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

Publication 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.

Metrics

  • 2,227
    Page views
  • 274
    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. 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

Further reading

    1. Cell Biology
    Agustin Leonardo Lujan, Ombretta Foresti ... Vivek Malhotra
    Research Article Updated

    We show that TANGO2 in mammalian cells localizes predominantly to mitochondria and partially at mitochondria sites juxtaposed to lipid droplets (LDs) and the endoplasmic reticulum. HepG2 cells and fibroblasts of patients lacking TANGO2 exhibit enlarged LDs. Quantitative lipidomics revealed a marked increase in lysophosphatidic acid (LPA) and a concomitant decrease in its biosynthetic precursor phosphatidic acid (PA). These changes were exacerbated in nutrient-starved cells. Based on our data, we suggest that TANGO2 function is linked to acyl-CoA metabolism, which is necessary for the acylation of LPA to generate PA. The defect in acyl-CoA availability impacts the metabolism of many other fatty acids, generates high levels of reactive oxygen species, and promotes lipid peroxidation. We suggest that the increased size of LDs is a combination of enrichment in peroxidized lipids and a defect in their catabolism. Our findings help explain the physiological consequence of mutations in TANGO2 that induce acute metabolic crises, including rhabdomyolysis, cardiomyopathy, and cardiac arrhythmias, often leading to fatality upon starvation and stress.

    1. Cell Biology
    2. Cancer Biology
    Chelsea U Kidwell, Joseph R Casalini ... Minna Roh-Johnson
    Research Article Updated

    Recent studies reveal that lateral mitochondrial transfer, the movement of mitochondria from one cell to another, can affect cellular and tissue homeostasis. Most of what we know about mitochondrial transfer stems from bulk cell studies and have led to the paradigm that functional transferred mitochondria restore bioenergetics and revitalize cellular functions to recipient cells with damaged or non-functional mitochondrial networks. However, we show that mitochondrial transfer also occurs between cells with functioning endogenous mitochondrial networks, but the mechanisms underlying how transferred mitochondria can promote such sustained behavioral reprogramming remain unclear. We report that unexpectedly, transferred macrophage mitochondria are dysfunctional and accumulate reactive oxygen species in recipient cancer cells. We further discovered that reactive oxygen species accumulation activates ERK signaling, promoting cancer cell proliferation. Pro-tumorigenic macrophages exhibit fragmented mitochondrial networks, leading to higher rates of mitochondrial transfer to cancer cells. Finally, we observe that macrophage mitochondrial transfer promotes tumor cell proliferation in vivo. Collectively these results indicate that transferred macrophage mitochondria activate downstream signaling pathways in a ROS-dependent manner in cancer cells, and provide a model of how sustained behavioral reprogramming can be mediated by a relatively small amount of transferred mitochondria in vitro and in vivo.