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Genomics

Single cell–cell communication

Nature Reviews Genetics volume 24, page 488 (2023)Cite this article

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Cell–cell communication (CCC) is critical for the proper development and homeostasis of multicellular organisms. Communication pathways mediated by ligand–receptor pairs can be inferred from single-cell RNA sequencing (scRNA-seq) data, but existing approaches perform analyses at the level of cell types or clusters, thereby losing valuable cell-specific information. Now, an article in Nature Biotechnology describes single-cell-resolved interaction analysis through binning (Scriabin), a framework for scalable CCC analysis of scRNA-seq data at the level of individual cells.

Using both previously published and newly generated datasets, the authors showed that Scriabin could identify known CCC events that agglomeration-based approaches had failed to detect. For example, when applied to a published single-cell atlas dataset comprising 76,592 cells from 4 regions of the developing fetal gut, Scriabin confirmed a communication pathway between a rare subset of fibroblast cells and intestinal stem cells. This interaction is important for maintenance of the intestinal stem-cell niche but, given the rarity of the cells involved, it is undetectable by agglomerative methods. Moreover, Scriabin was also able to detect new, biologically relevant CCC events and dynamics. For example, application of Scriabin to a published longitudinal dataset of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in human bronchial epithelial cells revealed that inflammatory responses were initiated by uninfected bystander cells and then amplified by infected cells.

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  1. Nature Reviews Genetics http://www.nature.com/nrg/

    Dorothy Clyde

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  1. Dorothy Clyde
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Correspondence to Dorothy Clyde.

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Clyde, D. Single cell–cell communication. Nat Rev Genet 24, 488 (2023). https://doi.org/10.1038/s41576-023-00631-8

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  • DOI: https://doi.org/10.1038/s41576-023-00631-8

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