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Direct Stochastic Optical Reconstruction Microscopy of Extracellular Vesicles in Three Dimensions

Published: August 26, 2021 doi: 10.3791/62845


Direct stochastic optical reconstruction microscopy (dSTORM) is used to bypass the typical diffraction limit of light microscopy and to view exosomes at the nanometer scale. It can be employed in both two and three dimensions to characterize exosomes.


Extracellular vesicles (EVs) are released by all cell types and play an important role in cell signaling and homeostasis. The visualization of EVs often require indirect methods due to their small diameter (40-250 nm), which is beneath the diffraction limit of typical light microscopy. We have developed a super-resolution microscopy-based visualization of EVs to bypass the diffraction limit in both two and three dimensions. Using this approach, we can resolve the three-dimensional shape of EVs to within +/- 20 nm resolution on the XY-axis and +/- 50 nm resolution along the Z-axis. In conclusion, we propose that super-resolution microscopy be considered as a characterization method of EVs, including exosomes, as well as enveloped viruses.


Extracellular vesicles (EVs) are membrane-bound vesicles released by all cell types. They contain lipids, proteins, metabolites, and nucleic acids and transfer these materials locally between cells and distally between tissues and organs. There are three primary subtypes of EVs: apoptotic bodies, microvesicles, and exosomes1,2. Here, we focus our discussion on exosomes and their associated proteins.

Exosomes are secreted vesicles originating from the inward budding of early endosomes into the multivesicular body (MVB). The MVB then fuses with the plasma membrane, releasing the exosomes into the extracellular space to travel to other cells3,4. Exosomes exist on a spectrum of sizes ranging from 40 to 150 nm and are enriched with endosomal transmembrane proteins known as tetraspanins (CD9, CD63, CD81), membrane-bound endosomal sorting complex required for the transport (ESCRT), and lipid raft-associated proteins1,2, 5,6,7.

Characterizing the biochemical makeup of exosomes has become a popular field for researchers to better understand their functional nature. Many methods exist for visualizing and characterizing exosomes, including nanoscale flow cytometry, nanoparticle tracking analysis (NTA), scanning and transmission electron microscopy (TEM), surface plasmon resonance, resistive pulse sensing, and traditional light microscopy, each of which contains intrinsic pros and cons8,9. TEM and cryo-EM can achieve nanometer-based resolution, but often require dehydrating and freeze-fracture steps, thereby shrinking or lysing EVs10,11. NTA relies on light scattering, allowing for the characterization of hundreds of EVs at a time, but is an indirect measurement of particle size and cannot easily distinguish between EVs, viruses, and protein aggregates12,13,14,15,16. Nanoscale flow cytometry employs light scattering from an excitation path, which can then be translated into size measurements, but is an emerging technology, and there is little consensus on what size of particles are within the linear range of detection for various instruments12,17,18.

Traditional light microscopy using fluorescent proteins or dyes has been one of the most heavily employed techniques for visualizing subcellular compartments, protein complexes, and signaling machinery within a cell. While this technique proves useful in visualizing the localization of complexes, the diffraction limit of traditional light microscopy (around 250-400 nm) prevents the clear resolution of proteins or structures in the typical size range of an exosome (40-150 nm)12,19,20.

Super-resolution microscopy, namely, direct stochastic optical reconstruction microscopy (dSTORM), distinguishes itself from conventional light microscopy by employing the photoswitchable properties of specific fluorophores and detecting these blinking events to reconstruct images down to nanometer precision21. Photoswitching events are collected using a high-framerate detection camera over the course of tens of thousands of individual exposures, and a point spread function is used to map with high confidence the exact location of the photoswitching fluorophore19,20,22. This allows dSTORM to bypass the diffraction limit of light microscopy. Several groups have reported the use of super-resolution techniques for visualizing and tracking exosomes and their associated proteins22,23,24,25. The final resolution depends on the biophysical properties of the fluorophore, but often ranges from +/-10-100 nm along the XY-axis, allowing single-molecule resolution.

The ability to resolve individual fluorophores at this scale on the XY-axis has revolutionized microscopy. However, there is little data on the three-dimensional (3-D) dSTORM of an exosome. Therefore, we sought to establish a standard operating procedure (SOP) for dSTORM-based visualization and characterization of purified EVs, including exosomes to nanometer precision in 3-D.

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1 Propagation and maintenance of cell lines

  1. Acquire human osteosarcoma cells (U2OS) and place the cells in the growth medium supplemented with 10% exosome-free Fetal Bovine Serum and 1x Penicillin/Streptomycin solution.
    NOTE: Exosome-free Fetal Bovine Serum was generated following the protocol presented in McNamara et. al.26.
  2. Maintain the U2OS cells in a copper-coated incubator at 37 °C in 5% CO2 and passage cells in T175 flasks26,27. The cells must be maintained in mid-logarithmic growth phase to prevent subpopulations from arising, or from the accumulation of apoptotic debris during the stationary phase.

2 Exosome isolation and purification

  1. Grow the U2OS cell lines to full confluency in 10 separate T175 flasks with 50 mL of media per flask. Remove the cell supernatant and successively passage it through a 0.45 µm and 0.22 µm vacuum filtration apparatus.
  2. Subject the supernatant to crossflow filtration (also known as tangential flow filtration) on a filtration system equipped with the 750 kDa hollow-fiber cartridge in order to remove smaller proteins or metabolites28.
    1. Passage the supernatant through the tangential flow filtration operator at a constant forward pressure of 30 psi, while maintaining a retention pressure of <20 psi to produce a Δ pressure of 10 or more psi. Place a magnetic stir bar in the retentate tank and set to 150 rpm26.
    2. Maintain the feed rate at 40 mL/min or higher. Collect the permeate in a reservoir and dispose of it.
  3. Concentrate the supernatant to 30 mL, and then equilibrate with four volumes of 1x PBS. Collect the crossflow filtered and equilibrated solution in a 50 mL conical tube.
  4. Precipitate the EVs at 4 °C overnight in a final concentration of 40 mg/mL polyethylene glycol with a molecular weight of 8,000 Da. Centrifuge the EVs at 1,200 x g at 4 °C for 1 h and resuspend in 500 µL of 1x PBS.
  5. Incubate the EVs with 50 µg/mL of photoswitchable red membrane intercalating dye and 50 µg/mL of RNase A in 1x PBS at 4 °C for 1 h.
  6. Remove excess dye through a column on a protein purification system attached to a fraction collector. Identify EV fractions through UV absorbance and pool them into a microcentrifuge tube26.
  7. Affinity-select a total of 200 µL of EVs using anti-CD81 magnetic beads equilibrated in 1x PBS.
    1. Dilute 100 µL of the anti-CD81 magnetic beads in 1x PBS to a total volume of 1 mL and allow them to bind at 4 °C for 2 h in a 2 mL microcentrifuge tube with continuous rocking.
  8. Wash the anti-CD81 beads and EV three times with 1x PBS. Elute CD81+ EV from the solution with 100 mM Glycine at pH 2.0 for 30 min at 37 °C.
  9. Pipette the purified CD81+ EV into an equal volume of 100 mM Tris-HCl at pH 7.5 in 1x PBS.
    ​NOTE: An aliquot of purified CD81+ EV solution may be reserved for Nanoparticle Tracking Analysis or electron microscopy in order to confirm the purity of the solution and presence of EVs26.

3 Fixation and preparation

  1. Place affinity-purified EVs onto glass-bottom µ-slide 8-well plates in a total volume of 200 µL (can dilute EV sample in 100 mM Tris-HCl at pH 7.5 in 1x PBS) and allow to adhere to the surface overnight at 4 °C.
  2. Without removing the existing solution from the 8-well plate, fix EVs onto the plates by adding 200 µL of 4% paraformaldehyde in 1x PBS to the EV-containing solution in each well and allow to incubate for 30 min at room temperature21.
  3. Carefully remove paraformaldehyde and excess solution with a micropipette in order to not disturb the EVs. Wash the EV with 1x PBS to remove excess paraformaldehyde. Perform the wash procedure three times. Remove excess 1x PBS.
  4. Prepare 250 µL of dSTORM B-cubed buffer solution per sample by creating a solution of 5 mM protocatechuate dioxygenase (Part A) diluted in imaging buffer (Part B) per manufacturer's protocol.
    NOTE: The concentration of the enzyme in the buffer may be doubled to 10 mM if photobleaching occurs.
    1. Add 250 µL of the prepared buffer to each well per manufacturer's protocol for 20 min at room temperature before imaging to scavenge oxidizing molecules.
      ​NOTE: The EV can then be either viewed immediately or stored at 4 °C for up to a week. Replace the buffer following storage before every visualization.

4 Direct stochastic optical reconstruction microscopy calibration

  1. Prepare the beads required for the calibration of the super-resolution microscope by diluting 100 nm microspheres to a concentration of 0.5% in molecular biology grade water and pipetting 200 µL into each well of a glass-bottom µ-slide 8-well plate.
    1. Allow the beads to settle in the wells for 1 h at room temperature.
  2. Without removing the existing solution, add 200 µL of 4% paraformaldehyde in PBS to each well to the calibration bead solution and allow to incubate for 30 min at room temperature.
  3. Carefully remove the paraformaldehyde with a micropipette to not disturb the beads and wash the beads three times with 1x PBS. Prepare the buffer according to step 3.4.
  4. Remove 1x PBS and add 250 µL of the prepared buffer to each well. Allow the buffer to sit for 20 min before visualization.
  5. Before placing anything on the stage, connect to the 3-D microscope using the Connect the Microscope button. Add 100x oil to the objective and place the center of the well on top of the objective. In the Acquire setting, turn on the 473 and 640 nm excitation lasers and click on View.
    1. Without the 3-D lens activated, view the beads under the photon saturation setting by clicking on Photon Counts in the Image Display options. Set the initial laser powers to 8.4 mW for the 473 nm laser and to 11.6 mW for the 640 nm laser.
    2. Decrease the focus of the laser to around -300 nm or the focal plane of the calibration beads to produce a clear resolution of the individual beads. Once the Z-plane is focused, further adjust the laser power levels to account for variation in each field of view.
  6. Under the instrument functions, complete 3-D mapping calibration and channel mapping calibration to obtain the errors on the X-, Y-, and Z-axis. Set the max number of FOVs to 20, the target number of points to 4,000, the max distance between channels to 5.0 pixels, and the exclusion radius between channels to 10.0 pixels during channel mapping calibration.
  7. Ensure that the calibration produces a point coverage of >90% and mapping quality that is good. Save the given calibration data for future image acquisitions.

5 Visualization of EV in three dimensions

  1. Add 100x oil onto the objective and place the prepared EVs into the microscope. Without the 3-D lens activated, turn on the 640 nm excitation laser and initially raise it to between 1.2 mW and 12.5 mW depending on the intensity of the signal and field of view to excite the red membrane intercalating dye stained EVs.
    1. Under the Image Display options, switch the viewing method from photon saturation to percentiles to better visualize the EVs. Adjust laser power to minimize noise, while maximizing signal. Maintain all the other parameters.
    2. Adjust the focus of the Z-plane by clicking the up or down icon on the Z-axis.
      NOTE: The Z-plane should be focused between -200 and -350 nm, but will vary depending on the field of view.
  2. Set the exposure time to 20 ms, the frame capture to 10,000 frames, and the initial laser power to between 1.2 mW and 12.5 mW, or the laser power determined in step 5.1, depending on the intensity of the signal and field of view.
    1. Activate the 3-D lens using the icon and start the acquisition by clicking on the Acquire button.
  3. Throughout image acquisition, raise the laser power by 3 increments of 10 every 1000 frames, or enough to maintain a high signal-to-noise ratio. Do not adjust the Z-plane during acquisition.
    ​NOTE: The laser may be raised to a maximum of 90 mW laser power.

6 Post-acquisition modification and EV tracing

  1. After the image acquisition, toggle over to the Analyze viewing window. Perform drift correction on the unfiltered image, and then activate filters. Adjust photon count, localization precision, sigmas, and frame index according to Table 1.
  2. Overlay an XYZ plane view tool along the X-axis of individual EVs from the field of view and export .CSV files of photoswitching events.
  3. Bisect individual EVs on the XY-axis in an X by Y field of view using a line histogram tool, which bins photoswitching events into set distance groups.
  4. Take images of single EVs and save them as .tiff files.
  5. Create 3-D videos of individual EVs using a 3-D visualization tool and color according to placement along the Z-axis.

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Representative Results

The goal of this study was to evaluate the effectiveness of super-resolution microscopy in visualizing individual EVs with nanometer resolution in three dimensions (3-D). To analyze the shape and size of individual EVs, we employed photoswitchable dye and incubated the EVs with a far-red, membrane intercalating dye, and removed excess dye through chromatography29. The affinity-captured anti-CD81 and red-stained EVs were then viewed in the super-resolution microscope under the 640 nm excitation laser. Following the calibration of the microscope that produced an average error of 16 nm on the XY-axis and 38 nm on the Z-axis (Figure 1A,B), the purified U2OS EVs were successfully visualized with a resolution of up to 20 nm on the XY-axis and 50 nm along the Z-axis.

Individual EVs visualized through dSTORM in 3-D photoswitched throughout the 10,000 frame exposure as the laser power was increased and were readily apparent in the acquired image (Figures 2A,B). Post-acquisition image correction of the Z-plane, photon counts, sigmas, and localization precision of the reconstructed image allowed for the clear resolution of the EV in 3-D (Figure 2C,D). The EV in Figure 2C photoswitched during only the first 7,000 frames, as seen by the legend in the upper-right corner. This is a result of photobleaching that may have been caused by raising the laser power too quickly. The histogram confirms that the majority of photoswitching events occurred within a 100 nm radius (Figure 2E), validating that the visualized EV is an exosome and that the isolation of EVs of a small diameter was successful.

Size distribution analysis was performed on other individually traced EVs using a line histogram tool and XYZ plane view tool to confirm that the majority of photoswitching events occurred within a 100 nm radius of the center (Figure 3A,C), further validating dSTORM's ability to visualize EVs of a small diameter. As seen by a 3-D visualization tool, error along the Z-axis is increased, producing an elongated final image of the EV along the axial axis (Figure 3D, Video 1). Photoswitching events were not correlated with EV size (Figure 3E), demonstrating that dSTORM-based characterization can be used for small EVs such as exosomes and small enveloped viruses less than 100 nm in diameter.

The correct parameters for Z-plane and sigma are integral to the proper resolution of the membrane in 3-D. Additionally, the correct exposure time, number of frames captured, and initial laser level are crucial to producing an image of an individual EV with a resolved membrane. Further investigation should be done on how to optimize the microscope and set both pre and post-acquisitional parameters to capture the highest resolution images of EVs.

Figure 1
Figure 1: Calibration of the super-resolution microscope in three dimensions using 100 nm microspheres. (A) Field of view in grayscale from calibration of the microscope with microspheres after post-acquisition image corrections. Scale bar in the lower right. (B) Absolute calibration errors on the XY-axis and the Z-axis were obtained through channel mapping calibration and 3-D mapping calibration, respectively. N = 10 biological replicates. Please click here to view a larger version of this figure.

Figure 2
Figure 2: dSTORM of a single EV in three dimensions. (A) Grayscale field of view of CD81+ affinity-purified EVs stained with photoswitchable red membrane intercalating dye and excited with the 640 nm excitation laser. Scale bar in the lower right. (B) Field of view from A labeled according to channel color. (C) Single EV from the zoomed-in view of the white box in A, labeled according to the frame index. The heat map in the upper right indicates the frame in which the photoswitching events were recorded. Scale bar in the lower right. (D) EV from C labeled according to channel color. (E) Size distribution analysis was created by bisecting the EV on the dashed line shown in D and separating the photoswitching event into 15.4 nm bins using a line histogram tool. Please click here to view a larger version of this figure.

Figure 3
Figure 3: Distribution of photoswitching events during the acquisition of a single EV in three dimensions. (A) Reconstructed image of a CD81+ affinity-purified EV labeled with photoswitchable red membrane intercalating dye and excited with the 640 nm excitation laser. Scale bar in the lower right. (B) Box and whisker plot of average diameters of CD81+ affinity-purified EVs obtained using the microscope's Line Histogram Tool along the XY-axis. (mean = 104 nm, standard deviation = 28 nm). (C) Location of individual photoswitching events along the XY dimension of the EV in A, recorded throughout the 10,000 frame exposure. (D) Location of individual photoswitching events along the XZ-axis of the EV in A, recorded throughout the 10,000 frame exposure. (E) Scatterplot of the number of photoswitching events recorded on individual EVs of varying diameters. R-squared value of 0.1065 demonstrates no correlation between the number of detected photoswitching events and EV diameter. Please click here to view a larger version of this figure.

Video 1: 3-D image of a single CD81+ affinity-purified EV labeled with photoswitchable red membrane intercalating dye and excited with the 640 nm excitation laser. The color scheme is labeled according to depth along the Z-axis. Error along the Z-axis is elongated. Please click here to download this Video.

Variable Min Max
Photon Count 200 10,000,000
Z-position (nm) -300 300
Localization Precision X (nm) 0 40
Localization Precision Y (nm) 0 40
Precision Sigma X (nm) 0 40
Precision Sigma Y (nm) 0 40
Sigma X (nm) (Channel 0, 640 nm laser) 100 350
Sigma Y (nm) (Channel 0, 640 nm laser) 100 350
Sigma X (nm) (Channel 1, 473, 561 nm lasers) 100 350
Sigma Y (nm) (Channel 1, 473, 561 nm lasers) 100 350
Frame Index 0 10,000

Table 1: Parameters for the super-resolution microscope during 3-D dSTORM acquisition.

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EVs have become a popular area of study due to their important role in many intracellular processes and cell-to-cell signaling1,30. However, their visualization proves to be difficult as their small size falls below the diffraction limit of light microscopy. Direct stochastic optical reconstruction microscopy (dSTORM) is a direct method of visualization that bypasses the diffraction limit by capturing photoswitching events of individual fluorophores over time and reconstructing an image based on these blinking events21,31. Super-resolution microscopy has been successfully performed in 3-D on several cellular structures such as actin filaments, microtubules, receptors embedded in the plasma membrane, and viral proteins in infected cells32,33,34,35,36. The purpose of this study was to evaluate the efficacy of super-resolution microscopy, specifically dSTORM, to visualize EVs in 3-D with nanometer resolution. We employed photoswitchable membrane intercalating dye to successfully visualize individual EVs from U2OS cells through dSTORM in up to +/- 20 nm resolution on the XY-axis and +/- 50 nm resolution on the Z-axis. Our previous work has shown that EVs from multiple cell lines and primary fluids have similar size distribution profiles as analyzed by NTA and TEM26,37. The use of a dSTORM-based characterization of EVs can add further confidence to this phenomenon, as well as potentially identify subpopulations in a single field of view. Further refinement of this method is warranted. One notable advantage to dSTORM is that the sample preparation does not require harsh or damaging steps that may alter the structure of the EVs. Our results further demonstrate that the biochemical nature of EVs is maintained during EV purification with anti-CD81 beads and acidic glycine26,37. We fixed the EVs with paraformaldehyde to avoid membrane permeabilizations caused by other fixatives such as methanol and ethanol. This allowed us to conclude that dSTORM accurately captures the morphology of EVs as they exist in solution. The use of Capto Core 700 is necessary, however, to purify the EVs effectively away from contaminants such as albumin and polyethylene glycol to below regulatory requirements38. One notable limitation of the protocol is that the binding efficiency between the EV and slides is not 100%, so some EVs are lost during sample preparation. Further investigation should be done on the efficacy of adhesive-coated slides to better bind EVs.

While the preparation of EVs for visualization is straightforward, the parameters during acquisition and especially during post-acquisitional modifications vary substantially from sample to sample, depending on the intensity and stability of the EVs and the fluorophore. One area of variability in the experiment is the intensity of the excitation lasers that must be delicately raised throughout exposure to maximize the signal but prevent photobleaching. Photobleaching, or when a fluorophore loses its ability to fluoresce, is a significant limitation throughout super-resolution microscopy12,39. To prevent photobleaching, the concentration of the enzyme in the buffer can be increased to 10 mM to better scavenge oxidizing molecules and prevent photobleaching. Additionally, setting the excitation laser power to a low initial level and slowly raising it throughout exposure to maintain a high signal is critical to prevent photobleaching.

We chose a red photoswitchable dye to stain the EVs due to its excitation wavelength, durability, and ability to withstand fixation29. However, the dye we chose may present issues during super-resolution microscopy when excited too quickly or at too high of an intensity. The fluorophores in the photoswitchable red membrane dye can photobleach after 10,000 frames or after the laser power exceeds 75.6 mW. Additionally, the membrane dye's intensity and ability to fluoresce decreases substantially after a week of storage at 4 °C. Finally, the membrane intercalating dyes have been shown to form micelles in an aqueous solution, so any excess dye still present in the EV sample after purification may be detected and mistaken for an EV if there is no other marker to identify the EV, such as a tetraspanin. Further investigation should be done using other membrane intercalating dyes to optimize for photo-stability31,40. Fluorescent antibodies conjugated to the EV may be a more suitable option as they tend to be more resistant to photobleaching and can amplify the signal41. However, the drawback of antibodies is that the signal from the fluorophore is slightly offset from the EV due to the distance from the epitope and fluorophore on the antibody.

Existing methods of EV visualization and characterization, such as NTA, flow cytometry, or EM, can require damaging preparation steps or are indirect methods of visualization. dSTORM requires little sample preparation, conserving the natural biochemical nature of EVs, and is a direct method of visualization that can bypass the diffraction limit and visualize EVs of a small diameter8,9,10,11,12,13,14,15,16,17,18,21,26. Other techniques of super-resolution microscopy can be optimized for EV characterization such as stimulated emission depletion (STED), spinning disc confocal microscopy (SDCM), and photo-activated localization microscopy (PALM)42,43. The current study exclusively focuses on dSTORM, but future work on optimizing super-resolution microscopy and comparing/contrasting these techniques is warranted. EVs have recently become a popular area of research as their role in virus progression has become more evident. Many evolutionarily distinct viruses, such as Epstein Barr Virus, HIV, and Hepatitis A Virus, have evolved to take advantage of the EV-signaling pathways to promote disease progression and evade the body's immune response37,44,45,46,47,48,49,50. These viruses have been shown to incorporate viral factors, such as mRNAs or viral proteins, into EVs that can then transfer these components to uninfected cells, while escaping immune detection6,51,52,53. These exosomal-associated viral factors can be detected and possibly employed as a biomarker for disease progression54,55. Therefore, dSTORM-based visualization of individual EVs and their associated proteins can be explored as a platform for disease biomarkers and, perhaps, disease progression of certain viruses54,55. Further research should be done to assess dSTORM's utility in visualizing both contents within an EV and proteins on its membrane.

In conclusion, we have demonstrated that super-resolution microscopy should be considered an effective technique for the visualization of EVs in 3-D with nanometer resolution. Results obtained by dSTORM are consistent with other EV characterizing techniques. A distinct advantage of dSTORM is the ability to directly visualize particles beneath the diffraction limit of light without dehydration or freeze fracture steps that can alter the biochemical nature of EVs.

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M.G.C. has no conflicts of interest to declare. R.P.M and D.P.D. receive material support from Oxford Nanoimaging (ONI) Inc. and Cytiva Inc. (formerly GE Healthcare). R.P.M. and D.P.D. declare competing interests for the possible commercialization of some of the information presented. These are managed by the University of North Carolina. The funding sources were not involved in the interpretations or writing of this manuscript.


We would like to thank Oxford Nanoimaging for their constructive feedback and guidance. This work was funded by the 5UM1CA121947-10 to R.P.M. and the 1R01DA040394 to D.P.D.


Name Company Catalog Number Comments
15 µ-Slide 8 well plates Ibidi 80827
1X PBS Gibco 14190-144
1X Penicillin Streptomycin solution Gibco 15140-122
50 mL conical tube Thermo Fisher 339652
500 mL 0.22 µm vacuum filtration apparatus Genesee 25-227
750 kDa hollow-fiber cartridge cutoff filter Cytiva 29-0142-95
AKTA Flux S Cytiva 29-0384-37
AKTA Start Cytiva 29022094-ECOMINSSW
Anti-CD81 magnetic beads Thermo Fisher 10616D
B-cubed buffer ONI  BCA0017
CellMask Red Thermo Fisher C10046
Dubelco's Modified Eagle Medium Thermo Fisher 10566016
Fetal Bovine Serum VWR 97068-085
Frac 30 Fraction collector Cytiva 29022094-ECOMINSSW
Glycine pH=2.0 Thermo Fisher BP381-5
HiTrap CaptoCore 700 Column Cytiva 17548151
Molecular Biology Grade Water Corning 9820003
Nanoimager Oxford Nanoimaging Custom
Paraformaldehhyde Electron Microscopy Sciences 15710
Polyethylene glycol Thermo Fisher BP233-1
RNase A Promega A797C
T175 Flasks Genesee 25-211
Tetraspek microspheres Invitrogen T7279
Tris- HCl pH=7.5 Thermo Fisher BP153-1
Unicorn V Cytiva 29022094-ECOMINSSW



  1. Pegtel, D. M., Gould, S. J. Exosomes. Annual Review of Biochemistry. 88, 487-514 (2019).
  2. Raposo, G., Stoorvogel, W. Extracellular vesicles: exosomes, microvesicles, and friends. The Journal of Cell Biology. 200 (4), 373-383 (2013).
  3. Théry, C., Zitvogel, L., Amigorena, S. Exosomes: composition, biogenesis and function. Nature Reviews. Immunology. 2 (8), 569-579 (2002).
  4. Cocozza, F., Grisard, E., Martin-Jaular, L., Mathieu, M., Théry, C. SnapShot: Extracellular vesicles. Cell. 182 (1), 262 (2020).
  5. Colombo, M., Raposo, G., Théry, C. Biogenesis, secretion, and intercellular interactions of exosomes and other extracellular vesicles. Annual Review of Cell and Developmental Biology. 30, 255-289 (2014).
  6. McNamara, R. P., Dittmer, D. P. Extracellular vesicles in virus infection and pathogenesis. Current Opinion in Virology. 44, 129-138 (2020).
  7. Schorey, J. S., Cheng, Y., Singh, P. P., Smith, V. L. Exosomes and other extracellular vesicles in host-pathogen interactions. EMBO Reports. 16 (1), 24-43 (2015).
  8. Akers, J. C., et al. Comparative analysis of technologies for quantifying Extracellular Vesicles (EVs) in Clinical Cerebrospinal Fluids (CSF). PLoS One. 11 (2), 0149866 (2016).
  9. Maas, S. L., et al. Possibilities and limitations of current technologies for quantification of biological extracellular vesicles and synthetic mimics. Journal of Controlled Release. 200, 87-96 (2015).
  10. Emelyanov, A., et al. Cryo-electron microscopy of extracellular vesicles from cerebrospinal fluid. PLoS One. 15 (1), 0227949 (2020).
  11. Noble, J. M., et al. Direct comparison of optical and electron microscopy methods for structural characterization of extracellular vesicles. Journal of Structural Biology. 210 (1), 107474 (2020).
  12. Panagopoulou, M. S., Wark, A. W., Birch, D. J. S., Gregory, C. D. Phenotypic analysis of extracellular vesicles: a review on the applications of fluorescence. Journal of Extracellular Vesicles. 9 (1), 1710020 (2020).
  13. Filipe, V., Hawe, A., Jiskoot, W. Critical evaluation of Nanoparticle Tracking Analysis (NTA) by NanoSight for the measurement of nanoparticles and protein aggregates. Pharmaceutical Research. 27 (5), 796-810 (2010).
  14. Carnell-Morris, P., Tannetta, D., Siupa, A., Hole, P., Dragovic, R. Analysis of extracellular vesicles using fluorescence nanoparticle tracking analysis. Methods in Molecular Biology. 1660, 153-173 (2017).
  15. Dragovic, R. A., et al. Sizing and phenotyping of cellular vesicles using Nanoparticle Tracking Analysis. Nanomedicine. 7 (6), 780-788 (2011).
  16. Bachurski, D., et al. Extracellular vesicle measurements with nanoparticle tracking analysis - An accuracy and repeatability comparison between NanoSight NS300 and ZetaView. Journal of Extracellular Vesicles. 8 (1), 1596016 (2019).
  17. Lacroix, R., Robert, S., Poncelet, P., Dignat-George, F. Overcoming limitations of microparticle measurement by flow cytometry. Seminars in Thrombosis and Hemostasis. 36 (8), 807-818 (2010).
  18. Lannigan, J., Erdbruegger, U. Imaging flow cytometry for the characterization of extracellular vesicles. Methods. 112, 55-67 (2017).
  19. Magenau, A., Gaus, K. 3D super-resolution imaging by localization microscopy. Methods in Molecular Biology. 1232, 123-136 (2015).
  20. Huang, B., Wang, W., Bates, M., Zhuang, X. Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy. Science. 319 (5864), 810-813 (2008).
  21. van de Linde, S., et al. Direct stochastic optical reconstruction microscopy with standard fluorescent probes. Nature Protocols. 6 (7), 991-1009 (2011).
  22. Chen, C., et al. Imaging and intracellular tracking of cancer-derived exosomes using single-molecule localization-based super-resolution microscope. ACS Applied Materials & Interfaces. 8 (39), 25825-25833 (2016).
  23. Grant, M. J., Loftus, M. S., Stoja, A. P., Kedes, D. H., Smith, M. M. Superresolution microscopy reveals structural mechanisms driving the nanoarchitecture of a viral chromatin tether. Proceedings of the National Academy of Sciences of the United States of America. 115 (19), 4992-4997 (2018).
  24. Nizamudeen, Z., et al. Rapid and accurate analysis of stem cell-derived extracellular vesicles with super resolution microscopy and live imaging. Biochimica et Biophysica Acta. Molecular Cell Research. 1865 (12), 1891-1900 (2018).
  25. Shen, X., et al. 3D dSTORM imaging reveals novel detail of ryanodine receptor localization in rat cardiac myocytes. The Journal of Physiology. 597 (2), 399-418 (2019).
  26. McNamara, R. P., et al. Large-scale, cross-flow based isolation of highly pure and endocytosis-competent extracellular vesicles. Journal of Extracellular Vesicles. 7 (1), 1541396 (2018).
  27. Plotkin, B. J., Sigar, I. M., Swartzendruber, J. A., Kaminski, A. Anaerobic growth and maintenance of mammalian cell lines. Journal of Visualized Experiments: JoVE. (137), (2018).
  28. Corso, G., et al. Reproducible and scalable purification of extracellular vesicles using combined bind-elute and size exclusion chromatography. Science Reports. 7 (1), 11561 (2017).
  29. Mönkemöller, V., et al. Imaging fenestrations in liver sinusoidal endothelial cells by optical localization microscopy. Physical Chemistry Chemical Physics. 16 (24), 12576-12581 (2014).
  30. Mathieu, M., Martin-Jaular, L., Lavieu, G., Théry, C. Specificities of secretion and uptake of exosomes and other extracellular vesicles for cell-to-cell communication. Nature Cell Biology. 21 (1), 9-17 (2019).
  31. Wang, L., Frei, M. S., Salim, A., Johnsson, K. Small-molecule fluorescent probes for live-cell super-resolution microscopy. Journal of the American Chemical Society. 141 (7), 2770-2781 (2019).
  32. Hu, Y. S., Cang, H., Lillemeier, B. F. Superresolution imaging reveals nanometer- and micrometer-scale spatial distributions of T-cell receptors in lymph nodes. Proceedings of the National Academy of Sciences of the United States of America. 113 (26), 7201-7206 (2016).
  33. Jayasinghe, I., et al. True molecular scale visualization of variable clustering properties of ryanodine receptors. Cell Reports. 22 (2), 557-567 (2018).
  34. Eggert, D., Rösch, K., Reimer, R., Herker, E. Visualization and analysis of hepatitis C virus structural proteins at lipid droplets by super-resolution microscopy. PLoS One. 9 (7), 102511 (2014).
  35. Mazloom-Farsibaf, H., et al. Comparing lifeact and phalloidin for super-resolution imaging of actin in fixed cells. PLoS One. 16 (1), 02246138 (2021).
  36. Huang, B., Jones, S. A., Brandenburg, B., Zhuang, X. Whole-cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution. Nature Methods. 5 (12), 1047-1052 (2008).
  37. McNamara, R. P., et al. Nef secretion into extracellular vesicles or exosomes is conserved across human and simian immunodeficiency viruses. mBio. 9 (1), 02344 (2018).
  38. Blom, H., et al. Efficient chromatographic reduction of ovalbumin for egg-based influenza virus purification. Vaccine. 32 (30), 3721-3724 (2014).
  39. Kalies, S., Kuetemeyer, K., Heisterkamp, A. Mechanisms of high-order photobleaching and its relationship to intracellular ablation. Biomedical Optics Express. 2 (4), 805-816 (2011).
  40. Mönkemöller, V., Øie, C., Hübner, W., Huser, T., McCourt, P. Multimodal super-resolution optical microscopy visualizes the close connection between membrane and the cytoskeleton in liver sinusoidal endothelial cell fenestrations. Scientific Reports. 5, 16279 (2015).
  41. Xu, J., Ma, H., Liu, Y. Stochastic Optical Reconstruction Microscopy (STORM). Current Protocols in Cytometry. 81, 1-27 (2017).
  42. Godin, A. G., Lounis, B., Cognet, L. Super-resolution microscopy approaches for live cell imaging. Biophysical Journal. 107 (8), 1777-1784 (2014).
  43. Azuma, T., Kei, T. Super-resolution spinning-disk confocal microscopy using optical photon reassignment. Optics Express. 23 (11), 15003-15011 (2015).
  44. Hurwitz, S. N., et al. CD63 regulates Epstein-Barr Virus LMP1 exosomal packaging, enhancement of vesicle production, and noncanonical NF-κB signaling. Journal of Virology. 91 (5), 02251 (2017).
  45. Hurwitz, S. N., Cheerathodi, M. R., Nkosi, D., York, S. B., Meckes, D. G. Tetraspanin CD63 bridges autophagic and endosomal processes to regulate exosomal secretion and intracellular signaling of Epstein-Barr Virus LMP1. Journal of Virology. 92 (5), 01969 (2018).
  46. Bukong, T. N., Momen-Heravi, F., Kodys, K., Bala, S., Szabo, G. Exosomes from hepatitis C infected patients transmit HCV infection and contain replication competent viral RNA in complex with Ago2-miR122-HSP90. PLoS Pathogens. 10 (10), 1004424 (2014).
  47. Khan, M. B., et al. Nef exosomes isolated from the plasma of individuals with HIV-associated dementia (HAD) can induce Aβ(1-42) secretion in SH-SY5Y neural cells. J Neurovirology. 22 (2), 179-190 (2016).
  48. Lee, J. H., et al. HIV-Nef and ADAM17-containing plasma extracellular vesicles induce and correlate with immune pathogenesis in chronic HIV infection. EBioMedicine. 6, 103-113 (2016).
  49. Meckes, D. G., et al. Modulation of B-cell exosome proteins by gamma herpesvirus infection. Proceedings of the National Academy of Sciences of the United States of America. 110 (31), 2925-2933 (2013).
  50. Raymond, A. D., et al. Microglia-derived HIV Nef+ exosome impairment of the blood-brain barrier is treatable by nanomedicine-based delivery of Nef peptides. Journal of Neurovirology. 22 (2), 129-139 (2016).
  51. Raab-Traub, N., Dittmer, D. P. Viral effects on the content and function of extracellular vesicles. Nature Reviews Microbiology. 15 (9), 559-572 (2017).
  52. Feng, Z., et al. A pathogenic picornavirus acquires an envelope by hijacking cellular membranes. Nature. 496 (7445), 367-371 (2013).
  53. Bandopadhyay, M., Bharadwaj, M. Exosomal miRNAs in hepatitis B virus related liver disease: a new hope for biomarker. Gut Pathogens. 12, 23 (2020).
  54. Hurwitz, S. N., et al. Proteomic profiling of NCI-60 extracellular vesicles uncovers common protein cargo and cancer type-specific biomarkers. Oncotarget. 7 (52), 86999-87015 (2016).
  55. Rodrigues, M., Fan, J., Lyon, C., Wan, M., Hu, Y. Role of extracellular vesicles in viral and bacterial infections: Pathogenesis, diagnostics, and therapeutics. Theranostics. 8 (10), 2709-2721 (2018).
Direct Stochastic Optical Reconstruction Microscopy of Extracellular Vesicles in Three Dimensions
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Chambers, M. G., McNamara, R. P.,More

Chambers, M. G., McNamara, R. P., Dittmer, D. P. Direct Stochastic Optical Reconstruction Microscopy of Extracellular Vesicles in Three Dimensions. J. Vis. Exp. (174), e62845, doi:10.3791/62845 (2021).

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