Transcriptome signatures preceding the induction of anti-stalk antibodies elicited by a chimeric hemagglutinin-based universal influenza virus vaccine

Abstract A phase 1 clinical trial to test the immunogenicity of a chimeric group 1 HA (cHA) universal influenza virus vaccine targeting the conserved stalk domain of the hemagglutinin of influenza viruses was carried out. Vaccination with adjuvanted-inactivated vaccines induced high anti-stalk antibody titers. We sought to identify gene expression signatures that correlate with such induction. Messenger-RNA sequencing in whole blood was performed on peripheral blood of 53 vaccinees, at early and late time points after priming and boosting. We generated longitudinal data on peripheral blood of 53 volunteers, at early (days 3 and 7) and late (28 days) time points after priming and boosting with cHAs. Differentially expressed gene analysis showed no differences between placebo and live-attenuated vaccine groups. However, an upregulation of genes involved in innate immune responses and type I interferon signaling was found at day 3 after vaccination with inactivated adjuvanted formulations. Cell type deconvolution analysis revealed a significant enrichment for monocytes and different subsets of dendritic cells as mediators for optimal B cell responses and significant increase of anti-stalk antibodies in sera. A significant upregulation of immunoglobulin related genes was only observed after administration of adjuvanted vaccines (either as primer or booster) with specific induction of anti-stalk IGVH1-69. This approach informed of specific immune signatures that correlate with robust anti-stalk antibody responses, while also helping to understand regulation of gene expression induced by cHA proteins under different vaccine regimens. Significance: Antibodies targeting the conserved stalk domain of the hemagglutinin protein of influenza viruses can prevent and reduce the severity of influenza virus infection. We have developed a chimeric HA vaccination strategy targeting these conserved regions and showed that vaccination induced high anti-stalk antibody titers in humans. Here we showed that anti-stalk vaccines elicit robust gene expression signatures similar to those described for subtype-specific influenza vaccines with an early upregulation of genes involved in innate immune response and type I interferon (IFN) signaling needed for an optimal B cell activation and proliferation. The current study provides a better understanding of the mechanism of regulation of gene expression and the transcriptional pathways that must be activated to induce optimal vaccine responses in the context of different universal vaccine strategies.