Spatial and functional specialization of human splenic innate lymphoid cells

Secondary lymphoid organs, including the spleen, integrate innate and adaptive immune responses. Studies in murine models and humans highlight Natural Killer (NK) cells and other innate lymphoid cells (ILC) as key organizers of splenic immune activity, yet their in situ organization and interactions within immune networks are incompletely understood. Here, we report a spatially resolved single-cell atlas of human splenic NK cells and ILCs. We identify CD39+TIGIT+CD56bright NK cells that localize with alternatively activated macrophages outside of B cell follicles. Splenic ILC2s, enriched in vascular-associated regions, express CD40L and can promote B cell survival and IgA secretion. Finally, we define three spatially and functionally distinct ILC3 subsets, namely KLF2⁺ progenitor-like ILC3s, follicle-associated CD38⁺ ILC3s, and IFNGR1⁺ ILC3s, that can promote B cell proliferation, IL-10 production, and IgG class switching. This spatially resolved atlas provides a comprehensive reference of human splenic ILC organization, specialization, and interaction networks. To date, the spatial and functional characterization of human splenic innate lymphoid cells (ILC) has remained limited. Here, the authors integrate CITE-seq and spatial transcriptomic data and present an atlas of human splenic NK and ILC cells and define high-resolution subset-specific spatial organization and interaction networks, providing insights into the presence of local immune niches in secondary lymphoid organs.