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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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QTV Provides Insights into Modulated Signaling Pathways, Related to Figure 3(A) The Toll-like receptor signaling pathway and its modulation during HCMV infection, based on the KEGG pathway (Kanehisa and Goto, 2000). Proteins (ovals) are shaded to correspond to their clusters (Figure 3B): red (downregulated), blue (unchanged), green (upregulated), gray (not quantified). Edges (from KEGG) are shaded green with arrows, to indicate that protein A activates protein B and pink to indicate that protein A inhibits protein B. A single gray/black edge with arrow indicates that protein A affects protein B - not labeled as activation or inhibition. A paired gray/black arrow between proteins A and B: protein A and B bind to or are associated with one another. Phosphorylation events are labeled with p+.(B) Immunoblots of HFFF infected with HCMV confirm proteomic profiles for three TLR-pathway members.(C) The gap junction pathway, shaded as for Figure S3A.(D) Modulation of cell surface wnt receptors. 11/13 quantified canonical and non-canonical wnt receptors were downregulated. The WCL2 β-catenin profile demonstrated a modest decline over time. Red diamonds – 12h after infection with irradiated HCMV.
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figs3: QTV Provides Insights into Modulated Signaling Pathways, Related to Figure 3(A) The Toll-like receptor signaling pathway and its modulation during HCMV infection, based on the KEGG pathway (Kanehisa and Goto, 2000). Proteins (ovals) are shaded to correspond to their clusters (Figure 3B): red (downregulated), blue (unchanged), green (upregulated), gray (not quantified). Edges (from KEGG) are shaded green with arrows, to indicate that protein A activates protein B and pink to indicate that protein A inhibits protein B. A single gray/black edge with arrow indicates that protein A affects protein B - not labeled as activation or inhibition. A paired gray/black arrow between proteins A and B: protein A and B bind to or are associated with one another. Phosphorylation events are labeled with p+.(B) Immunoblots of HFFF infected with HCMV confirm proteomic profiles for three TLR-pathway members.(C) The gap junction pathway, shaded as for Figure S3A.(D) Modulation of cell surface wnt receptors. 11/13 quantified canonical and non-canonical wnt receptors were downregulated. The WCL2 β-catenin profile demonstrated a modest decline over time. Red diamonds – 12h after infection with irradiated HCMV.

Mentions: The k-means method is useful to cluster proteins into a specified number of classes based on the similarity of temporal profiles. We clustered all 7,491 proteins from experiment WCL2 and 1,184 proteins from PM2 into three classes (corresponding to upregulation, downregulation, and no change) to identify novel pathways dysregulated during HCMV infection (Figure 3B). We then applied DAVID software (Huang et al., 2009) to determine which KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways were enriched in each class (Figures 3C and S3A). We made the discovery that multiple members of the TLR signaling pathway were downregulated (Figures S3A and S3B; Table S4A), suggesting that HCMV might employ a number of strategies to avoid this intrinsic immune mechanism. Fatty acid metabolism and oxidative phosphorylation were upregulated during infection (Figure 3C; Table S4A), corresponding to published literature (Koyuncu et al., 2013).


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)

QTV Provides Insights into Modulated Signaling Pathways, Related to Figure 3(A) The Toll-like receptor signaling pathway and its modulation during HCMV infection, based on the KEGG pathway (Kanehisa and Goto, 2000). Proteins (ovals) are shaded to correspond to their clusters (Figure 3B): red (downregulated), blue (unchanged), green (upregulated), gray (not quantified). Edges (from KEGG) are shaded green with arrows, to indicate that protein A activates protein B and pink to indicate that protein A inhibits protein B. A single gray/black edge with arrow indicates that protein A affects protein B - not labeled as activation or inhibition. A paired gray/black arrow between proteins A and B: protein A and B bind to or are associated with one another. Phosphorylation events are labeled with p+.(B) Immunoblots of HFFF infected with HCMV confirm proteomic profiles for three TLR-pathway members.(C) The gap junction pathway, shaded as for Figure S3A.(D) Modulation of cell surface wnt receptors. 11/13 quantified canonical and non-canonical wnt receptors were downregulated. The WCL2 β-catenin profile demonstrated a modest decline over time. Red diamonds – 12h after infection with irradiated HCMV.
© Copyright Policy - CC BY
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4048463&req=5

figs3: QTV Provides Insights into Modulated Signaling Pathways, Related to Figure 3(A) The Toll-like receptor signaling pathway and its modulation during HCMV infection, based on the KEGG pathway (Kanehisa and Goto, 2000). Proteins (ovals) are shaded to correspond to their clusters (Figure 3B): red (downregulated), blue (unchanged), green (upregulated), gray (not quantified). Edges (from KEGG) are shaded green with arrows, to indicate that protein A activates protein B and pink to indicate that protein A inhibits protein B. A single gray/black edge with arrow indicates that protein A affects protein B - not labeled as activation or inhibition. A paired gray/black arrow between proteins A and B: protein A and B bind to or are associated with one another. Phosphorylation events are labeled with p+.(B) Immunoblots of HFFF infected with HCMV confirm proteomic profiles for three TLR-pathway members.(C) The gap junction pathway, shaded as for Figure S3A.(D) Modulation of cell surface wnt receptors. 11/13 quantified canonical and non-canonical wnt receptors were downregulated. The WCL2 β-catenin profile demonstrated a modest decline over time. Red diamonds – 12h after infection with irradiated HCMV.
Mentions: The k-means method is useful to cluster proteins into a specified number of classes based on the similarity of temporal profiles. We clustered all 7,491 proteins from experiment WCL2 and 1,184 proteins from PM2 into three classes (corresponding to upregulation, downregulation, and no change) to identify novel pathways dysregulated during HCMV infection (Figure 3B). We then applied DAVID software (Huang et al., 2009) to determine which KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways were enriched in each class (Figures 3C and S3A). We made the discovery that multiple members of the TLR signaling pathway were downregulated (Figures S3A and S3B; Table S4A), suggesting that HCMV might employ a number of strategies to avoid this intrinsic immune mechanism. Fatty acid metabolism and oxidative phosphorylation were upregulated during infection (Figure 3C; Table S4A), corresponding to published literature (Koyuncu et al., 2013).

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