Unbiased recording and identification of thymic cellular interactomes using synthetic Notch receptors

Cellular interactions between thymocytes and other immune and stromal thymic cells play a key role in T cell maturation and homeostasis. Previous efforts delineating the cellular interactomes that support T cell development have mostly relied on imaging techniques, genetic deletion of essential molecular factors and bone marrow chimeras. Here, using synthetic NOTCH receptors we took a direct and unbiased genetic approach to fluorescently label cells in physical contact with CD4⁺ and CD4⁺CD8⁺ thymocytes in vivo in mice. Prospective isolation and transcriptional characterization at single-cell level of the interacting cells exposed the thymic cellular interactome that supports these T cells and how ageing erodes these interactions. Cellular interactors included, among others, dendritic cells, B cells, IL-17⁺ γδ T cells, fibroblast subsets and thymic epithelial cells. Ligand-receptor pair analyses highlighted signals involved in survival, differentiation and antigen presentation. Our work provides a new means to study thymic cellular interactions.