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.

Type 1 Diabetes (T1D) is a complex autoimmune disorder in which T cells destroy the pancreatic islets, leading to a loss of insulin production and hyperglycemia. The disease incidence has increased globally over the last decades, primarily in individuals with low to moderate genetic risk. There is evidence that environmental factors play a role alongside genetic risk to trigger the disease. An environmental factor that has global influence is adoption of the Western diet, characterized by increased consumption of n-6 fatty acids, including linoleic acid (LA), and decreased consumption of n-3 fatty acids. Increased n-6/n-3 ratios are associated with enhanced susceptibility to autoimmune diseases. We sought to understand how linoleic acid affects the survival and function of T cells from the non-obese diabetic (NOD) mouse, a model for T1D. We found that linoleic acid's presence during in vitro activation of T cells led to an increased expansion of the cells in culture. Additionally, CD4+ and CD8+ T cells activated in linoleic acid's presence produced increased levels of pro-diabetogenic cytokines, including Interleukin-21 (IL-21) and Interferon-gamma (IFN-γ). In contrast, linoleic acid reduced IL-10-producing CD4+ T cells, which are protective in T1D, significantly changing the balance between pro-and anti-inflammatory T cell subsets. Gene expression analysis of T cells exposed to linoleic acid during in vitro activation revealed decreased gene expression of lipid-regulated transcription factors, peroxisome proliferator-activated receptors (PPAR), PPARα and PPARγ. These data suggest a role for these transcription factors and their associated pathways in linoleic acid-mediated T cell functions. Finally, we tested whether the T cell fatty acid response is regulated by the cytokine IL-7, which modulates T cell immunometabolism. However, our data did not reveal a prominent role for IL-7 in regulating the T cell response to linoleic acid. Together, these studies add to evidence that fatty acids present in the microenvironment can directly alter T cell functions and that changes in dietary components may contribute to enhanced T1D susceptibility.

Les thérapies anti-tumorales se sont considérablement améliorées au cours de la dernière décennie. Toutefois, les traitements utilisés actuellement rencontrent d'importantes limitations, notamment dans le cas de cancers métastatiques, révélant l'urgence de développer de nouvelles approches. Ainsi, l'immunothérapie par transfert adoptif de cellules T représente une approche innovante particulièrement prometteuse. Son principe s'appuie sur l'injection de cellules T autologues spécifiques d'antigènes tumoraux, préalablement manipulées et amplifiées ex vivo, chez des patients rendus lymphopéniques par chimiothérapie et/ou radiothérapie. Toutefois, même si l'état lymphopénique est induit par ces 2 protocoles de conditionnements, leurs effets sur l'environnement de l'hôte ainsi que sur le devenir des cellules T greffées étaient, jusqu'à nos travaux, mal connus. Par le biais de modèles murins, nous avons pu démontrer que le devenir des cellules T diffère après transfert dans des souris irradiées ou traitées par chimiothérapie (Bu/Cy). Ainsi, après transfert dans des animaux irradiés, on observe une prolifération préférentielle des cellules T CD8, dépendante de l'IL-7, est observée alors qu'un transfert chez des souris traitées Bu/Cy se traduit par une prolifération rapide, indépendante de l'IL-7, des cellules T CD4. De plus, ces comportements sont associés à d'importantes modifications de l'environnement généré chez l'hôte. Plus spécifiquement, nous avons démontré, dans les organes lymphoïdes secondaires, que la localisation et la représentation des différentes sous-populations de cellules dendritiques présentes étaient différentiellement modulées par le type de conditionnement utilisé. Par ailleurs, l'élimination spécifique des cellules CD11c+ chez des souris traitées Bu/Cy était accompagnée d'une inhibition importante de la prolifération rapide des cellules T CD4 greffées. L'ensemble de nos travaux montrent que les traitements lymphopéniques génèrent des environnements distincts capables de moduler le devenir des cellules T greffées.Durant ma thèse, nous avons également abordé de façon originale un aspect novateur de l'environnement en étudiant le rôle potentiel des nutriments comme régulateurs métaboliques des fonctions effectrices des cellules T. La glutamine est l'acide aminé le plus abondant du plasma, pouvant contribuer aux besoins bionénergétiques et biosynthétiques des cellules T en prolifération. Nous avons démontré dans nos travaux qu'une carence en glutamine lors de l'activation de cellules T CD4 par leur TCR entrainait un délai dans l'activation de la voie mTOR, une réduction de la production intracellulaire d'ATP aux temps précoces et se traduisait par une diminution de la prolifération. De plus, ces conditions étaient associées à une augmentation de la conversion de cellules CD4 T naïves, via TGFβ, en cellules régulatrices Foxp3+ , y compris en condition de polarization Th1. Par contre, la carence en glutamine n'a pas inhibé la différenciation Th2. Les cellules T Foxp3+ ainsi générées en condition limitante de glutamine présentaient in vivo des fonctions suppressives aussi efficaces que celles des cellules régulatrices nTregs. En effet, elles ont la capacité de bloquer l'induction de la colite provoquée par la greffe de cellules T effectrices dans des souris Rag2-/- . Nos travaux démontrent ainsi que l'environnement métabolique peut être un régulateur clé de la différenciation des cellules T CD4. L'ensemble de mes travaux de thèse ont mis en évidence de nouveaux paramètres capables de potentiellement modifier la survie et la réactivité des cellules T greffées. / Anti-tumor therapies have improved significantly over the decade. However, the currently used treatments have important limitations, notably for metastatic cancers, and the development of new approaches is therefore a high priority. Adoptive T cell therapy (ACT) represents an innovative strategy that has shown much promise. This therapy is based on the infusion of tumor-specific T cells, which have been manipulated and expanded ex vivo, into patients who have been rendered lymphopenic by chemotherapy and/or irradiation. It is interesting to note that while lymphodepletion is attained by the vast majority of conditioning regimens, the effects of these protocols on the host environment and potentially, on the destiny of adoptively-transferred T cells had not been elucidated prior to the studies which we initiated. Using a murine model, we found that the fate of adoptively-transferred T cells differs markedly in mice rendered lymphopenic by sub-lethal irradiation as compared to a busulfan/cyclophosphamide (Bu/Cy) chemotherapy regimen. Irradiation-mediated lymphopenia resulted in a skewed IL-7-dependent proliferation of donor CD8+ T cells, whereas Bu/Cy treatment led to an increased IL-7-independent, rapid CD4+ T cell proliferation. These alterations in T cell proliferation were associated with striking changes in the host microenvironment. More specifically, we demonstrated that the proportion and localization of different dendritic cell (DC) subsets in lymphoid organs were differentially affected by the type of conditioning. Furthermore, we found that these DC controlled the rapid donor CD4+ T cell division detected in Bu/Cy-treated mice as depletion of CD11c+ DC inhibited this proliferation. Altogether, our studies demonstrate that lymphopenic regimens generate distinct host environments which modulate the fate of adoptively-transferred T cells. Durind my PhD, we also investigated an original and novel aspect of the microenvironement by studying the potential role of nutrients as metabolic regulators of T cell effector function. Glutamine is the most abundant amino acid in the plasma and contributes to the bioenergetic and biosynthetic requirements of proliferating T cells. Here, we demonstrated that activation of CD4+ T cells under glutamine-deprived conditions results in a delayed mTOR activation with reduced early ATP production and decreased proliferation. Moreover, these conditions resulted in the conversion of naïve CD4+ T cells into Foxp3+ regulatory T cells (Tregs). This de novo Treg differentiation occurred even under Th1-polarizing conditions and was TGFβ-dependent. Interestingly, glutamine deprivation did not inhibit Th2 differentiation. Importantly, these converted Foxp3+ T cells showed enhanced in vivo persistence and were highly suppressive, completely protecting Rag-deficient mice from the development of autoimmune inflammatory bowel disease as efficiently as natural-occuring Tregs. Thus, our data reveal the external metabolic environment to be a key regulator of a CD4 T lymphocyte's differentiation. Altogether, the data generated during my PhD provide new insights into the identification of parameters that can potentially alter the survival and reactivity of adoptively-transferred T cells.

La sclérose en plaques est une maladie inflammatoire et démyélinisante caractérisée par la formation de lésions multifocales à travers le système nerveux central. Les lymphocytes pro- inflammatoires CD4 Th1 et Th17 sont considérés pathogéniques en sclérose en plaques et dans son modèle animal, l’encéphalomyélite auto-immune expérimentale. L’obésité et la composition du microbiome intestinal sont associées à une exacerbation de l’inflammation et à la progression de la sclérose en plaques, faisant des approches thérapeutiques métaboliques une méthode de choix afin d’améliorer l’évolution de cette maladie. La méthionine est un acide aminé essentiel métabolisé en S-adénosylméthionine (SAM), considéré comme le donneur universel de groupements méthyl, influençant l’expression génique. La restriction en méthionine est quant à elle associée à une diminution de la prise de poids et de l’inflammation, et in vitro, permet de réduire l’expansion des cellules Th17. Notre hypothèse est donc que diminuer l’activité du cycle de la méthionine permettrait de limiter la progression de l’encéphalomyélite autoimmune expérimentale en modulant le métabolisme des cellules T, la barrière hémo-encéphalique et le microbiome intestinal. Pour ce faire, l’encéphalomyélite autoimmune expérimentale est induite chez des souris mâles et femelles exposées à une diète réduite en méthionine ou contrôle afin d’effectuer une évaluation clinique quotidienne. Des expériences de cytométrie en flux, d’immunofluorescence et de séquençage d’ADN ribosomal 16S sont effectuées afin de déterminer l’activité des cellules immunitaires, la perméabilité de la barrière hémo-encéphalique et la composition du microbiome intestinal. Nos résultats montrent que la diète réduite en méthionine est associée à un délai significatif de l’apparition des symptômes neurologiques, avec une évolution clinique différente entre les mâles et les femelles. Ceci est associé à une diminution du nombre de cellules immunitaires infiltrant le système nerveux central, en plus d’influencer la composition du microbiome intestinal, suggérant des changements vers un profil plutôt anti-inflammatoire. La diète réduite en méthionine semble donc améliorer la progression de l’encéphalomyélite autoimmune expérimentale de manière différente selon les sexes et pourrait représenter une nouvelle voie thérapeutique contre la sclérose en plaques. / Multiple sclerosis is an inflammatory demyelinating disease of the central nervous system with a sex bias towards women. Proinflammatory Th1 and Th17 cells are considered pathogenic in multiple sclerosis and its animal model, experimental autoimmune encephalomyelitis. Obesity, western diet and gut dysbiosis increase inflammation and influence the course of this disease. Contrarily, dietary methionine restriction is associated with lower weight gain and reduced inflammation. In vitro, T cells upregulate components of methionine metabolism, including S- adenosylmethionine, upon activation and proliferation, while methionine restriction in the milieu reduces the expansion of Th17 cells. Thus, we hypothesized that limiting the activity of the methionine cycle will improve experimental autoimmune encephalomyelitis course by modulating Th17 cells through sex-specific epigenetic mechanisms and modification of the gut microbiome. To test this hypothesis, active experimental autoimmune encephalomyelitis is induced in male and female mice exposed to a methionine restricted or control diet. Clinical scores, flow cytometry, immunofluorescence and 16S rRNA sequencing are used to characterize the properties of immune cells, the blood-brain barrier, and the gut microbiome. Our results show that dietary methionine restriction is associated with a significantly delayed onset of neurological symptoms, with clinical differences in disease evolution between males and females. This is associated with a reduced number of immune cells and pathogenic proinflammatory T cells in periphery, then in the central nervous system. Methionine restricted diet is moreover associated with modification of the gut microbiome, suggesting a shift towards an anti-inflammatory profile. Finally, methionine restriction also influences the expression of adherence molecules such as VCAM-1, present in the blood-brain barrier, suggesting a neuro-protective effect. Our data reveal that methionine restricted diet ameliorates the clinical course and neuroinflammatory processes in experimental autoimmune encephalomyelitis in a sex-dependent manner and could represent a new therapeutic avenue to improve multiple sclerosis course.