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Respiratory Mucosal Proteome Quantification in Human Influenza Infections.

Marion T, Elbahesh H, Thomas PG, DeVincenzo JP, Webby R, Schughart K - PLoS ONE (2016)

Bottom Line: Our results illustrate the utility of micro-proteomic technology for analysis of proteins in small volumes of respiratory mucosal samples.Most of the identified proteins were associated with the host immune response to infection, and changes in protein levels of 151 of the DEPs were significantly correlated with viral load.It establishes a precedent for micro-proteomic quantification of proteins that reflect ongoing response to respiratory infection.

View Article: PubMed Central - PubMed

Affiliation: University of Tennessee Health Science Center, Department of Microbiology, Immunology and Biochemistry, Memphis, United States of America.

ABSTRACT
Respiratory influenza virus infections represent a serious threat to human health. Underlying medical conditions and genetic make-up predispose some influenza patients to more severe forms of disease. To date, only a few studies have been performed in patients to correlate a selected group of cytokines and chemokines with influenza infection. Therefore, we evaluated the potential of a novel multiplex micro-proteomics technology, SOMAscan, to quantify proteins in the respiratory mucosa of influenza A and B infected individuals. The analysis included but was not limited to quantification of cytokines and chemokines detected in previous studies. SOMAscan quantified more than 1,000 secreted proteins in small nasal wash volumes from infected and healthy individuals. Our results illustrate the utility of micro-proteomic technology for analysis of proteins in small volumes of respiratory mucosal samples. Furthermore, when we compared nasal wash samples from influenza-infected patients with viral load ≥ 2(8) and increased IL-6 and CXCL10 to healthy controls, we identified 162 differentially-expressed proteins between the two groups. This number greatly exceeds the number of DEPs identified in previous studies in human influenza patients. Most of the identified proteins were associated with the host immune response to infection, and changes in protein levels of 151 of the DEPs were significantly correlated with viral load. Most important, SOMAscan identified differentially expressed proteins heretofore not associated with respiratory influenza infection in humans. Our study is the first report for the use of SOMAscan to screen nasal secretions. It establishes a precedent for micro-proteomic quantification of proteins that reflect ongoing response to respiratory infection.

No MeSH data available.


Related in: MedlinePlus

Functional analysis of DEPs from subset B.Pathway enrichment analysis for normalized log2–transformed expression values of proteins that were differentially expressed in IAV-positive versus IAV-negative patients from subset B is presented. Pathway terms that were enriched for the DEPs from subset B are indicated on the y-axis, the number of DEPs in the respective pathway category is indicated on the x-axis. The p-value for the probability that the observed distribution of expression occurred by chance is represented by colors of bars. The cut-off value for the pathway p-values was chosen at 0.05.
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pone.0153674.g003: Functional analysis of DEPs from subset B.Pathway enrichment analysis for normalized log2–transformed expression values of proteins that were differentially expressed in IAV-positive versus IAV-negative patients from subset B is presented. Pathway terms that were enriched for the DEPs from subset B are indicated on the y-axis, the number of DEPs in the respective pathway category is indicated on the x-axis. The p-value for the probability that the observed distribution of expression occurred by chance is represented by colors of bars. The cut-off value for the pathway p-values was chosen at 0.05.

Mentions: In subset A, sample ID_4043 segregated separately in the PCA (Fig 2) from the other influenza virus-positive samples and had low levels of CXCL10 and IL6 (data not shown). CXCL10 and IL6 are known to be highly elevated after influenza infection [29], and the previous cytokine-chemokine analysis [28] indicated that plasma CXCL10 was correlated with viral loads. Therefore, we analyzed a second subset (subset B) which was identical to subset A except that the outlier sample ID_4043 was deleted. Thus, subset B (S2 Table) consisted of six healthy controls (same as in subset A) and 11 influenza-infected patients (12 minus 1 from subset A). The corresponding PCA showed good segregation between uninfected control and influenza virus-positive groups (S3 Fig). Accordingly, analyses of IL6 and CXCL10 expression levels showed significant differences between the two groups (Kruskal-Wallis, p < 0.01 and p < 0.05, respectively) (S4 Fig), even though samples from two healthy controls had relatively elevated CXCL10 compared to the other healthy controls. Further analysis of subset B using LIMMA revealed a total of 162 DEPs, 63 increased and 99 decreased in samples from virally infected patients compared to uninfected individuals (log2-fold change ≥ 1 and adjusted p < 0.01) (S4 Table). Functional analysis of these DEPs using the Reactome pathway database showed enrichment for pathways that are activated during the host immune response (Fig 3). Furthermore, 151 of the 162 (up- or down-regulated) DEPs were also highly correlated with viral load. 56 of the 151 DEPs were positively and 95 were negatively correlated with viral load (0.6 < ρ <—0.6 and FDR < 0.01) (Fig 4, S5 Table).


Respiratory Mucosal Proteome Quantification in Human Influenza Infections.

Marion T, Elbahesh H, Thomas PG, DeVincenzo JP, Webby R, Schughart K - PLoS ONE (2016)

Functional analysis of DEPs from subset B.Pathway enrichment analysis for normalized log2–transformed expression values of proteins that were differentially expressed in IAV-positive versus IAV-negative patients from subset B is presented. Pathway terms that were enriched for the DEPs from subset B are indicated on the y-axis, the number of DEPs in the respective pathway category is indicated on the x-axis. The p-value for the probability that the observed distribution of expression occurred by chance is represented by colors of bars. The cut-off value for the pathway p-values was chosen at 0.05.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4835085&req=5

pone.0153674.g003: Functional analysis of DEPs from subset B.Pathway enrichment analysis for normalized log2–transformed expression values of proteins that were differentially expressed in IAV-positive versus IAV-negative patients from subset B is presented. Pathway terms that were enriched for the DEPs from subset B are indicated on the y-axis, the number of DEPs in the respective pathway category is indicated on the x-axis. The p-value for the probability that the observed distribution of expression occurred by chance is represented by colors of bars. The cut-off value for the pathway p-values was chosen at 0.05.
Mentions: In subset A, sample ID_4043 segregated separately in the PCA (Fig 2) from the other influenza virus-positive samples and had low levels of CXCL10 and IL6 (data not shown). CXCL10 and IL6 are known to be highly elevated after influenza infection [29], and the previous cytokine-chemokine analysis [28] indicated that plasma CXCL10 was correlated with viral loads. Therefore, we analyzed a second subset (subset B) which was identical to subset A except that the outlier sample ID_4043 was deleted. Thus, subset B (S2 Table) consisted of six healthy controls (same as in subset A) and 11 influenza-infected patients (12 minus 1 from subset A). The corresponding PCA showed good segregation between uninfected control and influenza virus-positive groups (S3 Fig). Accordingly, analyses of IL6 and CXCL10 expression levels showed significant differences between the two groups (Kruskal-Wallis, p < 0.01 and p < 0.05, respectively) (S4 Fig), even though samples from two healthy controls had relatively elevated CXCL10 compared to the other healthy controls. Further analysis of subset B using LIMMA revealed a total of 162 DEPs, 63 increased and 99 decreased in samples from virally infected patients compared to uninfected individuals (log2-fold change ≥ 1 and adjusted p < 0.01) (S4 Table). Functional analysis of these DEPs using the Reactome pathway database showed enrichment for pathways that are activated during the host immune response (Fig 3). Furthermore, 151 of the 162 (up- or down-regulated) DEPs were also highly correlated with viral load. 56 of the 151 DEPs were positively and 95 were negatively correlated with viral load (0.6 < ρ <—0.6 and FDR < 0.01) (Fig 4, S5 Table).

Bottom Line: Our results illustrate the utility of micro-proteomic technology for analysis of proteins in small volumes of respiratory mucosal samples.Most of the identified proteins were associated with the host immune response to infection, and changes in protein levels of 151 of the DEPs were significantly correlated with viral load.It establishes a precedent for micro-proteomic quantification of proteins that reflect ongoing response to respiratory infection.

View Article: PubMed Central - PubMed

Affiliation: University of Tennessee Health Science Center, Department of Microbiology, Immunology and Biochemistry, Memphis, United States of America.

ABSTRACT
Respiratory influenza virus infections represent a serious threat to human health. Underlying medical conditions and genetic make-up predispose some influenza patients to more severe forms of disease. To date, only a few studies have been performed in patients to correlate a selected group of cytokines and chemokines with influenza infection. Therefore, we evaluated the potential of a novel multiplex micro-proteomics technology, SOMAscan, to quantify proteins in the respiratory mucosa of influenza A and B infected individuals. The analysis included but was not limited to quantification of cytokines and chemokines detected in previous studies. SOMAscan quantified more than 1,000 secreted proteins in small nasal wash volumes from infected and healthy individuals. Our results illustrate the utility of micro-proteomic technology for analysis of proteins in small volumes of respiratory mucosal samples. Furthermore, when we compared nasal wash samples from influenza-infected patients with viral load ≥ 2(8) and increased IL-6 and CXCL10 to healthy controls, we identified 162 differentially-expressed proteins between the two groups. This number greatly exceeds the number of DEPs identified in previous studies in human influenza patients. Most of the identified proteins were associated with the host immune response to infection, and changes in protein levels of 151 of the DEPs were significantly correlated with viral load. Most important, SOMAscan identified differentially expressed proteins heretofore not associated with respiratory influenza infection in humans. Our study is the first report for the use of SOMAscan to screen nasal secretions. It establishes a precedent for micro-proteomic quantification of proteins that reflect ongoing response to respiratory infection.

No MeSH data available.


Related in: MedlinePlus