Name: direct stochastic optical reconstruction microscopy of extracellular vesicles in three dimensions
Uploaded: 2021-08-26T14:45:00
Description: Watch this Scientific Journal Video about Direct Stochastic Optical Reconstruction Microscopy of Extracellular Vesicles in Three Dimensions at JoVE.com

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.

1 Propagation and maintenance of cell lines
<ol>
	<li>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.</li>
	<li>Maintain the U2OS cells in a copper-coated incubator at 37 &#176;C in 5% CO2 and passage cells in T175 flasks26</sup...

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...

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.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>15 &#181;-Slide 8 well plates</td>
			<td>Ibidi</td>
			<td>80827</td>
			<td></td>
		</tr>
		<tr>
			<td>1X PBS</td>
			<td>Gibco</td>
			<td>14190-144</td>
			<td></td>
		</tr>
		<tr>
			<td>1X Penicillin Streptomycin solution</td>
			<td>Gibco</td>
			<td>15140-122</td>
			<td></td>
		</tr>
		<tr>
			<td>50 mL conical tube</td>
			<td>Thermo Fisher</td>
			<td>339652</td>
			<td></td>
		</tr>
		<tr>
			<td>500 mL 0.22 &#181;m vacuum filtration apparatus</td>
			<td>Genesee</td>
			<td>25-227</td>
			<td></td>
		</tr>
		<tr>
			<td>750 kDa hollow-fiber cartridge cutoff filter</td>
			<td>Cytiva</td>
			<td>29-0142-95</td>
			<td></td>
		</tr>
		<tr>
			<td>AKTA Flux S</td>
			<td>Cytiva</td>
			<td>29-0384-37</td>
			<td></td>
		</tr>
		<tr>
			<td>AKTA Start</td>
			<td>Cytiva</td>
			<td>29022094-ECOMINSSW</td>
			<td></td>
		</tr>
		<tr>
			<td>Anti-CD81 magnetic beads</td>
			<td>Thermo Fisher</td>
			<td>10616D</td>
			<td></td>
		</tr>
		<tr>
			<td>B-cubed buffer</td>
			<td>ONI</td>
			<td>&#160;BCA0017</td>
			<td></td>
		</tr>
		<tr>
			<td>CellMask Red</td>
			<td>Thermo Fisher</td>
			<td>C10046</td>
			<td></td>
		</tr>
		<tr>
			<td>Dubelco&#39;s Modified Eagle Medium</td>
			<td>Thermo Fisher</td>
			<td>10566016</td>
			<td></td>
		</tr>
		<tr>
			<td>Fetal Bovine Serum</td>
			<td>VWR</td>
			<td>97068-085</td>
			<td></td>
		</tr>
		<tr>
			<td>Frac 30 Fraction collector</td>
			<td>Cytiva</td>
			<td>29022094-ECOMINSSW</td>
			<td></td>
		</tr>
		<tr>
			<td>Glycine pH=2.0</td>
			<td>Thermo Fisher</td>
			<td>BP381-5</td>
			<td></td>
		</tr>
		<tr>
			<td>HiTrap CaptoCore 700 Column</td>
			<td>Cytiva</td>
			<td>17548151</td>
			<td></td>
		</tr>
		<tr>
			<td>Molecular Biology Grade Water</td>
			<td>Corning</td>
			<td>9820003</td>
			<td></td>
		</tr>
		<tr>
			<td>Nanoimager</td>
			<td>Oxford Nanoimaging</td>
			<td>Custom</td>
			<td></td>
		</tr>
		<tr>
			<td>Paraformaldehhyde</td>
			<td>Electron Microscopy Sciences</td>
			<td>15710</td>
			<td></td>
		</tr>
		<tr>
			<td>Polyethylene glycol</td>
			<td>Thermo Fisher</td>
			<td>BP233-1</td>
			<td></td>
		</tr>
		<tr>
			<td>RNase A</td>
			<td>Promega</td>
			<td>A797C</td>
			<td></td>
		</tr>
		<tr>
			<td>T175 Flasks</td>
			<td>Genesee</td>
			<td>25-211</td>
			<td></td>
		</tr>
		<tr>
			<td>Tetraspek microspheres</td>
			<td>Invitrogen</td>
			<td>T7279</td>
			<td></td>
		</tr>
		<tr>
			<td>Tris- HCl pH=7.5</td>
			<td>Thermo Fisher</td>
			<td>BP153-1</td>
			<td></td>
		</tr>
		<tr>
			<td>Unicorn V</td>
			<td>Cytiva</td>
			<td>29022094-ECOMINSSW</td>
			<td></td>
		</tr>
	</tbody>
</table>

direct stochastic optical reconstruction microscopy of extracellular vesicles in three dimensions

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.

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 las...

Watch this Scientific Journal Video about Direct Stochastic Optical Reconstruction Microscopy of Extracellular Vesicles in Three Dimensions at JoVE.com

Direct Stochastic Optical Reconstruction Microscopy of Extracellular Vesicles in Three Dimensions

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 ...

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