1. Biochemistry and Chemical Biology
  2. Medicine

Framework for rapid comparison of extracellular vesicle isolation methods

  1. Dmitry Ter-Ovanesyan
  2. Maia Norman
  3. Roey Lazarovits
  4. Wendy Trieu
  5. Ju-Hyun Lee
  6. George Church
  7. David R Walt  Is a corresponding author
  1. Wyss Institute for Biologically Inspired Engineering, United States
https://doi.org/10.7554/eLife.70725
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  1. Dmitry Ter-Ovanesyan
  2. Maia Norman
  3. Roey Lazarovits
  4. Wendy Trieu
  5. Ju-Hyun Lee
  6. George Church
  7. David R Walt
(2021)
Framework for rapid comparison of extracellular vesicle isolation methods
eLife 10:e70725.
https://doi.org/10.7554/eLife.70725
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Abstract

Extracellular vesicles (EVs) are released by all cells into biofluids and hold great promise as reservoirs of disease biomarkers. One of the main challenges in studying EVs is a lack of methods to quantify EVs that are sensitive enough and can differentiate EVs from similarly sized lipoproteins and protein aggregates. We demonstrate the use of ultrasensitive, single molecule array (Simoa) assays for the quantification of EVs using three widely expressed transmembrane proteins: the tetraspanins CD9, CD63, and CD81. Using Simoa to measure these three EV markers, as well as albumin to measure protein contamination, we were able to compare the relative efficiency and purity of several commonly used EV isolation methods in plasma and cerebrospinal fluid (CSF): ultracentrifugation, precipitation, and size exclusion chromatography (SEC). We further used these assays, all on one platform, to improve SEC isolation from plasma and CSF. Our results highlight the utility of quantifying EV proteins using Simoa and provide a rapid framework for comparing and improving EV isolation methods from biofluids.

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

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Author details

  1. Dmitry Ter-Ovanesyan

    Wyss Institute for Biologically Inspired Engineering, Boston, United States
    Competing interests
    Dmitry Ter-Ovanesyan, The authors have filed intellectual property related to methods for isolating extracellular vesicles..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1134-0073

  2. Maia Norman

    Wyss Institute for Biologically Inspired Engineering, Boston, United States
    Competing interests
    Maia Norman, The authors have filed intellectual property related to methods for isolating extracellular vesicles..

  3. Roey Lazarovits

    Wyss Institute for Biologically Inspired Engineering, Boston, United States
    Competing interests
    No competing interests declared.

  4. Wendy Trieu

    Wyss Institute for Biologically Inspired Engineering, Boston, United States
    Competing interests
    No competing interests declared.

  5. Ju-Hyun Lee

    Wyss Institute for Biologically Inspired Engineering, Boston, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6728-2071

  6. George Church

    Wyss Institute for Biologically Inspired Engineering, Boston, United States
    Competing interests
    George Church, GMC commercial interests: http://arep.med.harvard.edu/gmc/tech.html..

  7. David R Walt

    Wyss Institute for Biologically Inspired Engineering, Boston, United States
    For correspondence
    dwalt@bwh.harvard.edu
    Competing interests
    David R Walt, DRW has a financial interest in Quanterix Corporation, a company that develops an ultra-sensitive digital immunoassay platform. He is an inventor of the Simoa technology, a founder of the company and also serves on its Board of Directors. Dr. Walt's interests were reviewed and are managed by BWH. The authors have filed aprovisional patent (WO2021163416A1) on methods for EV isolationmeasuring andpurifying EVs..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5524-7348

Funding

Chan Zuckerberg Initiative (NDCN Collaborative Science Award)

  • Dmitry Ter-Ovanesyan
  • Maia Norman
  • Roey Lazarovits
  • Wendy Trieu
  • Ju-Hyun Lee
  • George Church
  • David R Walt

Open Philanthropy Project

  • Dmitry Ter-Ovanesyan
  • Maia Norman
  • Roey Lazarovits
  • Wendy Trieu
  • Ju-Hyun Lee
  • David R Walt

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

Copyright

© 2021, Ter-Ovanesyan 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. Dmitry Ter-Ovanesyan
  2. Maia Norman
  3. Roey Lazarovits
  4. Wendy Trieu
  5. Ju-Hyun Lee
  6. George Church
  7. David R Walt
(2021)
Framework for rapid comparison of extracellular vesicle isolation methods
eLife 10:e70725.
https://doi.org/10.7554/eLife.70725

Share this article

https://doi.org/10.7554/eLife.70725

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Further reading

    1. Biochemistry and Chemical Biology
    2. Medicine

    Improved isolation of extracellular vesicles by removal of both free proteins and lipoproteins

    Dmitry Ter-Ovanesyan, Tal Gilboa ... David R Walt
    Research Advance

    Extracellular vesicles (EVs) are released by all cells into biofluids such as plasma. The separation of EVs from highly abundant free proteins and similarly sized lipoproteins remains technically challenging. We developed a digital ELISA assay based on Single Molecule Array (Simoa) technology for ApoB-100, the protein component of several lipoproteins. Combining this ApoB-100 assay with previously developed Simoa assays for albumin and three tetraspanin proteins found on EVs (Ter-Ovanesyan, Norman et al., 2021), we were able to measure the separation of EVs from both lipoproteins and free proteins. We used these five assays to compare EV separation from lipoproteins using size exclusion chromatography with resins containing different pore sizes. We also developed improved methods for EV isolation based on combining several types of chromatography resins in the same column. We present a simple approach to quantitatively measure the main impurities of EV isolation in plasma and apply this approach to develop novel methods for enriching EVs from human plasma. These methods will enable applications where high-purity EVs are required to both understand EV biology and profile EVs for biomarker discovery.