Clinical Correlations of Transcriptional Profile in Patients Infected With Avian Influenza H7N9 Virus

Abstract

Background: Avian influenza A (H7N9) viruses emerged in China in 2013 and caused zoonotic disease associated with a case-fatality ratio of over 30%. Transcriptional profiles in peripheral blood reflect host responses and can help to elucidate disease pathogenesis.

Methods: We correlated serial blood transcriptomic profiles of patients with avian influenza A (H7N9) virus infection and determined the biological significances from the analysis.

Results: We found that specific gene expression profiles in the blood were strongly correlated with the Pao 2/Fio 2 ratio and viral load in the lower respiratory tract. Cell cycle and leukocyte-related immunity were activated at the acute stage of the infection while T-cell functions and various metabolic processes were associated with the recovery phase of the illness. A transition from systemic innate to adaptive immunity was found.

Conclusions: We developed a novel approach for transcriptomic analysis to identify key host responses that were strongly correlated with specific clinical and virologic parameters in patients with H7N9 infection.

Figure 1.

Overview of the microarray data. A–C, First 3 components (PC1–3) from principal component analysis of the gene expression profile are plotted. Ellipses represent 0.7 standard deviation from the mean value for the indicated categories (patient and control). D, The molecular distance to health (MDTH) for each sample is shown. E, Samples are categorized by week. The distribution of MDTH for each category is shown as a box plot. ** indicates a significant difference (P value < 2 × 10⁻⁵, Wilcoxon rank sum test) compared to the control.

Figure 2.

Correlation between molecular-distance-to-health (MDTH) and clinical parameters: A, Pao₂/Fio_{2 ratio}; B, lower respiratory tract (LRT) titer; C, upper respiratory tract (URT) titer; D, procalcitonin; E, hemoglobin; F, d-dimer. Control samples are blue; patient samples red. Pearson correlation and the corresponding P value are indicated. For controls, Pao₂/Fio₂ was assumed to be 450; viral titer at the upper and lower respiratory tracts were set as 0. MDTH values of 4 data points, namely patient No. 2 (day 13), patient No. 2 (day 15), Patient No. 3 (day 21), and patient No. 3 (day 28), were identified as outliers (see Materials and Methods) and were excluded from this analysis. Therefore, each plot includes a total of 15 control samples and 23 patient samples.

Figure 3.

Identification of genes with expression levels that correlated with clinical parameters. A, Number of genes identified with expression that showed a negative or positive correlation with clinical parameters of interest. B, Venn diagram showing numbers of genes which were identified from both the gene sets of Pao₂/Fio₂ ratio and viral titer at the LRT.

Figure 4.

Top 20 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways for each of the gene sets. Negative log-transformed adjusted P values for each of the top 20 KEGG pathways are plotted for (A) the overlapping gene set with negative Pao₂/Fio₂ and positive viral load at LRT correlation; and (B) the overlapping gene set with positive Pao₂/Fio₂ and negative viral load at LRT correlation. Red lines indicate an adjusted P value cutoff of 0.05. Bars are arranged in a descending order of negative log-transformed adjusted P values. A higher negative log-transformed adjusted P value indicates greater change in the corresponding pathway. Schematic gene pathways of (C) cell cycle and (D) T-cell receptor signaling with genes identified from our analysis marked with yellow.

Figure 4.

Top 20 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways for each of the gene sets. Negative log-transformed adjusted P values for each of the top 20 KEGG pathways are plotted for (A) the overlapping gene set with negative Pao₂/Fio₂ and positive viral load at LRT correlation; and (B) the overlapping gene set with positive Pao₂/Fio₂ and negative viral load at LRT correlation. Red lines indicate an adjusted P value cutoff of 0.05. Bars are arranged in a descending order of negative log-transformed adjusted P values. A higher negative log-transformed adjusted P value indicates greater change in the corresponding pathway. Schematic gene pathways of (C) cell cycle and (D) T-cell receptor signaling with genes identified from our analysis marked with yellow.