Early patterns of gene expression correlate with the humoral immune response to influenza vaccination in humans

Abstract

Background: Annual vaccination is the primary means for preventing influenza. However, great interindividual variability exists in vaccine responses, the cellular events that take place in vivo after vaccination are poorly understood, and appropriate biomarkers for vaccine responsiveness have not been developed.

Methods: We immunized a cohort of healthy male adults with a licensed trivalent influenza vaccine and performed a timed assessment of global gene expression before and after vaccination. We analyzed the relationship between gene expression patterns and the humoral immune response to vaccination.

Results: Marked up regulation of expression of genes involved in interferon signaling, positive IL-6 regulation, and antigen processing and presentation, were detected within 24 hours of immunization. The late vaccine response showed a transcriptional pattern suggestive of increased protein biosynthesis and cellular proliferation. Integrative analyses revealed a 494-gene expression signature--including STAT1, CD74, and E2F2--which strongly correlates with the magnitude of the antibody response. High vaccine responder status correlates with increased early expression of interferon signaling and antigen processing and presentation genes.

Conclusions: The results highlight the role of a systems biology approach in understanding the molecular events that take place in vivo after influenza vaccination and in the development of better predictors of vaccine responsiveness.

Figure 1.

The human transcriptional response to trivalent influenza vaccination shows three distinct patterns of gene expression. (A) Heatmap illustrating the patterns of expression for all differentially expressed genes. Yellow indicates a higher value. Three distinct patterns of expression are evident: early upregulation, late upregulation and downregulation. (B) Proportions of significant and nonsignificant Gene Ontology (GO) categories for each of the three expression patterns. (C) Selection of the most important GO terms for each expression pattern. Higher z scores indicate that a GO term is more likely to be enriched in a given set of differentially expressed genes.

Figure 2.

Early patterns of gene expression correlate with responsiveness to trivalent influenza vaccine. (A) Probability density estimate of the titer response index (TRI) in our cohort. A trimodal distribution for the vaccine response is observed. The hash marks below the curve are the TRI values for each individual, and the colors correspond to low, intermediate, and high responders. (B) STAT1 and E2F2 expression in the three responder groups at each time point. STAT1 expression increases after vaccination, most prominently on day 1 and in the high-responder group. E2F2 expression is downregulated after vaccination, most prominently on day 3 and with greater downregulation in the high-responder group. (C) Heatmap of the expression signature of vaccine responsiveness in the top 10 (left) and bottom 10 (right) responders. The expression values for each gene were standardized at each time point, and the day 1 and day 3 values were averaged. Yellow indicates a higher value. Each column represents an individual. The top row illustrates the TRI for each individual. The difference between STAT1 and E2F2 expression alone can differentiate individuals at the two extremes of the response spectrum, as illustrated in the second row. The bottom rows display the expression patterns for the 494 genes in the gene expression signature. (D) Cross-validation prediction data, illustrating how expression values can be used to predict the TRI.

Figure 3.

Interferon signaling and antigen presentation genes are preferentially upregulated in individuals with high vaccine responsiveness. (A) Top enriched pathways in the high responder group. The negative log P value, along the x-axis, increases as a pathway is more significantly associated. The ratio indicates the proportion of upregulated genes relative to all the genes present in a pathway. (B) Genes that act in the interferon pathway and which are preferentially upregulated in the high vaccine responders are shown in red. (C) Top functional network for genes that are preferentially upregulated in the high responder group, including genes that interact directly (solid lines) and indirectly (broken lines). Functionally, the network corresponds to antigen presentation, cellular growth and proliferation, and hematological system development and functions. Shades of red are used to display the level of expression for each gene in the high-responder relative to the low-responder groups.