Universal recording of immune cell interactions in vivo

Immune cells rely on transient physical interactions with other immune and non-immune populations to regulate their function. To study these “kiss-and-run” interactions directly in vivo, we previously developed LIPSTIC (Labeling Immune Partnerships by SorTagging Intercellular Contacts), an approach that uses enzymatic transfer of a labeled substrate between the molecular partners CD40L and CD40 to label interacting cells. Reliance on this pathway limited the use of LIPSTIC to measuring interactions between CD4+ helper T cells and antigen presenting cells, however. Here, we report the development of a universal version of LIPSTIC (uLIPSTIC), which can record physical interactions both among immune cells and between immune and non-immune populations irrespective of the receptors and ligands involved. We show that uLIPSTIC can be used, among other things, to monitor the priming of CD8+ T cells by dendritic cells, reveal the steady-state cellular partners of regulatory T (Treg) cells, and identify germinal center (GC)-resident T follicular helper (Tfh) cells based on their ability to interact cognately with GC B cells. By coupling uLIPSTIC with single-cell transcriptomics, we build a catalog of the immune populations that physically interact with intestinal epithelial cells (IECs) at steady state and profile the evolution of the interactome of lymphocytic choriomeningitis virus (LCMV)-specific CD8+ T cells in multiple organs upon systemic infection. Thus, uLIPSTIC provides a broadly useful technology for measuring and understanding cell–cell interactions across multiple biological systems. Overall design: uLIPSTIC interaction-dependent transcriptomics of the immune interacting partners of intestinal epithelial cells in steady-state mice and of LCMV-specific (P14) CD8+ T cells upon infection with lymphocytic choriomeningitis virus (LCMV) Armstrong cells in mediastinal lymph nodes, spleen, liver, and lung. Please note that the HTO, Barcode sequence, and hashtagged sample information is included in the 'readme.txt'.