In:
PLOS Computational Biology, Public Library of Science (PLoS), Vol. 18, No. 11 ( 2022-11-17), p. e1010715-
Abstract:
Cell-cell interactions shape cellular function and ultimately organismal phenotype. Interacting cells can sense their mutual distance using combinations of ligand-receptor pairs, suggesting the existence of a spatial code, i.e., signals encoding spatial properties of cellular organization. However, this code driving and sustaining the spatial organization of cells remains to be elucidated. Here we present a computational framework to infer the spatial code underlying cell-cell interactions from the transcriptomes of the cell types across the whole body of a multicellular organism. As core of this framework, we introduce our tool cell2cell , which uses the coexpression of ligand-receptor pairs to compute the potential for intercellular interactions, and we test it across the Caenorhabditis elegans ’ body. Leveraging a 3D atlas of C . elegans ’ cells, we also implement a genetic algorithm to identify the ligand-receptor pairs most informative of the spatial organization of cells across the whole body. Validating the spatial code extracted with this strategy, the resulting intercellular distances are negatively correlated with the inferred cell-cell interactions. Furthermore, for selected cell-cell and ligand-receptor pairs, we experimentally confirm the communicatory behavior inferred with cell2cell and the genetic algorithm. Thus, our framework helps identify a code that predicts the spatial organization of cells across a whole-animal body.
Type of Medium:
Online Resource
ISSN:
1553-7358
DOI:
10.1371/journal.pcbi.1010715
DOI:
10.1371/journal.pcbi.1010715.g001
DOI:
10.1371/journal.pcbi.1010715.g002
DOI:
10.1371/journal.pcbi.1010715.g003
DOI:
10.1371/journal.pcbi.1010715.g004
DOI:
10.1371/journal.pcbi.1010715.g005
DOI:
10.1371/journal.pcbi.1010715.g006
DOI:
10.1371/journal.pcbi.1010715.t001
DOI:
10.1371/journal.pcbi.1010715.s001
DOI:
10.1371/journal.pcbi.1010715.s002
DOI:
10.1371/journal.pcbi.1010715.s003
DOI:
10.1371/journal.pcbi.1010715.s004
DOI:
10.1371/journal.pcbi.1010715.s005
DOI:
10.1371/journal.pcbi.1010715.s006
DOI:
10.1371/journal.pcbi.1010715.s007
DOI:
10.1371/journal.pcbi.1010715.s008
DOI:
10.1371/journal.pcbi.1010715.s009
DOI:
10.1371/journal.pcbi.1010715.s010
DOI:
10.1371/journal.pcbi.1010715.s011
DOI:
10.1371/journal.pcbi.1010715.s012
DOI:
10.1371/journal.pcbi.1010715.s013
DOI:
10.1371/journal.pcbi.1010715.s014
DOI:
10.1371/journal.pcbi.1010715.s015
DOI:
10.1371/journal.pcbi.1010715.s016
DOI:
10.1371/journal.pcbi.1010715.s017
DOI:
10.1371/journal.pcbi.1010715.s018
DOI:
10.1371/journal.pcbi.1010715.s019
DOI:
10.1371/journal.pcbi.1010715.s020
DOI:
10.1371/journal.pcbi.1010715.r001
DOI:
10.1371/journal.pcbi.1010715.r002
DOI:
10.1371/journal.pcbi.1010715.r003
DOI:
10.1371/journal.pcbi.1010715.r004
Language:
English
Publisher:
Public Library of Science (PLoS)
Publication Date:
2022
detail.hit.zdb_id:
2193340-6
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