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Quantitative temporal viromics: an approach to investigate host-pathogen interaction.

Weekes MP, Tomasec P, Huttlin EL, Fielding CA, Nusinow D, Stanton RJ, Wang EC, Aicheler R, Murrell I, Wilkinson GW, Lehner PJ, Gygi SP - Cell (2014)

Bottom Line: QTV predicted natural killer and T cell ligands, as well as 29 viral proteins present at the cell surface, potential therapeutic targets.Temporal profiles of >80% of HCMV canonical genes and 14 noncanonical HCMV open reading frames were defined.QTV is a powerful method that can yield important insights into viral infection and is applicable to any virus with a robust in vitro model.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA; Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK. Electronic address: mpw1001@cam.ac.uk.

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Temporal WCL Analysis of HCMV-Infected Fibroblasts Demonstrates Exquisite Regulation of ISGs(A) Hierarchical cluster analysis of all proteins quantified in experiment WCL2, and enlargement of the top cluster A that included multiple IFN-induced antiviral proteins. Right panels, example temporal profiles. The y axis shows relative abundance of each protein. Red diamonds, 12 hr after infection with irradiated HCMV.(B) Immunoblots of HFFF infected with HCMV confirm proteomic profiles.(C) Interferon-induced proteins were more potently upregulated by productive infection than infection with irradiated HCMV. For each protein, signal:noise from the 12 hr irradiated virus or productive infection samples, and both mock samples was normalized to 1. The order of samples mock 1 and mock 2 was randomized into mock (a) and mock (b). The difference in normalized signal:noise was then calculated as indicated, and histograms were plotted. Where <0.05% of proteins were upregulated by infection with irradiated virus, 2% of proteins were upregulated by infection with live virus. These included 69 viral proteins and 84 human proteins, of which 39% are known ISGs.See also Figure S2 and Table S3.
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fig2: Temporal WCL Analysis of HCMV-Infected Fibroblasts Demonstrates Exquisite Regulation of ISGs(A) Hierarchical cluster analysis of all proteins quantified in experiment WCL2, and enlargement of the top cluster A that included multiple IFN-induced antiviral proteins. Right panels, example temporal profiles. The y axis shows relative abundance of each protein. Red diamonds, 12 hr after infection with irradiated HCMV.(B) Immunoblots of HFFF infected with HCMV confirm proteomic profiles.(C) Interferon-induced proteins were more potently upregulated by productive infection than infection with irradiated HCMV. For each protein, signal:noise from the 12 hr irradiated virus or productive infection samples, and both mock samples was normalized to 1. The order of samples mock 1 and mock 2 was randomized into mock (a) and mock (b). The difference in normalized signal:noise was then calculated as indicated, and histograms were plotted. Where <0.05% of proteins were upregulated by infection with irradiated virus, 2% of proteins were upregulated by infection with live virus. These included 69 viral proteins and 84 human proteins, of which 39% are known ISGs.See also Figure S2 and Table S3.

Mentions: We quantified 1,184 PM proteins (experiment PM2, Figure S1E) and 7,491 cellular proteins (experiment WCL2, Figure 2A). Protein temporal profiles correlated well between repeat time courses (Figures 1F and S1F). Data from all four experiments are shown in Table S2, where the worksheet “Plots” is interactive, enabling generation of overlayed temporal graphs of PM and WCL expression of any of the human and viral proteins quantified.


Quantitative temporal viromics: an approach to investigate host-pathogen interaction.

Weekes MP, Tomasec P, Huttlin EL, Fielding CA, Nusinow D, Stanton RJ, Wang EC, Aicheler R, Murrell I, Wilkinson GW, Lehner PJ, Gygi SP - Cell (2014)

Temporal WCL Analysis of HCMV-Infected Fibroblasts Demonstrates Exquisite Regulation of ISGs(A) Hierarchical cluster analysis of all proteins quantified in experiment WCL2, and enlargement of the top cluster A that included multiple IFN-induced antiviral proteins. Right panels, example temporal profiles. The y axis shows relative abundance of each protein. Red diamonds, 12 hr after infection with irradiated HCMV.(B) Immunoblots of HFFF infected with HCMV confirm proteomic profiles.(C) Interferon-induced proteins were more potently upregulated by productive infection than infection with irradiated HCMV. For each protein, signal:noise from the 12 hr irradiated virus or productive infection samples, and both mock samples was normalized to 1. The order of samples mock 1 and mock 2 was randomized into mock (a) and mock (b). The difference in normalized signal:noise was then calculated as indicated, and histograms were plotted. Where <0.05% of proteins were upregulated by infection with irradiated virus, 2% of proteins were upregulated by infection with live virus. These included 69 viral proteins and 84 human proteins, of which 39% are known ISGs.See also Figure S2 and Table S3.
© Copyright Policy - CC BY
Related In: Results  -  Collection

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fig2: Temporal WCL Analysis of HCMV-Infected Fibroblasts Demonstrates Exquisite Regulation of ISGs(A) Hierarchical cluster analysis of all proteins quantified in experiment WCL2, and enlargement of the top cluster A that included multiple IFN-induced antiviral proteins. Right panels, example temporal profiles. The y axis shows relative abundance of each protein. Red diamonds, 12 hr after infection with irradiated HCMV.(B) Immunoblots of HFFF infected with HCMV confirm proteomic profiles.(C) Interferon-induced proteins were more potently upregulated by productive infection than infection with irradiated HCMV. For each protein, signal:noise from the 12 hr irradiated virus or productive infection samples, and both mock samples was normalized to 1. The order of samples mock 1 and mock 2 was randomized into mock (a) and mock (b). The difference in normalized signal:noise was then calculated as indicated, and histograms were plotted. Where <0.05% of proteins were upregulated by infection with irradiated virus, 2% of proteins were upregulated by infection with live virus. These included 69 viral proteins and 84 human proteins, of which 39% are known ISGs.See also Figure S2 and Table S3.
Mentions: We quantified 1,184 PM proteins (experiment PM2, Figure S1E) and 7,491 cellular proteins (experiment WCL2, Figure 2A). Protein temporal profiles correlated well between repeat time courses (Figures 1F and S1F). Data from all four experiments are shown in Table S2, where the worksheet “Plots” is interactive, enabling generation of overlayed temporal graphs of PM and WCL expression of any of the human and viral proteins quantified.

Bottom Line: QTV predicted natural killer and T cell ligands, as well as 29 viral proteins present at the cell surface, potential therapeutic targets.Temporal profiles of >80% of HCMV canonical genes and 14 noncanonical HCMV open reading frames were defined.QTV is a powerful method that can yield important insights into viral infection and is applicable to any virus with a robust in vitro model.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA; Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK. Electronic address: mpw1001@cam.ac.uk.

Show MeSH
Related in: MedlinePlus