PMID- 33820623 OWN - NLM STAT- In-Process VI - 143 TI - Uncovering cellular networks in branching morphogenesis using single-cell transcriptomics. PG - 239-280 CI - Copyright © 2021 Elsevier Inc. All rights reserved. LA - eng PT - Journal Article PL - United States TA - Curr Top Dev Biol JT - Current topics in developmental biology JID - 0163114 IS - 1557-8933 (Electronic) LID - S0070-2153(20)30112-5 [pii] LID - 10.1016/bs.ctdb.2020.09.004 [doi] FAU - Goodwin, Katharine AU - Goodwin K AD - Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, United States. FAU - Nelson, Celeste M AU - Nelson CM AD - Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, United States; Department of Molecular Biology, Princeton University, Princeton, NJ, United States. Electronic address: celesten@princeton.edu. IS - 0070-2153 (Linking) SB - IM OTO - NOTNLM OT - *Diffusion analysis OT - *Kidney development OT - *Lineage tracing OT - *Lung development OT - *Mammary gland development OT - *Mechanical stress OT - *Morphodynamics OT - *Spatial transcriptomics LR - 20210726 DP - 2021 DEP - 20201105 AB - Single-cell RNA-sequencing (scRNA-seq) and related technologies to identify cell types and measure gene expression in space, in time, and within lineages have multiplied rapidly in recent years. As these techniques proliferate, we are seeing an increase in their application to the study of developing tissues. Here, we focus on single-cell investigations of branching morphogenesis. Branched organs are highly complex but typically develop recursively, such that a given developmental stage theoretically contains the entire spectrum of cell identities from progenitor to terminally differentiated. Therefore, branched organs are a highly attractive system for study by scRNA-seq. First, we provide an update on advances in the field of scRNA-seq analysis, focusing on spatial transcriptomics, computational reconstruction of differentiation trajectories, and integration of scRNA-seq with lineage tracing. In addition, we discuss the possibilities and limitations for applying these techniques to studying branched organs. We then discuss exciting advances made using scRNA-seq in the study of branching morphogenesis and differentiation in mammalian organs, with emphasis on the lung, kidney, and mammary gland. We propose ways that scRNA-seq could be used to address outstanding questions in each organ. Finally, we highlight the importance of physical and mechanical signals in branching morphogenesis and speculate about how scRNA-seq and related techniques could be applied to study tissue morphogenesis beyond just differentiation.