An atlas of neural crest lineages along the posterior developing zebrafish at single-cell resolution

Abstract

Neural crest cells (NCCs) are vertebrate stem cells that give rise to various cell types throughout the developing body in early life. Here, we utilized single-cell transcriptomic analyses to delineate NCC-derivatives along the posterior developing vertebrate, zebrafish, during the late embryonic to early larval stage, a period when NCCs are actively differentiating into distinct cellular lineages. We identified several major NCC/NCC- derived cell-types including mesenchyme, neural crest, neural, neuronal, glial, and pigment, from which we resolved over three dozen cellular subtypes. We dissected gene expression signatures of pigment progenitors delineating into chromatophore lineages, mesenchyme subtypes, and enteric NCCs transforming into enteric neurons. Global analysis of NCC derivatives revealed they were demarcated by combinatorial hox gene codes, with distinct profiles within neuronal cells. From these analyses, we present a comprehensive cell-type atlas that can be utilized as a valuable resource for further mechanistic and evolutionary investigations of NCC differentiation.

CHAF1A Blocks Neuronal Differentiation and Promotes Neuroblastoma Oncogenesis via Metabolic Reprogramming

“…Zebrafish Model: For single cell dataset analysis, publicly available single cell RNAseq data from 48-50 hpf and 68-70 hpf zebrafish embryos (GEO accession: GSE152906) were analyzed as described using www.advancedsciencenews.com www.advancedscience.com Seurat v3.1.1 software package for R. [77,78] Plots were generated using the FeaturePlot command. For HCR, probes against zebrafish chaf1a (NM_0 010 45013.2), sox9b (NM_131 644.1), crestin (AF195881.1), mycn (NM_212 614.2), and elavl3 (NM_131 449) transcripts were generated and purchased from Molecular Instruments, Inc.…”

Zebrafish: A Model Organism for Studying Enteric Nervous System Development and Disease

“…Also, the expression of various HSCR-causing genes including the Rearranged during transfection (ret ), GDNF family receptor alpha 1 ( gfra1) and zinc finger E-box binding homeobox ( zeb2) , is conserved (Roy-Carson et al, 2017 ). More recently, researchers started to determine the neural crest transcriptome at a single-cell resolution in late embryonic, to early larval stage (Howard et al, 2020 ). They shed light on the transcriptomes of enteric NCCs transforming into enteric neurons, and showed conserved enteric programs (Lasrado et al, 2017 ; Howard et al, 2020 ).…”

“…More recently, researchers started to determine the neural crest transcriptome at a single-cell resolution in late embryonic, to early larval stage (Howard et al, 2020 ). They shed light on the transcriptomes of enteric NCCs transforming into enteric neurons, and showed conserved enteric programs (Lasrado et al, 2017 ; Howard et al, 2020 ). Their data contain cells in a spectrum of differentiation states, enabling the identification of five subclusters of enteric neurons (Howard et al, 2020 ).…”

“…They shed light on the transcriptomes of enteric NCCs transforming into enteric neurons, and showed conserved enteric programs (Lasrado et al, 2017 ; Howard et al, 2020 ). Their data contain cells in a spectrum of differentiation states, enabling the identification of five subclusters of enteric neurons (Howard et al, 2020 ). For example, the onset of elavl3 expression reflects immature neurons, whereas the nos1 + / vipb + subpopulation represents cells further along a differentiation trajectory.…”