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Functional genomics highlights differential induction of antiviral pathways in the lungs of SARS-CoV-infected macaques.

de Lang A, Baas T, Teal T, Leijten LM, Rain B, Osterhaus AD, Haagmans BL, Katze MG - PLoS Pathog. (2007)

Bottom Line: The pathogenesis of severe acute respiratory syndrome coronavirus (SARS-CoV) is likely mediated by disproportional immune responses and the ability of the virus to circumvent innate immunity.As opposed to many in vitro experiments, SARS-CoV induced a wide range of type I interferons (IFNs) and nuclear translocation of phosphorylated signal transducer and activator of transcription 1 in the lungs of macaques.Using immunohistochemistry, we revealed that these antiviral signaling pathways were differentially regulated in distinctive subsets of cells.

View Article: PubMed Central - PubMed

Affiliation: Department of Virology, Erasmus Medical Center, Rotterdam, The Netherlands.

ABSTRACT
The pathogenesis of severe acute respiratory syndrome coronavirus (SARS-CoV) is likely mediated by disproportional immune responses and the ability of the virus to circumvent innate immunity. Using functional genomics, we analyzed early host responses to SARS-CoV infection in the lungs of adolescent cynomolgus macaques (Macaca fascicularis) that show lung pathology similar to that observed in human adults with SARS. Analysis of gene signatures revealed induction of a strong innate immune response characterized by the stimulation of various cytokine and chemokine genes, including interleukin (IL)-6, IL-8, and IP-10, which corresponds to the host response seen in acute respiratory distress syndrome. As opposed to many in vitro experiments, SARS-CoV induced a wide range of type I interferons (IFNs) and nuclear translocation of phosphorylated signal transducer and activator of transcription 1 in the lungs of macaques. Using immunohistochemistry, we revealed that these antiviral signaling pathways were differentially regulated in distinctive subsets of cells. Our studies emphasize that the induction of early IFN signaling may be critical to confer protection against SARS-CoV infection and highlight the strength of combining functional genomics with immunohistochemistry to further unravel the pathogenesis of SARS.

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Related in: MedlinePlus

Common and Unique Temporal Gene Responses to SARS-CoV Infection(A) The Venn diagram shows genes with an absolute fold change > 2 and p < 0.0001 in two out of the two day 1 samples (left circle) or two out of the four day 4 samples (right circle).(B) The heat map includes the 597 genes from the grey Venn diagram intersections. The right column highlights the 97 genes that are commonly regulated in all six samples with blue. All 97 genes are listed in Figure S1. All gene expression profiles are the results of comparing gene expression in lungs of experimental animals versus gene expression in lungs of mock-infected animals (pooled).(C) Functional annotation was used to categorize the 681 unique genes at day 1, and the 353 unique genes at day 4. The percentage of genes within the top functional categories is indicated in the day 1 and the day 4 bar graph, with a white line indicating the percentage of genes found at the alternative day. Cell-to-cell signaling and cell death, other top categories on day 1, and cell death, cellular growth, and proliferation, additional top categories on day 4, are not included in the bar graph, as these categories were observed to have more genes differentially expressed in the common signature.
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ppat-0030112-g003: Common and Unique Temporal Gene Responses to SARS-CoV Infection(A) The Venn diagram shows genes with an absolute fold change > 2 and p < 0.0001 in two out of the two day 1 samples (left circle) or two out of the four day 4 samples (right circle).(B) The heat map includes the 597 genes from the grey Venn diagram intersections. The right column highlights the 97 genes that are commonly regulated in all six samples with blue. All 97 genes are listed in Figure S1. All gene expression profiles are the results of comparing gene expression in lungs of experimental animals versus gene expression in lungs of mock-infected animals (pooled).(C) Functional annotation was used to categorize the 681 unique genes at day 1, and the 353 unique genes at day 4. The percentage of genes within the top functional categories is indicated in the day 1 and the day 4 bar graph, with a white line indicating the percentage of genes found at the alternative day. Cell-to-cell signaling and cell death, other top categories on day 1, and cell death, cellular growth, and proliferation, additional top categories on day 4, are not included in the bar graph, as these categories were observed to have more genes differentially expressed in the common signature.

Mentions: In order to elucidate common responses to SARS-CoV throughout the infection as well as unique responses at different time points after inoculation, a Venn diagram was generated with each set (circle) holding to the parameters of an absolute fold change > 2 and p < 0.0001 in at least two animals (Figure 3A). The day 1 set contained 1,278 genes and the day 4 set contained 950 genes. When examining host responses that were similar throughout the course of the infection, the intersection of the day 1 and day 4 sets indicates that 597 genes show shared responses. The heat map of these 597 genes is shown in Figure 3B. If more stringent criteria were used to find common responses in all six animals, using the 1,278 genes from the day 1 set and the 129 genes that are differentially expressed in all day 4 animals, a subset of 97 genes was identified. This subset included IFN-stimulated genes (ISGs), like IFITs, MX1, GBP1, and G1P2, and also various chemokines and cytokines, such as CXCL10 (IP-10), CCL2 (MCP-1), IL-6, and IL-8 (Figure S1). These same cytokines and chemokines have been reported to be up-regulated in human SARS cases [9–12]. This set also included cathepsin L (CTSL), which has been shown to be required for SARS-CoV entry into a cell [35]. Even though only 97 genes were commonly regulated in all animals, indicated with blue bars in Figure 3B, the heat map highlights that the other 500 genes show similar expression trends. Both sets of common-response genes showed similar functionality: cellular growth and proliferation, cell death, cellular movement, immune response, and cell-to-cell signaling.


Functional genomics highlights differential induction of antiviral pathways in the lungs of SARS-CoV-infected macaques.

de Lang A, Baas T, Teal T, Leijten LM, Rain B, Osterhaus AD, Haagmans BL, Katze MG - PLoS Pathog. (2007)

Common and Unique Temporal Gene Responses to SARS-CoV Infection(A) The Venn diagram shows genes with an absolute fold change > 2 and p < 0.0001 in two out of the two day 1 samples (left circle) or two out of the four day 4 samples (right circle).(B) The heat map includes the 597 genes from the grey Venn diagram intersections. The right column highlights the 97 genes that are commonly regulated in all six samples with blue. All 97 genes are listed in Figure S1. All gene expression profiles are the results of comparing gene expression in lungs of experimental animals versus gene expression in lungs of mock-infected animals (pooled).(C) Functional annotation was used to categorize the 681 unique genes at day 1, and the 353 unique genes at day 4. The percentage of genes within the top functional categories is indicated in the day 1 and the day 4 bar graph, with a white line indicating the percentage of genes found at the alternative day. Cell-to-cell signaling and cell death, other top categories on day 1, and cell death, cellular growth, and proliferation, additional top categories on day 4, are not included in the bar graph, as these categories were observed to have more genes differentially expressed in the common signature.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC1941749&req=5

ppat-0030112-g003: Common and Unique Temporal Gene Responses to SARS-CoV Infection(A) The Venn diagram shows genes with an absolute fold change > 2 and p < 0.0001 in two out of the two day 1 samples (left circle) or two out of the four day 4 samples (right circle).(B) The heat map includes the 597 genes from the grey Venn diagram intersections. The right column highlights the 97 genes that are commonly regulated in all six samples with blue. All 97 genes are listed in Figure S1. All gene expression profiles are the results of comparing gene expression in lungs of experimental animals versus gene expression in lungs of mock-infected animals (pooled).(C) Functional annotation was used to categorize the 681 unique genes at day 1, and the 353 unique genes at day 4. The percentage of genes within the top functional categories is indicated in the day 1 and the day 4 bar graph, with a white line indicating the percentage of genes found at the alternative day. Cell-to-cell signaling and cell death, other top categories on day 1, and cell death, cellular growth, and proliferation, additional top categories on day 4, are not included in the bar graph, as these categories were observed to have more genes differentially expressed in the common signature.
Mentions: In order to elucidate common responses to SARS-CoV throughout the infection as well as unique responses at different time points after inoculation, a Venn diagram was generated with each set (circle) holding to the parameters of an absolute fold change > 2 and p < 0.0001 in at least two animals (Figure 3A). The day 1 set contained 1,278 genes and the day 4 set contained 950 genes. When examining host responses that were similar throughout the course of the infection, the intersection of the day 1 and day 4 sets indicates that 597 genes show shared responses. The heat map of these 597 genes is shown in Figure 3B. If more stringent criteria were used to find common responses in all six animals, using the 1,278 genes from the day 1 set and the 129 genes that are differentially expressed in all day 4 animals, a subset of 97 genes was identified. This subset included IFN-stimulated genes (ISGs), like IFITs, MX1, GBP1, and G1P2, and also various chemokines and cytokines, such as CXCL10 (IP-10), CCL2 (MCP-1), IL-6, and IL-8 (Figure S1). These same cytokines and chemokines have been reported to be up-regulated in human SARS cases [9–12]. This set also included cathepsin L (CTSL), which has been shown to be required for SARS-CoV entry into a cell [35]. Even though only 97 genes were commonly regulated in all animals, indicated with blue bars in Figure 3B, the heat map highlights that the other 500 genes show similar expression trends. Both sets of common-response genes showed similar functionality: cellular growth and proliferation, cell death, cellular movement, immune response, and cell-to-cell signaling.

Bottom Line: The pathogenesis of severe acute respiratory syndrome coronavirus (SARS-CoV) is likely mediated by disproportional immune responses and the ability of the virus to circumvent innate immunity.As opposed to many in vitro experiments, SARS-CoV induced a wide range of type I interferons (IFNs) and nuclear translocation of phosphorylated signal transducer and activator of transcription 1 in the lungs of macaques.Using immunohistochemistry, we revealed that these antiviral signaling pathways were differentially regulated in distinctive subsets of cells.

View Article: PubMed Central - PubMed

Affiliation: Department of Virology, Erasmus Medical Center, Rotterdam, The Netherlands.

ABSTRACT
The pathogenesis of severe acute respiratory syndrome coronavirus (SARS-CoV) is likely mediated by disproportional immune responses and the ability of the virus to circumvent innate immunity. Using functional genomics, we analyzed early host responses to SARS-CoV infection in the lungs of adolescent cynomolgus macaques (Macaca fascicularis) that show lung pathology similar to that observed in human adults with SARS. Analysis of gene signatures revealed induction of a strong innate immune response characterized by the stimulation of various cytokine and chemokine genes, including interleukin (IL)-6, IL-8, and IP-10, which corresponds to the host response seen in acute respiratory distress syndrome. As opposed to many in vitro experiments, SARS-CoV induced a wide range of type I interferons (IFNs) and nuclear translocation of phosphorylated signal transducer and activator of transcription 1 in the lungs of macaques. Using immunohistochemistry, we revealed that these antiviral signaling pathways were differentially regulated in distinctive subsets of cells. Our studies emphasize that the induction of early IFN signaling may be critical to confer protection against SARS-CoV infection and highlight the strength of combining functional genomics with immunohistochemistry to further unravel the pathogenesis of SARS.

Show MeSH
Related in: MedlinePlus