CINTER-seq: Chemical profiling reveals interaction-dependent cell landscapes and gene signatures in vivo

Physical interactions between cells are essential for physiological functions, yet the in situ cellular interactome remains largely unexplored. In this study, we developed a photocatalytic chemistry to capture targeted physically interacting cells in living mice. Furthermore, we introduce sequencing of the cellular interactome (CINTER-seq), a quantitative approach for multiplexed indexing of the captured cellular interactome, enabled by the simultaneous ex situ sequencing of multidimensional parameters. Using this system, we have revealed interaction-dependent gene signatures of immune cells in vivo, providing molecular insights into their interactions. Notably, we find that the immune checkpoint lymphocyte-activation gene 3 (LAG3) can mediate stable T cell-antigen-presenting cell (APC) contacts only by interacting with major histocompatibility complex class II (MHC class II) molecules, while neutrophils are strongly activated through interactions with tumor cells to adopt a pro-tumor phenotype in an interaction-dependent manner. These results underscore the potential of the CINTER-seq platform to make in vivo cellular interactome decoding routines in future studies.