Profiling immune cell tissue niches in the spatial "omics" era.

Abstract

Immune responses require complex, spatially-coordinated interactions between immune cells and their tissue environment. For decades, we have imaged tissue sections to visualise a limited number of immune-related macromolecules in situ, functioning as surrogates for cell types or processes of interest. However, this inevitably provides a limited snapshot of the tissue's immune landscape. Recent developments in high-throughput spatial "omic" technologies, particularly spatial transcriptomics, and its application to human samples has facilitated a more comprehensive understanding of tissue immunity, by mapping fine-grained immune cell states to their precise tissue location, while providing contextual information about their immediate cellular and tissue environment. These data provide opportunities to investigate mechanisms underlying the spatial distribution of immune cells and its functional implications, including the identification of "immune niches", although the criteria used to define this term have been inconsistent. Here, we review recent technological and analytical advances in multi-parameter spatial profiling, focussing on how these methods have generated new insights in translational immunology. We propose a 3-step framework for the definition and characterisation of immune niches, which is powerfully facilitated by new spatial profiling methodologies. Finally, we summarise current approaches to analyse adaptive immune repertoires and lymphocyte clonal expansion in a spatially-resolved manner.