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Cytokine systems approach demonstrates differences in innate and pro-inflammatory host responses between genetically distinct MERS-CoV isolates.

Selinger C, Tisoncik-Go J, Menachery VD, Agnihothram S, Law GL, Chang J, Kelly SM, Sova P, Baric RS, Katze MG - BMC Genomics (2014)

Bottom Line: Using topological techniques, including persistence homology and filtered clustering, we performed a comparative transcriptional analysis of human Calu-3 cell host responses to the different MERS-CoV strains, with MERS-CoV Eng 1 inducing early kinetic changes, between 3 and 12 hours post infection, compared to MERS-CoV SA 1.Through our genomics-based approach, we found topological differences in the kinetics and magnitude of the host response to MERS-CoV SA 1 and MERS-CoV Eng 1, with differential expression of innate immune and pro-inflammatory responsive genes as a result of IFN, TNF and IL-1α signaling.Predicted activation for STAT3 mediating gene expression relevant for epithelial cell-to-cell adherens and junction signaling in MERS-CoV Eng 1 infection suggest that these transcriptional differences may be the result of amino acid differences in viral proteins known to modulate innate immunity during MERS-CoV infection.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, School of Medicine, University of Washington, Seattle, Washington, USA. csel@uw.edu.

ABSTRACT

Background: The recent emergence of a novel coronavirus in the Middle East (designated MERS-CoV) is a reminder of the zoonotic and pathogenic potential of emerging coronaviruses in humans. Clinical features of Middle East respiratory syndrome (MERS) include atypical pneumonia and progressive respiratory failure that is highly reminiscent of severe acute respiratory syndrome (SARS) caused by SARS-CoV. The host response is a key component of highly pathogenic respiratory virus infection. Here, we computationally analyzed gene expression changes in a human airway epithelial cell line infected with two genetically distinct MERS-CoV strains obtained from human patients, MERS-CoV SA 1 and MERS-CoV Eng 1.

Results: Using topological techniques, including persistence homology and filtered clustering, we performed a comparative transcriptional analysis of human Calu-3 cell host responses to the different MERS-CoV strains, with MERS-CoV Eng 1 inducing early kinetic changes, between 3 and 12 hours post infection, compared to MERS-CoV SA 1. Robust transcriptional changes distinguished the two MERS-CoV strains predominantly at the late time points. Combining statistical analysis of infection and cytokine-stimulated Calu-3 transcriptomics, we identified differential innate responses, including up-regulation of extracellular remodeling genes following MERS-CoV Eng 1 infection and differential pro-inflammatory responses.

Conclusions: Through our genomics-based approach, we found topological differences in the kinetics and magnitude of the host response to MERS-CoV SA 1 and MERS-CoV Eng 1, with differential expression of innate immune and pro-inflammatory responsive genes as a result of IFN, TNF and IL-1α signaling. Predicted activation for STAT3 mediating gene expression relevant for epithelial cell-to-cell adherens and junction signaling in MERS-CoV Eng 1 infection suggest that these transcriptional differences may be the result of amino acid differences in viral proteins known to modulate innate immunity during MERS-CoV infection.

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Differential cytokine stimulated gene expression in human airway epithelial cells infected with distinct MERS-CoVs. A. Venn diagram shows the number of genes which were DE after infection in any one virus or time point and their overlap within four sets of different cytokine stimulation. Whereas IFN-α, IFN-γ and IL-1α show a large number of specific genes, TNF stimulated DE genes share many genes with other cytokines B. Heatmap of 149 DE genes following either MERS-CoV SA 1 or MERS-CoV Eng 1 infection (MOI 5) that show strong contrasts at 18 and 24 hpi. The black bars on the left of the heatmap indicate whether genes were also DE after cytokine treatments (IFN-α, IFN-γ, IL-1α, TNF-α) in the same cell line system as the infection.
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Fig4: Differential cytokine stimulated gene expression in human airway epithelial cells infected with distinct MERS-CoVs. A. Venn diagram shows the number of genes which were DE after infection in any one virus or time point and their overlap within four sets of different cytokine stimulation. Whereas IFN-α, IFN-γ and IL-1α show a large number of specific genes, TNF stimulated DE genes share many genes with other cytokines B. Heatmap of 149 DE genes following either MERS-CoV SA 1 or MERS-CoV Eng 1 infection (MOI 5) that show strong contrasts at 18 and 24 hpi. The black bars on the left of the heatmap indicate whether genes were also DE after cytokine treatments (IFN-α, IFN-γ, IL-1α, TNF-α) in the same cell line system as the infection.

Mentions: There were no virus-specific differences in expression of pro-inflammatory cytokines, IL-1α or TNFα-IP3, which were highly up-regulated in response to both MERS-CoV Eng 1 and MERS-CoV SA 1. The cell migration-promoting factor, TNFα-IP2 [21], was highly up-regulated for MERS-CoV Eng 1 alone (Additional file 4: Figure S2). Cytokines appear to be important for MERS infection. To explore potential mechanisms regulating cytokine activity in response to MERS-CoV, we designed a microarray experiment to analyze Calu-3 responses to various cytokine treatments and develop signatures that were then examined in the context of MERS-CoV-infected Calu-3 cells. Calu-3 cells were treated with either human recombinant interferon IFN-α, IFN-γ, TNF or IL-1α, and cell lysates collected at different time points post-treatment for microarray. We found 399 DE genes responsive to recombinant IFN-α and 261 DE genes responsive to recombinant IFN-γ, and as expected, the majority of these genes were up-regulated following stimulation [22]. In response to pro-inflammatory cytokine treatment, we found 76 DE genes responsive to recombinant TNF and 383 DE genes responsive to recombinant IL-1α, which were also differentially expressed in response to MERS-CoV SA 1 or MERS-CoV Eng 1. Many of these genes showed cytokine-specific expression for IFN-α (260 DE genes), IFN-γ (107 DE genes), and IL-1α (209 DE genes (Figure 4A). TNF induced the least number of DE genes compared to the other cytokines (8 DE genes). Within the cytokine-stimulated genes we identified a set of 149 genes showing strong contrasts at late time points (18 and 24 hpi) between MERS-CoV SA 1 and MERS-CoV Eng 1 (Figure 4B).Figure 4


Cytokine systems approach demonstrates differences in innate and pro-inflammatory host responses between genetically distinct MERS-CoV isolates.

Selinger C, Tisoncik-Go J, Menachery VD, Agnihothram S, Law GL, Chang J, Kelly SM, Sova P, Baric RS, Katze MG - BMC Genomics (2014)

Differential cytokine stimulated gene expression in human airway epithelial cells infected with distinct MERS-CoVs. A. Venn diagram shows the number of genes which were DE after infection in any one virus or time point and their overlap within four sets of different cytokine stimulation. Whereas IFN-α, IFN-γ and IL-1α show a large number of specific genes, TNF stimulated DE genes share many genes with other cytokines B. Heatmap of 149 DE genes following either MERS-CoV SA 1 or MERS-CoV Eng 1 infection (MOI 5) that show strong contrasts at 18 and 24 hpi. The black bars on the left of the heatmap indicate whether genes were also DE after cytokine treatments (IFN-α, IFN-γ, IL-1α, TNF-α) in the same cell line system as the infection.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4522970&req=5

Fig4: Differential cytokine stimulated gene expression in human airway epithelial cells infected with distinct MERS-CoVs. A. Venn diagram shows the number of genes which were DE after infection in any one virus or time point and their overlap within four sets of different cytokine stimulation. Whereas IFN-α, IFN-γ and IL-1α show a large number of specific genes, TNF stimulated DE genes share many genes with other cytokines B. Heatmap of 149 DE genes following either MERS-CoV SA 1 or MERS-CoV Eng 1 infection (MOI 5) that show strong contrasts at 18 and 24 hpi. The black bars on the left of the heatmap indicate whether genes were also DE after cytokine treatments (IFN-α, IFN-γ, IL-1α, TNF-α) in the same cell line system as the infection.
Mentions: There were no virus-specific differences in expression of pro-inflammatory cytokines, IL-1α or TNFα-IP3, which were highly up-regulated in response to both MERS-CoV Eng 1 and MERS-CoV SA 1. The cell migration-promoting factor, TNFα-IP2 [21], was highly up-regulated for MERS-CoV Eng 1 alone (Additional file 4: Figure S2). Cytokines appear to be important for MERS infection. To explore potential mechanisms regulating cytokine activity in response to MERS-CoV, we designed a microarray experiment to analyze Calu-3 responses to various cytokine treatments and develop signatures that were then examined in the context of MERS-CoV-infected Calu-3 cells. Calu-3 cells were treated with either human recombinant interferon IFN-α, IFN-γ, TNF or IL-1α, and cell lysates collected at different time points post-treatment for microarray. We found 399 DE genes responsive to recombinant IFN-α and 261 DE genes responsive to recombinant IFN-γ, and as expected, the majority of these genes were up-regulated following stimulation [22]. In response to pro-inflammatory cytokine treatment, we found 76 DE genes responsive to recombinant TNF and 383 DE genes responsive to recombinant IL-1α, which were also differentially expressed in response to MERS-CoV SA 1 or MERS-CoV Eng 1. Many of these genes showed cytokine-specific expression for IFN-α (260 DE genes), IFN-γ (107 DE genes), and IL-1α (209 DE genes (Figure 4A). TNF induced the least number of DE genes compared to the other cytokines (8 DE genes). Within the cytokine-stimulated genes we identified a set of 149 genes showing strong contrasts at late time points (18 and 24 hpi) between MERS-CoV SA 1 and MERS-CoV Eng 1 (Figure 4B).Figure 4

Bottom Line: Using topological techniques, including persistence homology and filtered clustering, we performed a comparative transcriptional analysis of human Calu-3 cell host responses to the different MERS-CoV strains, with MERS-CoV Eng 1 inducing early kinetic changes, between 3 and 12 hours post infection, compared to MERS-CoV SA 1.Through our genomics-based approach, we found topological differences in the kinetics and magnitude of the host response to MERS-CoV SA 1 and MERS-CoV Eng 1, with differential expression of innate immune and pro-inflammatory responsive genes as a result of IFN, TNF and IL-1α signaling.Predicted activation for STAT3 mediating gene expression relevant for epithelial cell-to-cell adherens and junction signaling in MERS-CoV Eng 1 infection suggest that these transcriptional differences may be the result of amino acid differences in viral proteins known to modulate innate immunity during MERS-CoV infection.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, School of Medicine, University of Washington, Seattle, Washington, USA. csel@uw.edu.

ABSTRACT

Background: The recent emergence of a novel coronavirus in the Middle East (designated MERS-CoV) is a reminder of the zoonotic and pathogenic potential of emerging coronaviruses in humans. Clinical features of Middle East respiratory syndrome (MERS) include atypical pneumonia and progressive respiratory failure that is highly reminiscent of severe acute respiratory syndrome (SARS) caused by SARS-CoV. The host response is a key component of highly pathogenic respiratory virus infection. Here, we computationally analyzed gene expression changes in a human airway epithelial cell line infected with two genetically distinct MERS-CoV strains obtained from human patients, MERS-CoV SA 1 and MERS-CoV Eng 1.

Results: Using topological techniques, including persistence homology and filtered clustering, we performed a comparative transcriptional analysis of human Calu-3 cell host responses to the different MERS-CoV strains, with MERS-CoV Eng 1 inducing early kinetic changes, between 3 and 12 hours post infection, compared to MERS-CoV SA 1. Robust transcriptional changes distinguished the two MERS-CoV strains predominantly at the late time points. Combining statistical analysis of infection and cytokine-stimulated Calu-3 transcriptomics, we identified differential innate responses, including up-regulation of extracellular remodeling genes following MERS-CoV Eng 1 infection and differential pro-inflammatory responses.

Conclusions: Through our genomics-based approach, we found topological differences in the kinetics and magnitude of the host response to MERS-CoV SA 1 and MERS-CoV Eng 1, with differential expression of innate immune and pro-inflammatory responsive genes as a result of IFN, TNF and IL-1α signaling. Predicted activation for STAT3 mediating gene expression relevant for epithelial cell-to-cell adherens and junction signaling in MERS-CoV Eng 1 infection suggest that these transcriptional differences may be the result of amino acid differences in viral proteins known to modulate innate immunity during MERS-CoV infection.

Show MeSH
Related in: MedlinePlus