Monitoring of cell-cell communication and contact history in mammals

Abstract

Monitoring of cell-cell communication in multicellular organisms is fundamental to understanding diverse biological processes such as embryogenesis and tumorigenesis. To track cell-cell contacts in vivo, we developed an intercellular genetic technology to monitor cell-cell contact and to trace cell contact histories by permanently marking contacts between cells. In mice, we engineered an artificial Notch ligand into one cell (the sender cell) and an artificial receptor into another cell (the receiver cell). Contact between the sender and receiver cells triggered a synthetic Notch signaling that activated downstream transcriptional programs in the receiver cell, thereby transiently or permanently labeling it. In vivo cell-cell contact was observed during development, tissue homeostasis, and tumor growth. This technology may be useful for studying dynamic in vivo cell-cell contacts and cell fate plasticity.

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

“…Second, not all cells that are physically juxtaposed interact to the same extent, as exemplified by the low degree of labeling, if any, of conventional T cell or resident DC acceptors by Treg cell donors. uLIPSTIC thus differs from and complements methods such as synNotch variants, which, although they can be used to drive transcription of downstream reporter genes 26 , are based on molecular partners that bind each other with much higher (nanomolar) affinity, and thus are in theory themselves capable of driving cellular interactions 49 ; as well as methods based on label transfer by extracellular diffusion 25 , which can better be conceived of as approaches to mark close cellular neighborhoods rather than functional interactions. uLIPSTIC also has advantages over cell doublet-based methods 50 , in that uLIPSTIC labeling is continuous rather than binary, can study interactions that do not survive cell extraction and flow cytometry processing, and does not require computational deconvolution of single-cell transcriptional profiles from doublets, although our system has the disadvantage that it requires genetic engineering of its components.…”

“…An attractive strategy to overcome these limitations has been proximity-based labeling across cellular membranes [23][24][25][26][27] . These strategies rely on equipping "donor" cells with enzymes or other signals that act over short distances to identify "acceptor" cells in either close proximity or physical contact with these donors.…”

Perfect duet: Dual recombinases improve genetic resolution

“…New marker genes of specific cell subtypes locked on by dual recombinases can be identified by deep sequencing. Proximal cell and molecule profiling by gLCCC/gTCCC 96 and proximity labelling 97 that utilizes synNotch and HRP modules can be tamed by dual recombinases and combined with spatial transcriptomics or proteomics to unveil in vivo and in situ cell–cell interaction and the underlying molecular mechanisms. Moreover, live imaging with cell fate mapping allows for real‐time and in situ inspection of cellular processes and can facilitate the use of photoactivatable recombinases for light‐controlled recombination with tissue and temporal constraints 98,99 .…”

Bioorthogonal photocatalytic quinone methide decaging for cell-cell interaction labeling

“…The sensitivity and selectivity of the labeling method were demonstrated in the TCR-pMHC system and the broad utility was proven by detection of multiple cell types (including HEK293T, antigen-specific T cells and NK cells). By rational design and establishment of quinone methide probes and platforms, we provided a photocatalytic decaging method differing from those doublet-based methods requiring external computational assistant 41 or contact-dependent methods which may have concerns due to the artificial cellular interaction interference 42,43 . It is also complementary to the proximity labeling methods based on specific enzyme or chemical intermediates for intercellular interaction labeling.…”