Extracellular Vesicle-Derived microRNA Crosstalk Between Equine Chondrocytes and Synoviocytes—An In Vitro Approach
Abstract
1. Introduction
2. Results
2.1. Demographics of EV-Donor and EV-Recipient Cells
2.2. EV Concentration and Size
2.3. 5-EU RNA Capture from Recipient Cells
2.4. Sequencing Results
2.4.1. Data Overview
Predicted mRNA Targets of Unique miRNAs
Unsupervised Analysis
Differential Expression Analysis
Target Prediction and Pathway Analysis of Differentially Expressed miRNAs
3. Discussion
4. Materials and Methods
4.1. Tissue Collection
4.2. Isolation of Primary Chondrocytes and Synoviocytes
4.3. EV-Donor Cell Set Up and RNA Labelling
4.4. EV Isolation and Characterization
4.5. EV-Recipient Cell Setup and EV Incubation
4.6. RNA Extraction
4.7. Biotinylation of RNA and RNA Capture
4.8. Small RNA Sequencing
4.9. Data Analysis
4.9.1. Small RNA Sequencing Analysis
4.9.2. Target Prediction and Pathway Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
5-EU | 5-Ethynyl uridine |
BCL2 | B-cell lymphoma 2 apoptosis regulator |
CASR | Calcium-sensing receptor |
CI | Confidence interval |
CXCL12 | C-X-C motif chemokine ligand 12 |
DMEM | Dulbecco’s Modified Eagle Medium |
ECM | Extracellular matrix |
EV | Extracellular vesicle |
FASN | Fatty acid synthase |
FBS | Fetal bovine serum |
FDR | False discovery rate |
GRIA2 | Glutamate ionotropic receptor AMPA-type subunit 2 |
HES1 | Hes family bHLH transcription factor 1 |
IGF1 | Insulin-like growth factor 1 |
IGFBP5 | Insulin-like growth factor-binding protein 5 |
IL | Interleukin |
IL6R | Interleukin 6 receptor |
IPA | Ingenuity Pathway Analysis |
IRS1 | Insulin receptor substrate 1 |
lncRNA | Long non-coding RNA |
logFC | Log fold change |
Max | Maximum |
MCP | Metacarpophalangeal |
Min | Minimum |
MMP | Matrix metalloproteinase |
miRNA | microRNA |
mRNA | Messenger RNA |
NOTCH | Notch receptor |
OA | Osteoarthritis |
P | Passage |
PBS | Phosphate-buffered saline |
PCA | Principal component analysis |
Pen/Strep | Penicillin–streptomycin |
piRNA | Piwi-interfering RNA |
PPARG | Peroxisome proliferator-activated receptor gamma |
QC | Quality control |
RECK | Reversion-inducing cysteine-rich protein with Kazal motifs |
RPM | Reads per million |
rRNA | Ribosomal RNA |
RXRA | Retinoid X receptor alpha |
SEC | Size exclusion chromatography |
scRNA | Small conditional RNA |
SIRT1 | Sirtuin 1 |
SMAD4 | Mothers against decapentaplegic homolog 4 |
snRNA | Small nuclear RNA |
snoRNA | Small nucleolar RNA |
SF | Synovial fluid |
SD | Standard deviation |
THRB | Thyroid hormone receptor beta |
TNF | Tumor necrosis factor |
tRNA | Transfer RNA |
VCAM | Vascular cell adhesion molecule 1 |
VEGF | Vascular endothelial growth factor |
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Characteristics | EV-Donor Cells | EV-Recipient Cells | ||
---|---|---|---|---|
Chondrocytes (N = 8) | Synoviocytes (N = 9) | Chondrocytes (N = 5) | Synoviocytes (N = 4) | |
Age, years | ||||
Mean (SD) | 6.1 (2.6) | 5.8 (2.3) | 6.2 (4.4) | 5.5 (2.1) |
95% CI | 4.0–8.3 | 4.0–7.5 | 0.7–11.7 | 2.2–8.8 |
Min; Max | 3; 10 | 3; 10 | 3; 14 | 3; 8 |
p-value | 0.899 1 | 0.810 1 | ||
Sex, n (%) | ||||
Female | 3 (60.0) 2 | 5 (62.5) 3 | 0 (0.0) 4 | 3 (75.0) |
Male | 2 (40.0) 2 | 3 (37.5) 3 | 1 (100.0) 4 | 1 (25.0) |
p-value | 0.928 5 | – | ||
Joint macroscopic score (0–9) 6, n (%) | ||||
Scores | ||||
0 | 3 (37.5) | 2 (22.2) | 1 (20.0) | 0 (0.0) |
1 | 4 (50.0) | 1 (11.1) | 0 (0.0) | 1 (25.0) |
2 | 1 (12.5) | 5 (55.6) | 1 (20.0) | 2 (50.0) |
3 | 0 (0.0) | 1 (11.1) | 3 (60.0) | 1 (25.0) |
≥4 | 0 (0.0) | 0 (0.0) | 0 (0.0) | 0 (0.0) |
Mean (SD) | 0.8 (0.7) | 1.6 (1.0) | 2.2 (1.3) | 2.0 (0.8) |
95% CI | 0.2–1.3 | 0.8–2.3 | 0.6–3.8 | 0.7–3.3 |
Min; Max | 0; 2 | 0; 3 | 0; 3 | 1; 3 |
p-value | 0.092 7 | 0.635 1 |
EV Characteristics | Chondrocytes (N = 8) | Synoviocytes (N = 9) |
---|---|---|
EV concentration, particles/mL | ||
Mean (SD) | 1.7 × 109 (1.0 × 109) | 8.2 × 108 (9.6 × 108) |
95% CI | 8.5 × 108–1.5 × 109 | 5.3 × 108–1.1 × 109 |
Min; Max | 7.7 × 107; 3.0 × 109 | 7.9 × 107; 2.6 × 109 |
p-value | 0.115 1 | |
EV size, nm | ||
Mean (SD) | 186.3 (92.8) | 190.6 (71.7) |
95% CI | 157.2–215.4 | 168.9–212.3 |
Min; Max | 133.0; 274.8 | 136.3; 292.5 |
p-value | 0.815 1 |
5-EU-Labelled RNA | Experimental Samples | Control Samples | ||
---|---|---|---|---|
EV-Recipient Chondrocytes (N = 5) | EV-Recipient Synoviocytes (N = 4) | EV-Recipient Chondrocytes (N = 1) | EV-Recipient Synoviocytes (N = 1) | |
RNA concentration, ng/µL | ||||
Mean (SD) | 43.1 (5.6) | 62.8 (14.1) | 0.9 (0.0) | 1.8 (0.0) |
95% CI | 36.2–50.0 | 40.5–85.2 | – | – |
Min; Max | 33.6; 48.4 | 54.9; 83.9 | – | – |
p-value | 0.016 1 | – |
miRNA | logFC | p-Value | FDR | Significance |
---|---|---|---|---|
eca-miR-27b | −2.6 | <0.001 | <0.001 | Increased in EV-recipient chondrocytes (RNA originated from EV-donor synoviocytes) |
eca-miR-23b | −1.7 | 0.002 | 0.033 | Increased in EV-recipient chondrocytes (RNA originated from EV-donor synoviocytes) |
eca-miR-143 | 2.6 | 0.002 | 0.033 | Increased in EV-recipient synoviocytes RNA originated from EV-donor chondrocytes) |
eca-miR-31 | −4.9 | 0.003 | 0.033 | Increased in EV-recipient chondrocytes (RNA originated from EV-donor synoviocytes) |
eca-miR-21 | 0.8 | 0.013 | 0.110 | Increased in EV-recipient synoviocytes (RNA originated from EV-donor chondrocytes) |
eca-miR-181a | 2.2 | 0.015 | 0.110 | Increased in EV-recipient synoviocytes (RNA originated from EV-donor chondrocytes) |
eca-miR-191a | −0.6 | 0.016 | 0.110 | Increased in EV-recipient chondrocytes (RNA originated from EV-donor synoviocytes) |
eca-miR-181b | 1.8 | 0.018 | 0.110 | Increased in EV-recipient synoviocyte (RNA originated from EV-donor chondrocytes) |
eca-miR-199a-5p | −0.6 | 0.027 | 0.145 | Increased in EV-recipient chondrocytes (RNA originated from EV-donor synoviocytes) |
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Castanheira, C.I.G.D.; Anderson, J.R.; Clarke, E.J.; Hackl, M.; James, V.; Clegg, P.D.; Peffers, M.J. Extracellular Vesicle-Derived microRNA Crosstalk Between Equine Chondrocytes and Synoviocytes—An In Vitro Approach. Int. J. Mol. Sci. 2025, 26, 3353. https://doi.org/10.3390/ijms26073353
Castanheira CIGD, Anderson JR, Clarke EJ, Hackl M, James V, Clegg PD, Peffers MJ. Extracellular Vesicle-Derived microRNA Crosstalk Between Equine Chondrocytes and Synoviocytes—An In Vitro Approach. International Journal of Molecular Sciences. 2025; 26(7):3353. https://doi.org/10.3390/ijms26073353
Chicago/Turabian StyleCastanheira, Catarina I. G. D., James R. Anderson, Emily J. Clarke, Matthias Hackl, Victoria James, Peter D. Clegg, and Mandy J. Peffers. 2025. "Extracellular Vesicle-Derived microRNA Crosstalk Between Equine Chondrocytes and Synoviocytes—An In Vitro Approach" International Journal of Molecular Sciences 26, no. 7: 3353. https://doi.org/10.3390/ijms26073353
APA StyleCastanheira, C. I. G. D., Anderson, J. R., Clarke, E. J., Hackl, M., James, V., Clegg, P. D., & Peffers, M. J. (2025). Extracellular Vesicle-Derived microRNA Crosstalk Between Equine Chondrocytes and Synoviocytes—An In Vitro Approach. International Journal of Molecular Sciences, 26(7), 3353. https://doi.org/10.3390/ijms26073353