Systematic Identification of Cell-Cell Communication Networks in the Developing Brain

Abstract

SummarySince the generation of cell-type specific knockout models, the importance of inter-cellular communication between neural, vascular, and microglial cells during neural development has been increasingly appreciated. However, the extent of communication between these major cell populations remains to be systematically mapped. Here, we describe EMBRACE (embryonic brain cell extraction using FACS), a method to simultaneously isolate neural, mural, endothelial, and microglial cells to more than 94% purity in ∼4 h. Utilizing EMBRACE we isolate, transcriptionally analyze, and build a cell-cell communication map of the developing mouse brain. We identify 1,710 unique ligand-receptor interactions between neural, endothelial, mural, and microglial cells in silico and experimentally confirm the APOE-LDLR, APOE-LRP1, VTN-KDR, and LAMA4-ITGB1 interactions in the E14.5 brain. We provide our data via the searchable “Brain interactome explorer”, available at https://mpi-ie.shinyapps.io/braininteractomeexplorer/. Together, this study provides a comprehensive map that reveals the richness of communication within the developing brain.

Deciphering cell–cell interactions and communication from gene expression

“…In addition, immunofluorescence was used to colocalize the expression of four ligand–receptor interactions (APOE–LRP1, APOE–LDLR, VTN–KDR and LAMA4–ITGB1) to adjacent cells in mouse brain on embryonic day 14.5 (ref. 22 ), supporting the relevance of these interactions to the developing brain. Thus, these approaches confirm spatial colocalization of predicted interactions.…”

“…Tissue and organ development also depends on signals that progenitor cells send and receive 21 . The analysis of brain CCC showed crosstalk involved in neurogenesis and identified novel mediators 16 , 22 , such as apolipoprotein E (APOE), a protein associated with Alzheimer disease. CCC analysis also elucidated how erythroblasts interact with macrophages during haematopoiesis in the fetal liver 23 and was applied to liver organoid development to investigate how multilineage communication shapes the differentiation of hepatic cells 24 .…”

“…Several high-quality lists of ligand–receptor pairs exist for model organisms 7 , 14 – 16 , 22 , 29 , 30 , 32 , 33 , 38 , 53 – 55 , 67 , 84 . However, studying cell–cell communication in organisms with fewer protein–protein interaction (PPI) data requires additional effort, especially in imputing ligand–receptor pairs through heuristic approaches and subsequent manual curation to increase the confidence in the list.…”

Secondary single-cell transcriptomic analysis reveals common molecular signatures of cerebrovascular injury between traumatic brain injury and aging

“…In addition, we also found several PC-specific mTBI responsive genes. For instance, Gprc5c, a marker for mural cells (Sheikh et al, 2019), was suppressed by mTBI in PC and could serve as a potential marker for brain injury induced PC alteration (Fig. 2E); Smad7, a negative regulator of TGF-b signaling (Lee et al, 2017), was significantly increased in mTBI, suggesting that TGF-b signaling may be involved in mTBI-induced BBB dysfunction (Fig.…”

COMUNET: a tool to explore and visualize intercellular communication

“…Single-cell RNA sequencing (scRNA-seq) has been extensively used in the last few years to analyse intercellular communication in tissues (see, e.g., (Camp et al , 2017;Puram et al , 2017;Zepp et al , 2017;Zhou et al , 2017;Cohen et al , 2018;Halpern et al , 2018;Skelly et al , 2018;Vento-Tormo et al , 2018;Kumar et al , 2018;Schiebinger et al , 2019;Bonnardel et al , 2019;Sheikh et al , 2019) ). Several algorithms to perform these analyses have been published (for instance, (Efremova et al , 2019;Vento-Tormo et al , 2018;Rieckmann et al , 2017;Boisset et al , 2018;Ramilowski et al , 2015) and they all start from a database of interacting partners (e.g., ligand and receptor pairs) to infer, from their expression patterns, a list of potential communication pathways between cell types.…”