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Specific mutations in H5N1 mainly impact the magnitude and velocity of the host response in mice.

Tchitchek N, Eisfeld AJ, Tisoncik-Go J, Josset L, Gralinski LE, Bécavin C, Tilton SC, Webb-Robertson BJ, Ferris MT, Totura AL, Li C, Neumann G, Metz TO, Smith RD, Waters KM, Baric R, Kawaoka Y, Katze MG - BMC Syst Biol (2013)

Bottom Line: Using a new geometrical representation method and two criteria, we show that inoculation concentrations and four specific mutations in VN1203 mainly impact the magnitude and velocity of the host response kinetics, rather than specific sets of up- and down- regulated genes.These kinetic properties imply that time-matched comparisons of 'omics profiles to viral infections give limited views to differentiate host-responses.Moreover, these results demonstrate that a fast activation of the host-response at the earliest time points post-infection is critical for protective mechanisms against fast replicating viruses.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Microbiology, University of Washington, Seattle, WA 98195 USA.

ABSTRACT

Background: Influenza infection causes respiratory disease that can lead to death. The complex interplay between virus-encoded and host-specific pathogenicity regulators - and the relative contributions of each toward viral pathogenicity - is not well-understood.

Results: By analyzing a collection of lung samples from mice infected by A/Vietnam/1203/2004 (H5N1; VN1203), we characterized a signature of transcripts and proteins associated with the kinetics of the host response. Using a new geometrical representation method and two criteria, we show that inoculation concentrations and four specific mutations in VN1203 mainly impact the magnitude and velocity of the host response kinetics, rather than specific sets of up- and down- regulated genes. We observed analogous kinetic effects using lung samples from mice infected with A/California/04/2009 (H1N1), and we show that these effects correlate with morbidity and viral titer.

Conclusions: We have demonstrated the importance of the kinetics of the host response to H5N1 pathogenesis and its relationship with clinical disease severity and virus replication. These kinetic properties imply that time-matched comparisons of 'omics profiles to viral infections give limited views to differentiate host-responses. Moreover, these results demonstrate that a fast activation of the host-response at the earliest time points post-infection is critical for protective mechanisms against fast replicating viruses.

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MDS Projections of the VN1203 mutants infected transcriptomic profiles over the VN1203-WT Reference Map. (A) Multidimensional Scaling Projection (MDS Projection) of the transcriptomic profiles of the VN1203-PB2627E dosage condition over the VN1203 wild-type Multidimensional Scaling Reference Map (MDS Ref Map). (B) MDS Projection of the transcriptomic profiles of the VN1203-HAavir dosage condition over the VN1203 wild-type MDS Ref Map. (C) MDS Projection of the transcriptomic profiles of the VN1203-PB1F2del dosage conditions over the VN1203 wild-type MDS Ref Map. (D) MDS Projection of the transcriptomic profiles of the VN1203-NS1trunc dosage conditions over the VN1203 wild-type MDS Ref Map. Each dot is the transcriptomic profile of a biological sample plotted in the intensity space of gene expression. Pairwise distances between the dots are proportional to the transcriptomic distances between the samples. MDS Projections allow to project additional ‘omics profiles over a predefined MDS representation (MDS Ref Map). Transcriptomic distances have been calculated based on the signature of 5,660 transcripts that significantly correlate with one eigentranscript. Dots are colored in order to indicate the dosage conditions, and biological conditions are indicated by the convex hull (i.e. the smallest convex set containing the points [30]) of the set of biological replicates and labeled to indicate the time point post-infection. Samples and biological conditions of the H5N1 VN1203 wild-type 104 PFU infection dosage are indicated by gray dots and gray convex hulls. Hence the grey spots that are connected represent the -omics profiles of mice lung infected by the VN1203 wild-type virus at 104 PFU, while the ones not connected represent the -omics profiles for the other infection concentrations. The Kruskal Stress shown in each representation quantifies the quality of the geometrical representation as a fraction of the information lost during the dimensionality reduction procedure.
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Figure 5: MDS Projections of the VN1203 mutants infected transcriptomic profiles over the VN1203-WT Reference Map. (A) Multidimensional Scaling Projection (MDS Projection) of the transcriptomic profiles of the VN1203-PB2627E dosage condition over the VN1203 wild-type Multidimensional Scaling Reference Map (MDS Ref Map). (B) MDS Projection of the transcriptomic profiles of the VN1203-HAavir dosage condition over the VN1203 wild-type MDS Ref Map. (C) MDS Projection of the transcriptomic profiles of the VN1203-PB1F2del dosage conditions over the VN1203 wild-type MDS Ref Map. (D) MDS Projection of the transcriptomic profiles of the VN1203-NS1trunc dosage conditions over the VN1203 wild-type MDS Ref Map. Each dot is the transcriptomic profile of a biological sample plotted in the intensity space of gene expression. Pairwise distances between the dots are proportional to the transcriptomic distances between the samples. MDS Projections allow to project additional ‘omics profiles over a predefined MDS representation (MDS Ref Map). Transcriptomic distances have been calculated based on the signature of 5,660 transcripts that significantly correlate with one eigentranscript. Dots are colored in order to indicate the dosage conditions, and biological conditions are indicated by the convex hull (i.e. the smallest convex set containing the points [30]) of the set of biological replicates and labeled to indicate the time point post-infection. Samples and biological conditions of the H5N1 VN1203 wild-type 104 PFU infection dosage are indicated by gray dots and gray convex hulls. Hence the grey spots that are connected represent the -omics profiles of mice lung infected by the VN1203 wild-type virus at 104 PFU, while the ones not connected represent the -omics profiles for the other infection concentrations. The Kruskal Stress shown in each representation quantifies the quality of the geometrical representation as a fraction of the information lost during the dimensionality reduction procedure.

Mentions: Having characterized VN1203-WT dynamics, we were now able to determine how each specific VN1203 mutant altered the kinetics of the host responses. In particular, our aim was to better quantify the magnitude differences between WT and mutants that were introduced with Figure 2. We next developed a new geometrical representation method in order to compare the kinetics of the host response to the various VN1203 mutants relative to the host response to VN1203-WT at the transcriptomic level. Using the MDS representation presented in Figure 3C as a reference, we projected the transcriptomic profiles of samples infected by the four VN1203 mutant viruses individually at 104 PFU (Figure 5A-D) and, in the case of VN1203-NS1trunc and VN1203-PB1F2del, at 103 and 104 PFU dosages (Figure 5C and D). While traditional MDS methods project a set of high dimensional objects into a lower dimensional space for visualization purposes, the MDS method that we developed allows for projection of additional objects over a predefined MDS representation (see Methods section). Thus, the resulting representation allows us to visualize the similarities and differences between the WT and mutant samples, and MC and VC allow us to quantify the kinetic changes in the host response related to magnitude and velocity, as previously described for VN1203-WT. The reference representation is named a MDS Reference Map and the resulting projections are named MDS Projections. Quantification of magnitude and velocity revealed different information about each mutant.


Specific mutations in H5N1 mainly impact the magnitude and velocity of the host response in mice.

Tchitchek N, Eisfeld AJ, Tisoncik-Go J, Josset L, Gralinski LE, Bécavin C, Tilton SC, Webb-Robertson BJ, Ferris MT, Totura AL, Li C, Neumann G, Metz TO, Smith RD, Waters KM, Baric R, Kawaoka Y, Katze MG - BMC Syst Biol (2013)

MDS Projections of the VN1203 mutants infected transcriptomic profiles over the VN1203-WT Reference Map. (A) Multidimensional Scaling Projection (MDS Projection) of the transcriptomic profiles of the VN1203-PB2627E dosage condition over the VN1203 wild-type Multidimensional Scaling Reference Map (MDS Ref Map). (B) MDS Projection of the transcriptomic profiles of the VN1203-HAavir dosage condition over the VN1203 wild-type MDS Ref Map. (C) MDS Projection of the transcriptomic profiles of the VN1203-PB1F2del dosage conditions over the VN1203 wild-type MDS Ref Map. (D) MDS Projection of the transcriptomic profiles of the VN1203-NS1trunc dosage conditions over the VN1203 wild-type MDS Ref Map. Each dot is the transcriptomic profile of a biological sample plotted in the intensity space of gene expression. Pairwise distances between the dots are proportional to the transcriptomic distances between the samples. MDS Projections allow to project additional ‘omics profiles over a predefined MDS representation (MDS Ref Map). Transcriptomic distances have been calculated based on the signature of 5,660 transcripts that significantly correlate with one eigentranscript. Dots are colored in order to indicate the dosage conditions, and biological conditions are indicated by the convex hull (i.e. the smallest convex set containing the points [30]) of the set of biological replicates and labeled to indicate the time point post-infection. Samples and biological conditions of the H5N1 VN1203 wild-type 104 PFU infection dosage are indicated by gray dots and gray convex hulls. Hence the grey spots that are connected represent the -omics profiles of mice lung infected by the VN1203 wild-type virus at 104 PFU, while the ones not connected represent the -omics profiles for the other infection concentrations. The Kruskal Stress shown in each representation quantifies the quality of the geometrical representation as a fraction of the information lost during the dimensionality reduction procedure.
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Figure 5: MDS Projections of the VN1203 mutants infected transcriptomic profiles over the VN1203-WT Reference Map. (A) Multidimensional Scaling Projection (MDS Projection) of the transcriptomic profiles of the VN1203-PB2627E dosage condition over the VN1203 wild-type Multidimensional Scaling Reference Map (MDS Ref Map). (B) MDS Projection of the transcriptomic profiles of the VN1203-HAavir dosage condition over the VN1203 wild-type MDS Ref Map. (C) MDS Projection of the transcriptomic profiles of the VN1203-PB1F2del dosage conditions over the VN1203 wild-type MDS Ref Map. (D) MDS Projection of the transcriptomic profiles of the VN1203-NS1trunc dosage conditions over the VN1203 wild-type MDS Ref Map. Each dot is the transcriptomic profile of a biological sample plotted in the intensity space of gene expression. Pairwise distances between the dots are proportional to the transcriptomic distances between the samples. MDS Projections allow to project additional ‘omics profiles over a predefined MDS representation (MDS Ref Map). Transcriptomic distances have been calculated based on the signature of 5,660 transcripts that significantly correlate with one eigentranscript. Dots are colored in order to indicate the dosage conditions, and biological conditions are indicated by the convex hull (i.e. the smallest convex set containing the points [30]) of the set of biological replicates and labeled to indicate the time point post-infection. Samples and biological conditions of the H5N1 VN1203 wild-type 104 PFU infection dosage are indicated by gray dots and gray convex hulls. Hence the grey spots that are connected represent the -omics profiles of mice lung infected by the VN1203 wild-type virus at 104 PFU, while the ones not connected represent the -omics profiles for the other infection concentrations. The Kruskal Stress shown in each representation quantifies the quality of the geometrical representation as a fraction of the information lost during the dimensionality reduction procedure.
Mentions: Having characterized VN1203-WT dynamics, we were now able to determine how each specific VN1203 mutant altered the kinetics of the host responses. In particular, our aim was to better quantify the magnitude differences between WT and mutants that were introduced with Figure 2. We next developed a new geometrical representation method in order to compare the kinetics of the host response to the various VN1203 mutants relative to the host response to VN1203-WT at the transcriptomic level. Using the MDS representation presented in Figure 3C as a reference, we projected the transcriptomic profiles of samples infected by the four VN1203 mutant viruses individually at 104 PFU (Figure 5A-D) and, in the case of VN1203-NS1trunc and VN1203-PB1F2del, at 103 and 104 PFU dosages (Figure 5C and D). While traditional MDS methods project a set of high dimensional objects into a lower dimensional space for visualization purposes, the MDS method that we developed allows for projection of additional objects over a predefined MDS representation (see Methods section). Thus, the resulting representation allows us to visualize the similarities and differences between the WT and mutant samples, and MC and VC allow us to quantify the kinetic changes in the host response related to magnitude and velocity, as previously described for VN1203-WT. The reference representation is named a MDS Reference Map and the resulting projections are named MDS Projections. Quantification of magnitude and velocity revealed different information about each mutant.

Bottom Line: Using a new geometrical representation method and two criteria, we show that inoculation concentrations and four specific mutations in VN1203 mainly impact the magnitude and velocity of the host response kinetics, rather than specific sets of up- and down- regulated genes.These kinetic properties imply that time-matched comparisons of 'omics profiles to viral infections give limited views to differentiate host-responses.Moreover, these results demonstrate that a fast activation of the host-response at the earliest time points post-infection is critical for protective mechanisms against fast replicating viruses.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Microbiology, University of Washington, Seattle, WA 98195 USA.

ABSTRACT

Background: Influenza infection causes respiratory disease that can lead to death. The complex interplay between virus-encoded and host-specific pathogenicity regulators - and the relative contributions of each toward viral pathogenicity - is not well-understood.

Results: By analyzing a collection of lung samples from mice infected by A/Vietnam/1203/2004 (H5N1; VN1203), we characterized a signature of transcripts and proteins associated with the kinetics of the host response. Using a new geometrical representation method and two criteria, we show that inoculation concentrations and four specific mutations in VN1203 mainly impact the magnitude and velocity of the host response kinetics, rather than specific sets of up- and down- regulated genes. We observed analogous kinetic effects using lung samples from mice infected with A/California/04/2009 (H1N1), and we show that these effects correlate with morbidity and viral titer.

Conclusions: We have demonstrated the importance of the kinetics of the host response to H5N1 pathogenesis and its relationship with clinical disease severity and virus replication. These kinetic properties imply that time-matched comparisons of 'omics profiles to viral infections give limited views to differentiate host-responses. Moreover, these results demonstrate that a fast activation of the host-response at the earliest time points post-infection is critical for protective mechanisms against fast replicating viruses.

Show MeSH
Related in: MedlinePlus