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bioRxiv · 10.1101/2022.02.04.479174

LRLoop: Feedback loops as a design principle of cell-cell communication

Xin, Y.·Lyu, P.·Jiang, J.·Zhou, F.·Wang, J.·Blackshaw, S.·Qian, J.
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Abstract

Genome-wide gene expression profiling, and single-cell RNA-seq in particular, allows the predictions of molecular mechanisms regulating cell-cell communication based on the expression of known ligand-receptor pairs. Currently available techniques for predicting ligand-receptor interactions are one-directional from sender to receiver cells. Here we describe LRLoop, a new method for analyzing cell-cell communication that is based on bi-directional ligand-receptor interactions, where two pairs of ligand-receptor interactions are identified that are responsive to each other, and thereby form a closed feedback loop. We assessed LRLoop using both bulk and single-cell datasets and found our method significantly reduces the false positive rate seen with existing methods. Finally, we applied LRLoop to the single-cell datasets obtained from retinal development and discovered many new bi-directional ligand-receptor interactions among individual cell types that potentially control proliferation, neurogenesis and/or cell fate specification.

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Xin, Y., Lyu, P., Jiang, J., Zhou, F., Wang, J., Blackshaw, S., Qian, J.. 2022-02-08. LRLoop: Feedback loops as a design principle of cell-cell communication. https://doi.org/10.1101/2022.02.04.479174

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