New avenues for systematically inferring cell-cell communication: through single-cell transcriptomics data

Abstract

For multicellular organisms, cell-cell communication is essential to numerous biological processes. Drawing upon the latest development of single-cell RNA-sequencing (scRNA-seq), high-resolution transcriptomic data have deepened our understanding of cellular phenotype heterogeneity and composition of complex tissues, which enables systematic cell-cell communication studies at a single-cell level. We first summarize a common workflow of cell-cell communication study using scRNA-seq data, which often includes data preparation, construction of communication networks, and result validation. Two common strategies taken to uncover cell-cell communications are reviewed, e.g., physically vicinal structure-based and ligand-receptor interaction-based one. To conclude, challenges and current applications of cell-cell communication studies at a single-cell resolution are discussed in details and future perspectives are proposed.

Deciphering cell–cell interactions and communication from gene expression

“…Single-cell analyses have considered cell location in mouse bone marrow 53 , 128 , demonstrating that cell proximity is key to the study of intercellular communication. The study of spatial proximity in interacting cells is an emerging approach 129 . One technology for profiling these physical interactions, PIC-seq, uses cell sorting to acquire and transcriptionally profile physically interacting cells (PICs) through massively parallel single-cell RNA-seq 130 .…”

Inference and analysis of cell-cell communication using CellChat

“…While most current scRNA-seq data analysis approaches allow detailed cataloging of cell types and prediction of cellular differentiation trajectories, they have limited capability in probing underlying intercellular communications that often drive heterogeneity and cell state transitions. Yet, scRNA-seq data inherently contains gene expression information that could be used to infer such intercellular communications 6 , 7 .…”

The emerging role of angiotensinogen in cardiovascular diseases

“…Digital PCR can perform absolute quantitative analysis of nucleic acid and has higher accuracy and sensitivity than traditional quantitative PCR (Denis et al, 2019). In contrast, single‐cell RNA sequencing technologies can facilitate the in‐depth analysis of the transcriptome of each cell at a high resolution, which allows the unbiased assessment of cellular heterogeneity as well as the identification of new cellular states and populations (Chavkin & Hirschi, 2020; Paik, Cho, Tian, Chang, & Wu, 2020; Shao, Lu, Liao, Chen, & Fan, 2020). Therefore, we can anticipate the potential future progress in the determination of cardiac AGT expression by using these two novel technologies.…”