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Nirbhaya V, Chandra R, Kumar S. Nanoengineered phosphorus doped graphitic carbon nitride based ultrasensitive biosensing platform for Swine flu detection. Colloids Surf B Biointerfaces 2023; 230:113504. [PMID: 37597493 DOI: 10.1016/j.colsurfb.2023.113504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 08/02/2023] [Accepted: 08/05/2023] [Indexed: 08/21/2023]
Abstract
In the present study, we developed an amino-polyindole modified phosphorus doped graphitic carbon nitride nanomaterial (APIN/P-g-C3N4) based immunosensing biochip for Serum amyloid A (SAA) biomarker towards early diagnosis of Swine flu. The P-g-C3N4 was synthesis via polycondensation and functionalized with APIN. Further, the biochip was fabricated by modifying the working area of SPE with APIN/P-g-C3N4 using drop cast method, APIN introduced the larger loading of -NH2 group moieties onto P-g-C3N4 matrix and benefitted to reinforced the biomolecules via covalent linkages. The monoclonal anti-SAA was conjugated onto APIN/P-g-C3N4/SPE using EDC-NHS chemistry and BSA was added for non-specific site blocking. The structural, chemical, composition and morphological characteristics of the synthesized, functionalized nanomaterial and fabricated biochips were investigated by XRD, XPS, FT-IR spectroscopy, SEM, FE-SEM and TEM techniques. Further, the electrochemical characterization and response studies of fabricated biochip were analyzed using the CV and DPV techniques. Based on the analytical performance of the proposed immunosensing biochip i.e. BSA/anti-SAA/APIN/P-g-C3N4/SPE, it is capable to detect SAA protein with ultra sensitivity of 79.5 μA log (mL ng-1) cm-2, ultralow limit of detection of 5 ng mL-1 and wider linear detection range of 5 ng mL-1-500 μg mL-1 with quick response time of 10 min. Moreover, the fabricated immunosensing biochips was used to analyse SAA protein in spiked serum samples and the achieved results demonstrated the good agreement with the electrochemical response observed in standard SAA protein samples in analytical solution. The proposed biochip can provide insights for developing a wide range of clinical screening tools for detecting various contagious diseases.
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Affiliation(s)
- Vishakha Nirbhaya
- Department of Chemistry, University of Delhi, Delhi 110007, India; Department of Applied Science, Meerut Institute of Engineering and Technology, Meerut 250005, India
| | - Ramesh Chandra
- Department of Chemistry, University of Delhi, Delhi 110007, India; Institute of Nano Medical Sciences, University of Delhi, Delhi 110007, India
| | - Suveen Kumar
- Department of Chemistry, University of Delhi, Delhi 110007, India.
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Sigdel TK, Boada P, Kerwin M, Rashmi P, Gjertson D, Rossetti M, Sur S, Munar D, Cimino J, Ahn R, Pickering H, Sen S, Parmar R, Fatou B, Steen H, Schaenman J, Bunnapradist S, Reed EF, Sarwal MM. Plasma proteome perturbation for CMV DNAemia in kidney transplantation. PLoS One 2023; 18:e0285870. [PMID: 37205661 DOI: 10.1371/journal.pone.0285870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 05/03/2023] [Indexed: 05/21/2023] Open
Abstract
BACKGROUND Cytomegalovirus (CMV) infection, either de novo or as reactivation after allotransplantation and chronic immunosuppression, is recognized to cause detrimental alloimmune effects, inclusive of higher susceptibility to graft rejection and substantive impact on chronic graft injury and reduced transplant survival. To obtain further insights into the evolution and pathogenesis of CMV infection in an immunocompromised host we evaluated changes in the circulating host proteome serially, before and after transplantation, and during and after CMV DNA replication (DNAemia), as measured by quantitative polymerase chain reaction (QPCR). METHODS LC-MS-based proteomics was conducted on 168 serially banked plasma samples, from 62 propensity score-matched kidney transplant recipients. Patients were stratified by CMV replication status into 31 with CMV DNAemia and 31 without CMV DNAemia. Patients had blood samples drawn at protocol times of 3- and 12-months post-transplant. Additionally, blood samples were also drawn before and 1 week and 1 month after detection of CMV DNAemia. Plasma proteins were analyzed using an LCMS 8060 triple quadrupole mass spectrometer. Further, public transcriptomic data on time matched PBMCs samples from the same patients was utilized to evaluate integrative pathways. Data analysis was conducted using R and Limma. RESULTS Samples were segregated based on their proteomic profiles with respect to their CMV Dnaemia status. A subset of 17 plasma proteins was observed to predict the onset of CMV at 3 months post-transplant enriching platelet degranulation (FDR, 4.83E-06), acute inflammatory response (FDR, 0.0018), blood coagulation (FDR, 0.0018) pathways. An increase in many immune complex proteins were observed at CMV infection. Prior to DNAemia the plasma proteome showed changes in the anti-inflammatory adipokine vaspin (SERPINA12), copper binding protein ceruloplasmin (CP), complement activation (FDR = 0.03), and proteins enriched in the humoral (FDR = 0.01) and innate immune responses (FDR = 0.01). CONCLUSION Plasma proteomic and transcriptional perturbations impacting humoral and innate immune pathways are observed during CMV infection and provide biomarkers for CMV disease prediction and resolution. Further studies to understand the clinical impact of these pathways can help in the formulation of different types and duration of anti-viral therapies for the management of CMV infection in the immunocompromised host.
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Affiliation(s)
- Tara K Sigdel
- Department of Surgery, University of California San Francisco, San Francisco, CA, United States of America
| | - Patrick Boada
- Department of Surgery, University of California San Francisco, San Francisco, CA, United States of America
| | - Maggie Kerwin
- Department of Surgery, University of California San Francisco, San Francisco, CA, United States of America
| | - Priyanka Rashmi
- Department of Surgery, University of California San Francisco, San Francisco, CA, United States of America
| | - David Gjertson
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA, United States of America
| | - Maura Rossetti
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA, United States of America
| | - Swastika Sur
- Department of Surgery, University of California San Francisco, San Francisco, CA, United States of America
| | - Dane Munar
- Department of Surgery, University of California San Francisco, San Francisco, CA, United States of America
| | - James Cimino
- Department of Surgery, University of California San Francisco, San Francisco, CA, United States of America
| | - Richard Ahn
- Department of Microbiology and Immunology, University of California Los Angeles, Los Angeles, CA, United States of America
| | - Harry Pickering
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA, United States of America
| | - Subha Sen
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA, United States of America
| | - Rajesh Parmar
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA, United States of America
| | - Benoit Fatou
- Department of Pathology, Harvard Medical School, Boston, MA, United States of America
| | - Hanno Steen
- Department of Pathology, Harvard Medical School, Boston, MA, United States of America
| | - Joanna Schaenman
- Department of Medicine, University of California Los Angeles, Los Angeles, CA, United States of America
| | - Suphamai Bunnapradist
- Department of Medicine, University of California Los Angeles, Los Angeles, CA, United States of America
| | - Elaine F Reed
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA, United States of America
| | - Minnie M Sarwal
- Department of Surgery, University of California San Francisco, San Francisco, CA, United States of America
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Kwon JT, Kim Y, Choi S, Yoon BL, Kim HS, Shim I, Sul D. Pulmonary Toxicity and Proteomic Analysis in Bronchoalveolar Lavage Fluids and Lungs of Rats Exposed to Copper Oxide Nanoparticles. Int J Mol Sci 2022; 23:13265. [PMID: 36362054 PMCID: PMC9655042 DOI: 10.3390/ijms232113265] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/14/2022] [Accepted: 10/25/2022] [Indexed: 07/21/2023] Open
Abstract
Copper oxide nanoparticles (CuO NPs) were intratracheally instilled into lungs at concentrations of 0, 0.15, and 1.5 mg/kg bodyweight to 7-week-old Sprague-Dawley rats. The cytotoxicity, immunotoxicity, and oxidative stress were evaluated, followed by proteomic analysis of bronchoalveolar lavage fluid (BALF) and lungs of rats. The CuO NPs-exposed groups revealed dose-dependent increases in total cells, polymorphonuclear leukocytes, lactate dyhydrogenase, and total protein levels in BALF. Inflammatory cytokines, including macrophage inflammatory protein-2 and tumor necrosis factor-α, were increased in the CuO NPs-treated groups. The expression levels of catalase, glutathione peroxidase-1, and peroxiredoxin-2 were downregulated, whereas that of superoxide dismutase-2 was upregulated in the CuO NPs-exposed groups. Five heat shock proteins were downregulated in rats exposed to high concentrations of CuO NPs. In proteomic analysis, 17 proteins were upregulated or downregulated, and 6 proteins were validated via Western blot analysis. Significant upregulation of 3-hydroxy-3-methylglutaryl-CoA synthase and fidgetin-like 1 and downregulation of annexin II, HSP 47 and proteasome α1 occurred in the CuO NPs exposed groups. Taken together, this study provides additional insight into pulmonary cytotoxicity and immunotoxicity as well as oxidative stress in rats exposed to CuO NPs. Proteomic analysis revealed potential toxicological biomarkers of CuO NPs, which also reveals the toxicity mechanisms of CuO NPs.
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Affiliation(s)
- Jung-Taek Kwon
- Environmental Health Research Department, National Institute of Environmental Research, Incheon 22689, Korea
| | - Yoonjin Kim
- Environmental Health Research Department, National Institute of Environmental Research, Incheon 22689, Korea
| | - Seonyoung Choi
- Graduate School of Medicine, Korea University, 73 Inchon-ro, Sungbuk-ku, Seoul 136-705, Korea
| | - Byung-ll Yoon
- College of Veterinary Medicine and Institute of Veterinary Science, Kangwon National University, Chuncheon 24341, Korea
| | - Hyun-Sook Kim
- Department of Biomedical Laboratory Science, College of Health Science, Cheongju University, Cheongju 28503, Korea
| | - Ilseob Shim
- Environmental Health Research Department, National Institute of Environmental Research, Incheon 22689, Korea
| | - Donggeun Sul
- Graduate School of Medicine, Korea University, 73 Inchon-ro, Sungbuk-ku, Seoul 136-705, Korea
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Nephrotoxicity evaluation and proteomic analysis in kidneys of rats exposed to thioacetamide. Sci Rep 2022; 12:6837. [PMID: 35477741 PMCID: PMC9046159 DOI: 10.1038/s41598-022-11011-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 04/18/2022] [Indexed: 11/18/2022] Open
Abstract
Thioacetamide (TAA) was administered orally at 0, 10, and 30 mg/kg body weight (BW) daily to Sprague–Dawley rats aged 6–7 weeks for 28 consecutive days. Nephrotoxicity and proteomics were evaluated in the kidneys of rats exposed to TAA. The BW decreased, however, the relative kidneys weight increased. No significant histopathologic abnormalities were found in the kidneys. The numbers of monocytes and platelets were significantly increased. However, the mean corpuscular volume and hematocrit values were decreased significantly in rats exposed to 30 mg/kg BW TAA. The expression levels of Kim-1 and NGAL were increased 4 to 5-fold in the kidneys, resulting in significant nephrotoxicity. Proteomic analysis was conducted and a total of 5221 proteins spots were resolved. Of these, 3 and 21 protein spots were up- and downregulated, respectively. The validation of seven proteins was performed by Western blot analysis. The expression level of ASAP2 was significantly upregulated, whereas RGS14, MAP7Dl, IL-3Rα, Tmod1, NQO2, and MUP were reduced. Sixteen isoforms of MUP were found by the 2DE immunoblot assay and were significantly downregulated with increasing exposure to TAA. MUP isoforms were compared in the liver, kidneys, and urine of untreated rats and a total of 43 isoforms were found.
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Jain R, Nirbhaya V, Chandra R, Kumar S. Nanostructured Mesoporous Carbon Based Electrochemical Biosensor for Efficient Detection of Swine Flu. ELECTROANAL 2022. [DOI: 10.1002/elan.202100242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Raghav Jain
- Department of Chemistry University of Delhi Delhi 110007 India
| | | | - Ramesh Chandra
- Department of Chemistry University of Delhi Delhi 110007 India
| | - Suveen Kumar
- Department of Chemistry University of Delhi Delhi 110007 India
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Nirbhaya V, Chaudhary C, Chauhan D, Chandra R, Kumar S. Multiwalled carbon nanotube nanofiller-polyindole polymer matrix-based efficient biosensor for the rapid detection of swine flu. NEW J CHEM 2022. [DOI: 10.1039/d1nj06173a] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Pictorial representation of the synthesis of the electrode material, fabrication and electrochemical response of the biosensing platform for swine flu detection.
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Affiliation(s)
| | - Chhaya Chaudhary
- Department of Chemistry, University of Delhi, Delhi-110007, India
| | - Dipti Chauhan
- Department of Chemistry, University of Delhi, Delhi-110007, India
| | - Ramesh Chandra
- Department of Chemistry, University of Delhi, Delhi-110007, India
| | - Suveen Kumar
- Department of Chemistry, University of Delhi, Delhi-110007, India
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Nirbhaya V, Kumar Y, Chandra R, Kumar S. 3D-phosphorus doped mesoporous graphitic carbon nitride based immunosensor for swine flu detection. NEW J CHEM 2022. [DOI: 10.1039/d2nj03205h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Illustrative representation of the immunosensing platform and its electrochemical response for the detection of swine flu.
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Affiliation(s)
| | - Yogesh Kumar
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Ramesh Chandra
- Institute of Nano Medical Sciences, University of Delhi, Delhi 110007, India
| | - Suveen Kumar
- Department of Chemistry, University of Delhi, Delhi 110007, India
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Zhou J, Huang S, Fan B, Niu B, Guo R, Gu J, Gao S, Li B. iTRAQ-based proteome analysis of porcine group A rotavirus-infected porcine IPEC-J2 intestinal epithelial cells. J Proteomics 2021; 248:104354. [PMID: 34418579 DOI: 10.1016/j.jprot.2021.104354] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 07/20/2021] [Accepted: 08/10/2021] [Indexed: 11/25/2022]
Abstract
Porcine rotavirus (PoRV), particularly group A, is one of the most important swine pathogens, causing substantial economic losses in the animal husbandry industry. To improve understanding of host responses to PoRV infection, we applied isobaric tags for relative and absolute quantification (iTRAQ) labeling coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS) to quantitatively identify the differentially expressed proteins in PoRV-infected IPEC-J2 cells and confirmed the differentially accumulated proteins (DAPs) expression differences by performing RT-qPCR and Western blot analysis. Herein, in PoRV- and mock-infected IPEC-J2 cells, relative quantitative data were identified for 4724 proteins, 223 of which were DAPs (125 up-accumulated and 98 down-accumulated). Bioinformatics analyses further revealed that a majority of the DAPs are involved in numerous crucial biological processes and signaling pathways, such as metabolic process, immune system process, amino acid metabolism, energy metabolism, immune system, MHC class I peptide loading complex, Hippo signaling pathway, Th1 and Th2 cell differentiation, antigen processing and presentation, and tubule bicarbonate reclamation. The cellular localization prediction analysis indicated that these DAPs may be located in the Golgi apparatus, nucleus, peroxisomal, cytoplasm, mitochondria, extracellular, plasma membrane, and endoplasmic reticulum (ER). Expression levels of three up-accumulated (VAMP4, IKBKE, and TJP3) or two down-accumulated (SOD3 and DHX9) DAPs upon PoRV infection, were further validated by RT-qPCR and Western blot analysis. Collectively, this work is the first time to investigate the protein profile of PoRV-infected IPEC-J2 cells using quantitative proteomics; these findings provide valuable information to better understand the mechanisms underlying the host responses to PoRV infection in piglets. SIGNIFICANCE: The proteomics analysis of this study uncovered the target associated with PoRV-induced innate immune response or cellular damage, and provided relevant insights into the molecular functions, biological processes, and signaling pathway in these targets. Out of these 223 DAPs, the expression levels of three up-accumulated (VAMP4, IKBKE, and TJP3) and two down-accumulated (SOD3 and DHX9) DAPs upon PoRV infection, have been further validated using RT-qPCR and Western blot analysis. These outcomes could uncover how PoRV manipulated the cellular machinery, which could further our understanding of PoRV pathogenesis in piglets.
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Affiliation(s)
- Jinzhu Zhou
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, Jiangsu, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, PR China
| | - Shimeng Huang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, Jiangsu, China
| | - Baochao Fan
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, Jiangsu, China; School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Beibei Niu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, Jiangsu, China; College of Veterinary Medicine, Nanjing Agricultural University, No.1 Wei-gang, Nanjing 210095, China
| | - Rongli Guo
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, Jiangsu, China
| | - Jun Gu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, Jiangsu, China; School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Song Gao
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, PR China
| | - Bin Li
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, Jiangsu, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, PR China; School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China; School of Life Sciences, Jiangsu University, Zhenjiang 212013, China.
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Milewska A, Ner‐Kluza J, Dabrowska A, Bodzon‐Kulakowska A, Pyrc K, Suder P. MASS SPECTROMETRY IN VIROLOGICAL SCIENCES. MASS SPECTROMETRY REVIEWS 2020; 39:499-522. [PMID: 31876329 PMCID: PMC7228374 DOI: 10.1002/mas.21617] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 12/15/2019] [Indexed: 05/24/2023]
Abstract
Virology, as a branch of the life sciences, discovered mass spectrometry (MS) to be the pivotal tool around two decades ago. The technique unveiled the complex network of interactions between the living world of pro- and eukaryotes and viruses, which delivered "a piece of bad news wrapped in protein" as defined by Peter Medawar, Nobel Prize Laureate, in 1960. However, MS is constantly evolving, and novel approaches allow for a better understanding of interactions in this micro- and nanoworld. Currently, we can investigate the interplay between the virus and the cell by analyzing proteomes, interactomes, virus-cell interactions, and search for the compounds that build viral structures. In addition, by using MS, it is possible to look at the cell from the broader perspective and determine the role of viral infection on the scale of the organism, for example, monitoring the crosstalk between infected tissues and the immune system. In such a way, MS became one of the major tools for the modern virology, allowing us to see the infection in the context of the whole cell or the organism. © 2019 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Aleksandra Milewska
- Malopolska Centre of BiotechnologyJagiellonian UniversityGronostajowa 7A30‐387KrakowPoland
| | - Joanna Ner‐Kluza
- Department of Biochemistry and Neurobiology, Faculty of Materials Sciences and CeramicsAGH University of Science and TechnologyMickiewicza 30 Ave.30‐059KrakowPoland
| | - Agnieszka Dabrowska
- Malopolska Centre of BiotechnologyJagiellonian UniversityGronostajowa 7A30‐387KrakowPoland
- Faculty of Biochemistry, Biophysics and BiotechnologyJagiellonian UniversityGronostajowa 730‐387KrakowPoland
| | - Anna Bodzon‐Kulakowska
- Department of Biochemistry and Neurobiology, Faculty of Materials Sciences and CeramicsAGH University of Science and TechnologyMickiewicza 30 Ave.30‐059KrakowPoland
| | - Krzysztof Pyrc
- Malopolska Centre of BiotechnologyJagiellonian UniversityGronostajowa 7A30‐387KrakowPoland
| | - Piotr Suder
- Department of Biochemistry and Neurobiology, Faculty of Materials Sciences and CeramicsAGH University of Science and TechnologyMickiewicza 30 Ave.30‐059KrakowPoland
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Bian J, Liang M, Ding S, Wang L, Ni W, Xiong S, Li W, Bao X, Gao X, Wang R. iTRAQ-based high-throughput proteomics analysis reveals alterations of plasma proteins in patients infected with human bocavirus. PLoS One 2019; 14:e0225261. [PMID: 31751365 PMCID: PMC6872134 DOI: 10.1371/journal.pone.0225261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 10/31/2019] [Indexed: 12/18/2022] Open
Abstract
Human bocavirus (HBoV) is a member of the genus Bocavirus, family Parvoviridae, and subfamily Parvovirus and was first identified in nasopharyngeal aspirates of Swedish children with acute respiratory tract infection (ARTI) in 2005. It is the causative agent of nasopharyngeal aspirate disease and death in children. The HboV genomic structure is a linear single-stranded DNA (ssDNA). Its clinical pathogenic characteristics have been extensively studied, however, at present the molecular mechanism underlying the pathogenesis of HBoV infection is not completely clear. In this study, a total of 293 differentially expressed proteins (DEPs) between ARTI cases and healthy plasma samples were characterized using isobaric tags for relative and absolute quantitation (iTRAQ)-coupled bioinformatics analysis, among which 148 were up-regulated and 135 were down-regulated. Gene Ontology (GO) and Cluster of Orthologous Groups of proteins (COG) annotated an enrichment of DEPs in complement activation and biological processes like immunity, inflammation, signal transduction, substance synthesis, and metabolism. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis enriched DEPs mainly in the Wnt signaling pathway (ko04310), PPAR signaling pathway (ko03320), intestinal immune network for IgA production (ko04672), complement and coagulation cascades (ko04610), Toll-like receptor signaling pathway (ko04620) and B cell receptor signaling pathway (ko04662). Further, expression levels of three candidate proteins (upregulated PPP2R1A and CUL1, and downregulated CETP) were validated using western blotting. Our investigation is the first analysis of the proteomic profile of HBoV-infected ARTI cases using the iTRAQ approach, providing a foundation for a better molecular understanding of the pathogenesis of ARTI in children.
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Affiliation(s)
- Junmei Bian
- Tongren Hospital of Wuhan University (Wuhan Third Hospital), Wuhan, PR China
| | - Min Liang
- Tongren Hospital of Wuhan University (Wuhan Third Hospital), Wuhan, PR China
| | - Shuxian Ding
- Tongren Hospital of Wuhan University (Wuhan Third Hospital), Wuhan, PR China
| | - Liyan Wang
- Tongren Hospital of Wuhan University (Wuhan Third Hospital), Wuhan, PR China
| | - Wenchang Ni
- Tongren Hospital of Wuhan University (Wuhan Third Hospital), Wuhan, PR China
| | - Shisi Xiong
- Tongren Hospital of Wuhan University (Wuhan Third Hospital), Wuhan, PR China
| | - Wan Li
- Tongren Hospital of Wuhan University (Wuhan Third Hospital), Wuhan, PR China
| | - Xingxing Bao
- Tongren Hospital of Wuhan University (Wuhan Third Hospital), Wuhan, PR China
| | - Xue Gao
- Tongren Hospital of Wuhan University (Wuhan Third Hospital), Wuhan, PR China
| | - Rong Wang
- Tongren Hospital of Wuhan University (Wuhan Third Hospital), Wuhan, PR China
- * E-mail:
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11
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Yang S, Pei Y, Zhao A. iTRAQ-based Proteomic Analysis of Porcine Kidney Epithelial PK15 cells Infected with Pseudorabies virus. Sci Rep 2017; 7:45922. [PMID: 28374783 PMCID: PMC5379687 DOI: 10.1038/srep45922] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 03/03/2017] [Indexed: 12/18/2022] Open
Abstract
Pseudorabies virus (PRV) is one of the most important pathogens of swine, resulting in severe economic losses to the pig industry. To improve our understanding of the host responses to PRV infection, we applied isobaric tags for relative and absolute quantification (iTRAQ) labeling coupled with liquid chromatography-tandem mass spectrometry to quantitatively identify the differentially expressed cellular proteins in PRV-infected PK15 cells. In total, relative quantitative data were identified for 4333 proteins in PRV and mock- infected PK15 cells, among which 466 cellular proteins were differentially expressed, including 234 upregulated proteins and 232 downregulated proteins. Bioinformatics analysis disclosed that most of these differentially expressed proteins were involved in metabolic processes, cellular growth and proliferation, endoplasmic reticulum (ER) stress response, cell adhesion and cytoskeleton. Moreover, expression levels of four representative proteins, beta-catenin, STAT1, GRB2 and PCNA, were further confirmed by western blot analysis. This is the first attempt to analyze the protein profile of PRV-infected PK15 cells using iTRAQ technology, and our findings may provide valuable information to help understand the host response to PRV infection.
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Affiliation(s)
- Songbai Yang
- College of Animal Science and Technology, Zhejiang A&F University, Lin'an, Zhejiang 311300, China
| | - Yue Pei
- College of Animal Science and Technology, Zhejiang A&F University, Lin'an, Zhejiang 311300, China
| | - Ayong Zhao
- College of Animal Science and Technology, Zhejiang A&F University, Lin'an, Zhejiang 311300, China
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Lautridou J, Pichereau V, Artigaud S, Buzzacott P, Wang Q, Bernay B, Driad S, Mazur A, Lambrechts K, Théron M, Guerrero F. Effect of simulated air dive and decompression sickness on the plasma proteome of rats. Proteomics Clin Appl 2016; 10:614-20. [DOI: 10.1002/prca.201600017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 03/01/2016] [Accepted: 04/06/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Jacky Lautridou
- Laboratoire ORPHY EA 4324; Université de Bretagne Occidentale; Brest France
| | - Vianney Pichereau
- LEMAR UMR 6539 CNRS/UBO/IRD/Ifremer; Université de Bretagne Occidentale; Brest France
| | - Sébastien Artigaud
- LEMAR UMR 6539 CNRS/UBO/IRD/Ifremer; Université de Bretagne Occidentale; Brest France
| | - Peter Buzzacott
- Laboratoire ORPHY EA 4324; Université de Bretagne Occidentale; Brest France
| | - Qiong Wang
- Laboratoire ORPHY EA 4324; Université de Bretagne Occidentale; Brest France
| | - Benoit Bernay
- Proteogen SFR ICORE 4206; Université de Caen; Caen France
| | - Sabrina Driad
- Laboratoire ORPHY EA 4324; Université de Bretagne Occidentale; Brest France
| | - Aleksandra Mazur
- Laboratoire ORPHY EA 4324; Université de Bretagne Occidentale; Brest France
| | - Kate Lambrechts
- Laboratoire ORPHY EA 4324; Université de Bretagne Occidentale; Brest France
| | - Michael Théron
- Laboratoire ORPHY EA 4324; Université de Bretagne Occidentale; Brest France
| | - François Guerrero
- Laboratoire ORPHY EA 4324; Université de Bretagne Occidentale; Brest France
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Marion T, Elbahesh H, Thomas PG, DeVincenzo JP, Webby R, Schughart K. Respiratory Mucosal Proteome Quantification in Human Influenza Infections. PLoS One 2016; 11:e0153674. [PMID: 27088501 PMCID: PMC4835085 DOI: 10.1371/journal.pone.0153674] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 04/01/2016] [Indexed: 01/08/2023] Open
Abstract
Respiratory influenza virus infections represent a serious threat to human health. Underlying medical conditions and genetic make-up predispose some influenza patients to more severe forms of disease. To date, only a few studies have been performed in patients to correlate a selected group of cytokines and chemokines with influenza infection. Therefore, we evaluated the potential of a novel multiplex micro-proteomics technology, SOMAscan, to quantify proteins in the respiratory mucosa of influenza A and B infected individuals. The analysis included but was not limited to quantification of cytokines and chemokines detected in previous studies. SOMAscan quantified more than 1,000 secreted proteins in small nasal wash volumes from infected and healthy individuals. Our results illustrate the utility of micro-proteomic technology for analysis of proteins in small volumes of respiratory mucosal samples. Furthermore, when we compared nasal wash samples from influenza-infected patients with viral load ≥ 28 and increased IL-6 and CXCL10 to healthy controls, we identified 162 differentially-expressed proteins between the two groups. This number greatly exceeds the number of DEPs identified in previous studies in human influenza patients. Most of the identified proteins were associated with the host immune response to infection, and changes in protein levels of 151 of the DEPs were significantly correlated with viral load. Most important, SOMAscan identified differentially expressed proteins heretofore not associated with respiratory influenza infection in humans. Our study is the first report for the use of SOMAscan to screen nasal secretions. It establishes a precedent for micro-proteomic quantification of proteins that reflect ongoing response to respiratory infection.
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Affiliation(s)
- Tony Marion
- University of Tennessee Health Science Center, Department of Microbiology, Immunology and Biochemistry, Memphis, United States of America
| | - Husni Elbahesh
- University of Tennessee Health Science Center, Department of Microbiology, Immunology and Biochemistry, Memphis, United States of America
| | - Paul G. Thomas
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, United States of America
| | - John P. DeVincenzo
- University of Tennessee Health Science Center, Department of Microbiology, Immunology and Biochemistry, Memphis, United States of America
- University of Tennessee Health Science Center, Department of Pediatrics, Memphis, United States of America
- Children’s Foundation Research Center at Le Bonheur Children’s Hospital, Memphis, United States of America
| | - Richard Webby
- Department of Infectious Diseases, St Jude Children’s Research Hospital, Memphis, United States of America
| | - Klaus Schughart
- University of Tennessee Health Science Center, Department of Microbiology, Immunology and Biochemistry, Memphis, United States of America
- Department of Infection Genetics, Helmholtz Centre for Infection Research, Braunschweig, Germany
- University of Veterinary Medicine Hannover, Hannover, Germany
- * E-mail:
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14
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Scumaci D, Tammè L, Fiumara CV, Pappaianni G, Concolino A, Leone E, Faniello MC, Quaresima B, Ricevuto E, Costanzo FS, Cuda G. Plasma Proteomic Profiling in Hereditary Breast Cancer Reveals a BRCA1-Specific Signature: Diagnostic and Functional Implications. PLoS One 2015; 10:e0129762. [PMID: 26061043 PMCID: PMC4465499 DOI: 10.1371/journal.pone.0129762] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 05/13/2015] [Indexed: 12/16/2022] Open
Abstract
Background Breast cancer (BC) is a leading cause of death among women. Among the major risk factors, an important role is played by familial history of BC. Germ-line mutations in BRCA1/2 genes account for most of the hereditary breast and/or ovarian cancers. Gene expression profiling studies have disclosed specific molecular signatures for BRCA1/2-related breast tumors as compared to sporadic cases, which might help diagnosis and clinical follow-up. Even though, a clear hallmark of BRCA1/2-positive BC is still lacking. Many diseases are correlated with quantitative changes of proteins in body fluids. Plasma potentially carries important information whose knowledge could help to improve early disease detection, prognosis, and response to therapeutic treatments. The aim of this study was to develop a comprehensive approach finalized to improve the recovery of specific biomarkers from plasma samples of subjects affected by hereditary BC. Methods To perform this analysis, we used samples from patients belonging to highly homogeneous population previously reported. Depletion of high abundant plasma proteins, 2D gel analysis, liquid chromatography-tandem mass spectrometry (LC-MS/MS) and bioinformatics analysis were used into an integrated approach to investigate tumor-specific changes in the plasma proteome of BC patients and healthy family members sharing the same BRCA1 gene founder mutation (5083del19), previously reported by our group, with the aim to identify specific signatures. Results The comparative analysis of the experimental results led to the identification of gelsolin as the most promising biomarker. Conclusions Further analyses, performed using a panel of breast cancer cell lines, allowed us to further elucidate the signaling network that might modulate the expression of gelsolin in breast cancer.
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Affiliation(s)
- Domenica Scumaci
- Dpt. of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Salvatore Venuta University Campus, Catanzaro, Italy
- * E-mail:
| | - Laura Tammè
- Dpt. of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Salvatore Venuta University Campus, Catanzaro, Italy
| | - Claudia Vincenza Fiumara
- Dpt. of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Salvatore Venuta University Campus, Catanzaro, Italy
| | - Giusi Pappaianni
- Dpt. of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Salvatore Venuta University Campus, Catanzaro, Italy
| | - Antonio Concolino
- Dpt. of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Salvatore Venuta University Campus, Catanzaro, Italy
| | - Emanuela Leone
- Dpt. of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Salvatore Venuta University Campus, Catanzaro, Italy
| | - Maria Concetta Faniello
- Dpt. of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Salvatore Venuta University Campus, Catanzaro, Italy
| | - Barbara Quaresima
- Dpt. of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Salvatore Venuta University Campus, Catanzaro, Italy
| | - Enrico Ricevuto
- Medical Oncology, S. Salvatore Hospital, University of L'Aquila, L'Aquila, Italy
| | - Francesco Saverio Costanzo
- Dpt. of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Salvatore Venuta University Campus, Catanzaro, Italy
| | - Giovanni Cuda
- Dpt. of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Salvatore Venuta University Campus, Catanzaro, Italy
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