• The impact of the non-immune chemiome on T cell activation

      Rosenberg, Kenneth; Singh, Nevil; 0000-0002-1231-7836 (2020)
      T cells are critical organizers of the immune response and rigid control over their activation is necessary for balancing host defense and immunopathology. It takes 3 signals provided by dendritic cells (DC) to fully activate a T cell response – T cell receptor (TCR) engagement of antigen on MHC (Signal 1), co-stimulatory signals (Signal 2) and cytokines (Signal 3). Yet, even before activation T cells are typically exposed to a universe of chemicals (a “chemiome”) including drugs, metabolites, hormones etc. which are not typically ascribed an immunological role. In this thesis, we hypothesized that members of this non-immune chemiome acting on T cells, prior to antigen encounter, flavor specific signaling pathways to differentially influence subsequent T cell activation and fate. Unraveling these signals, which we termed “Signal 0”, could help us understand and manipulate tissue and time specific flavoring of immunity. In this thesis we first developed a pharmacological model for signal 0, by treating T cells with drugs that activate only subsets of the TCR-signaling network prior to full antigen exposure. We found that pharmacological pre-activation of the PKCƟ/ERK pathways modulates long time survival of T cells without changing proliferation or cytokine production. Next, we examined receptors for the non-immune chemiome that resting T cells express and identified neurotransmitter receptors (NR) as a major family. All T cells expressed a core NR signature, but very few NR were also modulated in a T cell lineage-specific fashion. Of these, we focused on VPAC1, the receptor for vasoactive intestinal peptide (VIP). We found that VIP signaling attenuates ERK phosphorylation, but paradoxically drives increased differentiation towards IL-17 and IL-22 secretion. In addition ERK signaling induced by drugs (phorbol esters) versus the TCR followed differential kinetics and recruited non-overlapping negative feedback mechanisms, suggesting that even the same branch of TCR signaling is subject to different localization and temporal controls. Taken together, our data suggest that the branches of the TCR-signaling network integrate pre-existing signals (Signal 0) into the activation program of T cells, allowing localized cues, including neurotransmitter levels, to modify the long-term trajectory of the immune response.
    • Mathematical models in the study of the amino acid sequence of HLA class I molecules in reference to their ability to present peptides

      Fan, Bo; Cano, Pedro, M.D., M.B.A. (2000)
      T cell recognition of antigen requires that peptides derived from foreign or self-altered antigen be displayed within the cleft of a MHC molecule on the membrane of a cell. Considerable effort has focused on characterizing the specificity of MHC molecules in order to predict peptide binding. The similarity of HLA alleles in reference to their ability to present peptides to T cells is evaluated by calculating the correlation matrix between the binding affinity tables for the sets of peptides presented by each allele. This correlation matrix is an empirical similarity matrix between HLA alleles, and it is modeled in terms of possible structures defined in the metric space of HLA class I amino acid sequences. The following clusters of HLA class I molecules are identified in reference to their ability to present peptides: (Cluster I) HLA-A3/HLA-A11/HLA-A31/HLA-A33/HLA-A68; (Cluster II) HLA-B35/HLA-B51/HLA-B53/HLA-B54/HLA-B7/; and (Cluster III) HLA-A29/HLA-B61/HLA-B44. In modeling these natural clusters, the geometric structures with more predictive power confirm the importance of those positions in the peptide-binding groove, particularly those in the B pocket. Other positions (46, 79, 113, 144, and 177) not noticed before are also revealed to bear relevance in determining peptide-binding specificity. In addition, all known HLA class I alleles are classified into different clusters at four different levels. The binding specificity of peptides to MHC molecules is studied by representing amino acid sequences as vectors in a metric feature-space whose transformations make conceptual models of MHC peptide binding in terms of the amino acid sequence of the respective MHC alleles. Such models allow the prediction of peptide binding not only for those HLA class I alleles with sufficient data, but also for those alleles for which peptide binding data is not yet available. The use of this novel metric space approach with the application of geometric and algebraic concepts to study amino acid sequences and peptide-binding lead to the successful development of computational algorithms for MHC peptide-binding predictions which have important implications for the design of new peptide vaccines for clinical interventions.
    • Regulation of intrinsic activation thresholds of T cells

      Matson, Courtney; Singh, Nevil; 0000-0002-9817-4986 (2020)
      T cells are activated when their T cell receptor (TCR) senses peptide-MHC (pMHC) molecules from pathogens and tumors. A network of signaling molecules downstream of the TCR drives the extent and nature of subsequent cellular responses. The activation threshold (AT) of these signaling pathways is a critical checkpoint for T cell responses. Here, we examined mechanisms by which the AT of a T cell is first determined and how it changes during the course of responding to antigen. The initial AT of a T cell is set during development by calibrating to how strongly it senses pMHC in the thymus. This calibration affects the surface levels of a receptor CD5, whose subsequent role is poorly defined. We found that CD5, independent of the TCR, sets basal levels of IκBα in T cells. Since IκBα critically modulates the transcription factor NFκB, which regulates multiple T cell functions including cell-survival, we hypothesized that variations in basal AT of T cells stem from varying NFκB depots maintained by CD5. Indeed, blocking NFκB abolished differences in cell-survival of thymocytes with different CD5 levels. The initial heterogeneities are further modified when peripheral T cells encounter antigen. Resulting memory T cells acquired higher CD5 levels and continuously required CD5 expression to maintain higher IκBα expression. If the stimulating antigen was not cleared efficiently, peripheral T cells further ‘tuned’ their AT in the opposite direction and resulted in loss of sensitivity to antigen (as seen in exhausted T cells). Importantly, this AT tuning involved additional regulation of TCR-proximal kinases such as Zap70 and was reversible in vivo, but not in vitro. We also found that rather than just the duration of antigen exposure, AT-tuning was potentially influenced by the rate at which antigen changes in vivo. This can help us understand how different persistent pathogens or tumors affect T cell responses, potentially based on the rates at which they replicate in the host. Finally, we characterized compounds that can target a T cell’s AT, identified in a high-throughput pharmacological screen, to potentially isolate drugs for altering T cell function during these physiological contexts.