Quantitative Proteomic Analysis of the Human Immune Response Following Influenza Vaccination
Galassie, Allison Caitlin
Vaccines are one of the greatest public health successes; yet there is an incomplete understanding of which genes and proteins are induced by vaccines and how they contribute to the development of protective immune responses. While genomics and transcriptomics have facilitated understanding of the immune response, a systems approach including proteomics creates a more comprehensive view of vaccine responses. Most systems vaccinology studies utilize PBMCs in their analysis, which can be problematic if predominant cells overwhelm the responses of underrepresented cell types. This work outlines the development and application of a cell-based quantitative proteomic method to assess the contribution of individual cell types following influenza vaccination. First, immune cell populations (B cells, monocytes, neutrophils, natural killer cells, and T cells) were purified from blood before and after a seasonal influenza vaccination to optimize the 8-plex iTRAQ multiplexing approach. Pooling the individual cell types, rather than individual time points, resulted in the identification of more cell-type specific protein clusters whose levels changed after vaccination. Further, proteomic expression profiles and biological networks generated from purified immune cells differed significantly from PBMCs, indicating a more complete understanding of the immune response can be achieved from this method. This cell-based method was applied in a clinical trial assessing the molecular immune responses of an AS03-adjuvanted H5N1 influenza vaccine. Distinct responses were observed in all cells, but monocytes demonstrated the strongest differential signal. Immunological pathways, including MHC class I-mediated antigen processing and presentation, inflammation and oxidative stress proteins, and immunoproteasome subunits were enriched in monocytes and neutrophils after the first AS03-adjuvanted vaccine dose. These proteins were then identified as being predictive of seroprotective antibody responses 28 days after the second vaccine dose. Finally, comparison between proteomic and transcriptomic results showed little overlap, but confirmed enrichment of Class I antigen processing and presentation pathways. By investigating each individual immune cell population using quantitative proteomic methods, a more complete understanding of the complex immune response can be achieved.