CD4+ and CD8+ T cell behavior in the landscape of intestinal damage

Intestinal damage can be the result of different types of injury, for instance resulting from chemotherapy or sustained inflammation. This thesis investigates the behavior of CD4+ and CD8+ T lymphocytes in the context of intestinal epithelial damage. We focused on (intestinal) graft-versus-host disease (GVHD), a devastating complication of hematopoietic stem cell translation (HSCT), as tissue damage is a risk factor and a result of GVHD development. To study T cell behavior in the context of tissue damage, we developed an ex-vivo 3D model system using adult stem cell-derived small intestinal epithelial organoids, self-assembling 3D structures that resemble the native tissue of origin, and T cells isolated from peripheral blood of healthy donors. This platform enables to characterize how different types of damage affect intestinal epithelial cells, and how this damage influences T cells in turn. This thesis provides an overview of GVHD pathogenesis, T cell contribution to pathology, T cell response to damage and potential of using organoid models for immunological research (Chapter 1). The model system presented in this thesis was used to investigate the impact of chemotherapy on intestinal epithelial cells, and the resulting T cell responses (Chapter 2). Exposure of intestinal organoids to chemotherapeutics used in HSCT patients, namely Busulfan, Fludarabine and Clofarabine, induces damage-related responses affecting both the capacity to regenerate and transcriptional reprogramming. Damage from chemotherapy determines the release of galectin-9 (Gal-9), a protein that promotes T cell migration and activation in this system. As Gal-9 has pleiotropic effects on T cells depending on the context, we provided a comprehensive review of Gal-9’s immunomodulatory effects on T cells (Chapter 3). Moreover, we studied the effect of interferon-gamma (IFNγ)-induced damage, a form of damage typical of inflammatory conditions such as (intestinal) GVHD and inflammatory bowel disease (IBD) (Chapter 4). IFNγ-treatment of organoids leads to transcriptional reprogramming, marked by a switch to a pro-inflammatory gene expression profile, including transcriptional upregulation of the chemokines CXCL9, CXCL10, and CXCL11. IFNγ-treatment of organoids leads to enhanced T cell migration in a CXCL11-dependent manner without affecting T cell activation status. In addition, we further characterized T cells exposed to damaged organoids on a transcriptional level, showing that they respond to different types of damage in a distinct manner (Chapter 5). Chemotherapy-induced damage results in an augmented metabolic and proliferative response, while IFNγ-induced damage determines a pro-inflammatory, metabolically inactive and quiescent transcriptional state. Lastly, the findings presented in this thesis are contextualized and are used to provide a future outlook for follow-up research (Chapter 6). Taken together, our findings provide a foundation for follow-up preclinical and prospective clinical investigations aimed at manipulating Gal-9 and CXCL11 to regulate T cell responses in the intestine. This thesis offers significant insights into the pathogenesis of T cell-mediated gastrointestinal diseases such as GVHD.