scRNA-sequencing in chick suggests a probabilistic model for cell fate allocation at the neural plate border

  1. Alexandre P Thiery
  2. Ailin Leticia Buzzi
  3. Eva Hamrud
  4. Chris Cheshire
  5. Nicholas M Luscombe
  6. James Briscoe
  7. Andrea Streit  Is a corresponding author
  1. King's College London, United Kingdom
  2. The Francis Crick Institute, United Kingdom

Abstract

The vertebrate 'neural plate border' is a transient territory located at the edge of the neural plate containing precursors for all ectodermal derivatives: the neural plate, neural crest, placodes and epidermis. Elegant functional experiments in a range of vertebrate models have provided an in-depth understanding of gene regulatory interactions within the ectoderm. However, these experiments conducted at tissue level raise seemingly contradictory models for fate allocation of individual cells. Here, we carry out single cell RNA sequencing of chick ectoderm from primitive streak to neurulation stage, to explore cell state diversity and heterogeneity. We characterise the dynamics of gene modules, allowing us to model the order of molecular events which take place as ectodermal fates segregate. Furthermore, we find that genes previously classified as neural plate border 'specifiers' typically exhibit dynamic expression patterns and are enriched in either neural, neural crest or placodal fates, revealing that the neural plate border should be seen as a heterogeneous ectodermal territory and not a discrete transitional transcriptional state. Analysis of neural, neural crest and placodal markers reveals that individual NPB cells co-express competing transcriptional programmes suggesting that their ultimate identify is not yet fixed. This population of 'border located undecided progenitors' (BLUPs) gradually diminishes as cell fate decisions take place. Considering our findings, we propose a probabilistic model for cell fate choice at the neural plate border. Our data suggest that the probability of a progenitor's daughters to contribute to a given ectodermal derivative is related to the balance of competing transcriptional programmes, which in turn are regulated by the spatiotemporal position of a progenitor.

Data availability

10x single cell RNAseq was carried out in two batches and is available under two separate accession numbers (ArrayExpress: E-MTAB-10408 and E-MTAB-1144). Our NGS alignments and downstream analysis have been wrapped into custom Nextflow pipelines allowing for full reproducibility. For the code used in this analysis, including links to our Docker containers, see our GitHub repository at https://github.com/alexthiery/10x_neural_plate_border. Finally, we have developed a user friendly ShinyApp to allow public exploration of our single cell RNAseq data at https://shiny.crick.ac.uk/thiery_neural_plate_border/.

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Alexandre P Thiery

    Centre for Craniofacial and Regenerative Biology, King's College London, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  2. Ailin Leticia Buzzi

    Centre for Craniofacial and Regenerative Biology, King's College London, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  3. Eva Hamrud

    Centre for Craniofacial and Regenerative Biology, King's College London, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  4. Chris Cheshire

    Bioinformatics and Computational Biology Laboratory, The Francis Crick Institute, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  5. Nicholas M Luscombe

    Bioinformatics and Computational Biology Laboratory, The Francis Crick Institute, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  6. James Briscoe

    Bioinformatics and Computational Biology Laboratory, The Francis Crick Institute, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1020-5240
  7. Andrea Streit

    Centre for Craniofacial and Regenerative Biology, King's College London, London, United Kingdom
    For correspondence
    andrea.streit@kcl.ac.uk
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7664-7917

Funding

Biotechnology and Biological Sciences Research Council (BB/S005536/1)

  • Alexandre P Thiery
  • Ailin Leticia Buzzi
  • Andrea Streit

Biotechnology and Biological Sciences Research Council (BB/R006342/1)

  • Alexandre P Thiery
  • Ailin Leticia Buzzi
  • Andrea Streit

Wellcome Trust (108874/B/15/Z)

  • Nicholas M Luscombe

Wellcome Trust (FC001051)

  • Chris Cheshire
  • Nicholas M Luscombe
  • James Briscoe

Cancer Research UK (FC001051)

  • Chris Cheshire
  • Nicholas M Luscombe
  • James Briscoe

Medical Research Council (FC001051)

  • Chris Cheshire
  • Nicholas M Luscombe
  • James Briscoe

Wellcome Trust (108874/Z/15/Z)

  • Eva Hamrud

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Richard A Schneider, University of California, San Francisco, United States

Version history

  1. Preprint posted: February 16, 2022 (view preprint)
  2. Received: August 15, 2022
  3. Accepted: August 1, 2023
  4. Accepted Manuscript published: August 2, 2023 (version 1)
  5. Version of Record published: August 14, 2023 (version 2)

Copyright

© 2023, Thiery et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Alexandre P Thiery
  2. Ailin Leticia Buzzi
  3. Eva Hamrud
  4. Chris Cheshire
  5. Nicholas M Luscombe
  6. James Briscoe
  7. Andrea Streit
(2023)
scRNA-sequencing in chick suggests a probabilistic model for cell fate allocation at the neural plate border
eLife 12:e82717.
https://doi.org/10.7554/eLife.82717

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https://doi.org/10.7554/eLife.82717

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