Innate lymphoid cell differentiation and functions in intestinal homeostasis and disease

The gastrointestinal (GI) tract, which includes the small and the large intestine, is considered the largest immunological organ that plays a pivotal role in food digestion, nutrient absorption and fuel generation. Inflammatory Bowel Disease (IBD), which is broadly divided into Crohn’s disease (CD) and Ulcerative Colitis (UC), are multifactorial chronic intestinal inflammatory conditions that affect both pediatric and adult patients. Patients with IBD have a significantly increased risk of developing colorectal cancer (CRC). The immune system is undoubtably a major factor in disease pathogenesis and understanding what goes awry to cause disease is of great importance. This thesis focuses on a particular immune cell type called innate lymphoid cells (ILCs), and follows our journey to understand their role in the intestine of pediatric and adult patients with IBD as well as in CRC.

Since the discovery of ILCs is fairly recent, a lot remains unknown regarding their phenotype and function at steady and disease state, particularly in humans. In this thesis we performed immunophenotypic, functional, transcriptional as well as epigenetic assays to understand many aspects of their biology, differentiation and interactions with their adaptive counterparts, T cells.

In Paper I, we described the presence of CD45RA+ ILCs with naïve features in the tonsil that are transcriptionally, epigenetically and functionally distinct from the differentiated ILC subsets. We demonstrated that (CD45RA+)CD62L−ILCs were accumulated in the inflamed gut of adult patients with IBD and compared to their tonsil counterpart, these cells showed preferential differentiation towards IL22-producing ILC3s.

In Paper II, we determined the landscape of innate and adaptive lymphocytes in pediatric IBD (pIBD) through single-cell RNA sequencing. First, we demonstrated that ILCs are altered in pIBD, and in line with Paper I, we show that increased frequency of CD62L−ILCs is also a feature in pediatric IBD patients. Also, we were able to uncover shared and unique transcriptional signatures between ILCs and T cells and identify with a neighbor-based computational method the most and least inflamed cells in our dataset.

In Paper III, we explored the antigen-presenting properties of circulating and tissue-resident intestinal ILCs. Specifically, we were able to demonstrate that human circulating HLADR+ ILCs were able to internalize, process and present antigen to memory CD4+ T cells, and that this process is regulated by IL-1β through NF-κΒ signaling while it is suppressed by TGF-β. Additionally, via confocal microscopy we found that intestinal HLADR+ ILCs were located in close proximity to T cells, raising the possibility that the antigen presentation by ILCs could occur in vivo.

Overall, the research work included in this thesis contributes to advancing our understanding of ILCs in intestinal homeostasis and disease. The characterization of novel ILC states and functions in complex intestinal diseases such as IBD and CRC could pave the way for unraveling mechanisms that drive these diseases and potentially facilitate the development of more effective therapies for those patients.

List of scientific papers

I. Efthymia Kokkinou, Ram Vinay Pandey, Luca Mazzurana, Irene Gutierrez-Perez, Christopher Andrew Tibbitt, Whitney Weigel, Tea Soini, Anna Carrasco, Anna Rao, Maho Nagasawa, Suzanne M Bal, Mattias Jangard, Danielle Friberg, Ulrik Lindforss, Caroline Nordenvall, Malin Ljunggren, Staffan Haapaniemi, Åsa V Keita, Johan Söderholm, Charlotte Hedin, Hergen Spits, Yenan T. Bryceson, Jenny Mjösberg. CD45RA+CD62L− ILCs in human tissues represent a quiescent local reservoir for the generation of differentiated ILCs. Science Immunology. 2022 Apr 15;7(70).
https://doi.org/10.1126/sciimmunol.abj8301

II. Efthymia Kokkinou, Tea Soini*, Ram Vinay Pandey*, Aline van Acker*, Jakob Theorell, Paulo Czarnewski, Egle Kvedaraite, Niels Vandamme, Magda Lourda, Chiara Sorini, Whitney Weigel, Anna Carrasco, Christopher Andrew Tibbitt, Heinrich Schlums, Ulrik Lindforss, Caroline Nordenvall, Malin Ljunggren, Maja Ideström, Mattias Svensson, Jan-Inge Henter, Eduardo J. Villablanca, Yenan T. Bryceson, Helena Rolandsdotter, Jenny Mjösberg. The single-cell transcriptional landscape of innate and adaptive lymphocytes in pediatric-onset colitis. *Equal contribution. [Submitted]

III. Anna Rao, Otto Strauss*, Efthymia Kokkinou*, Mélanie Bruchard, Kumar P. Tripathi, Heinrich Schlums, Anna Carrasco-Garcia, Luca Mazzurana, Viktoria Konya, Eduardo J. Villablanca, Niklas K Björkström, Ulrik Lindforss, Hergen Spits, Jenny Mjösberg. Cytokines regulate the antigen-presenting characteristics of human circulating and tissue-resident intestinal ILCs. Nature Communications. 2020 Apr 27;11(1):2049. *Equal contribution.
https://doi.org/10.1038/s41467-020-15695-x