
- TEDA International Cardiovascular Hospital and The Affiliated Hospital, Hangzhou Normal University, Tianjin and Hangzhou, China
| | - Chao Xuan
- TEDA International Cardiovascular Hospital, Tianjin, China
| | - Qin Yang
- TEDA International Cardiovascular Hospital and The Affiliated Hospital, Hangzhou Normal University, Tianjin and Hangzhou, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Xiao-Cheng Liu
- TEDA International Cardiovascular Hospital, Tianjin, China
| | - Zhi-Gang Liu
- TEDA International Cardiovascular Hospital, Tianjin, China
| | - Guo-Wei He
- TEDA International Cardiovascular Hospital and The Affiliated Hospital, Hangzhou Normal University, Tianjin and Hangzhou, China
- Department of Surgery, Oregon Health and Science University, Portland, Oregon, United States of America
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Coombs KM. HeLa cell response proteome alterations induced by mammalian reovirus T3D infection. Virol J 2013; 10:202. [PMID: 23799967 PMCID: PMC3847587 DOI: 10.1186/1743-422x-10-202] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 06/14/2013] [Indexed: 01/04/2023] Open
Abstract
Background Cells are exposed to multiple stressors that induce significant alterations in signaling pathways and in the cellular state. As obligate parasites, all viruses require host cell material and machinery for replication. Virus infection is a major stressor leading to numerous induced modifications. Previous gene array studies have measured infected cellular transcriptomes. More recently, mass spectrometry-based quantitative and comparative assays have been used to complement such studies by examining virus-induced alterations in the cellular proteome. Methods We used SILAC (stable isotope labeling with amino acids in cell culture), a non-biased quantitative proteomic labeling technique, combined with 2-D HPLC/mass spectrometry and reciprocal labeling to identify and measure relative quantitative differences in HeLa cell proteins in purified cytosolic and nuclear fractions after reovirus serotype 3 Dearing infection. Protein regulation was determined by z-score analysis of each protein’s label distribution. Results A total of 2856 cellular proteins were identified in cytosolic fractions by 2 or more peptides at >99% confidence and 884 proteins were identified in nuclear fractions. Gene ontology analyses indicated up-regulated host proteins were associated with defense responses, immune responses, macromolecular binding, regulation of immune effector processes, and responses to virus, whereas down-regulated proteins were involved in cell death, macromolecular catabolic processes, and tissue development. Conclusions These analyses identified numerous host proteins significantly affected by reovirus T3D infection. These proteins map to numerous inflammatory and innate immune pathways, and provide the starting point for more detailed kinetic studies and delineation of virus-modulated host signaling pathways.
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Affiliation(s)
- Kevin M Coombs
- Department of Medical Microbiology, Faculty of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
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Berard AR, Cortens JP, Krokhin O, Wilkins JA, Severini A, Coombs KM. Quantification of the host response proteome after mammalian reovirus T1L infection. PLoS One 2012; 7:e51939. [PMID: 23240068 PMCID: PMC3519901 DOI: 10.1371/journal.pone.0051939] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 11/13/2012] [Indexed: 12/24/2022] Open
Abstract
All viruses are dependent upon host cells for replication. Infection can induce profound changes within cells, including apoptosis, morphological changes, and activation of signaling pathways. Many of these alterations have been analyzed by gene arrays to measure the cellular "transcriptome." We used SILAC (stable isotope labeling by amino acids in cell culture), combined with high-throughput 2-D HPLC/mass spectrometry, to determine relative quantitative differences in host proteins at 6 and 24 hours after infecting HEK293 cells with reovirus serotype 1 Lang (T1L). 3,076 host proteins were detected at 6 hpi, of which 132 and 68 proteins were significantly up or down regulated, respectively. 2,992 cellular proteins, of which 104 and 49 were up or down regulated, respectively, were identified at 24 hpi. IPA and DAVID analyses indicated proteins involved in cell death, cell growth factors, oxygen transport, cell structure organization and inflammatory defense response to virus were up-regulated, whereas proteins involved in apoptosis, isomerase activity, and metabolism were down-regulated. These proteins and pathways may be suitable targets for intervention to either attenuate virus infection or enhance oncolytic potential.
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Affiliation(s)
- Alicia R. Berard
- Department of Medical Microbiology, Faculty of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
- Manitoba Center for Proteomics and Systems Biology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - John P. Cortens
- Manitoba Center for Proteomics and Systems Biology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Oleg Krokhin
- Manitoba Center for Proteomics and Systems Biology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - John A. Wilkins
- Department of Medical Microbiology, Faculty of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
- Manitoba Center for Proteomics and Systems Biology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Alberto Severini
- Department of Medical Microbiology, Faculty of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
- National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - Kevin M. Coombs
- Department of Medical Microbiology, Faculty of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
- Manitoba Center for Proteomics and Systems Biology, University of Manitoba, Winnipeg, Manitoba, Canada
- Manitoba Institute of Child Health, University of Manitoba, Winnipeg, Manitoba, Canada
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Oda T, Shimizu K, Yamaguchi A, Satoh K, Matsumoto KI. Hypothermia produces rat liver proteomic changes as in hibernating mammals but decreases endoplasmic reticulum chaperones. Cryobiology 2012; 65:104-12. [DOI: 10.1016/j.cryobiol.2012.05.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Revised: 04/24/2012] [Accepted: 05/10/2012] [Indexed: 12/25/2022]
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Xie N, Huang K, Zhang T, Lei Y, Liu R, Wang K, Zhou S, Li J, Wu J, Wu H, Deng C, Zhao X, Nice EC, Huang C. Comprehensive proteomic analysis of host cell lipid rafts modified by HBV infection. J Proteomics 2012; 75:725-39. [DOI: 10.1016/j.jprot.2011.09.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2011] [Revised: 08/26/2011] [Accepted: 09/17/2011] [Indexed: 12/29/2022]
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Zheng J, Sugrue RJ, Tang K. Mass spectrometry based proteomic studies on viruses and hosts--a review. Anal Chim Acta 2011; 702:149-59. [PMID: 21839192 PMCID: PMC7094357 DOI: 10.1016/j.aca.2011.06.045] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 06/20/2011] [Accepted: 06/21/2011] [Indexed: 02/07/2023]
Abstract
In terms of proteomic research in the 21st century, the realm of virology is still regarded as an enormous challenge mainly brought by three aspects, namely, studying on the complex proteome of the virus with unexpected variations, developing more accurate analytical techniques as well as understanding viral pathogenesis and virus-host interaction dynamics. Progresses in these areas will be helpful to vaccine design and antiviral drugs discovery. Mass spectrometry based proteomics have shown exceptional display of capabilities, not only precisely identifying viral and cellular proteins that are functionally, structurally, and dynamically changed upon virus infection, but also enabling us to detect important pathway proteins. In addition, many isolation and purification techniques and quantitative strategies in conjunction with MS can significantly improve the sensitivity of mass spectrometry for detecting low-abundant proteins, replenishing the stock of virus proteome and enlarging the protein-protein interaction maps. Nevertheless, only a small proportion of the infectious viruses in both of animal and plant have been studied using this approach. As more virus and host genomes are being sequenced, MS-based proteomics is becoming an indispensable tool for virology. In this paper, we provide a brief review of the current technologies and their applications in studying selected viruses and hosts.
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Affiliation(s)
- Jie Zheng
- Division of Chemical Biology and Biotechnology, School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Richard J. Sugrue
- Division of Molecular and Cell Biology, School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Kai Tang
- Division of Chemical Biology and Biotechnology, School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
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Hammer E, Goritzka M, Ameling S, Darm K, Steil L, Klingel K, Trimpert C, Herda LR, Dörr M, Kroemer HK, Kandolf R, Staudt A, Felix SB, Völker U. Characterization of the Human Myocardial Proteome in Inflammatory Dilated Cardiomyopathy by Label-free Quantitative Shotgun Proteomics of Heart Biopsies. J Proteome Res 2011; 10:2161-71. [DOI: 10.1021/pr1008042] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Elke Hammer
- Interfakultäres Institut für Genetik und Funktionelle Genomforschung, Ernst-Moritz-Arndt-Universität Greifswald, Germany
| | - Michelle Goritzka
- Interfakultäres Institut für Genetik und Funktionelle Genomforschung, Ernst-Moritz-Arndt-Universität Greifswald, Germany
| | - Sabine Ameling
- Interfakultäres Institut für Genetik und Funktionelle Genomforschung, Ernst-Moritz-Arndt-Universität Greifswald, Germany
| | - Katrin Darm
- Interfakultäres Institut für Genetik und Funktionelle Genomforschung, Ernst-Moritz-Arndt-Universität Greifswald, Germany
| | - Leif Steil
- Interfakultäres Institut für Genetik und Funktionelle Genomforschung, Ernst-Moritz-Arndt-Universität Greifswald, Germany
| | - Karin Klingel
- Abteilung Molekulare Pathologie, Universitätsklinikum Tübingen, Germany
| | | | - Lars R. Herda
- Klinik für Innere Medizin B, Universitätsmedizin Greifswald, Germany
| | - Marcus Dörr
- Klinik für Innere Medizin B, Universitätsmedizin Greifswald, Germany
| | - Heyo K. Kroemer
- Institut für Pharmakologie, Universitätsmedizin Greifswald, Germany
| | - Reinhard Kandolf
- Abteilung Molekulare Pathologie, Universitätsklinikum Tübingen, Germany
| | - Alexander Staudt
- Klinik für Innere Medizin B, Universitätsmedizin Greifswald, Germany
| | - Stephan B. Felix
- Klinik für Innere Medizin B, Universitätsmedizin Greifswald, Germany
| | - Uwe Völker
- Interfakultäres Institut für Genetik und Funktionelle Genomforschung, Ernst-Moritz-Arndt-Universität Greifswald, Germany
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