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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 Plasma Membrane Profiling of HCMV-Infected Fibroblasts(A) Workflow of experiments PM1 and WCL1.(B) Hierarchical cluster analysis of all proteins quantified in experiment PM1 and annotated “plasma membrane,” “cell surface,” “extracellular,” or “short GO” (Figure S1A).(C) All ABC transporters quantified. One-way ANOVA with multiple hypothesis correction: ∗p < 0.005, ∗∗p < 0.0001.(D) Quantitation of all HCMV proteins reported present at the surface of infected fibroblasts. gB, gH, gL, gO, and UL132 are virion envelope glycoproteins expressed late in infection. One-way ANOVA with multiple hypothesis correction: ∗p < 0.005, ∗∗p < 0.0001.(E) Principal component analysis of all quantified proteins from experiments PM1 and WCL1 confirmed that biological replicates were highly reproducible and suggested that the major source of variability within a given experiment was duration of infection.(F) Correlation between proteins quantified in experiments PM1 and PM2.See also Figure S1 and Table S1.
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fig1: Temporal Plasma Membrane Profiling of HCMV-Infected Fibroblasts(A) Workflow of experiments PM1 and WCL1.(B) Hierarchical cluster analysis of all proteins quantified in experiment PM1 and annotated “plasma membrane,” “cell surface,” “extracellular,” or “short GO” (Figure S1A).(C) All ABC transporters quantified. One-way ANOVA with multiple hypothesis correction: ∗p < 0.005, ∗∗p < 0.0001.(D) Quantitation of all HCMV proteins reported present at the surface of infected fibroblasts. gB, gH, gL, gO, and UL132 are virion envelope glycoproteins expressed late in infection. One-way ANOVA with multiple hypothesis correction: ∗p < 0.005, ∗∗p < 0.0001.(E) Principal component analysis of all quantified proteins from experiments PM1 and WCL1 confirmed that biological replicates were highly reproducible and suggested that the major source of variability within a given experiment was duration of infection.(F) Correlation between proteins quantified in experiments PM1 and PM2.See also Figure S1 and Table S1.

Mentions: We infected primary human fetal foreskin fibroblasts (HFFFs) with HCMV strain Merlin and initially used 8-plex TMT to quantify changes in PM protein expression. We assessed in biological duplicate three of the reference time points in productive HCMV infection and mock infection (experiment “PM1”, Figure 1A). We quantified 927 PM proteins (Figure S1A available online). Surprisingly, 56% of proteins changed >2-fold and 33% >3-fold by 72 hr of infection. Replicates clustered tightly (Figure 1B).


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 Plasma Membrane Profiling of HCMV-Infected Fibroblasts(A) Workflow of experiments PM1 and WCL1.(B) Hierarchical cluster analysis of all proteins quantified in experiment PM1 and annotated “plasma membrane,” “cell surface,” “extracellular,” or “short GO” (Figure S1A).(C) All ABC transporters quantified. One-way ANOVA with multiple hypothesis correction: ∗p < 0.005, ∗∗p < 0.0001.(D) Quantitation of all HCMV proteins reported present at the surface of infected fibroblasts. gB, gH, gL, gO, and UL132 are virion envelope glycoproteins expressed late in infection. One-way ANOVA with multiple hypothesis correction: ∗p < 0.005, ∗∗p < 0.0001.(E) Principal component analysis of all quantified proteins from experiments PM1 and WCL1 confirmed that biological replicates were highly reproducible and suggested that the major source of variability within a given experiment was duration of infection.(F) Correlation between proteins quantified in experiments PM1 and PM2.See also Figure S1 and Table S1.
© Copyright Policy - CC BY
Related In: Results  -  Collection

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

fig1: Temporal Plasma Membrane Profiling of HCMV-Infected Fibroblasts(A) Workflow of experiments PM1 and WCL1.(B) Hierarchical cluster analysis of all proteins quantified in experiment PM1 and annotated “plasma membrane,” “cell surface,” “extracellular,” or “short GO” (Figure S1A).(C) All ABC transporters quantified. One-way ANOVA with multiple hypothesis correction: ∗p < 0.005, ∗∗p < 0.0001.(D) Quantitation of all HCMV proteins reported present at the surface of infected fibroblasts. gB, gH, gL, gO, and UL132 are virion envelope glycoproteins expressed late in infection. One-way ANOVA with multiple hypothesis correction: ∗p < 0.005, ∗∗p < 0.0001.(E) Principal component analysis of all quantified proteins from experiments PM1 and WCL1 confirmed that biological replicates were highly reproducible and suggested that the major source of variability within a given experiment was duration of infection.(F) Correlation between proteins quantified in experiments PM1 and PM2.See also Figure S1 and Table S1.
Mentions: We infected primary human fetal foreskin fibroblasts (HFFFs) with HCMV strain Merlin and initially used 8-plex TMT to quantify changes in PM protein expression. We assessed in biological duplicate three of the reference time points in productive HCMV infection and mock infection (experiment “PM1”, Figure 1A). We quantified 927 PM proteins (Figure S1A available online). Surprisingly, 56% of proteins changed >2-fold and 33% >3-fold by 72 hr of infection. Replicates clustered tightly (Figure 1B).

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