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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

PCA analysis of normalized protein expression values of subset A.Principle component analysis (PCA) was performed with normalized log2–transformed protein expression values from nasal washes for 18 samples from the subset A that was selected based viral load being higher than > 28. The first two principal components are shown representing 42% and 16%, respectively, of the total variation. Healthy controls are labelled gray and IAV-positive samples are labelled red. In addition, sample identities (e.g., ID_4002) are shown. Horizontal and vertical axis represent principle component 1 and 2, respectively.
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pone.0153674.g002: PCA analysis of normalized protein expression values of subset A.Principle component analysis (PCA) was performed with normalized log2–transformed protein expression values from nasal washes for 18 samples from the subset A that was selected based viral load being higher than > 28. The first two principal components are shown representing 42% and 16%, respectively, of the total variation. Healthy controls are labelled gray and IAV-positive samples are labelled red. In addition, sample identities (e.g., ID_4002) are shown. Horizontal and vertical axis represent principle component 1 and 2, respectively.

Mentions: A comparison of all 18 samples from infected patients with the six samples from healthy individuals did not identify statistically significant differentially expressed proteins (DEPs). This result is consistent with the incomplete segregation of positive and negative samples in the PCA (Fig 1) and previous chemokine and cytokine measurements in samples from the entire patient cohort from which the samples analyzed herein were obtained [28]. The low viral load in some of the infected patients (S1 Table) may account for this result. It is well known from animal experiments that immune responses and pathologies depend largely on viral loads (reviewed in [30]). Furthermore, the distribution of viral loads among all of the infected patients in the entire patient cohort [28] was bimodal (S2 Fig). Based upon the bimodal distribution between patients with higher versus lower viral RNA levels in the entire influenza infected patient cohort, we selected a subset of patients with a minimum viral load of 28 (subset A, S2 Table) to identify proteins that were differentially expressed between infected patients (12 samples) and healthy controls (6 samples). Fig 2 shows the PCA for this subset. Comparison of the SOMAscan results between virally-infected patients and healthy controls from subset A by LIMMA revealed a total of 23 DEPs, 5 increased and 18 decreased (log2-fold change ≥ 1 and adjusted p < 0.01) (S3 Table).


Respiratory Mucosal Proteome Quantification in Human Influenza Infections.

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

PCA analysis of normalized protein expression values of subset A.Principle component analysis (PCA) was performed with normalized log2–transformed protein expression values from nasal washes for 18 samples from the subset A that was selected based viral load being higher than > 28. The first two principal components are shown representing 42% and 16%, respectively, of the total variation. Healthy controls are labelled gray and IAV-positive samples are labelled red. In addition, sample identities (e.g., ID_4002) are shown. Horizontal and vertical axis represent principle component 1 and 2, respectively.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0153674.g002: PCA analysis of normalized protein expression values of subset A.Principle component analysis (PCA) was performed with normalized log2–transformed protein expression values from nasal washes for 18 samples from the subset A that was selected based viral load being higher than > 28. The first two principal components are shown representing 42% and 16%, respectively, of the total variation. Healthy controls are labelled gray and IAV-positive samples are labelled red. In addition, sample identities (e.g., ID_4002) are shown. Horizontal and vertical axis represent principle component 1 and 2, respectively.
Mentions: A comparison of all 18 samples from infected patients with the six samples from healthy individuals did not identify statistically significant differentially expressed proteins (DEPs). This result is consistent with the incomplete segregation of positive and negative samples in the PCA (Fig 1) and previous chemokine and cytokine measurements in samples from the entire patient cohort from which the samples analyzed herein were obtained [28]. The low viral load in some of the infected patients (S1 Table) may account for this result. It is well known from animal experiments that immune responses and pathologies depend largely on viral loads (reviewed in [30]). Furthermore, the distribution of viral loads among all of the infected patients in the entire patient cohort [28] was bimodal (S2 Fig). Based upon the bimodal distribution between patients with higher versus lower viral RNA levels in the entire influenza infected patient cohort, we selected a subset of patients with a minimum viral load of 28 (subset A, S2 Table) to identify proteins that were differentially expressed between infected patients (12 samples) and healthy controls (6 samples). Fig 2 shows the PCA for this subset. Comparison of the SOMAscan results between virally-infected patients and healthy controls from subset A by LIMMA revealed a total of 23 DEPs, 5 increased and 18 decreased (log2-fold change ≥ 1 and adjusted p < 0.01) (S3 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