ILCs

Innate lymphoid cells (ILCs) are a highly heterogenous family of lymphocytes primarily found residing in mucosal tissues, where they respond rapidly to local stimuli to produce potent, antigen-independent, cytokine responses. Here, they engage extensively with their microenvironment, interacting with epithelial, stromal and neuronal cells. In addition, they have been shown to communicate with T cells, exhibiting antigen-presenting capabilities. Consequentially, ILCs play critical roles in the maintenance of barrier integrity, shaping microbial colonisation and regulating local immune responses under both homeostatic and inflammatory conditions.

Often considered the innate counterpart to adaptive T cells, ILCs can be split into 5 subtypes based on their development, transcription factor dependence, surface marker expression, and effector functions. These comprise natural killer (NK) cells, lymphoid tissue inducer cells, and the helper-like type 1, 2 and 3 ILCs (ILC1, ILC2, and ILC3, respectively)¹.

Broadly speaking, NK cells functionally parallel cytotoxic CD8+ T cells, whilst the helper-like ILCs mirror their CD4+ counterparts¹:

• ILC1s resemble Th1 cells: T-bet⁺ and produce IFN-γ as their main cytokine.
• ILC2s resemble Th2: GATA3⁺, producing IL-5 and IL-13.
• ILC3s resemble Th17/Th22 cells: RORγt⁺, producing IL-17 and IL-22.

However, this paradigm is an oversimplification as ILCs display considerable functional diversity. For example, ILC3s can also produce IL-2, GM-CSF and TGF-b. Moreover, a clear delineation between subsets, particularly NK cells and ILC1s, remains an area of active debate in humans.

Complicating matters further, ILCs display marked tissue specificity, varying in both frequency and phenotype. Furthermore, within tissues, they exhibit substantial transcriptional heterogeneity and plasticity². For example, research in mice has shown that in homeostasis, ILC3s form the major ILC population in the intestine; however, in response to an infection or IL-12 signalling, resident ILC3s are depleted, replaced by an expansion of IFN-γ-producing “ex-ILC3s”, exhibiting a phenotype near-indistinguishable from ILC1s³.

This plasticity may have important implications in human tissues. Alterations in ILC composition have been observed in inflammatory bowel disease, with the reduction in the relative frequency of ILC3s coupled to the increased presence of cytotoxic ILC1 / ILC1-like cells forming a hallmark of active inflammation. Yet, whether this reflects ILC3-to-ILC1 plasticity or selective recruitment remains unclear³.

The low abundance, tissue restriction, and under-representation of ILCs in many single-cell atlases form a major bottleneck into research on human ILCs. As a result, much of our foundational knowledge has been derived from mouse models, yet the extent to which these findings translate to humans remains poorly understood. For example, ILC2s are abundantly found in the murine small intestine, whilst being exceedingly rare in the human one.

Previously, one of the main ways to generate large numbers of human ILCs in vitro was to culture ILC precursors on stromal feeder cell lines. Using this method, specific conditions are required to induce the differentiation of specific ILC subtypes; however, not all families of ILCs were able to be generated at once. More recently, organoid-based co-culture systems have emerged, in which easily accessible human ILC precursors are cultured with stem cell- or biopsy-derived intestinal organoids⁴. These systems provide a reductionist yet physiologically relevant model to study ILC development and function within a tissue-specific context, with scope for increasing complexity through the incorporation of additional cell types, such as neurons.

Text by Isabelle Coales, King’s College London

 

References

1. Vivier, E. et al. Innate Lymphoid Cells: 10 Years On. Cell 174, 1054–1066 (2018).
2. Meininger, I. et al. Tissue-Specific Features of Innate Lymphoid Cells. Trends Immunol. 41, 902–917 (2020).
3. Coman, D., Coales, I., Roberts, L. B. & Neves, J. F. Helper-Like Type-1 Innate Lymphoid Cells in Inflammatory Bowel Disease. Front. Immunol. 13, (2022).
4. Jowett, G. M. et al. Organoids capture tissue-specific innate lymphoid cell development in mice and humans. Cell Rep. 40, (2022).