Genome-wide interrogation of extracellular vesicle biology using barcoded miRNAs

  1. Albert Lu  Is a corresponding author
  2. Paulina Wawro
  3. David W Morgens
  4. Fernando Portela
  5. Michael C Bassik
  6. Suzanne R Pfeffer  Is a corresponding author
  1. Stanford University School of Medicine, United States

Abstract

Extracellular vesicles mediate transfer of biologically active molecules between neighboring or distant cells, and these vesicles may play important roles in normal physiology and the pathogenesis of multiple disease states including cancer. However, the underlying molecular mechanisms of their biogenesis and release remain unknown. We designed artificially barcoded, exosomal microRNAs (bEXOmiRs) to monitor extracellular vesicle release quantitatively using deep sequencing. We then expressed distinct pairs of CRISPR guide RNAs and bEXOmiRs, enabling identification of genes influencing bEXOmiR secretion from Cas9-edited cells. This approach uncovered genes with unrecognized roles in multivesicular endosome exocytosis, including critical roles for Wnt signaling in extracellular vesicle release regulation. Coupling bEXOmiR reporter analysis with CRISPR-Cas9 screening provides a powerful and unbiased means to study extracellular vesicle biology and for the first time, to associate a nucleic acid tag with individual membrane vesicles.

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. Albert Lu

    Department of Biochemistry, Stanford University School of Medicine, Stanford, United States
    For correspondence
    alulopez@stanford.edu
    Competing interests
    No competing interests declared.
  2. Paulina Wawro

    Department of Biochemistry, Stanford University School of Medicine, Stanford, United States
    Competing interests
    No competing interests declared.
  3. David W Morgens

    Department of Genetics, Stanford University School of Medicine, Stanford, United States
    Competing interests
    No competing interests declared.
  4. Fernando Portela

    Department of Biochemistry, Stanford University School of Medicine, Stanford, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0238-9251
  5. Michael C Bassik

    Department of Genetics, Stanford University School of Medicine, Stanford, United States
    Competing interests
    No competing interests declared.
  6. Suzanne R Pfeffer

    Department of Biochemistry, Stanford University School of Medicine, Stanford, United States
    For correspondence
    pfeffer@stanford.edu
    Competing interests
    Suzanne R Pfeffer, Reviewing editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6462-984X

Funding

National Institutes of Health (NIDDK 37332)

  • Suzanne R Pfeffer

National Institutes of Health (DP2HD084069)

  • Michael C Bassik

National Institutes of Health (T32 HG000044)

  • David W Morgens

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

Reviewing Editor

  1. Christopher G Burd, Yale School of Medicine, United States

Version history

  1. Received: August 27, 2018
  2. Accepted: December 17, 2018
  3. Accepted Manuscript published: December 17, 2018 (version 1)
  4. Version of Record published: December 31, 2018 (version 2)
  5. Version of Record updated: January 4, 2019 (version 3)

Copyright

© 2018, Lu 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. Albert Lu
  2. Paulina Wawro
  3. David W Morgens
  4. Fernando Portela
  5. Michael C Bassik
  6. Suzanne R Pfeffer
(2018)
Genome-wide interrogation of extracellular vesicle biology using barcoded miRNAs
eLife 7:e41460.
https://doi.org/10.7554/eLife.41460

Share this article

https://doi.org/10.7554/eLife.41460

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