Abstract

During embryonic development cells acquire identity at the same time as they are proliferating, implying that an intrinsic facet of cell fate choice requires coupling lineage decisions to rates of cell division. How is the cell cycle regulated to promote or suppress heterogeneity and differentiation? We explore this question combining time lapse imaging with single cell RNA-seq in the contexts of self-renewal, priming and differentiation of mouse embryonic stem cells (ESCs) towards the Primitive Endoderm lineage (PrE). Since ESCs are derived from the Inner Cell Mass of the mammalian blastocyst, ESCs in standard culture conditions are transcriptionally heterogeneous containing subfractions that are primed for either of the two ICM lineages, Epiblast and PrE. These subfractions represent dynamic states that can readily interconvert in culture, and the PrE subfraction is functionally primed for endoderm differentiation. Here we find that differential regulation of cell cycle can tip the balance between these primed populations, such that naïve ESC culture conditions promote Epiblast-like expansion and PrE differentiation stimulates the selective survival and proliferation of PrE-primed cells. In endoderm differentiation, we find that this change is accompanied by a counter-intuitive increase in G1 length that also appears replicated in vivo. While FGF/ERK signalling is a known key regulator of ESCs and PrE differentiation, we find it is not just responsible for ESCs heterogeneity, but also cell cycle synchronisation, required for the inheritance of similar cell cycles between sisters and cousins. Taken together, our results point to a tight relationship between transcriptional heterogeneity and cell cycle regulation in the context of lineage priming, with primed cell populations providing a pool of flexible cell types that can be expanded in a lineage-specific fashion while allowing plasticity during early determination.

Data availability

The sc-RNAseq data used in this study has been deposited in the Gene Expression Omnibus and are available under the accession number GSE200534. Previously published Nowotschin et al., 2019 data that were used here are available under accession number GSE123046.

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

Article and author information

Author details

  1. Marta Perera

    The Novo Nordisk Foundation Center for Stem Cell Medicine, University of Copenhagen, Copenhagen, Denmark
    Competing interests
    No competing interests declared.
  2. Silas Boye Nissen

    Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9473-4755
  3. Martin Proks

    The Novo Nordisk Foundation Center for Stem Cell Medicine, University of Copenhagen, Copenhagen, Denmark
    Competing interests
    No competing interests declared.
  4. Sara Pozzi

    The Novo Nordisk Foundation Center for Stem Cell Medicine, University of Copenhagen, Copenhagen, Denmark
    Competing interests
    No competing interests declared.
  5. Rita Soares Monteiro

    The Novo Nordisk Foundation Center for Stem Cell Medicine, University of Copenhagen, Copenhagen, Denmark
    Competing interests
    No competing interests declared.
  6. Ala Trusina

    Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1945-454X
  7. Joshua M Brickman

    The Novo Nordisk Foundation Center for Stem Cell Medicine, University of Copenhagen, Copenhagen, Denmark
    For correspondence
    Joshua.brickman@sund.ku.dk
    Competing interests
    Joshua M Brickman, Reviewing editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1580-7491

Funding

Lundbeckfonden (R198-2015-412)

  • Joshua M Brickman

Danish Agency for Science and Higher Education (DFF- 8020-00100B)

  • Joshua M Brickman

Danish National Research Foundation (DNRF116)

  • Joshua M Brickman

Lundbeckfonden (R286-2018-1534)

  • Marta Perera

Lundbeckfonden (R303-2018-2939)

  • Rita Soares Monteiro

Danish National Research Foundation (DNRF116)

  • Ala Trusina

Novo Nordisk Fonden (NNF21CC0073729)

  • Joshua M Brickman

Novo Nordisk Fonden (NNF17CC002785)

  • Joshua M Brickman

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

Reviewing Editor

  1. Carole LaBonne, Northwestern University, United States

Version history

  1. Received: March 25, 2022
  2. Preprint posted: April 5, 2022 (view preprint)
  3. Accepted: August 12, 2022
  4. Accepted Manuscript published: August 15, 2022 (version 1)
  5. Version of Record published: August 26, 2022 (version 2)
  6. Version of Record updated: September 1, 2022 (version 3)

Copyright

© 2022, Perera 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.

Metrics

  • 1,928
    Page views
  • 308
    Downloads
  • 5
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Marta Perera
  2. Silas Boye Nissen
  3. Martin Proks
  4. Sara Pozzi
  5. Rita Soares Monteiro
  6. Ala Trusina
  7. Joshua M Brickman
(2022)
Transcriptional heterogeneity and cell cycle regulation as central determinants of primitive endoderm priming
eLife 11:e78967.
https://doi.org/10.7554/eLife.78967

Share this article

https://doi.org/10.7554/eLife.78967

Further reading

    1. Developmental Biology
    2. Immunology and Inflammation
    Amir Hossein Kayvanjoo, Iva Splichalova ... Elvira Mass
    Research Article Updated

    During embryogenesis, the fetal liver becomes the main hematopoietic organ, where stem and progenitor cells as well as immature and mature immune cells form an intricate cellular network. Hematopoietic stem cells (HSCs) reside in a specialized niche, which is essential for their proliferation and differentiation. However, the cellular and molecular determinants contributing to this fetal HSC niche remain largely unknown. Macrophages are the first differentiated hematopoietic cells found in the developing liver, where they are important for fetal erythropoiesis by promoting erythrocyte maturation and phagocytosing expelled nuclei. Yet, whether macrophages play a role in fetal hematopoiesis beyond serving as a niche for maturing erythroblasts remains elusive. Here, we investigate the heterogeneity of macrophage populations in the murine fetal liver to define their specific roles during hematopoiesis. Using a single-cell omics approach combined with spatial proteomics and genetic fate-mapping models, we found that fetal liver macrophages cluster into distinct yolk sac-derived subpopulations and that long-term HSCs are interacting preferentially with one of the macrophage subpopulations. Fetal livers lacking macrophages show a delay in erythropoiesis and have an increased number of granulocytes, which can be attributed to transcriptional reprogramming and altered differentiation potential of long-term HSCs. Together, our data provide a detailed map of fetal liver macrophage subpopulations and implicate macrophages as part of the fetal HSC niche.

    1. Developmental Biology
    2. Neuroscience
    Smrithi Prem, Bharati Dev ... Emanuel DiCicco-Bloom
    Research Article Updated

    Autism spectrum disorder (ASD) is defined by common behavioral characteristics, raising the possibility of shared pathogenic mechanisms. Yet, vast clinical and etiological heterogeneity suggests personalized phenotypes. Surprisingly, our iPSC studies find that six individuals from two distinct ASD subtypes, idiopathic and 16p11.2 deletion, have common reductions in neural precursor cell (NPC) neurite outgrowth and migration even though whole genome sequencing demonstrates no genetic overlap between the datasets. To identify signaling differences that may contribute to these developmental defects, an unbiased phospho-(p)-proteome screen was performed. Surprisingly despite the genetic heterogeneity, hundreds of shared p-peptides were identified between autism subtypes including the mTOR pathway. mTOR signaling alterations were confirmed in all NPCs across both ASD subtypes, and mTOR modulation rescued ASD phenotypes and reproduced autism NPC-associated phenotypes in control NPCs. Thus, our studies demonstrate that genetically distinct ASD subtypes have common defects in neurite outgrowth and migration which are driven by the shared pathogenic mechanism of mTOR signaling dysregulation.