Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal.

The clinical efficacy of adoptive T cell therapies including CAR T therapy are limited by poor in vivo persistence and moderate anti-tumor efficacy. According to the literature, metabolism plays a critical role in the phenotypic state and fate of T cells during antigen-driven expansion. During different stages of a T cell life cycle, the predominant pathway used for metabolism changes. Naïve T rely on oxidative phosphorylation, but as the T cells becomes activated, their metabolic profile switches to become more reliant on glycolysis. Most T cells become terminally differentiated and become senescent once they have performed their cytotoxic function. A minority of the activated T cells gradually start to rely on oxidative phosphorylation once again and become memory T cells. Memory T cells can become either effector memory or central memory T cells. These memory T cells, specifically central memory T cells, are the key to T cells persistence during both ex vivo and in vivo expansion and following disappearance of the antigenic stimulus. Since the metabolic profile of the T cells plays a critical role in its differentiation state, we tested the hypothesis that inhibitors of intermediary metabolism could promote a metabolic profile that is more desirable for the optimal phenotype consistent with the memory phenotype that would favor persistence in spite of strong activation signals. The four inhibitors screened were: a PFKFB3 inhibitor, an inhibitor of a key step in glycolysis; ibrutinib, an inhibitor of Bruton’s tyrosine kinase; idelalisib, an inhibitor of PI3K subunit; and duvelisib, an inhibitor of PI3K and PI3K gamma subunits. To test this hypothesis, T cells were cultured with or without each compound and then the analysis included: phenotypic analysis by flow cytometry, quantitative analysis by counting cells with ethidium bromide acridine orange, and metabolic profiling by the Seahorse assay. This study was conducted using T cells from a human healthy volunteer that were collected by apheresis. T cells were cultured in a G-Rex plate for 15 days with complete media supplemented with recombinant human IL-2 (30 U/mL). Cells were activated on day 1 and day 8 by the addition of anti-CD3/CD28 beads and test metabolic inhibitor compounds were added every 4 days. T cells cultured with idelalisib, duvelisib, and ibrutinib had increased expansion (approximately50-fold: idelalisib/ duvelisib and 21-fold ibrutinib) when compared to control (cells with beads alone) with only 6-fold expansion. Phenotypic analysis performed using flow cytometry showed an increased percentage of CD27+ CD28+ in the CD8+ and CD4+ T cell cell populations in the idelalisib treated group and decreased number of senescent T cells that are double negative for CD27 and CD28. Consistent with our hypothesis, metabolic analysis showed that cells treated with idelalisib and duvelisib were more reliant on oxidative phosphorylation, rather than glycolysis as compared to the control cultures. Cells treated with duvelisib also showed an increased spare respiratory capacity (SRC), which is associated with more efficacious memory T cells. The results of these studies show that metabolism plays a critical role in the long-term survival of T cells. We demonstrate that inhibiting intermediary metabolism, specifically inhibiting PI3K, favorably alters the metabolic state of the T cells leading to increased cell numbers and T cells with a phenotype consistent with enhanced ex vivo and in vivo proliferation and persistence.

The immune system recognizes and eliminates an enormous array of pathogens due to the diverse antigen receptor repertoire of T and B lymphocytes. However, the development of lymphocytes bearing receptors with unique specificities requires the generation of programmed double strand breaks (DSB) coupled with bursts of proliferation, rendering lymphocytes susceptible to mutations and oncogenic transformation. Thus, mechanisms responsible for monitoring global genomic integrity, such as those coordinated by the ATM (ataxia-telangiectasia mutated) kinase, must be activated during lymphocyte development to limit the oncogenic potential of antigen receptor locus recombination. I show that ATM deficiency compromises TCRα recombination and the post-mitotic survival of T-cell receptor αβ (TCRαβ+) CD4+CD8+ (DP) thymocytes, providing a molecular and developmental basis for the immunodeficiency characteristic of ATM loss. Moreover, I show that in early thymocyte progenitors undergoing TCRβ recombination, ATM loss leads to cell cycle defects and developmental arrest, likely facilitating the acquisition of mutations that contribute to leukemogenesis. Using ATM deficiency as a murine model of T cell precursor acute lymphoblastic leukemia (T-ALL), I demonstrate that IL-7 signaling, a critical survival and proliferation signal during early stages of normal thymocyte development, is also required for leukemic maintenance. Moreover, we show for the first time that in normal and leukemic thymocyte precursors, interleukin 7 receptor (IL-7R) expression and function are controlled by Notch signaling, a key determinant of T cell fate. Collectively, these findings provide insight into the mechanisms by which ATM promotes normal lymphocyte development and protects from neoplastic transformation, while establishing the groundwork for assessing the molecular events that lead to the initiation and stepwise progression of T cell leukemogenesis.

Long-term survival of cardiac transplant recipients continues to be severely limited by the development of a pathological, chronic rejection process, termed allograft vasculopathy (AV). This remains to be the case despite dramatic improvements in the areas of surgical techniques, pre- and post-operative care, and immunosuppression. To model the clinical setting we used calcineurin inhibitor (CNI) immunosuppression, the cornerstone of post-transplant immunosuppression, in a murine aortic interposition transplant model for our analysis of AV development. This model mimics the presentation of AV in human cardiac transplants through the development of a progressively occlusive neointimal lesion. Our previous work in this model has demonstrated that CD8+, but not CD4+, T cells play a role in neointimal lesion formation. Further investigation also highlighted a specific requirement for either CD8+ T cell-derived IFN-γ or direct cytotoxicity in the development of lesion formation. In the current study we confirmed that CD8+ T cell-derived IFN-γ also leads to the loss of medial smooth muscle cells, an event which inversely correlates with lesion formation. The Fas/FasL direct cytotoxic pathway was also significantly involved in neointimal lesion formation and medial remodeling. This work clarified the pathways utilized by CD8+ T cells in their role as mediators of AV development. Recognizing the threat that CD8+ T cells pose to cardiac transplant recipients in the presence of CNI immunosuppression, and a growing concern with the presence of anti-donor memory T cells in transplant recipients, we next explored the development of memory CD8+ T cells in the presence of CNI immunosuppression. We first established that memory CD8+ T cells could not develop when CNI immunosuppression was initiated immediately post-challenge. Next, we hypothesized that the clinical practice of CNI delay post-transplant would permit the development of de novo memory CD8+ T cells. Immediate and early initiation was sufficient to prevent the development of de novo memory CD8+ T cells. However, later delay to within a clinically practiced timeframe did permit the development of de novo memory CD8+ T cells. Our analysis revealed that this population demonstrated equivalent functionality to de novo memory CD8+ T cells generated in the absence of CNI immunosuppression.

abstract: There are many biological questions that require single-cell analysis of gene sequences, including analysis of clonally distributed dimeric immunoreceptors on lymphocytes (T cells and B cells) and/or the accumulation of driver/accessory mutations in polyclonal tumors. Lysis of bulk cell populations results in mixing of gene sequences, making it impossible to know which pairs of gene sequences originated from any particular cell and obfuscating analysis of rare sequences within large populations. Although current single-cell sorting technologies can be used to address some of these questions, such approaches are expensive, require specialized equipment, and lack the necessary high-throughput capacity for comprehensive analysis. Water-in-oil emulsion approaches for single cell sorting have been developed but droplet-based single-cell lysis and analysis have proven inefficient and yield high rates of false pairings. Ideally, molecular approaches for linking gene sequences from individual cells could be coupled with next-generation high-throughput sequencing to overcome these obstacles, but conventional approaches for linking gene sequences, such as by transfection with bridging oligonucleotides, result in activation of cellular nucleases that destroy the template, precluding this strategy. Recent advances in the synthesis and fabrication of modular deoxyribonucleic acid (DNA) origami nanostructures have resulted in new possibilities for addressing many current and long-standing scientific and technical challenges in biology and medicine. One exciting application of DNA nanotechnology is the intracellular capture, barcode linkage, and subsequent sequence analysis of multiple messenger RNA (mRNA) targets from individual cells within heterogeneous cell populations. DNA nanostructures can be transfected into individual cells to capture and protect mRNA for specific expressed genes, and incorporation of origami-specific bowtie-barcodes into the origami nanostructure facilitates pairing and analysis of mRNA from individual cells by high-throughput next-generation sequencing. This approach is highly modular and can be adapted to virtually any two (and possibly more) gene target sequences, and therefore has a wide range of potential applications for analysis of diverse cell populations such as understanding the relationship between different immune cell populations, development of novel immunotherapeutic antibodies, or improving the diagnosis or treatment for a wide variety of cancers. / Dissertation/Thesis / Doctoral Dissertation Microbiology 2017

Human Immunodeficiency Virus 1 (HIV-1) remains a significant public health concern due to the lack of a cure. In spite of anti-retroviral therapies, HIV-1 persists within infected cells as integrated transcriptionally silent proviruses. Re-activation after therapy interruption results in new HIV-1 replication. Attempts to clear this reservoir through the use of latency reversing agents by targeting cellular mechanisms that maintain HIV-1 in a latent state have been unsuccessful. In addition, subsets of latently infected cells exist within the reservoir that display differential capacities for provirus induction. In order to understand the nature of the reservoir and manipulate it therapeutically, more knowledge is needed regarding factors that bias a virus towards latency or replication at the time of infection. Because multiple mechanisms that regulate HIV-1 transcription, including chromatin remodeling, transcription factor activation and polymerase pausing, are regulated by the T cell receptor (TCR), I hypothesized that signaling at the time of infection determines proviral fate. I transduced Jurkat cell lines and primary CD4+ T cells with chimeric antigen receptors (CARs) that mimicked signaling from the TCR. These CARs spanned a 3-log range of binding affinities for their ligand, providing a tunable model. High levels of TCR stimulation during infection biased cells towards productive replication and the formation of an inducible latent reservoir. Examination of the mechanisms downstream from TCR signaling revealed that robust cellular activation led to a release of the repressor Negative Elongation Factor from the paused RNA Polymerase II, facilitating transcriptional elongation. Because signaling determined the presence of repressive factors, I sought to manipulate the balance between latency and expression through recruitment of repressors to the HIV-1 provirus using a nuclease-deficient CRISPR Associated Protein 9 fused to a Krüppel Associated Box Domain. I screened a pool of guide RNAs that mediated transcriptional repression of HIV-1. Our lab discovered that guides bound to the HIV-1 Long Terminal Repeat prevented viral re-activation in an integrated cell model of HIV-1 latency. The research presented here confirms my hypothesis that signals during infection have prolonged effects on latency reversal. I provide evidence that manipulation of these mechanisms represent therapeutic targets for cure efforts.

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Daniel R Frederick