Innate lymphoid cell heterogeneity in human tissues at steady state and during inflammation

Abstract

The family of innate lymphoid cells (ILCs) is the most recently identified group of innate immune cells. The ILC classification groups the cells according to their transcription factor and cytokine profile into ILC1, ILC2 and ILC3, paralleling the classification of T cells. ILCs are increasingly recognized for their important functions in the innate immune response, largely mediated through the production of high levels of cytokines. ILCs perform a variety of protective functions in a variety of situations such as the defense against bacterial, viral or helminth infections and the direct regulation of T cell responses, especially at mucosal barrier surfaces. In addition, they are known to be important for lymphoid tissue development, tissue repair and intestinal tolerance towards commensal bacteria. However, immune responses mediated by ILCs can also cause and sustain tissue damage and ILCs are implicated in various inflammatory and autoimmune disorders of the intestine, lung and skin.

This thesis focuses on ILCs in the human body at steady state and during inflammatory diseases. In the first study, we explored the transcriptome of tonsil ILCs using single-cell RNA sequencing and for each ILC subset revealed the expression of previously unrecognized genes which indicate a number of novel functions for ILCs. Furthermore, the analysis of ILC heterogeneity identified three subpopulations of ILC3 that were confirmed by FACS analysis and showed different functionality. In the second study, we present the first detailed characterization of the ILC compartment in the human liver, revealing unique features of ILC composition in adult as well as fetal liver. Furthermore, we detected a correlation between liver fibrosis and an increased frequency of intrahepatic ILC2. In light of the involvement of ILC2 in tissue remodeling, this could indicate that deregulated ILC2 activity contributes to the development of liver fibrosis in humans. The third study addresses the role of ILCs in inflammatory bowel disease (IBD), through systematically analyzing the alterations in ILC subset frequencies in the intestinal mucosa and blood of Crohn’s disease (CD) and ulcerative colitis (UC) patients compared to non-IBD controls. Thus, we identified specific changes in the mucosal ILC composition that were unique to newly diagnosed CD and UC patients respectively. In contrast, we show that in established CD and UC, the ILC distribution is similar but significantly different when compared to non-IBD patients. Overall, a reduction of NKp44+ ILC3 correlated with disease score in IBD. In addition, we investigated the homing marker expression seen in blood ILCs and observed unique expression profiles for each ILC subset. However, treatment with vedolizumab, an anti-a4b7 antibody, did not have an effect on ILC frequencies in the blood.

In summary, the work in this thesis contributes knowledge to aid a better understanding and characterization of ILCs in the human body. The identification of novel potential functions of these cells will help to advance the ILC field. Furthermore, the studies that indicate an involvement of ILCs in liver fibrosis and IBD suggest that ILCs are worth considering when developing new treatment targets in future investigations.