(91c) Analysis of Transcriptomic Data for CD4 Naïve T Cells Stimulated By Cytokines

Novel cancer therapeutics rely on the immune system to attack a pathogen of interest. Most pre-exhaustive therapies deplete the immune system of vital T cells, rendering the immune system un-prepared for swiftly destroying pathogens. Some of the most important T cells are naïve CD4+ T cells, which, upon coming into contact with a pathogen, will proliferate and differentiate into Helper T, Regulatory T or Follicular Helper T cells [1]. Some of the same cellular signaling pathways which govern differentiation of naïve CD4+ T cells also govern the proliferation of T cells, which is a desirable effect given the state of most immunodepleted cancer patients. Cytokines have a strong interdependent relationship with T cells and can both regulate and be produced from T cells in order to sponsor proportional immune responses, both in proliferation and differentiation [2]. Three cytokines: IL-2, IL-7 and IL-15, have been suggested in literature as having a profound impact on the proliferation of naïve T cells [3]. Here, we have engaged in a design of experiments to understand the influence of each of the three cytokines to gain insight into how to best stimulate proliferation of Naïve CD4+ T cells. We have studied the Naïve CD4+ T cell transcriptome over time using RNA Sequencing. Using EdgeR, we are able to sort through and identify genes with high magnitudes of change in the differential gene expression [4]. The output of this sorting technique is the input for further consolidation of genes of interest using principal component analysis (PCA). We identify outliers which may have unique impact to the pathways inducing proliferation in the T cells. From the PCA analysis, we use GeneMania software to find connections between the genes of interest, and the function of these genes in how they relate to proliferative pathways [5]. We also link these genes to a genome scale model for CD4+ T cells to overlap these genes and isolate the most important genes associated with key pathways [6]. We find that most of the genes linked with IL-2 stimulation are associated with cell chemotaxis and cell migration. Genes linked with IL-7 stimulation are associated heavily with electrolyte transport and chemotaxis, and genes linked with IL-15 stimulation are associated with metal ion response and regulation of growth. We can make associations using the transcriptome to highlight why the combination of cytokines we have chosen happens to be a useful path to T cell proliferation. Finally, we also correlate the growth rate time profile with the transcriptome time profile of genes sampled at the same time points to understand whether these genes can be positively correlated with the rate of proliferation of the T cells. Our findings lay the groundwork for further work in regulating CD4+ naïve T cell growth with cytokines in clinical setting.

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