Name: Proteome/Phosphoproteome Analysis of the Extracellular Vesicle (EV) Samples Using LC-MS/MS
Uploaded: 2023-10-27T13:10:00
Description: Watch this Scientific Journal Video about Proteome/Phosphoproteome Analysis of the Extracellular Vesicle EV Samples Using LC-MS/MS at JoVE.com

proteome/phosphoproteome analysis of the extracellular vesicle (ev) samples using lc-ms/ms

Enhancing EV Isolation for Precise Biofluid Analysis

Extracellular vesicles (EVs) are membrane-encapsulated nanoparticles secreted by all types of cells and are present in biofluids such as blood, urine, saliva, etc.1,2,3,4. EVs carry a cargo of diverse bioactive molecules which reflect the physiological and pathological state of their host cells and, therefore function as crucial factors in disease progression4,5,6. Moreover, extensive studies have established that EV-based disease markers can be identified prior to the onset of symptoms or the physiological detection of tumors5,6,7.
Phosphorylation acts as a key mechanism in cellular signaling and regulation. Therefore, phosphoproteins provide a valuable source for biomarker discovery as aberrant phosphorylation events are associated with dysregulated cellular signaling pathways and metastatic disease development such as cancer8,9,10. Although profiling phosphorylation dynamics allows for the identification of disease-specific phosphoprotein signatures as potential biomarkers, the low abundance and dynamic nature of phosphoproteins pose major challenges in developing phosphoproteins as biomarkers11,12. Notably, the low-abundant phosphoproteins encapsulated within EVs are protected from external enzymatic digestion in the extracellular environment8. Consequently, EVs and EV-derived phosphoproteins offer an ideal source for biomarker discovery in the early-stage detection of cancer and other diseases.
Although analysis of protein phosphorylation in EVs offers a valuable resource for understanding cancer signaling and early-stage disease diagnosis, the lack of efficient EV isolation methods presents a major barrier. EV isolation is commonly achieved through differential ultracentrifugation (DUC)13. However, this method is time-consuming and is not suitable for clinical implications due to low throughput and poor reproducibility13,14. Alternative EV isolation approaches, such as polymer-induced precipitation15, are limited by low specificity due to co-precipitation of non-EV proteins. Affinity-based approaches, including antibody-based affinity capture16 and affinity filtration17, offer enhanced specificity but are restricted to a relatively low recovery rate due to small volume.
To address the issues in exploring phosphoprotein dynamics in EVs, our group has developed extracellular vesicles total recovery and purification (EVtrap) technique based on chemical affinity to capture EVs onto functionalized magnetic beads18. Previous results have demonstrated that this magnetic bead-based EV isolation method is highly effective in isolating EVs from a wide range of biofluid samples and is able to achieve much higher EV yield while minimizing contamination compared to DUC and other existing isolation methods18,19. We have successfully utilized EVtrap and a titanium-based phosphopeptide enrichment method developed by our group20 to profile the phosphoproteome of EVs derived from diverse biofluids and to detect potential phosphoprotein biomarkers for various diseases19,21,22.
Here, we present a protocol based on EVtrap for the isolation of circulating EVs. The protocol focuses on the urinary EVs. We also demonstrate the characterization of isolated EVs using western blotting. We then detail the sample preparation and mass spectrometry (MS) acquisition for both proteomics and phosphoproteomics analyses. This protocol provides an efficient and reproducible workflow for profiling the urinary EV proteome and phosphoproteome, which will facilitate further studies on EVs and their clinical applications23.

Author Spotlight: Advancing EVtrap for High-Throughput Proteomics in Disease Biomarker Discovery 

Chemical Affinity-Based Isolation of Extracellular Vesicles from Biofluids for Proteomics and Phosphoproteomics Analysis

We are working on extracellular vesicle-based biomarker discovery. One important step is to isolate them efficiently and selectively. EVtrap, which is based on magnetic bead-based separation, can really help us by providing high throughput, easy to use, in particular, easy for clinical applications.We have been using this protocol for discovery in proteins and the phosphoprotein biomarkers for different diseases such as breast cancer, kidney cancers, and Parkinson's Disease. This biomarker is derived from biofluid. EVs can potentially be used for liquid biopsies, which can further improve clinical diagnosis and the treatment.Currently, the most commonly used approach for extracellular vesicle isolation are ultracentrifugation and precipitation, but those methods are limited to co-isolation of contaminants and also low efficiency. So our EVtrap method will provide a more effective way for isolating EVs, which will allow for a more reproducible and sensitive method and also will benefit downstream analysis. We are working on two things.First, we are continue developing the methods and protocols for EV isolation and a downstream analysis, in particular, a mass backup-based analysis. Second one is we are exploring different application in clinical field because of the advantage by the EVtrap.

Watch this Scientific Journal Video about Proteome/Phosphoproteome Analysis of the Extracellular Vesicle EV Samples Using LC-MS/MS at JoVE.com

Proteome/Phosphoproteome Analysis of the Extracellular Vesicle (EV) Samples Using LC-MS/MS  

To begin, prepare proteome and phosphoproteome samples of the extracellular vesicles isolated from the urine samples using the EVtrap approach. Inject the samples into the trapped ion-mobility time-of-flight mass spectrometer through the liquid chromatography system. Separate the peptides into a 15-centimeter C18 column.For proteomics analysis, acquire data using the dia-PASEF method with a mass range per ramp to span from 300 to 1200 mass-to-charge ratio and ion-mobility constant from 0.6 to 1.50 1/Knot. For phosphoproteomics analysis, acquire data using a dia-PASEF acquisition method. Set the mass range per ramp to span from 400 to 1550 mass-to-charge ratio in ion-mobility constant from 0.6 to 1.50 1/Knot.Load the raw files into proteomic software. Set up the search parameters in the homo sapiens database. For Digest Type, select Specific, and under Enzymes, select TrypsinP.Define the Peptide Length to a minimum of 7 and a maximum of 52 and allow two missed cleavages. Then set the Maximum Variable Modifications to 5. The Fixed Modification should be Carbamidomethyl at Cystine, while the Variable Modifications should include Acetyl Protein N-Terminal, Oxidation at Methionine, and Phosphorylation at Serine, Threonine, and Tyrosine.Finally, set the false discovery rate for peptide spectrum match, peptide, and protein group to 0.01. In the LCMS and MS proteomic profiling, 2%of each sample revealed over 11, 000 unique peptides from approximately 2, 200 proteins. Notably, 72%of unique proteins were consistently found in all three replicates and 90 top EV markers and proteins were identified compared to the ExoCarta database.Quantitative precision was confirmed with a low-medium coefficient of variation of 5.7%signifying high reproducibility and reliability. For phosphoproteomics, 98%of each peptide sample yielded 800 unique phosphopeptides and 350 phosphoproteins. The enrichment resulted in 72%phosphoserine, 22%phosphothreonine, and 6%phosphotyrosine peptides.42%of phosphopeptides were identified in all replicates in a medium coefficient of variation of 21.8%was observed, indicating acceptable quantitative reproducibility.

proteomephosphoproteome-analysis-extracellular-vesicle-ev-samples

Research

JoVE Journal

Biochemistry

Extracellular vesicles (EVs) from biofluids have recently gained significant attention in the field of liquid biopsy. Released by almost every type of cell, they provide a real-time snapshot of host cells and contain a wealth of molecular information, including proteins, in particular those with post-translational modifications (PTMs) such as phosphorylation, as the main player of cellular functions and disease onset and progression. However, the isolation of EVs from biofluids remains challenging due to low yields and impurities from current EV isolation methods, making the downstream analysis of EV cargo, such as EV phosphoproteins, difficult. Here, we describe a rapid and effective EV isolation method based on functionalized magnetic beads for EV isolation from biofluids such as human urine and downstream proteomics and phosphoproteomics analysis following EV isolation. The protocol enabled a high recovery yield of urinary EVs and sensitive profiles of EV proteome and phosphoproteome. Furthermore, the versatility of this protocol and relevant technical considerations are also addressed here.

The present protocol provides detailed descriptions for the efficient isolation of urinary extracellular vesicles utilizing functionalized magnetic beads. Moreover, it encompasses subsequent analyses, including western blotting, proteomics, and phosphoproteomics.

Extracellular vesicles (EVs) from biofluids have recently gained significant attention in the field of liquid biopsy. Released by almost every type of ...

Extracellular Vesicle (EV) Isolation from Human Urine Samples Using the EVtrap Approach

To begin, collect the urine samples from healthy individuals. Centrifuge 12 milliliters of sample in a 15 milliliter conical tube to eliminate cell debris in large apoptotic bodies. Then, transfer 10 milliliters of the supernatant into a fresh 15 milliliter tube.Add one milliliter of loading buffer and 200 microliters of EV trap bead slurry to the sample. Incubate the sample at room temperature for 30 minutes with end over end rotation. To pellet the sample, place the 15 milliliter conical tube on a magnetic separator rack.Carefully remove the supernatant and re-suspend the beads in one milliliter of washing buffer. Then, transfer the suspension to a 1.5 milliliter micro centrifuge tube and gently pipette to re-suspend the extracellular vesicle or EV-bound beads. Place the micro centrifuge tube on a magnetic separator rack for 1.5 milliliter tubes.Using a P200 pipette, carefully aspirate the supernatant. Now, wash the beads with one milliliter of washing buffer, followed by two washes with one milliliter of PBS at room temperature. Incubate the beads with 100 microliters of freshly prepared 100 millimolar Triethanolamine for five minutes.Using 1.5 milliliter micro centrifuge tube magnetic separator rack, collect the eluded solution containing EVs. After combining the eluded solutions, dry the eluit, using a vacuum centrifuge concentrator at four degrees Celsius.

Preparation of Dried Extracellular Vesicle (EV) Sample for Proteomics and Phosphoproteomics Analysis

To begin, take the dried extracellular vesicle sample obtained from the human urine using the EV trap approach. Prepare a fresh lysis buffer with the shown components. Then add 100 microliters of lysis buffer to solubilize the dried EV sample.Heat the sample at 95 degrees Celsius for 10 minutes while shaking at 1, 100 RPM. After cooling the sample to room temperature, dilute it fivefold by adding 400 microliters of 50 millimolar TEAB. Measure the protein concentration using a BCA assay kit according to the manufacturer's instructions.Add trypsin and lysine C mix to the sample an incubate at 37 degrees celsius overnight with shaking at 1, 100 RPM. Then add 50 microliters of 10%trifluoroacetic acid or TFA to acidify the sample. Further, add 600 microliters of ethyl acetate to the samples and vortex the mixture for two minutes.Centrifuge the sample for three minutes at 20, 000 G and carefully remove the upper layer without disturbing the interface. Dry the aqueous phase using a vacuum centrifuge concentrator. Now resuspend the dried sample in 200 microliters of 0.1%TFA to acidify peptides.To desalt the sample, use a CA18 desalting tip and condition it with 200 microliters of 0.1%TFA and 80%acetonitrile, followed by two washes with 200 microliters of 0.1%TFA. Load the acidified peptide sample into the tip and wash it three times with 200 microliters of 0.1%TFA. Elute the peptides with 200 microliters of 0.1%TFA and 80%acetonitrile.After drawing the eluent as demonstrated, resuspend the dried to phosphoproteomics sample in 200 microliters of loading buffer for phosphopeptide enrichment. Add 50 microliters of the beads to the sample and vigorously shake for 20 minutes at room temperature. Load the sample with the beads into the fritted tip and centrifuge for one minute at 100 G.Wash the tip successively with 200 microliters of loading buffer, washing buffers one and two.Place the tip with beads into a new tube to collect the eluded phosphopeptides. Add 50 microliters of elution buffer to the tip and centrifuge for two minutes at 20 G.Then dry the eluded phosphopeptides using a vacuum centrifuge concentrator.