Tissue-specific adaptation and function of innate lymphoid cells

Abstract

Immune cell phenotype and function is strongly shaped by the tissue microenvironment. Adaptation of immune cells to tissue-specific microenvironment is, therefore, an essential process in homeostasis and inflammation. Innate lymphoid cells (ILCs) exhibit tissue-specific heterogeneity and function and are known to be key players as early responders in tissue inflammation and injury. However, the factors influencing ILC phenotype and function remain to be elucidated. Therefore, we aimed to the study the role of ILCs in the context of tissue adaptation and function under homeostasis and disease conditions. In the first study, we focused on the phenotypic adaptation of type 2 ILCs (ILC2s) in different organs and the factors influencing this process. We show that the murine effector ILC2s derived from various organs are capable in repopulating the niche of ILC2s at other anatomical locations where they undergo phenotypic adaptation specific to the tissue microenvironment. Using single-cell RNA sequencing of ILC2 populations, we observed an upregulation in the retinoic acid (RA) signalling in ILC2s adapting to the small-intestinal microenvironment. We also observed RA signalling-mediated reprogramming of ILC2s to the intestinal phenotype in vitro and in vivo. In the absence of RA signalling, ILC2s failed to acquire the intestinal phenotype and exhibited impaired worm expulsion during Strongyloides ratti infection, indicating the functional importance of tissue-specific imprinting of ILC2s. In conclusion, our study highlights an important attribute of effector ILC2s in retaining flexibility to adapt to changing tissue-specific microenvironment, enabling them to exert tissue-specific functions such as controlling intestinal helminth infections. In the second study, we aimed to characterise natural cytotoxicity receptor (NCR) and T-bet expressing ILC populations in murine kidney and study their functional role in crescentic glomerulonephritis. Detailed profiling of NCR+ T-bet+ ILCs in murine kidney revealed conventional natural killer (cNK) cells and type 1 ILCs (ILC1s) as two major subsets. In a mouse model of crescentic glomerulonephritis, induction of renal inflammation did not have a substantial influence on the abundance and phenotype of NK cells or ILC1s. We utilized widely used depletion antibodies for total NCR+ ILCs (anti-NK1.1 antibody) and for cNK cells (anti-asialoGM1 serum) to perform the functional analyses in this model. However, these strategies proved to be unreliable tools as they were associated with significant off-target depletion of kidney natural killer T cells (NKT; anti-NK1.1) and CD8+ T cells (anti-asialoGM1). Furthermore, we observed that neither the depletion of cNK and ILC1s in NKT cell-deficient mice and CD8+ T cell-deficient mice nor the specific genetic deletion of cNK cells in Ncr1Cre/wt × Eomesfl/fl mice altered the progression of disease in experimental glomerulonephritis. In summary, we show that cNK cells and ILC1s do not play a vital role in initiation and progression of glomerulonephritis and suggest caution while using standard antibody depletion methods to study the functional role of NCR+ T-bet+ ILCs in mouse models.