Dissection of intercellular communication using the transcriptome-based framework ICELLNET

Nat Commun. 2021 Feb 17;12(1):1089. doi: 10.1038/s41467-021-21244-x.

Abstract

Cell-to-cell communication can be inferred from ligand-receptor expression in cell transcriptomic datasets. However, important challenges remain: global integration of cell-to-cell communication; biological interpretation; and application to individual cell population transcriptomic profiles. We develop ICELLNET, a transcriptomic-based framework integrating: 1) an original expert-curated database of ligand-receptor interactions accounting for multiple subunits expression; 2) quantification of communication scores; 3) the possibility to connect a cell population of interest with 31 reference human cell types; and 4) three visualization modes to facilitate biological interpretation. We apply ICELLNET to three datasets generated through RNA-seq, single-cell RNA-seq, and microarray. ICELLNET reveals autocrine IL-10 control of human dendritic cell communication with up to 12 cell types. Four of them (T cells, keratinocytes, neutrophils, pDC) are further tested and experimentally validated. In summary, ICELLNET is a global, versatile, biologically validated, and easy-to-use framework to dissect cell communication from individual or multiple cell-based transcriptomic profiles.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cell Communication / genetics*
  • Cells, Cultured
  • Computational Biology / methods*
  • Databases, Factual*
  • Dendritic Cells / cytology
  • Dendritic Cells / metabolism
  • Gene Expression Profiling / methods*
  • Humans
  • Keratinocytes / cytology
  • Keratinocytes / metabolism
  • Neutrophils / cytology
  • Neutrophils / metabolism
  • Sequence Analysis, RNA / methods
  • Single-Cell Analysis / methods
  • T-Lymphocytes / cytology
  • T-Lymphocytes / metabolism
  • Transcriptome / genetics*