Transcriptional Analysis of TH2 Primed Dendritic Cells and T cells

Allergy is a condition affecting between 10 and 30% of the world’s population, with incidence rising every year. It is primarily mediated by THelper (TH) 0 cells reacting to an ordinarily harmless environmental antigen to induce an adaptive TH2 response. TH0 cells are presented the antigen by dendritic cells (DC), the immune systems most proficient antigen presenting cell, which act as the bridge between the innate and adaptive immune system. Dendritic cells specific to this study termed Triple Negative (TN) and CD11b+ are able to prime T cells to become TH2 cells, but current research has been unable to fully determine the proteins that mediate this TH2 priming. TN and CD11b+ DC exhibit transcriptional and functional distinction within the TH2 response, but the individual functions they take on during TH2 responses have not fully been determined. Some evidence suggests that the cell surface protein OX40L and the secreted protein TSLP are capable of inducing TH2 priming, but this is not conserved across all TH2 models. In an effort to determine other specific proteins that induce TH2 priming, RNA-sequencing has been utilized on TN and CD11b+ dendritic cells in TH2 inducing conditions. This thesis aims to analyse RNA-sequencing data generated from purified TH2 antigen positive TN and CD11b+ dendritic cells that have taken up a TH2-inducing stimulus – fluorescently labelled (AF488) non-viable Nippostrongylus brasiliensis. Due to the majority of DC-TH0 interactions occurring at the cell surface interface, the bioinformatic analysis was focused on genes belonging to the surface and secreted compartments.

Here I show that AF488-Nippostrongylus brasiliensis positive TN and CD11b+ DC are transcriptionally distinct from each other. Functional roles of differentially expressed genes (DEG) were also markedly distinct. Superfamily analysis revealed TN genes associated with signal transduction and proteases, whereas CD11b+ DEG were linked to cell adhesion and immune responses. This suggests that the different DC subsets have different roles in an immune response, and potentially different roles in the induction of TH2 immune responses. Network analysis of DEG from DC subsets and proteins expressed by TH0 and TH2 cell surfaces identified over 300 predicted interactions. Notably, 33 identified were known interactions – validating the bioinformatic methods used. Finally, I have been developing a method to assess novel interactions via flow cytometry methods that allows detection of binding and identification of the cell population that is bound. This has shown promise with the detection of generated proteins bound to TN and CD11b+ DC during TH2 stimulating conditions, paving the way for future novel interaction analyses.