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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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Modulation of Intracellular Signaling Pathways during HCMV Infection(A) Quantitation of interferon induction and response pathways. The temporal profile of each protein is shown over 96 hr of infection, and colored red (downregulation), blue (unchanged), or green (upregulation). Data were derived from experiment WCL2 apart from IFNAR1 and IFNAR2, from PM2. Expression of certain ISGs is known to occur in the absence of IFN, in an IRF3-dependent manner. PRR, pattern recognition receptors.(B) Average temporal profiles from 3-class k-means clustering of proteins quantified in experiments WCL2 and PM2. The three classes divided proteins into downregulated (red), unchanged (blue), or upregulated (green).(C) Enrichment of KEGG pathways within each class was determined using DAVID software, against a background of all quantified proteins. Benjamini-Hochberg adjusted p values are shown for each indicated bar (∗p < 0.00001, ∗∗p < 0.0001, ∗∗∗p < 0.01, ∗∗∗∗p < 0.05). Individual pathways are shown in Figures S3A–S3C, and pathway members are shown in Table S4.
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fig3: Modulation of Intracellular Signaling Pathways during HCMV Infection(A) Quantitation of interferon induction and response pathways. The temporal profile of each protein is shown over 96 hr of infection, and colored red (downregulation), blue (unchanged), or green (upregulation). Data were derived from experiment WCL2 apart from IFNAR1 and IFNAR2, from PM2. Expression of certain ISGs is known to occur in the absence of IFN, in an IRF3-dependent manner. PRR, pattern recognition receptors.(B) Average temporal profiles from 3-class k-means clustering of proteins quantified in experiments WCL2 and PM2. The three classes divided proteins into downregulated (red), unchanged (blue), or upregulated (green).(C) Enrichment of KEGG pathways within each class was determined using DAVID software, against a background of all quantified proteins. Benjamini-Hochberg adjusted p values are shown for each indicated bar (∗p < 0.00001, ∗∗p < 0.0001, ∗∗∗p < 0.01, ∗∗∗∗p < 0.05). Individual pathways are shown in Figures S3A–S3C, and pathway members are shown in Table S4.

Mentions: The activity of a signaling pathway can be modulated either by posttranslational modification, or regulation of expression of a pathway member. Changes in protein expression can be quantified by QTV. We have shown that after an initial activation, the expression of ISG is rapidly reduced during HCMV infection, but how is this achieved? We quantified 13/15 key members of IFN induction and signaling pathways (Figure 3A, reviewed in Amsler et al., 2013). We confirmed known effects of HCMV infection on Jak1, STAT2, and IRF9 (Le et al., 2008) and demonstrated that, apart from STAT1, expression of the final effectors in both interferon induction and response pathways were all progressively diminished during infection (Figure 3A). An effect of HCMV infection on IRF3 has not previously been reported.


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)

Modulation of Intracellular Signaling Pathways during HCMV Infection(A) Quantitation of interferon induction and response pathways. The temporal profile of each protein is shown over 96 hr of infection, and colored red (downregulation), blue (unchanged), or green (upregulation). Data were derived from experiment WCL2 apart from IFNAR1 and IFNAR2, from PM2. Expression of certain ISGs is known to occur in the absence of IFN, in an IRF3-dependent manner. PRR, pattern recognition receptors.(B) Average temporal profiles from 3-class k-means clustering of proteins quantified in experiments WCL2 and PM2. The three classes divided proteins into downregulated (red), unchanged (blue), or upregulated (green).(C) Enrichment of KEGG pathways within each class was determined using DAVID software, against a background of all quantified proteins. Benjamini-Hochberg adjusted p values are shown for each indicated bar (∗p < 0.00001, ∗∗p < 0.0001, ∗∗∗p < 0.01, ∗∗∗∗p < 0.05). Individual pathways are shown in Figures S3A–S3C, and pathway members are shown in Table S4.
© Copyright Policy - CC BY
Related In: Results  -  Collection

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

fig3: Modulation of Intracellular Signaling Pathways during HCMV Infection(A) Quantitation of interferon induction and response pathways. The temporal profile of each protein is shown over 96 hr of infection, and colored red (downregulation), blue (unchanged), or green (upregulation). Data were derived from experiment WCL2 apart from IFNAR1 and IFNAR2, from PM2. Expression of certain ISGs is known to occur in the absence of IFN, in an IRF3-dependent manner. PRR, pattern recognition receptors.(B) Average temporal profiles from 3-class k-means clustering of proteins quantified in experiments WCL2 and PM2. The three classes divided proteins into downregulated (red), unchanged (blue), or upregulated (green).(C) Enrichment of KEGG pathways within each class was determined using DAVID software, against a background of all quantified proteins. Benjamini-Hochberg adjusted p values are shown for each indicated bar (∗p < 0.00001, ∗∗p < 0.0001, ∗∗∗p < 0.01, ∗∗∗∗p < 0.05). Individual pathways are shown in Figures S3A–S3C, and pathway members are shown in Table S4.
Mentions: The activity of a signaling pathway can be modulated either by posttranslational modification, or regulation of expression of a pathway member. Changes in protein expression can be quantified by QTV. We have shown that after an initial activation, the expression of ISG is rapidly reduced during HCMV infection, but how is this achieved? We quantified 13/15 key members of IFN induction and signaling pathways (Figure 3A, reviewed in Amsler et al., 2013). We confirmed known effects of HCMV infection on Jak1, STAT2, and IRF9 (Le et al., 2008) and demonstrated that, apart from STAT1, expression of the final effectors in both interferon induction and response pathways were all progressively diminished during infection (Figure 3A). An effect of HCMV infection on IRF3 has not previously been reported.

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