Tissue-niches and cellular interactions of mouse and human ILCs at single-cell resolution

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Emerging evidence suggests that ILCs residing in a given tissue canin principle be generated from different cellular sources (i.e. localresident versus recruited cells) and at different timepoints duringontogeny (e.g. embryonic, neonatal, adult). The local pools of ILCscan undergo substantial changes during inflammation and infection.We are only beginning to understand the relationship ofheterogeneous subtypes of tissue-ILCs, their “division of labor” aswell as their local interactions. With the advent of single-celltechnologies we have started to decipher the heterogeneity of ILCs.However, the tissue microenvironment of ILCs remains largelyunexplored due to the lack of experimental methods enabling thehigh-resolution profiling of cell types in their tissue context. Molecularcontrol exerted by tissue-niches, e.g. via paracrine signaling, likelyaffects the maintenance and local differentiation of progenitor cells,and controls tissue-adaptation of ILCs to facilitate particular functions.Revealing the cell type composition of the microenvironment fordistinct ILC sub-types residing in a given tissue context would allow topredict sub-type- or differentiation stage-specific niches and to testmolecules involved in these cellular interactions. These contextdependentmechanisms are challenging to study, particularly inhuman tissues, and novel approaches to validate findings from mousemodels and to address these questions in patient samples areurgently needed. Our findings obtained during the first funding periodunderscore that by combining single-cell RNA-Seq, the in silicoprediction of differentiation trajectories and the in vivo validation indisease models, we are able to infer early differentiation stages ofILCs and to reveal the developmental and functional heterogeneity ofthese cells as well as the dynamic changes occurring during immunechallenge. We have now developed novel approaches to combine thepower of single-cell RNA-Seq in cell type identification with the spatialresolution of single-molecule FISH, multiplexed across >100 genes, inorder to map cell types in situ. On this basis, we propose toinvestigate human and mouse ILCs and their in situ tissue-context inthe liver during homeostasis, tissue-damage and repair. The essentialgoal of the project is to reveal functionally distinct sub-types and theirdifferentiation dynamics and to identify the mechanisms of intercellularcross-talk involved in the emergence and regulation of thesepopulations in health and disease. To this end, we will build on ourcombined established expertise in the experimental in vivo study ofILCs in models of hepatic tissue damage and regeneration and ourexperience in scRNA-seq, in-depth bioinformatical analyses andspatial reconstruction of the liver microenvironment.