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

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 monocyte markers 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. A randomized, placebo-controlled, observer-blind, phase I clinical study was conducted at Cincinnati Children’s Hospital Medical Center (Cincinnati, OH, USA) and Duke Early Phase Clinical Research Unit (Durham, NC, USA). This clinical trial was designed to assess the safety and immunogenicity of a chimeric hemagglutinin-based vaccine approach; and its ability to elicit broadly cross-reactive antibodies against the hemagglutinin stalk domain of influenza viruses. Briefly, 66 participants were block-randomized in each site and received LAIV8-IIV5/AS03 (Group 1, G1), LAIV8-IIV5 (Group 2, G2), SALINE-PBS (Group 3, G3), IIV8/AS03-IIV5/AS03 (Group 4, G4) or PBS-PBS (Group 5, G5). To note, LAIV8 was administered intranasal while the IIV5 and IIV5/AS03 vaccines were given intramuscularly. The Cincinnati Children’s Hospital Medical Center Institutional Review Board (IRB) served as the central IRB of record for review, approval and oversight of this study on behalf of the Icahn School of Medicine at Mount Sinai IRB, Duke IRB and PATH Research Ethics Committee. All patients provided written informed consent prior to participation. ClinicalTrials.gov identifier NCT03300050. De-identified samples were made available for this analysis (Icahn School of Medicine at Mount Sinai IRB approval #IRB-17-01779).