Homeostasis is the ability of our body to maintain a stable internal environment within narrow ranges while adjusting to the changing environment. The immune system is important in the maintenance of homeostasis by continually surveying and responding to challenges with a self-limiting inflammatory response. In this thesis we have further explored the programming and adaptation of T(reg)-cells in humans at tissue sites in both homeostatic and chronic inflammatory conditions, where the inflammatory response is not self-limiting anymore. Two of these chronic inflammatory conditions are juvenile idiopathic arthritis (JIA) and Crohn’s disease. JIA encompasses all forms of arthritis in childhood. Crohn’s disease is a chronic relapsing-remitting inflammatory disease of the gastro-intestinal tract. Despite the myriad of studies and enormous progress made over the past decades towards deciphering the pathogenesis of and treatment for both diseases we still lack an understanding especially in the human setting. Further fundamental insight in the differentiation and adaptation of immune cells to their respective sites of function will improve our understanding of the pathogenesis and relapsing-remitting course of these inflammatory diseases, and may lead to identification of new therapeutic targets and the fine-tuning of therapeutic strategies.
In chapter 2 we show that inflammation-derived functional Treg cells have a transcriptional profile characterized by upregulation of both a core Treg cell and effector program. We identify a specific human eTreg cell signature that includes the vitamin D receptor as a predicted regulator in eTreg cell differentiation. Furthermore, we show that the Treg cell profile has striking overlap with tumor-infiltrating Treg cells. We extend on this in chapter 3 using single cell RNA-sequencing. We reveal that there is a heterogeneous population of Tregs at the site of inflammation in JIA. SF Treg differentiate to a classical eTreg profile with a more dominant suppressive or cytotoxic profile that share a similar TCR repertoire, or towards GPR56+CD161+CXCL13+ Tregs with a more distinct TCR repertoire. Genes characterizing GPR56+CD161+CXCL13+ Tregs were also mirrored in other T cell subsets in both the tumor and autoimmune setting. Then, in chapter 4 we combine publicly available Treg datasets to explored shared and distinct genes, pathways and key regulators characterizing the transcriptional program of Tregs comparing PB to homeostatic tissue, and homeostatic tissue to inflammatory/tumor tissue. Tregs first adapt to the tissue microenvironment regulated by HOX genes followed by activation, interaction with and influence on the local tissue architecture and eTreg differentiation. BATF is an important transcription factor in tissue adaptation and differentiation independent of the state of the tissue. FOXP3, HDGF and NR3C2 are shared regulators of the transcriptional program in both inflamed and tumor tissue-derived Tregs. Overall, our data demonstrate that human tissue-derived Treg cells acquire a conserved and specific eTreg cell profile which is fine-tuned by environment-specific adaptations.
The last three chapters focus on the adaptation of T cells residing in the mucosal barrier. This barrier consists of the epithelium and the lamina propria which are separated by a 7 µm basal membrane. In chapter 5 we have reviewed the homeostatic and pathogenic functions of T cells residing in the epithelium of the intestinal mucosa in humans.
Chapter 6 focuses on CD4 T cells and chapter 7 on CD8 T cells in patients with Crohn’s disease and control subjects without a chronic inflammatory conditions of the gut. We observed differential and tightly regulated adaptation of T cells to the epithelium and lamina propria. Inflammation in Crohn’s disease patients primarily induces changes within the epithelium and not the lamina propria. The main consequence of epithelial adaptation, irrespective of inflammation, seems to be an overall dampening of broad (pro-inflammatory) responses and tight regulation of lifespan. These data suggest differential regulation of the lamina propria and epithelium, with a specific regulatory role in the inflamed epithelium.
Lastly, in chapter 8 the findings in this thesis together with unpublished data were discussed and put in a broader perspective.