1. Computational and Systems Biology
  2. Stem Cells and Regenerative Medicine
Download icon

Single cell RNA-seq identifies the origins of heterogeneity in efficient cell transdifferentiation and reprogramming

  1. Mirko Francesconi
  2. Bruno Di Stefano
  3. Clara Berenguer
  4. Luisa de Andrés-Aguayo
  5. Marcos Plana-Carmona
  6. Maria Mendez-Lago
  7. Amy Guillaumet-Adkins
  8. Gustavo Rodriguez-Esteban
  9. Marta Gut
  10. Ivo G Gut
  11. Holger Heyn
  12. Ben Lehner  Is a corresponding author
  13. Thomas Graf  Is a corresponding author
  1. Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Spain
  2. Harvard University, United States
Research Article
  • Cited 14
  • Views 6,828
  • Annotations
Cite this article as: eLife 2019;8:e41627 doi: 10.7554/eLife.41627

Abstract

Forced transcription factor expression can transdifferentiate somatic cells into other specialized cell types or reprogram them into induced pluripotent stem cells (iPSCs) with variable efficiency. To better understand the heterogeneity of these processes, we used single-cell RNA sequencing to follow the transdifferentation of murine pre-B cells into macrophages as well as their reprogramming into iPSCs. Even in these highly efficient systems, there was substantial variation in the speed and path of fate conversion. We predicted and validated that these differences are inversely coupled and arise in the starting cell population, with Mychigh large pre-BII cells transdifferentiating slowly but reprogramming efficiently and Myclow small pre-BII cells transdifferentiating rapidly but failing to reprogram. Strikingly, differences in Myc activity predict the efficiency of reprogramming across a wide range of somatic cell types. These results illustrate how single cell expression and computational analyses can identify the origins of heterogeneity in cell fate conversion processes.

Data availability

Single cell gene expression data have been deposited in the National Center for Biotechnology Information Gene Expression Omnibus (GEO) under accession number GSE112004

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

Article and author information

Author details

  1. Mirko Francesconi

    Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
    Competing interests
    The authors declare that no competing interests exist.
  2. Bruno Di Stefano

    Department of Stem Cell and Regenerative Biology, Harvard University, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2532-3087
  3. Clara Berenguer

    Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
    Competing interests
    The authors declare that no competing interests exist.
  4. Luisa de Andrés-Aguayo

    Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
    Competing interests
    The authors declare that no competing interests exist.
  5. Marcos Plana-Carmona

    Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1976-7506
  6. Maria Mendez-Lago

    Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
    Competing interests
    The authors declare that no competing interests exist.
  7. Amy Guillaumet-Adkins

    Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
    Competing interests
    The authors declare that no competing interests exist.
  8. Gustavo Rodriguez-Esteban

    Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
    Competing interests
    The authors declare that no competing interests exist.
  9. Marta Gut

    Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
    Competing interests
    The authors declare that no competing interests exist.
  10. Ivo G Gut

    Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7219-632X
  11. Holger Heyn

    Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
    Competing interests
    The authors declare that no competing interests exist.
  12. Ben Lehner

    Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
    For correspondence
    lehner.ben@gmail.com
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8817-1124
  13. Thomas Graf

    Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
    For correspondence
    Thomas.Graf@crg.eu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2774-4117

Funding

H2020 European Research Council

  • Thomas Graf

H2020 European Research Council

  • Ben Lehner

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

Ethics

Animal experimentation: The protocol was approved by the Committee on the Ethics of Animal Experiments of the Generalitat de Catalunya (Permit Number: JMC-071001P3). All surgery was performed under sodium pentobarbital anesthesia, and every effort was made to minimize suffering.

Reviewing Editor

  1. Chris P Ponting, University of Edinburgh, United Kingdom

Publication history

  1. Received: September 1, 2018
  2. Accepted: March 11, 2019
  3. Accepted Manuscript published: March 12, 2019 (version 1)
  4. Accepted Manuscript updated: March 21, 2019 (version 2)
  5. Version of Record published: March 26, 2019 (version 3)

Copyright

© 2019, Francesconi 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

  • 6,828
    Page views
  • 1,007
    Downloads
  • 14
    Citations

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

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)

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

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

  1. Further reading

Further reading

    1. Chromosomes and Gene Expression
    2. Computational and Systems Biology
    Torahiko L Higashi et al.
    Research Article

    The cohesin complex topologically encircles DNA to promote sister chromatid cohesion. Alternatively, cohesin extrudes DNA loops, thought to reflect chromatin domain formation. Here, we propose a structure-based model explaining both activities. ATP and DNA binding promote cohesin conformational changes that guide DNA through a kleisin N-gate into a DNA gripping state. Two HEAT-repeat DNA binding modules, associated with cohesin’s heads and hinge, are now juxtaposed. Gripping state disassembly, following ATP hydrolysis, triggers unidirectional hinge module movement, which completes topological DNA entry by directing DNA through the ATPase head gate. If head gate passage fails, hinge module motion creates a Brownian ratchet that, instead, drives loop extrusion. Molecular-mechanical simulations of gripping state formation and resolution cycles recapitulate experimentally observed DNA loop extrusion characteristics. Our model extends to asymmetric and symmetric loop extrusion, as well as z-loop formation. Loop extrusion by biased Brownian motion has important implications for chromosomal cohesin function.

    1. Computational and Systems Biology
    Pierpaolo Sorrentino et al.
    Short Report Updated

    Brain activity during rest displays complex, rapidly evolving patterns in space and time. Structural connections comprising the human connectome are hypothesized to impose constraints on the dynamics of this activity. Here, we use magnetoencephalography (MEG) to quantify the extent to which fast neural dynamics in the human brain are constrained by structural connections inferred from diffusion MRI tractography. We characterize the spatio-temporal unfolding of whole-brain activity at the millisecond scale from source-reconstructed MEG data, estimating the probability that any two brain regions will significantly deviate from baseline activity in consecutive time epochs. We find that the structural connectome relates to, and likely affects, the rapid spreading of neuronal avalanches, evidenced by a significant association between these transition probabilities and structural connectivity strengths (r = 0.37, p<0.0001). This finding opens new avenues to study the relationship between brain structure and neural dynamics.