Methods for Extracellular Vesicle Isolation: Relevance for Encapsulated miRNAs in Disease Diagnosis and Treatment
Abstract
:1. Introduction
2. EVs: Biogenesis, Function, and Clinical Potential
2.1. Biogenesis of EVs
2.2. EV Function
2.3. EVs Clinical Potential
3. Methods to Isolate EVs
3.1. UC
3.1.1. dUC
3.1.2. DGUC
3.2. Precipitation
3.3. Immunoaffinity
3.4. FACSCanto and EV Sorting
3.5. UF
3.6. SEC
3.7. Microfluidics
3.8. EV Isolation Methods Overview
3.9. EV Quantification and Characterization
4. Biogenesis and Function of microRNAs
4.1. microRNA Biogenesis
4.2. microRNA Function
4.3. microRNAs in Therapy
4.4. microRNAs in Diagnosis
5. Methods to Assess miRNA Levels
5.1. Quantitative Real-Time PCR (qRT-PCR)
5.2. Microarray Analysis
5.3. Next-Generation Sequencing (NGS)
5.4. In Situ Hybridization
5.5. Northern Blotting
5.6. Biosensors
5.7. Digital Droplet PCR (ddPCR)
5.8. NanoString
5.9. Overview of Methods to Quantify miRNA Levels
6. microRNAs Encapsulated in Extracellular Vesicle in Diagnosis and Treatment
Biomarker | Associated Disease | Isolation and Detection Methodology | Reference |
---|---|---|---|
miR-21, miR-126, miR-146a | COVID-19 | UC for EV isolation; qRT-PCR for miRNA detection | [266] |
miR-21, miR-155 | Lung Cancer | UC for EV isolation; qRT-PCR for miRNA detection | [29] |
miR-122, miR-192 | Hepatocellular Carcinoma | UC for EV isolation; NGS for miRNA detection | [267] |
miR-29a, miR-181b | Alzheimer’s Disease | UC for EV isolation; Surface-Enhanced Raman Scattering (SERS) for miRNA detection | [268] |
miR-21, miR-141 | Prostate Cancer | UC for EV isolation; qRT-PCR for miRNA detection | [269] |
miR-21, miR-1246 | Esophageal Squamous Cell Carcinoma | Glycosylated EV capture strategy; qRT-PCR for miRNA detection | [270] |
miR-155, miR-210 | Diffuse Large B-Cell Lymphoma | UC for EV isolation; qRT-PCR for miRNA detection | [271] |
miR-21, miR-29a | Colorectal Cancer | UC for EV isolation; qRT-PCR for miRNA detection | [272] |
miR-1246, miR-4644 | Pancreatic Cancer | UC for EV isolation; qRT-PCR for miRNA detection | [273] |
miR-21, miR-221 | Glioblastoma | UC for EV isolation; qRT-PCR for miRNA detection | [274] |
Clinical Status
7. Discussion
8. Conclusions
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
Abbreviations
EV | Extracellular vesicle |
miRNA | microRNA |
MVBs | Multivesicular bodies |
ESCRT | Endosomal Sorting Complexes Required for Transport |
MSC | Mesenchymal Stem Cell |
UC | Ultracentrifugation |
dUC | Differential Ultracentrifugation |
DGUC | Density Gradient Ultracentrifugation |
PEG | Polyethylene Glycol |
TEIR | Total Exosome Isolation Reagent |
FSC | Forward Scattered |
SSC | Side Scattered |
sEV | Small extracellular vesicle |
MWCO | Molecular Weight Cutoff |
UF | Ultrafiltration |
TFF | Tangential Flow Filtration |
SEC | Size exclusion chromatography |
RInSE | Rapid Inertial Solution Exchange |
PEEK | Polyetheretherketone |
TBS | Tris-Buffered Saline |
IgG | Immunoglobulin G |
pre-miRNA | miRNA precursor |
DGCR8 | DiGeorge Syndrome Critical Region 8 |
RISC | RNA-induced silencing complex |
mRNA | messenger RNA |
Ago2 | Argonaute 2 |
RBP | RNA-binding protein |
lncRNAs | long non-coding RNAs |
UTR | Untranslated Region |
ASO | Antisense Oligonucleotide |
HCV | Hepatitis C Virus |
qPCR | quantitative Polymerase Chain Reaction |
qRT-PCR | Quantitative Real-Time PCR |
RT | reverse transcription |
cDNA | complementary DNA |
NGS | Next-Generation Sequencing |
ISH | In Situ Hybridization |
smRNA | Single-molecule RNA |
NB | Northern Blot |
SERS | Surface-enhanced Raman scattering |
EM | Electromagnetic Mechanism |
CM | Chemical-enhancement Mechanism |
PI-SPR | Phase Imaging Surface Plasmon Resonance |
ddPCR | Digital Droplet PCR |
MS | Mass Spectrometry |
LC | Liquid Chromatography |
DLS | Dynamic Light Scattering |
NTA | Nanoparticle Tracking Analysis |
AFM | Atomic Force Microscopy |
TIRF-M | Total Internal Reflection Microscopy |
SEM | Scanning Electron Microscopy |
TEM | Transmission Electron Microscopy |
cryo-TEM | Cryo-Transmission Electron Microscopy |
TRPS | Tunable Resistive Pulse Sensing |
IRIS | Interference Reflectance Imaging Sensor |
SMLM | Single-Molecule Localization Microscopy |
STED | Stimulated Emission Depletion |
RS | Raman Spectroscopy |
SERS | Surface-enhanced Raman scattering |
TERS | Tip-Enhanced Raman Scattering |
FT-IR | Fourier-Transform Infrared |
FCS | Fluorescence Correlation Spectroscopy |
micro-CT | Micro-Computed Tomography |
ELISA | Enzyme-Linked Immunosorbent Assay |
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Isolation Method | Advantages | Disadvantages | References |
---|---|---|---|
UC | Large sample amounts can be obtained. Easy to use. Low processing costs, capacity to handle large sample volumes, simultaneous separation of multiple EV samples, and no additional reagents are needed. DGUC: EV subtype isolation capacity. | Requirement of specialized equipment. EV structure may be disrupted. EV loss, fusion, distortion, and co-isolation of contaminants. Requires large sample volumes. Time-consuming. Dependent on the rotor, the temperature, and viscosity of the sample. Exosome aggregation can be induced. DGUC: Additional purification procedures are required to remove gradient solution in downstream applications. | [70,71,72,73,77] |
Precipitation | Does not require specialized equipment, is quick, simple, affordable, and the volume required is low. EVs are not damaged. High isolation yield. | Poor EV purity, and protein contamination is generally high (pretreatment with proteases might help). | [82,83] |
Immunoaffinity | High purity of isolated EVs by a rather simple process. | EV structure can be impacted by the non-neutral pH and non-physiological elution buffers. | [93,98] |
EV sorting | Enables high-throughput analysis and categorization of EV based on biomarker expression. | High costs for modifying equipment and time-consuming. Detection limits in particle size. | [102,103] |
UF | Fast, simple, and quick. It does not require special equipment. | It can damage EVs from shear stress, particle aggregation might compromise EV yields and consistency. | [67,97,106] |
SEC | EVs maintain their integrity, important for biological activity assessment assays. High yields and low contamination. | Optimized SEC columns according to sample volume and type are required. | [113,114] |
Microfluidics | Very high purity and recovery rate. EVs maintain their biological function. | Time-consuming | [131] |
miR-15a and miR-16 | Chronic Lymphocytic Leukemia | qRT-PCR | [208] |
miR-21 | Various Cancers (e.g., breast, lung, prostate) | qRT-PCR | [209] |
miR-126 | Lung Cancer | Microarray Analysis | [210] |
miR-122 | Hepatocellular Carcinoma | Northern Blot and qRT-PCR | [211] |
miR-155 | Diffuse Large B-Cell Lymphoma | qRT-PCR | [212] |
miR-21, miR-126, miR-146a | COVID-19 | qRT-PCR | [213] |
miR-196b, miR-31, miR-891a, miR-34c, miR-653 | Lung Adenocarcinoma | Transcriptome Analysis | [214] |
miR-21, miR-155 | Breast Cancer | Electrochemical Biosensors | [215] |
miR-122, miR-192 | Hepatocellular Carcinoma | NGS | [216] |
miR-29a, miR-181b | Alzheimer’s Disease | Surface-Enhanced Raman Scattering (SERS) Biosensors | [217] |
Detection Method | Advantages | Disadvantages | Reference |
---|---|---|---|
qRT-PCR | High sensitivity and specificity. Quantitative and widely used. | Requires prior sequence knowledge. Limited detection of novel miRNAs. | [232] |
Microarray Analysis | High-throughput detection of multiple miRNAs. Suitable for comparative expression profiling. | Lower sensitivity than qRT-PCR. Detects only known miRNAs. | [231] |
NGS | Allows discovery of novel miRNAs. High sensitivity and dynamic range. | Expensive and requires complex bioinformatics. Long turnaround time. | [236] |
ISH | Provides spatial distribution of miRNA expression. Single-cell resolution. | Less quantitative than qRT-PCR/NGS. Requires high-quality tissue samples. | [240,241] |
NB | Confirms miRNA integrity and size. | Labor-intensive and requires large RNA amounts. Low sensitivity. | [245,248] |
Biosensors | Rapid and real-time detection. Potential for portable diagnostics. | Requires careful design and optimization. May be affected by biological sample complexity. | [250,257,261,262] |
ddPCR | Absolute quantification without a standard curve. High sensitivity, even for low-abundance miRNAs. Resistant to PCR inhibitors. | More expensive than qRT-PCR. Limited multiplexing capabilities. | [257,258] |
NanoString | Direct and absolute quantification. High specificity due to sequence-specific probes. Multiplexing capability. Works well with low RNA input and degraded samples. High reproducibility and ease of use. | Lower sensitivity compared to qPCR for low-abundance miRNAs. Higher cost per sample compared to some qPCR-based methods. Requires specialized equipment (nCounter system). | [259,260] |
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Ljungström, M.; Oltra, E. Methods for Extracellular Vesicle Isolation: Relevance for Encapsulated miRNAs in Disease Diagnosis and Treatment. Genes 2025, 16, 330. https://doi.org/10.3390/genes16030330
Ljungström M, Oltra E. Methods for Extracellular Vesicle Isolation: Relevance for Encapsulated miRNAs in Disease Diagnosis and Treatment. Genes. 2025; 16(3):330. https://doi.org/10.3390/genes16030330
Chicago/Turabian StyleLjungström, Maria, and Elisa Oltra. 2025. "Methods for Extracellular Vesicle Isolation: Relevance for Encapsulated miRNAs in Disease Diagnosis and Treatment" Genes 16, no. 3: 330. https://doi.org/10.3390/genes16030330
APA StyleLjungström, M., & Oltra, E. (2025). Methods for Extracellular Vesicle Isolation: Relevance for Encapsulated miRNAs in Disease Diagnosis and Treatment. Genes, 16(3), 330. https://doi.org/10.3390/genes16030330