Single-cell transcriptome analysis of the zebrafish embryonic trunk

Metikala, Sanjeeva; Chetty, Satish Casie; Sumanas, Saulius

doi:10.1371/journal.pone.0254024

Cited by 19 publications

(11 citation statements)

References 47 publications

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“…We have previously reported transcriptomic profiles of arterial and venous endothelial cells identified by scRNA-seq analaysis of zebrafish trunks at 30 hpf 46 . A substantial overlap was observed between 24 and 30 hpf datasets in both arterial and venous marker expression (Table S5 ).…”

Section: Resultsmentioning

confidence: 99%

Single-cell transcriptomic analysis of vascular endothelial cells in zebrafish embryos

Gurung

Restrepo

Chestnut

et al. 2022

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Vascular endothelial cells exhibit substantial phenotypic and transcriptional heterogeneity which is established during early embryogenesis. However, the molecular mechanisms involved in establishing endothelial cell diversity are still not well understood. Zebrafish has emerged as an advantageous model to study vascular development. Despite its importance, the single-cell transcriptomic profile of vascular endothelial cells during zebrafish development is still missing. To address this, we applied single-cell RNA-sequencing (scRNA-seq) of vascular endothelial cells isolated from zebrafish embryos at the 24 hpf stage. Six distinct clusters or subclusters related to vascular endothelial cells were identified which include arterial, two venous, cranial, endocardial and endothelial progenitor cell subtypes. Furthermore, we validated our findings by characterizing novel markers for arterial, venous, and endocardial cells. We experimentally confirmed the presence of two transcriptionally different venous cell subtypes, demonstrating heterogeneity among venous endothelial cells at this early developmental stage. This dataset will be a valuable resource for future functional characterization of vascular endothelial cells and interrogation of molecular mechanisms involved in the establishment of their heterogeneity and cell-fate decisions.

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Section: Resultsmentioning

confidence: 99%

Single-cell transcriptomic analysis of vascular endothelial cells in zebrafish embryos

Gurung

Restrepo

Chestnut

et al. 2022

Sci Rep

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“…This technology has been successfully applied to normal cell, induced pluripotent stem cell (iPSC), and organoids research (53,54) (Fig. 3(B)), but most of the time, scRNA-seq data are obtained from the model animals, such as Drosophila (55), planaria (56), Caenorhabditis elegans (57), Ciona (58), Zebrafish (59), Xenopus (60), mouse (61), etc., and nonmodel animals (62) (Fig. 3(C)).…”

Section: Single-cell Transcriptome In Healthmentioning

confidence: 99%

Single-Cell Transcriptome Analysis in Health and Disease

Bhattachan,

Jeschke

2023

Shock

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The analysis of the single-cell transcriptome has emerged as a powerful tool to gain insights of the basic mechanisms of health and disease. It is widely used to reveal the cellular diversity and complexity of tissues at cellular resolution by RNA sequencing of the whole transcriptome from a single cell. Equally, it is applied to discover an unknown, rare population of cells in the tissue. The prime advantage of single-cell transcriptome analysis is the detection of stochastic nature of gene expression of the cell in tissue. Moreover, the availability of multiple platforms for the single-cell transcriptome has broadened its approaches to using cells of different sizes and shapes, including the capture of short or full-length transcripts, which is helpful in the analysis of challenging biological samples. And with the development of numerous packages in R and Python, new directions in the computational analysis of single-cell transcriptomes can be taken to characterize healthy versus diseased tissues to obtain novel pathological insights. To further examine the biology of different cell types, downstream analysis such as differential gene expression analysis, GO term analysis, KEGG pathway analysis, cell-cell interaction analysis, and trajectory analysis has become standard practice in the workflow of single-cell transcriptome analysis. Here, we provide a broad overview of single-cell transcriptome analysis in health and disease conditions currently applied in various studies.

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“…At larval stages in the trunk, kitlga is expressed in the developing sense organs and pigment precursors, whereas kitlgb is expressed in the skin, similar to mammalian SCF/ KITLG expression (Hultman et al, 2007). Recent single-cell RNA-seq (Metikala et al, 2021) and bulk RNA-seq of different skin layers (Cokus et al, 2019) of embryonic and larval zebrafish indicate that both layers of the zebrafish skin, the basal cells and periderm, express Kitlgb at 30, 52, and 72 hpf. In particular, expression levels of Kitlgb at 52 and 72 hpf are virtually the same in both skin cell populations (Cokus et al, 2019).…”

Section: Kitb Has An Early Role In Regulating Cutaneous Axon Densitymentioning

confidence: 99%

c-Kit Receptor Maintains Sensory Axon Innervation of the Skin through Src Family Kinases

et al. 2022

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Peripheral somatosensory neurons innervate the skin and sense the environment. Whereas many studies focus on initial axon outgrowth and pathfinding, how signaling pathways contribute to maintenance of the established axon arbors and terminals within the skin is largely unknown. This question is particularly relevant to the many types of neuropathies that affect mature neuronal arbors. We show that a receptor tyrosine kinase (RTK), c-Kit, contributes to maintenance, but not initial development, of cutaneous axons in the larval zebrafish before sex determination. Downregulation of Kit signaling rapidly induced retraction of established axon terminals in the skin and a reduction in axonal density. Conversely, misexpression of c-Kit ligand in the skin in larval zebrafish induced increases in local sensory axon density, suggesting an important role for Kit signaling in cutaneous axon maintenance. We found Src family kinases (SFKs) act directly downstream to mediate Kit's role in regulating cutaneous axon density. Our data demonstrate a requirement for skin-to-axon signaling to maintain axonal networks and elucidate novel roles for Kit and SFK signaling in this context. This Kit-SFK signaling axis offers a potential pathway to therapeutically target in sensory neuropathies and to further explore in other neurobiological processes.

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Single-cell transcriptome analysis of the zebrafish embryonic trunk

Cited by 19 publications

References 47 publications

Single-cell transcriptomic analysis of vascular endothelial cells in zebrafish embryos

Single-cell transcriptomic analysis of vascular endothelial cells in zebrafish embryos

Single-Cell Transcriptome Analysis in Health and Disease

c-Kit Receptor Maintains Sensory Axon Innervation of the Skin through Src Family Kinases

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