Abstract
Systems biology is an approach to comprehensively study complex interactions within a biological system. Most published systems vaccinology studies have utilized whole blood or peripheral blood mononuclear cells (PBMC) to monitor the immune response after vaccination. Because human blood is comprised of multiple hematopoietic cell types, the potential for masking responses of under-represented cell populations is increased when analyzing whole blood or PBMC. To investigate the contribution of individual cell types to the immune response after vaccination, we established a rapid and efficient method to purify human T and B cells, natural killer (NK) cells, myeloid dendritic cells (mDC), monocytes, and neutrophils from fresh venous blood. Purified cells were fractionated and processed in a single day. RNA-Seq and quantitative shotgun proteomics were performed to determine expression profiles for each cell type prior to and after inactivated seasonal influenza vaccination. Our results show that transcriptomic and proteomic profiles generated from purified immune cells differ significantly from PBMC. Differential expression analysis for each immune cell type also shows unique transcriptomic and proteomic expression profiles as well as changing biological networks at early time points after vaccination. This cell type-specific information provides a more comprehensive approach to monitor vaccine responses.
Highlights
Systems biology is a comprehensive approach to describe complex interactions between multiple components in a biological system[1]
To develop a comprehensive systems biology model for studying immune responses following vaccination, we developed an efficient protocol to purify from human blood six immune cell types that contribute to both innate and adaptive immune responses: T cells, B cells, natural killer (NK) cells, myeloid dendritic cells, monocytes, and neutrophils
Average numbers of peripheral blood mononuclear cells (PBMC) and PMN obtained from 90mL of fresh blood were 232.9 ± 96.6x106 and 113.1 ± 70.0x106, respectively. These cells were stained with a cocktail of antibodies to identify and quantify six targeted immune cell types: CD3+ T cells, CD14+ monocytes, CD15+ neutrophils, CD19+ B cells, CD11c+ myeloid dendritic cells (mDC), and CD56+ NK cells (Fig. 1A)
Summary
Systems biology is a comprehensive approach to describe complex interactions between multiple components in a biological system[1]. The first systems biological studies to dissect human vaccine-induced responses utilized the yellow fever vaccine, YF-17D[6,7] In these pioneering studies, both CD8+ T cell and B cell signatures identified in microarray profiles were correlated with protective cell-mediated and antibody responses, providing predictive signatures. Both CD8+ T cell and B cell signatures identified in microarray profiles were correlated with protective cell-mediated and antibody responses, providing predictive signatures Since these studies, several other vaccines have been studied, including live and inactivated influenza and pneumococcal polysaccharide vaccines [8,9,10]. Using the Nakaya dataset, Tan et al identified immunoglobulin and complement genes as well as proliferation-associated genes to be predictors of protective antibody production in response to TIV vaccination. They concluded that enrichment of these particular gene sets at 7 days post-TIV vaccination was likely due to increased representation of proliferating plasmablasts in subjects with elevated antibody responses[11]
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