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Streptococcus pneumoniae nasopharyngeal colonization induces type I interferons and interferon-induced gene expression.

Joyce EA, Popper SJ, Falkow S - BMC Genomics (2009)

Bottom Line: Subsequent to this initial inflammatory response, we observed increases in transcripts associated with T cell development and activation, as well as wounding, basement membrane remodeling, and cell proliferation.Examining multiple time points over six weeks of colonization demonstrated that asymptomatic carriage stimulates a dynamic host response characterized by temporal waves with distinct biological programs.Our data suggest that the usual response to the presence of the pneumocccus is an initial controlled inflammatory response followed by activation of host physiological processes such as response to wounding, basement membrane remodeling, and increasing cellular numbers that ultimately allow the host to maintain an intact epithelium and eventually mount a preventive adaptive immune response.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94131, USA. ejoyce@stanford.edu

ABSTRACT

Background: We employed DNA microarray technology to investigate the host response to Streptococcus pneumoniae in a mouse model of asymptomatic carriage. Over a period of six weeks, we profiled transcript abundance and complexity in the Nasal Associated Lymphoid Tissue (NALT) to identify genes whose expression differed between pneumococcal-colonized and uncolonized states.

Results: Colonization with S. pneumoniae altered the expression of hundreds of genes over the course of the study, demonstrating that carriage is a dynamic process characterized by increased expression of a set of early inflammatory responses, including induction of a Type I Interferon response, and the production of several antimicrobial factors. Subsequent to this initial inflammatory response, we observed increases in transcripts associated with T cell development and activation, as well as wounding, basement membrane remodeling, and cell proliferation. Our analysis suggests that microbial colonization induced expression of genes encoding components critical for controlling JAK/STAT signaling, including stat1, stat2, socs3, and mapk1, as well as induction of several Type I Interferon-inducible genes and other antimicrobial factors at the earliest stages of colonization.

Conclusion: Examining multiple time points over six weeks of colonization demonstrated that asymptomatic carriage stimulates a dynamic host response characterized by temporal waves with distinct biological programs. Our data suggest that the usual response to the presence of the pneumocccus is an initial controlled inflammatory response followed by activation of host physiological processes such as response to wounding, basement membrane remodeling, and increasing cellular numbers that ultimately allow the host to maintain an intact epithelium and eventually mount a preventive adaptive immune response.

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NALT transcript analysis identifying genes that differentiate between mock-infected and pneumococcal-infected mice. Comparisons were made between infected samples and mock-infected controls using Statistical Analysis for Microarrays (SAM) and the Fligner-Killeen Test for equality of variance. These analyses identified 112 transcripts that consistently differed during infection [SAM (FDR = 5%)] and the 358 transcripts (top 5%) that varied more during carriage as compared to control mice. (A) A union of the gene sets was clustered using a self-organizing map algorithm; each row represents a single gene, and each column a single animal. Black indicates the median level of expression, red indicates greater expression than the median, green less expression, and gray missing data. Numerically labeled horizontal gray bars above the samples indicate day post-colonization. (B) Expression profiles for the five functional categories identified. Heat maps illustrating the individual genes comprising each category are shown. An average expression profile for each category was calculated and plotted to illustrate the temporal characteristics of each category. Purple: Early Immune Response; Green: Immune System Process; Orange: Response to Wounding; Blue: Basement Membrane; Yellow: Cell Cycle/DNA Replication.
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Figure 2: NALT transcript analysis identifying genes that differentiate between mock-infected and pneumococcal-infected mice. Comparisons were made between infected samples and mock-infected controls using Statistical Analysis for Microarrays (SAM) and the Fligner-Killeen Test for equality of variance. These analyses identified 112 transcripts that consistently differed during infection [SAM (FDR = 5%)] and the 358 transcripts (top 5%) that varied more during carriage as compared to control mice. (A) A union of the gene sets was clustered using a self-organizing map algorithm; each row represents a single gene, and each column a single animal. Black indicates the median level of expression, red indicates greater expression than the median, green less expression, and gray missing data. Numerically labeled horizontal gray bars above the samples indicate day post-colonization. (B) Expression profiles for the five functional categories identified. Heat maps illustrating the individual genes comprising each category are shown. An average expression profile for each category was calculated and plotted to illustrate the temporal characteristics of each category. Purple: Early Immune Response; Green: Immune System Process; Orange: Response to Wounding; Blue: Basement Membrane; Yellow: Cell Cycle/DNA Replication.

Mentions: Complementing these ontological analyses, we visualized a union of both data sets, which is illustrated in Figure 2A. Samples were arranged by time post-infection and genes clustered using a Self Organizing Map (SOM) algorithm [23]. Visualizing the data in this way graphically illustrates the dynamic changes in gene expression during colonization as compared with mock-infection. These patterns roughly corresponded to gene subsets whose expression was induced early in the time course (1–13 days), during carriage (13–21 days), and at later stages when the organisms were disappearing from the nasal cavity (21–42 days). We examined the genes associated with these temporal categories to identify additional biological functions potentially associated with colonization that weren't revealed in the GeneTrail analyses. A set of 16 genes with a marked increase in expression on Day 1 was characteristic of early immune responses. 13 of the 16 genes are known to be stimulated by a Type I Interferon Response. A few of these genes were identified by both the SAM and variance analyses (irg1, ifit3, and socs3). These 16 Early Immune Response genes are listed in Table 3. We extracted the data for these 16 genes, as well as all of the genes in each of the GO or KEGG categories identified by the GeneTrail analyses, and calculated an average expression value at each time point. These data were plotted to give an average expression profile for each functional category over the course of infection. Several of the categories, like Mitosis, Cell Division, Cell Cycle, Microtubule-based Processes, and DNA Replication had similar expression profiles. Since these categories correspond to related processes, they were combined into a single group. Figure 2B illustrates both the average gene expression profiles for the major functional categories associated with carriage and the heat maps of the individual members of these categories. We were thus able to map the temporal expression pattern of the biological themes associated with asymptomatic colonization. Transcripts associated with the Early Immune Response cluster were most abundant between Days 1 and 6-post infection, after which their abundance declined, whereas transcript abundance for most of the genes involved in Cell Cycle and DNA Replication did not increase until Day 6 and continued throughout the time course, with maximal differences seen at Day 42. The genes comprising the Immune System Process category showed more variability in the timing of their induction but were, on average, most highly induced midway through the time course. Alterations in the expression profiles for the Basement Membrane and Response to Wound Healing categories were more modest, with initial changes seen during the first two weeks followed by a return to baseline expression levels.


Streptococcus pneumoniae nasopharyngeal colonization induces type I interferons and interferon-induced gene expression.

Joyce EA, Popper SJ, Falkow S - BMC Genomics (2009)

NALT transcript analysis identifying genes that differentiate between mock-infected and pneumococcal-infected mice. Comparisons were made between infected samples and mock-infected controls using Statistical Analysis for Microarrays (SAM) and the Fligner-Killeen Test for equality of variance. These analyses identified 112 transcripts that consistently differed during infection [SAM (FDR = 5%)] and the 358 transcripts (top 5%) that varied more during carriage as compared to control mice. (A) A union of the gene sets was clustered using a self-organizing map algorithm; each row represents a single gene, and each column a single animal. Black indicates the median level of expression, red indicates greater expression than the median, green less expression, and gray missing data. Numerically labeled horizontal gray bars above the samples indicate day post-colonization. (B) Expression profiles for the five functional categories identified. Heat maps illustrating the individual genes comprising each category are shown. An average expression profile for each category was calculated and plotted to illustrate the temporal characteristics of each category. Purple: Early Immune Response; Green: Immune System Process; Orange: Response to Wounding; Blue: Basement Membrane; Yellow: Cell Cycle/DNA Replication.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2743716&req=5

Figure 2: NALT transcript analysis identifying genes that differentiate between mock-infected and pneumococcal-infected mice. Comparisons were made between infected samples and mock-infected controls using Statistical Analysis for Microarrays (SAM) and the Fligner-Killeen Test for equality of variance. These analyses identified 112 transcripts that consistently differed during infection [SAM (FDR = 5%)] and the 358 transcripts (top 5%) that varied more during carriage as compared to control mice. (A) A union of the gene sets was clustered using a self-organizing map algorithm; each row represents a single gene, and each column a single animal. Black indicates the median level of expression, red indicates greater expression than the median, green less expression, and gray missing data. Numerically labeled horizontal gray bars above the samples indicate day post-colonization. (B) Expression profiles for the five functional categories identified. Heat maps illustrating the individual genes comprising each category are shown. An average expression profile for each category was calculated and plotted to illustrate the temporal characteristics of each category. Purple: Early Immune Response; Green: Immune System Process; Orange: Response to Wounding; Blue: Basement Membrane; Yellow: Cell Cycle/DNA Replication.
Mentions: Complementing these ontological analyses, we visualized a union of both data sets, which is illustrated in Figure 2A. Samples were arranged by time post-infection and genes clustered using a Self Organizing Map (SOM) algorithm [23]. Visualizing the data in this way graphically illustrates the dynamic changes in gene expression during colonization as compared with mock-infection. These patterns roughly corresponded to gene subsets whose expression was induced early in the time course (1–13 days), during carriage (13–21 days), and at later stages when the organisms were disappearing from the nasal cavity (21–42 days). We examined the genes associated with these temporal categories to identify additional biological functions potentially associated with colonization that weren't revealed in the GeneTrail analyses. A set of 16 genes with a marked increase in expression on Day 1 was characteristic of early immune responses. 13 of the 16 genes are known to be stimulated by a Type I Interferon Response. A few of these genes were identified by both the SAM and variance analyses (irg1, ifit3, and socs3). These 16 Early Immune Response genes are listed in Table 3. We extracted the data for these 16 genes, as well as all of the genes in each of the GO or KEGG categories identified by the GeneTrail analyses, and calculated an average expression value at each time point. These data were plotted to give an average expression profile for each functional category over the course of infection. Several of the categories, like Mitosis, Cell Division, Cell Cycle, Microtubule-based Processes, and DNA Replication had similar expression profiles. Since these categories correspond to related processes, they were combined into a single group. Figure 2B illustrates both the average gene expression profiles for the major functional categories associated with carriage and the heat maps of the individual members of these categories. We were thus able to map the temporal expression pattern of the biological themes associated with asymptomatic colonization. Transcripts associated with the Early Immune Response cluster were most abundant between Days 1 and 6-post infection, after which their abundance declined, whereas transcript abundance for most of the genes involved in Cell Cycle and DNA Replication did not increase until Day 6 and continued throughout the time course, with maximal differences seen at Day 42. The genes comprising the Immune System Process category showed more variability in the timing of their induction but were, on average, most highly induced midway through the time course. Alterations in the expression profiles for the Basement Membrane and Response to Wound Healing categories were more modest, with initial changes seen during the first two weeks followed by a return to baseline expression levels.

Bottom Line: Subsequent to this initial inflammatory response, we observed increases in transcripts associated with T cell development and activation, as well as wounding, basement membrane remodeling, and cell proliferation.Examining multiple time points over six weeks of colonization demonstrated that asymptomatic carriage stimulates a dynamic host response characterized by temporal waves with distinct biological programs.Our data suggest that the usual response to the presence of the pneumocccus is an initial controlled inflammatory response followed by activation of host physiological processes such as response to wounding, basement membrane remodeling, and increasing cellular numbers that ultimately allow the host to maintain an intact epithelium and eventually mount a preventive adaptive immune response.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94131, USA. ejoyce@stanford.edu

ABSTRACT

Background: We employed DNA microarray technology to investigate the host response to Streptococcus pneumoniae in a mouse model of asymptomatic carriage. Over a period of six weeks, we profiled transcript abundance and complexity in the Nasal Associated Lymphoid Tissue (NALT) to identify genes whose expression differed between pneumococcal-colonized and uncolonized states.

Results: Colonization with S. pneumoniae altered the expression of hundreds of genes over the course of the study, demonstrating that carriage is a dynamic process characterized by increased expression of a set of early inflammatory responses, including induction of a Type I Interferon response, and the production of several antimicrobial factors. Subsequent to this initial inflammatory response, we observed increases in transcripts associated with T cell development and activation, as well as wounding, basement membrane remodeling, and cell proliferation. Our analysis suggests that microbial colonization induced expression of genes encoding components critical for controlling JAK/STAT signaling, including stat1, stat2, socs3, and mapk1, as well as induction of several Type I Interferon-inducible genes and other antimicrobial factors at the earliest stages of colonization.

Conclusion: Examining multiple time points over six weeks of colonization demonstrated that asymptomatic carriage stimulates a dynamic host response characterized by temporal waves with distinct biological programs. Our data suggest that the usual response to the presence of the pneumocccus is an initial controlled inflammatory response followed by activation of host physiological processes such as response to wounding, basement membrane remodeling, and increasing cellular numbers that ultimately allow the host to maintain an intact epithelium and eventually mount a preventive adaptive immune response.

Show MeSH
Related in: MedlinePlus