1. Computational and Systems Biology
  2. Stem Cells and Regenerative Medicine
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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 13
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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.

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