Purification of High Yield Extracellular Vesicle Preparations Away from Virus

Summary

This protocol isolates extracellular vesicles (EVs) away from virions with high efficiency and yield by incorporating EV precipitation, density gradient ultracentrifugation, and particle capture to allow for a streamlined workflow and a reduction of starting volume requirements, resulting in reproducible preparations for use in all EV research.

Abstract

One of the major hurdles in the field of extracellular vesicle (EV) research today is the ability to achieve purified EV preparations in a viral infection setting. The presented method is meant to isolate EVs away from virions (i.e., HIV-1), allowing for a higher efficiency and yield compared to conventional ultracentrifugation methods. Our protocol contains three steps: EV precipitation, density gradient separation, and particle capture. Downstream assays (i.e., Western blot, and PCR) can be run directly following particle capture. This method is advantageous over other isolation methods (i.e., ultracentrifugation) as it allows for the use of minimal starting volumes. Furthermore, it is more user friendly than alternative EV isolation methods requiring multiple ultracentrifugation steps. However, the presented method is limited in its scope of functional EV assays as it is difficult to elute intact EVs from our particles. Furthermore, this method is tailored towards a strictly research-based setting and would not be commercially viable.

Introduction

Research centered around extracellular vesicles (EVs), specifically exosomes, a type of EV ranging 30-120 nm and characterized by the presence of three tetraspanin markers CD81, CD9, and CD63, has largely been shaped by the development of methods to isolate and purify the vesicles of interest. The ability to dissect multifaceted mechanisms has been hindered due to complex and time-consuming techniques which generate samples composed of a heterogeneous population of vesicles generated via different pathways with a wide range of contents, sizes, and densities. While this is an issue for nearly all EV research, it is of particular importance when studying EVs in the context of viral infection, as virions and virus-like particles (VLPs) can be similar in diameter to the vesicles of interest. For example, the Human Immunodeficiency Virus Type 1 (HIV-1) is approximately 100 nm in diameter, which is roughly the same size as many types of EVs. For this reason, we have designed a novel EV isolation workflow to address these issues.

The current gold standard of EV isolation is ultracentrifugation. This technique makes use of the various vesicle densities, which allows the vesicles to be separated by centrifugation with differential sedimentation of higher density particles versus lower density particles at each stage ^1,2. Several low-speed centrifugation steps are required to remove intact cells (300-400 x g for 10 min), cell debris (~2,000 x g for 10 min), and apoptotic bodies/large vesicles (~10,000 x g for 10 min). These initial purifications are followed by high speed ultracentrifugation (100,000-200,000 x g for 1.5-2 h) to sediment EVs. Wash steps are performed to further ensure EV purity, however, this results in the reduction of the number of isolated EVs, thereby lowering total yield ^3,4. This method’s utility is further limited by the requirement of a large number of cells (approximately 1 x 10⁸) and a large sample volume (> 100 mL) to achieve adequate results.

To address the growing concerns, precipitation of vesicles with hydrophilic polymers has become a useful technique in recent years. Polyethylene glycol (PEG), or other related precipitation reagents, allows the user to pull down the vesicles, viruses, and protein or protein-RNA aggregates within a sample by simply incubating the sample with the reagent of choice, followed by a single low-speed centrifugation^1,2,5. We have previously reported that use of PEG or related methods to precipitate EVs in comparison to traditional ultracentrifugation results in a significantly higher yield⁶. This strategy is fast, easy, does not require additional expensive equipment, is readily scalable, and retains EV structure. However, due to the promiscuous nature of this method, the resulting samples contain a variety of products including free proteins, protein complexes, a range of EVs, and virions thus requiring further purification to obtain the desired population^1,2,7,8.

To overcome the heterogeneity of EVs obtained from various precipitation methods, density gradient ultracentrifugation (DG) is utilized to better separate particles based upon their density. This method is carried out using a stepwise gradient using a density gradient medium, such as iodixanol or sucrose, which allows for the separation of EVs from proteins, protein complexes, and virus or virus-like particles (VLPs). It is important to note that, while it was once thought that DG allowed for more precise separation of EV subpopulations, it is now known that sizes and densities of various vesicles can overlap. For example, exosomes are known to have flotation densities of 1.08-1.22 g/mL⁹, while vesicles isolated from the Golgi (COPI⁺ or clathrin⁺) have densities of 1.05-1.12 g/mL and those from the endoplasmic reticulum (COPII⁺) sediment at 1.18-1.25 g/mL^1,2,3,4,9. Additionally, if one desires to compare exosomal fractions against fractions containing viral particles, this may become more difficult depending upon the density of the virus of interest—there are viruses other than HIV-1 that likely equilibrate at the same densities as exosomal positive fractions².

Finally, enrichment of EV preps for downstream visualization and functional assays is vital to EV research. The use of EV-enriching nanoparticles, specifically, multi-functional hydrogel particles that range 700-800 nm in diameter, are a critical step in achieving concentrated EV preps. They possess a high affinity aromatic bait which encapsulated by a porous outer sieving shell to promote selectivity. The nanoparticles utilized in this study include two distinct preparations with different core baits (Reactive Red 120 NT80; and Cibacron Blue F3GA NT82) which have shown to increase capture of EVs from various reagents and biofluids (see the Table of Materials)^{6,10,11,12,13,14,15}. The particles offer easy enrichment of EVs from numerous starting materials including iodixanol fractions, cell culture supernatant, as well as patient biofluids such as plasma, serum, cerebral spinal fluids (CSF), and urine^6,13.

The method presented here improves the efficiency of current EV purification techniques by combining several technologies; EV precipitation, density gradient ultracentrifugation, and particle capture, to streamline the workflow, reduce sample requirements, and increase yield to obtain a more homogenous EV sample for use in all EV research. This method is particularly useful in the investigation of EVs and their contents during viral infection as it includes a 0.22 µm filtration step to exclude large, unwanted vesicles and VLPs and separation of the total EV population based on density to effectively isolate EVs from virions.

Protocol

1. Filtration and Precipitation of Extracellular Vesicles (EVs)

1. To prepare the culture supernatant from infected or transfected cells (i.e., cell lines and/or primary cells), culture approximately 10 mL of late-log cells for 5 days at 37 °C and 5% CO₂ in appropriate culture medium (i.e., RPMI or DMEM with 10% fetal bovine serum [FBS]).
   NOTE: All culture medium reagents should be free of EVs, and can be either purchased (see Table of Materials) or prepared in-house by pre-ultracentrifugation of serum at 100,000 x g for 90 min. This protocol has been successful for several commonly-used cell lines including: CEM, Jurkat, 293T, U937 (uninfected lines), U1, J1.1, ACH2, HUT102, MT-2 (HIV-1 and HTLV-1 infected lines), multiple transfected cells, and primary myeloid and T-cells (both infected and uninfected); however, this protocol can be used for any cell type, including those that require specialized media or culture conditions. Density of cells may need to be optimized for different cell types. It is recommended that the highest density be used with minimal cell death after 5 days.
2. Centrifuge the culture at 3,000 x g for 5 min to pellet cells and discard the pellet.
3. Filter the culture supernatant using a sterile 0.22 µm filter and collect filtrate in a clean tube.
4. Add equal volume of PEG precipitation reagent (1:1 ratio) to filtered supernatant. Invert tube several times to ensure a homogenous mixture.
   NOTE: Do NOT vortex.
5. Incubate mixture at 4 °C overnight (O/N).
6. Centrifuge mixture at 1,500 x g for 30 min at room temperature (RT) to yield a heterogeneous EV pellet.
   NOTE: EV pellet should appear white or off-white in color.
7. Discard the EV-depleted culture supernatant.
8. Resuspend the EV pellet in 150–300 µL of 1x phosphate-buffered saline without calcium and magnesium (PBS) and keep on ice.

2. Construction of a Density Gradient

1. Mix iodixanol density gradient medium with 1x PBS to create 11 different 1 mL density fractions from 6 to 18% iodixanol in 1.2% increments in separate microcentrifuge tubes as shown in Figure 1A.
2. Vortex each tube to mix.
3. Layer density fractions into a pre-cleaned and dry swinging bucket ultracentrifuge tube starting with fraction #18 and ending with fraction #6 as indicated in Figure 1B.
   NOTE: All tubes should be sanitized using a 10% bleach spray followed by followed by rinsing 3x with deionized water and a final wash of sterile deionized water prior to loading of the gradient fractions.
4. Add resuspended EV pellet (300 µL) to the top of the layered gradient in the ultracentrifuge tube.
5. Ultracentrifuge at 100,00 x g at 4 °C for 90 min.
6. Carefully remove the 1 mL fractions from the ultracentrifuge tube and transfer each fraction into new microcentrifuge tubes.

3. Enrichment of EV Fractions uUsing Nanoparticles

1. Create a 30% slurry of nanoparticles using equal volumes of NT80, NT82, and 1x PBS.
   NOTE: The mixture should be vortexed prior to use to ensure homogeneity.
2. Add 30 µL of the slurry to each microcentrifuge tube containing the density fractions and pipette/invert them several times to mix.
3. Rotate EV-enriching nanoparticle-containing density fraction microcentrifuge tubes O/N at 4 °C at approximately 20 rpm.
4. Centrifuge density fraction microcentrifuge tubes at 20,000 x g for 5 min at RT.
5. Discard the liquid and wash EV pellet twice with 1x PBS.
   NOTE: Nanoparticle pellets can be frozen at -20 °C or immediately used for various downstream assays (i.e., PCR, Western blot, mass spectrometry, and other assays).

4. Recommended Preparation of Nanoparticle Pellet for Downstream Assays

1. For RNA isolation
   1. Resuspend the pellet in 50 µL of autoclaved deionized water treated with 0.001% diethyl pyrocarbonate (DEPC) filtered through a 0.2 µm filter and isolate RNA according to the kit manufacturer’s protocol.
2. For gel electrophoresis
   1. Resuspend the pellet directly in 15 µL of Laemmli buffer.
   2. Heat sample 3x at 95 °C for 3 min. Vortex gently and spin down between each heat cycle.
   3. Centrifuge sample for 15 s at 20,000 x g and load all eluted material directly onto the gel.
      NOTE: For best results, limit the amount of particles loaded onto the gel and run the gel at 100 V to ensure any remaining particles are contained to the wells.
3. For trypsin digestion
   1. Resuspend the pellet in 20 µL of urea prior to alkylation and trypsinization of sample. Nanoparticles can be pelleted by a 14,000 x g centrifugation at RT for 10 min. Sample containing the trypsinized peptide can be transferred into a clean collection tube.

Results

PEG precipitation increases EV yield
Our combination approach to EV isolation is significantly more efficient in terms of EV recovery as compared to traditional ultracentrifugation, as evident by the 90% reduction in the volume of starting material required. Ultracentrifugation, the current gold standard in EV isolation, requires approximately 100 mL of culture supernatant to produce an adequate EV prep for downstream assays, whereas our novel protocol requires only 1...

Discussion

The outlined method allows for enhanced EV yield and the separation of virus from EVs using a combination approach to isolation. Relatively large quantities of starting material (i.e., cell supernatant) can be filtered prior to EV isolation by precipitation, DG separation, and nanoparticle enrichment, resulting in a final volume of ~30 µL, allowing for immediate usage in a variety of downstream assays. The use of nanoparticle enrichment is essential as, compared to traditional ultracentrifugation, these EV-enriching...

Materials

List of materials used in this article

Name	Company	Catalog Number	Comments
CEM CD4+ Cells	NIH AIDS Reagent Program	117	CEM
DPBS without Ca and Mg (1x)	Quality Biological	114-057-101
ExoMAX Opti-Enhancer	Systems Biosciences	EXOMAX24A-1	PEG precipitation reagent
Exosome-Depleted FBS	Thermo Fisher Scientific	A2720801
Fetal Bovine Serum	Peak Serum	PS-FB3	Serum
HIV-1 infected U937 Cells	NIH AIDS Reagent Program	165	U1
Nalgene Syringe Filter 0.2 µm SFCA	Thermo Scientific	723-2520
Nanotrap (NT80)	Ceres Nanosciences	CN1030	Reactive Red 120 core
Nanotrap (NT82)	Ceres Nanosciences	CN2010	Cibacron Blue F3GA core
Optima XE-980 Ultracentrifuge	Beckman Coulter	A94471
OptiPrep Density Gradient Medium	Sigma-Aldrich	D1556-250mL	Iodixanol
SW 41 Ti Swinging-Bucket Rotor	Beckman Coulter	331362
Ultra-Clear Tube, 14 mm x 89 mm	Beckman Coulter	344059