Genetic dissection of intercellular interactions in vivo by membrane-permeable protein

Abstract

Unraveling cell–cell interaction is fundamental to understanding many biological processes. To date, genetic tools for labeling neighboring cells in mammals are not available. Here, we developed a labeling strategy based on the Cre-induced intercellular labeling protein (CILP). Cre-expressing donor cells release a lipid-soluble and membrane-permeable fluorescent protein that is then taken up by recipient cells, enabling fluorescent labeling of neighboring cells. Using CILP, we specifically labeled endothelial cells surrounding a special population of hepatocytes in adult mice and revealed their distinct gene signatures. Our results highlight the potential of CILP as a platform to reveal cell–cell interactions and communications in vivo.

Application of New Lineage Tracing Techniques in Cardiovascular Development and Physiology

“…Therefore, the new technique independent of cell-cell contact should be explored. For example, the use of the recently reported lipid-soluble and membrane-permeable fluorescence protein 78,79 or sortase-mediated intercellular labeling 80 could also be used for genetic tracing. In the future, coupling intercellular genetic tracing technology with orthogonal recombinase-mediated genome editing may provide new opportunities for understanding the cell origin and fate plasticity in cardiovascular development and pathogenesis.…”

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

“…Labelled neighbours were then extracted and profiled to characterise the tumour microenvironment ( Nolan et al, 2022 ; Ombrato et al, 2019 ). A Cre-inducible version of Cherry-niche has also been used to study homeostatic interactions between hepatocytes and endothelial cells in adult mice ( Zhang et al, 2023 )…”

Decoding the Complexity of Immune–Cancer Cell Interactions: Empowering the Future of Cancer Immunotherapy

“…Most proximity-based methods are dependent on cell–cell contact and interaction. Cherry-niche, caged luciferins, and CLIP (cre-induced intercellular labeling protein) are three approaches that do not solely rely on direct cell–cell contact for labeling [ 41 , 42 , 44 ]. In the Cherry-niche method, cells are engineered to express the enzyme Cherry-tagged ligase, which can attach a fluorophore to nearby cells expressing a complementary Cherry-tagged receptor [ 41 ].…”

“…Upon activation, the caged luciferins produce luminescent signals that can be detected and used to identify neighboring cells in the vicinity [ 42 ]. CLIP has an interesting methodology in that it can label cells that are in direct contact as well as those that are not in direct contact but are in proximity to each other [ 44 ]. This method involves the engineering of both the donor and receiver cells, where the donor cell secretes a lipid-soluble tag containing mCherry that labels the recipient cells [ 44 ].…”

“…CLIP has an interesting methodology in that it can label cells that are in direct contact as well as those that are not in direct contact but are in proximity to each other [ 44 ]. This method involves the engineering of both the donor and receiver cells, where the donor cell secretes a lipid-soluble tag containing mCherry that labels the recipient cells [ 44 ]. These approaches provide additional tools for studying cell–cell interactions, offering different mechanisms for labeling and detection beyond direct cell–cell contact.…”