The landscape of cell–cell communication through single-cell transcriptomics

TLDR

Cell‑cell communication, a fundamental process shaping tissues, has historically been limited to a few cell types and genes, but single‑cell transcriptomics now enables unprecedented scale and depth of analysis. This review aims to comprehensively describe cell‑cell communication by surveying recent methods for inferring interactions from single‑cell transcriptomics and proposing future directions. The authors discuss methods that infer cell‑cell communication from both non‑spatial and spatial single‑cell transcriptomics, highlighting their complementary strengths and limitations.

Abstract

Cell-cell communication is a fundamental process that shapes biological tissue. Historically, studies of cell-cell communication have been feasible for one or two cell types and a few genes. With the emergence of single-cell transcriptomics, we are now able to examine the genetic profiles of individual cells at unprecedented scale and depth. The availability of such data presents an exciting opportunity to construct a more comprehensive description of cell-cell communication. This review discusses the recent explosion of methods that have been developed to infer cell-cell communication from non-spatial and spatial single-cell transcriptomics, two promising technologies which have complementary strengths and limitations. We propose several avenues to propel this rapidly expanding field forward in meaningful ways.