Multiplex live single-cell transcriptional analysis demarcates cellular functional heterogeneity

  1. Ayhan Atmanli  Is a corresponding author
  2. Dongjian Hu
  3. Frederik Ernst Deiman
  4. Annebel Marjolein van de Vrugt
  5. Lauren Deems Black
  6. Ibrahim Domian
  1. Massachusetts General Hospital, United States
  2. Tufts University, United States

Abstract

A fundamental goal in the biological sciences is to determine how individual cells with varied gene expression profiles and diverse functional characteristics contribute to development, physiology, and disease. Here, we report a novel strategy to assess gene expression and cell physiology in single living cells. Our approach utilizes fluorescently-labeled mRNA-specific anti-sense RNA probes and dsRNA-binding protein to identify the expression of specific genes in real-time at single-cell resolution via FRET. We use this technology to identify distinct myocardial subpopulations expressing the structural proteins myosin heavy chain α and myosin light chain 2a in real-time during early differentiation of human pluripotent stem cells. We combine this live-cell gene expression analysis with detailed physiologic phenotyping to capture the functional evolution of these early myocardial subpopulations during lineage specification and diversification. This live-cell mRNA imaging approach will have wide ranging application wherever heterogeneity plays an important biological role.

Data availability

All data generated or analysed during this study are included in the manuscript and supporting files.

Article and author information

Author details

  1. Ayhan Atmanli

    Cardiovascular Research Center, Massachusetts General Hospital, Boston, United States
    For correspondence
    ayhan.atmanli@gmail.com
    Competing interests
    Ayhan Atmanli, Inventor of pending patent (PCT/US2016/029972).
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6951-8893
  2. Dongjian Hu

    Cardiovascular Research Center, Massachusetts General Hospital, Boston, United States
    Competing interests
    No competing interests declared.
  3. Frederik Ernst Deiman

    Cardiovascular Research Center, Massachusetts General Hospital, Boston, United States
    Competing interests
    No competing interests declared.
  4. Annebel Marjolein van de Vrugt

    Cardiovascular Research Center, Massachusetts General Hospital, Boston, United States
    Competing interests
    No competing interests declared.
  5. Lauren Deems Black

    Department of Biomedical Engineering, Tufts University, Medford, United States
    Competing interests
    No competing interests declared.
  6. Ibrahim Domian

    Cardiovascular Research Center, Massachusetts General Hospital, Boston, United States
    Competing interests
    Ibrahim Domian, Inventor of a pending patent (PCT/US2016/029972).

Funding

American Heart Association (Predoctoral Fellowship)

  • Ayhan Atmanli

National Heart, Lung, and Blood Institute (Progenitor Cell Biology Consortium (PCBC) Jump Start Award)

  • Ayhan Atmanli

National Heart, Lung, and Blood Institute (U01HL100408-01)

  • Ibrahim Domian

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

Reviewing Editor

  1. Sean Wu, Stanford

Version history

  1. Received: June 23, 2019
  2. Accepted: October 7, 2019
  3. Accepted Manuscript published: October 8, 2019 (version 1)
  4. Version of Record published: November 18, 2019 (version 2)

Copyright

© 2019, Atmanli 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. Ayhan Atmanli
  2. Dongjian Hu
  3. Frederik Ernst Deiman
  4. Annebel Marjolein van de Vrugt
  5. Lauren Deems Black
  6. Ibrahim Domian
(2019)
Multiplex live single-cell transcriptional analysis demarcates cellular functional heterogeneity
eLife 8:e49599.
https://doi.org/10.7554/eLife.49599

Share this article

https://doi.org/10.7554/eLife.49599

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