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Isolation and characterization of extracellular vesicle subpopulations from tissues

Nature Protocols volume 16, pages 1548–1580 (2021)Cite this article

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Abstract

Extracellular vesicles (EVs) are lipid bilayered membrane structures released by all cells. Most EV studies have been performed by using cell lines or body fluids, but the number of studies on tissue-derived EVs is still limited. Here, we present a protocol to isolate up to six different EV subpopulations directly from tissues. The approach includes enzymatic treatment of dissociated tissues followed by differential ultracentrifugation and density separation. The isolated EV subpopulations are characterized by electron microscopy and RNA profiling. In addition, their protein cargo can be determined with mass spectrometry, western blot and ExoView. Tissue-EV isolation can be performed in 22 h, but a simplified version can be completed in 8 h. Most experiments with the protocol have used human melanoma metastases, but the protocol can be applied to other cancer and non-cancer tissues. The procedure can be adopted by researchers experienced with cell culture and EV isolation.

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Fig. 1: Representative electron microscopy section of human colon cancer tissue.
Fig. 2: Schematic overview of the isolation procedure for tissue-derived EVs.
Fig. 3: EV characterization (Step 40).
Fig. 4: Iodixanol cushion separation instead of discontinuous iodixanol gradient (Step 40B).
Fig. 5: Step-by-step visualization of the tissue EV isolation procedure.

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Data availability

All identified proteins and their expression are provided in the supporting primary research article by Crescitelli et al35. The full-length, unprocessed blots and gels related to Extended Data Fig. 5 have been submitted to the figshare repository (https://figshare.com/articles/figure/Isolation_and_characterization_of_extracellular_vesicles_from_tissues_WesternBlot_Extended_data_Fig_4_pdf/12854744). All the information regarding flow cytometry experiments is available as supplementary information (Supplementary Tables 1 and 2) to this article. All parameters have been submitted to EVtrack (http://evtrack.org/) in the original publication35 (http://evtrack.org/search_results.php?evtraqid=EV190108&pmid=&author=&compl_score=&biofluid=&study_aim=&isolation_method=&species=&prot_methods=&keyword=&part_methods=&year=&submit=1).

The MS proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE90 partner repository with the dataset identifier PXD021694.

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Acknowledgements

We thank the Centre for Cellular Imaging at the University of Gothenburg and the National Microscopy Infrastructure (VR-RFI 2016-00968)) for microscopy support and, in particular, M. Micaroni for his assistance in buffer preparation for sample preparation and image acquisition. We thank the Proteomic Core Facility at the University of Gothenburg for performing the LC-tandem MS analysis, in particular, A. Thorsell, J. Fuchs and B.-M. Olsson. The Proteomics Core Facility is grateful to the Inga-Britt and Arne Lundbergs Forskningsstiftlese for the donation of the Orbitrap Fusion Tribrid MS instrument. We thank R. Cattaneo for his assistance with figure preparation. We thank the VBG Group Herman Krefting Foundation for Asthma and Allergy Research for supporting the Krefting Research Centre at the University of Gothenburg. This work was funded by the Swedish Research Council (K2014-85X-22504-01-3), the Swedish Heart and Lung Foundation (20120528), the Swedish Cancer Foundation (CAN2014/844) and the Knut and Alice Wallenberg Foundation (Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Sweden).

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Authors and Affiliations

  1. Krefting Research Centre, Institute of Medicine at the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden

    Rossella Crescitelli, Cecilia Lässer & Jan Lötvall

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  1. Rossella Crescitelli
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  2. Cecilia Lässer
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Contributions

R.C. performed most of the experiments and analyzed the data. R.C., C.L. and J.L. designed the study. C.L. performed the flow cytometry and proteomics data analysis. The data were interpreted collectively, and the manuscript was written by R.C. with the support of C.L. and J.L. All authors have read, commented on and given approval of the final version of the manuscript.

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Correspondence to Rossella Crescitelli.

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Competing interests

The authors have developed multiple EV-associated patents for putative clinical utilization: US20200088734A1, United States, R.C., J.L.; WO2020146390A1, WIPO (PCT), R.C., J.L.; GB2574785A, United Kingdom, C.L., J.L.; US20070298118A1, United States, J.L.; CA3017586A1, Canada, J.L.; US20200163998A1, United States, J.L.; and WO2014076137A1, WIPO (PCT), J.L. J.L. owns equity in Codiak BioSciences Inc. and Exocure Biosciences Inc. and consults in the field of EVs through Vesiclebio AB. R.C. and C.L. own equity in Exocure Bioscience Inc.

Additional information

Peer review information Nature Protocols thanks Rienk Nieuwland and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Related links

Key references using this protocol

Crescitelli, R. et al. J. Extracell. Vesicles 9, 1722433 (2020): https://doi.org/10.1080/20013078.2020.1722433

Jang, S. C. et al. J. Extracell. Vesicles 8, 1635420 (2019): https://doi.org/10.1080/20013078.2019.1635420

Extended data

Extended Data Fig. 1 Representative sections of mouse and human tissue and EVs isolated from these tissues.

a and b, Sections of mouse tissues from subcutaneous melanoma tissue (a) and colon cancer (b) are shown. EVs isolated from subcutaneous melanoma and colon cancer tissue shown in a1–3 and b1–3 are as follows: lEVs (1), sEVs (2) and a mixture of both lEVs and sEVs isolated by using the iodixanol cushion separation (3). c and d, Sections of tissues isolated from human colon mucosa (c) and colon cancer (d) are shown. EVs in the extracellular space are indicated with red arrows. Mixtures of both lEVs and sEVs isolated by using iodixanol cushion separation from colon mucosa and tumor tissue are shown in c1 and d1 (scale bars: a = 1 µm, a1–a3 = 500 nm, b = 1 µm, b1–b3 = 200 nm, c = 2 µm, the higher-magnification panel in c = 500 nm, c1 = 200 nm, d = 1 µm, the higher-magnification panel in d = 500 nm, d1 = 200 nm). Human samples were collected and processed in alignment with the Regional Ethical Review Board at the University of Gothenburg, Sweden (melanoma metastases #096-12 and #995-16; colon cancer and colon mucosa #118-15) and according to institutional animal use and care guidelines (Directive 2010/63/EU on the protection of animals used for scientific purposes).

Extended Data Fig. 2 Protocol optimization: enzymatic treatment applied at different steps of the procedure.

a, The 2018 Protocol was used to isolate EVs without using collagenase D and DNase I (blue arrows). In the 2019 Protocol, collagenase and DNase I treatment was applied to the re-suspended vesicle-enriched pellets (green arrows). In the Final Protocol, collagenase D and DNase I treatment were applied directly to the tissue pieces after the dissociating step (red arrows). b and c, Micrograms of proteins isolated from lEVs (b) and sEVs (c) normalized to the grams of tissue for each protocol; 2018 Protocol, n = 4; 2019 Protocol, n = 2; Final Protocol 3, n = 13. Human samples were collected and processed in alignment with the Regional Ethical Review Board at the University of Gothenburg, Sweden (#096-12 and #995-16). The patient provided informed written consent. The image is modified from Crescitelli et al.35.

Extended Data Fig. 3 Evaluation of the molecular effects of collagenase D and DNase I on CD9, CD63 and CD81.

a and b, Flow cytometry analysis showing the gating and the expression of CD9, CD63 and CD81 after collagenase D and DNase I treatment of HMC-1 cells (a) and lEVs and sEVs (b). The EVs were bound to anti-CD63 beads before analysis. The viability of HMC-1 cells after enzymatic treatment was evaluated with flow cytometry and 7-AAD. The information about the antibodies, cell line, EV-binding beads, instruments and software used to perform flow cytometry experiments is listed in Supplementary Table 1. The information about the cell and EV populations analyzed in the flow cytometry experiments is given in Supplementary Table 2. c, The expression of CD9, CD63 and CD81 on EVs after collagenase D and DNase I treatment was investigated by ExoView. Enzymatic treatment was performed on HMC1 cells and their conditional media (containing EVs), and the media were loaded onto the chips. The results are presented as the mean, but individual values from three different experiments are shown as well. n = 3. FSC-A, forward scatter area; K, thousand; PE, phycoerithrin; SSC-A, side scatter area. The image is modified from Crescitelli et al.35.

Extended Data Fig. 4 Quantitative proteomic analysis (tandem mass tag (TMT)) of the EV subpopulations isolated from cutaneous melanoma metastatic tissues.

Lists of the top 100 proteins identified from three online EV databases (EVpedia, ExoCarta and VesiclePedia87,88,89) were used to construct a list of common EV proteins. Furthermore, new markers suggested by Kowal and colleagues15 and the protein AGO2 were added to the list. After the duplicates were removed, a multi-group comparison was performed in Qlucore. Proteins differentially expressed in our dataset (P = 0.01, Q = 0.02) are shown in the heat map. Human samples were collected and processed in alignment with the Regional Ethical Review Board at the University of Gothenburg, Sweden (#096-12 and #995-16). The patient provided informed written consent. The image is modified from Crescitelli et al.35.

Extended Data Fig. 5 Validation of EV proteins by western blot.

a, Western blot was used to investigate the presence of vesicle markers in lEVs and sEVs, including CD63, flotillin-1, CD9 and CD81, as well as the endoplasmatic reticulum protein calnexin. 10 μg of proteins was loaded per sample. b, Western blot was performed to validate a selection of proteins from the TMT analysis in all six EV subpopulations from two cutaneous melanoma metastatic tissues, including ADAM10, mitofillin, flotillin-1 and CD81. 4 μg of total protein was loaded per sample except for the western blot of large HD EVs from tumor 1 and 2 and the western blot of small HD EVs from tumor 2. The EV yield was insufficient; thus, 36 µl (maximum volume) of EVs was loaded instead, and they corresponded to 0.6, 0.7 and 2.5 µg of proteins. Human samples were collected and processed in alignment with the Regional Ethical Review Board at the University of Gothenburg, Sweden (#096-12 and #995-16). The patient provided informed written consent. The image is modified from Crescitelli et al.35.

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Supplementary Information

Supplementary Tables 1 and 2 supporting Extended Data Fig. 3.

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Crescitelli, R., Lässer, C. & Lötvall, J. Isolation and characterization of extracellular vesicle subpopulations from tissues. Nat Protoc 16, 1548–1580 (2021). https://doi.org/10.1038/s41596-020-00466-1

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