Universal recording of cell-cell contactsin vivofor interaction-based transcriptomics

Abstract

Cellular interactions are essential for tissue organization and functionality. In particular, immune cells rely on direct and usually transient interactions with other immune and non-immune populations to specify and 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 cellular partners of regulatory T cells in steady state, 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) and identify a receptor-ligand pair necessary for the interaction between IECs and intraepithelial lymphocytes (IELs). Thus, uLIPSTIC provides a broadly useful technology for measuring and understanding cell-cell interactions across multiple biological systems.

Spatial transcriptomics elucidates medulla niche supporting germinal center response in myasthenia gravis thymoma

“…Interestingly, in thymomas, both single-positive T cells and migratory DCs (migDCs) expressed CCR7 , suggesting that the medullary characteristics of thymomas facilitate the mobilization of migDCs. Ligands for CCR4 specific to Treg Eff, such as CCL17 and CCL22 , were expressed by migDCs in thymomas, suggesting their role in maintaining Treg Eff in the medulla 20 (Figures 4A,B). Similarly, CXCL16 , the ligand for CXCR6 specific to Treg Eff, was expressed in cDC1, cDC2, and migDCs (Figures 4A,B).…”

Enabling neighbour labelling: using synthetic biology to explore how cells influence their neighbours

“…at its N terminus. When in proximity of an extracellular membrane-tethered N-terminal pentaglycine peptide (G5) on receiver cells, SrtA catalyses the covalent addition of the label onto the G5 peptide on receiver cells, allowing tracking of historical interactions ( Nakandakari-Higa et al, 2023 preprint; Pasqual et al, 2018 ). TMD, transmembrane domain.…”

Reprogramming dendritic cells through the immunological synapse: A two‐way street

“…To increase the degree of generality and robustness, it would be important to determine whether postsynaptic reprogramming occurs using “natural” CD4 + T‐cell partners, that is, T cells bearing TCRs of various affinities for a wider array of peptide‐loaded MHC‐II molecules. Novel techniques, for example, universal LIPSTIC technology [62] and PIC‐seq [54] may allow ascertaining the effect of polyclonal synaptic interactions on psDCs. Giladi and co‐workers used PIC‐seq to show that the genes upregulated in psDCs upon immunization with the helminth Nippostrongylus brasiliensis , which include Fscn1 or Ccl22 [54], may be conserved regardless of the clonality of the interaction.…”