A Thesis submitted to The University of Arizona College of Medicine - Phoenix in partial fulfillment of the requirements for the Degree of Doctor of Medicine. / Recent advances in cancer immunology, highlighted by immune checkpoint inhibitors, have demonstrated that immunotherapy is a viable option in the oncologist’s armamentarium. Despite these advances, many patients are nonresponders. Preliminary studies have suggested that non-responders lack a de-novo anti-tumor antigen immune response that can be unmasked by checkpoint blockade; thus, strategies to induce anti-tumor immune responses are needed. We hypothesized that many tumor associated antigens (Ag) are readily susceptible to immune attack, but only in the context of identifying the tumor antigen epitopes that can reliably initiate an immune response, regardless of individual patient human leukocyte antigen (HLA) haplotype restrictions. We further hypothesized that epitope prediction strategies which seek to identify pan- or highly promiscuous-HLA binding epitopes would reduce the number of potential candidates and be more likely to accurately identify high-priority tumor Ag epitopes. Utilizing known HLA-serotype frequencies and setting a threshold of ninety percent of population coverage, regardless of race or ethnicity, twenty-nine different HLA-DRB1 haplotypes were chosen for antigen prediction utilizing the open source epitope prediction algorithm netMHCIIpan. Predictions were also performed for HLA-A serotypes utilizing the open source algorithm netMHCpan. Predicted epitopes were synthesized in the form of synthetic long peptides and tested in immune system sensitization assays involving unfractionated peripheral blood mononuclear cells (PBMC). Briefly, PBMC were subjected to a two-step culture, first synchronizing their exposure to the long peptides with aggressive surrogate activation of innate immunity, followed by IL-7-modulated T-cell hyperexpansion. Predictions resulted in identification of highly promiscuous-HLA binding epitopes. Unexpectedly, these epitopes clustered together forming high priority regions: unique “hot spots” with high densities of promiscuous HLA-binding epitopes from the widely expressed oncoproteins MUC1, HER2/neu and CMV-pp65 (p<0.0001, for predicted HLA-DRB1 binding affinities, compared to non-hot spot regions). Added synthetic long peptides (>20aa) derived from “hot spot” regions of MUC1, HER2/neu, and CMVpp65 reliably produced selective and sustained expansion of both CD4+ and CD8+ peptide-specific, interferon-γ (IFNγ)-producing Tcells when synchronized with step 2 exposure to exogenous IL-7 (p<0.0001 and p=0.0048, for CD4+ and CD8+ Ag-specific T-cells, respectively, compared to T-cells directed against peptides from non-hot spot regions). “Hot spot” peptide Ag-specific T-cells preferentially recognized endogenous tumor derived MUC1, either in MUC1 expressing tumor cell killing assays (p=0.038, compared to non-peptide Ag-specific T-cells) or as MUC1 tumor lysate when pulsed onto restimulatory PBMC (p=0.022 and 0.025, for CD4+ and CD8+ T-cells, respectively, compared to T-cells directed against peptides from non-hot spot regions). This mechanistically rational antigen selection sequence, effective even for unvaccinated donors, regardless of HLA-haplotype, enables rapid identification of tumor protein regions relevant for cancer immunology, including adoptive immunotherapy, vaccines, and even identification of tumor neo-antigens unique to each patient.

The prevailing view of signal transduction is that it proceeds through the linear relay of information via sequential bimolecular interactions, involving, for example, Src homology (SH) 2 domains. It has been assumed that such interactions are highly selective, i.e. that the affinities of these interactions are several orders of magnitude higher than that for non-specific interactions. However, recent studies have suggested that the difference in affinities between so-called specific and non-specific interactions is not sufficient to support such a proposal. This therefore raises the question of how signalling pathway specificity is generated at all. To address this, we have taken a systems approach by expressing and purifying >90% of the SH2 domains identified in a T cell line using a next-generation sequencing-based transcriptomic analysis, and performed a systematic survey of the interaction of these SH2 domains with a set of potential phosphorylated peptides derived from the key signalling receptors of the T cell (including CD28, CTLA-4, PD-1, ICOS, BTLA, LAT and the CD3 subunits of the TCR complex), using surface plasmon resonance-based binding assays. Our results show that, instead of being highly selective for certain SH2 domains, the T cell-expressed receptors are very cross-reactive, such that each receptor is found to interact with ~50 different SH2 domains on average. In silico analysis based on these results confirms the expectation that affinity itself is not the sole determining factor for receptor specificity. Further exploration of the system using in silico simulations incorporating the absolute concentrations of SH2 domain-containing proteins measured in T cells using a proteomics-based approach, suggests instead that the specificity of SH2 domain recruitment by T-cell receptors is the result of systems effects, with expression levels of the signalling proteins being a major factor. Surprisingly, LCK, the most highly expressed SH2 domain in resting Jurkat, is predicted to dominate the binding of most receptors, suggesting a novel mechanism of Src kinase activation and function.

Tissue-resident memory T cells (TRM) are a non-circulating subset of memory that are maintained at sites of pathogen entry and mediate optimal protection against reinfection. Lung TRM can be generated in response to respiratory infection or vaccination, however, the molecular pathways involved in CD4+TRM establishment have not been defined. Here, we performed transcriptional profiling of influenza-specific lung CD4+TRM following influenza infection to identify pathways implicated in CD4+TRM generation and homeostasis. Lung CD4+TRM displayed a unique transcriptional profile distinct from spleen memory, including up-regulation of a gene network induced by the transcription factor IRF4, a known regulator of effector T cell differentiation. In addition, the gene expression profile of lung CD4+TRM was enriched in gene sets previously described in tissue-resident regulatory T cells. Up-regulation of immunomodulatory molecules such as CTLA-4, PD-1, and ICOS, suggested a potential regulatory role for CD4+TRM in tissues. Using loss-of-function genetic experiments in mice, we demonstrate that IRF4 is required for the generation of lung-localized pathogen-specific effector CD4+T cells during acute influenza infection. Influenza-specific IRF4−/− T cells failed to fully express CD44, and maintained high levels of CD62L compared to wild type, suggesting a defect in complete differentiation into lung-tropic effector T cells. This finding identifies IRF4 as an important regulator of CD4+TRM generation in response to respiratory infection. Furthermore, comparing whole transcriptome profiling of mouse and human lung memory T cell subsets, we define a lung CD4+TRM gene signature common to mice and humans. IRF4 protein was specifically up-regulated in lung CD4+TRM but not in circulating memory subsets, in both humans and mice previously infected with influenza. This result suggest that high expression of IRF4 contributes to a cross-species conserved molecular pathway of long term maintenance of CD4+TRM in the lung. Overall, our findings confirm lung CD4+TRM as a unique memory T cell subset regulated by tissue-specific transcription factors. These results have important implications in focusing future studies of tissue resident memory T cells to factors with translational potential. Importantly, by determining the lung CD4+TRM gene signature common to mice and humans, we motivate future genetic studies that could lead to the complete identification of the mechanisms of TRM maintenance in humans.

University of Macau / Institute of Chinese Medical Sciences

Adoptive cell transfer (ACT) has garnered significant interest in recent years within the medical field due to its potential in providing an effective form of personalized medicine for patients suffering from a wide range of chronic illnesses, including but not limited to cancer. By leveraging the patient’s own cells as the therapeutic agent, concerns over patient compatibility and adverse reactions are significantly reduced. Central to this therapy is the ability to optimize cell quantity and cell activation in order to produce a more robust infusion to the patient. This thesis focuses on two main aspects. The first is the materials synthesis and development of a novel platform for the ex vivo expansion of human T cells for ACT, while the second aims to elucidate the underlying structural mechanics of this platform. This platform, which consists of an electrospun mesh of micron and sub-micron diameter poly (dimethyl siloxane)-based fibers, aims to maintain the high surface-area to volume ratio characteristic of the current clinical gold standard. This also simultaneously allows for effective leveraging of T cell mechanosensing, a phenomenon previously discovered by our lab that is the ability of a human T cell to respond differently to surface mechanical cues. By modulating the concentration of poly (ε-caprolactone) in these fibers, a biocompatible polymer, the mesh mechanical rigidity was varied: this effectively allowed for the leverage of T cell mechanosensing by maintaining a low and tunable Young’s modulus throughout. Additionally, safety concerns involving transfusion of the expansion platform into the patient were addressed by having a single continuous substrate instead of an array of disjoint ferromagnetic beads. Our results thus far indicate that this soft mesh platform can produce upwards of 5.6-12.5 times more T cells in healthy patients than the clinical gold standard while maintaining comparable levels of cellular activation and phenotypic distributions as measured through IFNγ secretion and expression of surface proteins CD107b, CD45RO, and CCR7, respectively. Additionally, this platform demonstrates the ability to produce improved expansion of exhausted (PD-1high) T cells from CLL patients compared to the clinical gold standard across all analyzed Rai stages. Finally, experiments have shown our platform to be scalable to produce clinically relevant levels of cells (> 50 million) from a given starting population, thus indicating its potential in adaptation in larger scale in vitro systems. The currently demonstrated capabilities of our mesh platform thus hold significant promise in the clinical development and adoption of ACT, as well as the development of larger scale in vitro systems. In order to elucidate the underlying structural mechanics of our platform, quantitative AFM studies have indicated a force-dependency in rigidity measurement, thus indicating that standard Hertzian contact models and their derivatives (DMT, Sneddon, etc.), may not be ideal in calculating the rigidity of this material. In order to better model the effective Young’s modulus (E_eff) of the mesh and account for cantilever beam-bending type mechanical deformation, a modification of Euler-Bernoulli theory was established. This mathematical model was subsequently used to correlate fiber geometry parameters to bending stiffness, thus allowing for us to estimate E_eff for a range of meshes. Subsequent T cell expansions and comparison of data to previous expansions on planar surfaces provided verification of our model.

No description available.

The thymus is the primary lymphoid organ responsible for the development and maturation of T lymphocytes (aka T-cells) in vertebrates. The complex architecture of the thymic microenvironment orchestrates the formation of a diverse and self-tolerant T-cell repertoire capable of supporting the development and maintenance of a functional immune system. The main component of this microenvironment, the thymic epithelium, is crucially required to direct thymus organogenesis and homeostasis, and to mediate T-cell repertoire development and selection. The thymic epithelial progenitor cells (TEPCs) from which the mature thymus develops originate from the endoderm of the 3rd pharyngeal pouch by embryonic day 9 in mouse development (or early week 6 in human embryos). Expression of the transcription factor FOXN1 is required to drive TEPCs differentiation in each thymic epithelial lineage (TEC), while the absence of functional FOXN1 causes athymia. Moreover, forced expression of Foxn1 in mouse embryonic fibroblasts (MEFs) converts these MEFs into TECs that can support the development of a normal thymic system. Despite the great therapeutic potential that TEPCs present in regenerative medicine, there is currently no detailed model describing regulation of the TEPC state and its differentiation into cortical (c) and medullary (m) TECs, or explaining the dominant role of FOXN1 in the thymic epithelial system. Comparative transcriptomics analysis in conjunction with pathway enrichment analysis of the developing TEPCs could reveal the signalling pathways that regulate the early TEPC state and progression into differentiation. Additionally, integrative bioinformatics analysis of transcriptomics and genomics datasets could identify the functional networks that are directly regulated by FOXN1 during early TEC progression. In this thesis I provide, for the first time, an in silico model explaining fetal TEPC differentiation into the functionally distinct TEC lineages, in the cellular, molecular and signalling contexts of thymus early development. Furthermore, I present evidence which suggests that FOXN1 could be a pioneer factor, capable of fully establishing the transcriptional programme that underpins thymic epithelial cell identity and function. Finally, in this thesis, I introduce the development of an interactive thymic-specific database that provides a platform for easy access, analysis and integration of curated bioinformatics datasets.

T cells are at the heart of the adaptive immune response. They mediate many important immunological processes that provide protection against viruses, bacteria and other pathogens. The aim of the work described in this thesis was to use gene expression profiling to gain insights into different aspects of T cell biology. In particular we wanted to examine the mechanisms and identify the genes that underlie T cell effector function. IFN-g-producing Th1 cells are a major effector subset that protects against intracellular pathogens, while Th2 cells produce IL-4, IL-5 and IL-13 and mediate protection against large extracellular pathogens. Microarray profiling of gene expression in mouse and human Th1 and Th2 cells, as well as mouse Tc1 and Tc2 cells, identified a number of novel markers of these T cells which may have important roles in T cell differentiation/function. We found that T cell type, host species and differentiation conditions significantly influenced gene expression profiles generated during T cell polarization. Providing help to B cells for antibody production is the major function of the third effector subset of CD4+ T cells termed T follicular homing or TFH cells. Relatively little is known about the generation of these cells, and the mechanisms of their effector function. Using oligonucleotide microarrays we identified a TFH-specific gene expression signature, which included many novel genes which will undoubtedly enable better identification and characterization of this novel subset. A comprehensive study profiling all the major leukocyte subsets revealed their distinct gene expression signatures and numerous leukocyte subset specific genes. A detailed examination of most major T cell subsets identified distinguishing features of each subset together with gene expression changes associated with T cell activation and exposure to cell culture conditions. In addition, we described a distinctive transcriptional profile for gd T cells and examined the differences between central and effector memory T cells. We also showed that specific gene expression signatures provide a powerful tool for subset classification. Taken together this work provides important insights into T cell differentiation and effector function, and presents a basis for future work examining numerous novel genes relevant to T cell biology.

The activation and effector function of CD4+ T cells are critical points of regulation during an antigen specific T cell response. Dysregulation of these processes can lead to the development of human diseases, encompassing both immunodeficiency and autoimmunity. Members of the TNF superfamily have recently emerged as important regulators of T cell responses, with their overexpression causing autoimmune inflammation in animal models. As overproduction of the novel TNF superfamily ligand BAFF is associated with several autoimmune conditions, we sought to examine the potential role of BAFF as a regulator of T cell activation and effector function. We initially demonstrated BAFF costimulation of T cell activation in vitro. Generation of specific monoclonal antibodies identified BAFF-R as the only BAFF receptor present on T cells, and showed that it was expressed in an activation-dependent and subset-specific manner. Impaired BAFF costimulation in BAFF-R deficient mice indicated that BAFF-R was crucial for mediating BAFF effects in T cells. Analysis of T cell responses in vivo revealed that BAFF transgenic mice have increased T cell priming and recall responses to protein antigens, and showed a corresponding increase in the DTH model of Th1 cell-dependent inflammation. In addition, Th2-dependent allergic airway responses are suppressed in BAFF transgenic mice. Crossing to a B cell deficient background revealed that the proinflammatory effects of BAFF on T cell priming and DTH rely on the presence of B cells, while the suppressive effects during allergic airway inflammation are B cell independent. These data demonstrated that BAFF regulated the outcome of T cell responses in vivo and identified BAFF dependent crosstalk between T and B cells. Stimulation of B cells with BAFF induced the upregulation of MHC class II and ICOS-L both in vitro and in vivo. Induction of these cell surface molecules was associated with an increased capacity to induce T cell proliferation, however this effect was independent of ICOS-L expression. Thus it was demonstrated that BAFF regulated T cell activation and effector function both directly, via stimulation of BAFF-R, and indirectly, by altering the function of B cells. These data suggest that BAFF dependent alterations in T cell function may be an additional causative factor in the association between elevated BAFF levels and the generation of autoimmunity.

Cytotoxic T lymphocytes (CTL) are differentiated CD8+ T cells that eliminate virally infected cells and tumor cells. CTL lyse target cells by at least two distinct mechanisms: degranulation of cytolytic molecules and cell surface expression of Fas ligand (FasL), which induces apoptosis of Fas-expressing target cells. In addition to their defense function, these two cytolytic mechanisms also play crucial roles in homeostatic regulation and contribute to pathogenesis in many different model systems. To fully exploit killer cells in tumor and virus elimination, or dampen the immune response in, for example, autoimmune diseases, it is essential to understand the mechanisms that CTL employ to destroy target cells. In contrast to the well-characterized degranulation mechanism, the regulation of FasL expression on the CTL cell surface remains elusive and even controversial. The prevailing model at the time I initiated my studies was that FasL is stored in cytolytic granules and that FasL cell surface expression would be subject to the same controls as degranulation. In this thesis, I revealed for the first time that there are two waves of FasL cell surface expression upon target cell engagement, which are differentially regulated by TCR signaling and perform distinct roles in CTL mediated responses. I demonstrated that CTL degranulation and FasL lytic mechanisms are fully independent with respect to stored component localization and regulation. Finally, based on cell fractionation and imaging studies, I suggested that FasL is stored in a recycling endosome associated compartment, which is located in a special niche between the ER and mitochondria and uses a novel microtubule-independent secretory mechanism to translocate to the cell surface. Together, these findings provide important insight into the regulation and role of FasL in CTL mediated responses. / Immunology