Methodological Approaches to Study Extracellular Vesicle miRNAs in Epstein–Barr Virus-Associated Cancers
Abstract
:1. Introduction
2. EBV miRNAs in EBV-Associated Cancers
2.1. Nasopharyngeal Carcinoma (NPC)
2.2. Diffuse Large B-Cell Lymphoma (DLBCL) and Natural Killer/T-Cell Lymphoma (NKTL)
2.3. BL and Lymphoblastoid Cells (LCL)
2.4. Gastric Carcinoma (GC)
2.5. Comprehensive Studies
3. EBV miRNAs and EV
4. EV Isolation Methods
4.1. Ultracentrifugation (UC)
4.2. Ultrafiltration (UF)
4.3. Size-Exclusion Chromatography (SEC)
4.4. Anion Exchange Chromatography (AIEX)
4.5. Precipitation Methods
4.6. Immunoaffinity Isolation
4.7. Microfluidic Devices
4.8. Combination Approaches
4.9. Comparison of EV Isolation Methods for miRNA Detection
5. Methods for miRNA Detection
5.1. RT-qPCR
5.2. DNA Probes
5.3. NGS
5.4. Surface Plasmon Resonance (SPR)
5.5. Localized Surface Plasmon Resonance (LSPR)
5.6. Surface-Enhanced Raman Scattering (SERS)
6. Conclusions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
AIEX | Anion exchange chromatography |
BART | BamHI A rightward transcripts |
BHRF | BamHI fragment H rightward open reading frame |
BL | Burkitt′s lymphoma |
DC | Differential ultracentrifugation |
DLBCL | Diffuse large B-cell lymphoma |
EBV | Epstein–Barr-virus |
EV | Extracellular vesicle |
GC | Gastric carcinoma |
HL | Hodgkin’s lymphoma |
LCL | Lymphoblastoid cell line |
LSPR | Localized surface plasmon resonance |
MB | Molecular beacon |
NGS | Next-generation sequencing |
NKTL | Nasal NK/T-cell lymphoma |
NPC | Nasopharyngeal carcinoma |
NTA | Nanoparticle tracking analysis |
PAP | Poly(A) polymerase |
PTLD | Post-transplant lymphoproliferative disease |
RT-qPCR | Reverse transcription quantitative polymerase chain reaction |
SEC | Size-exclusion chromatography |
SERS | Surface-enhanced Raman scattering |
SPR | Surface plasmon resonance |
TFF | Tangential flow filtration |
UC | Ultracentrifugation |
UF | Ultrafiltration |
UMI | Unique Molecular Identifier |
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Tumor Type | Sample | Latency Type | BHRF1 Cluster | BART Cluster 1 | BART Cluster 2 | BART-2 | Method | Ref. |
---|---|---|---|---|---|---|---|---|
BL | MUTUI/ OUS/ BL41/95, Marm. B95.8 | I/ II/ III | −/ +/ + | 1 | + | Northern blot | [35] | |
BC-1/ Jijoye/ Raji/ BL41/95/ MUTU III, Namalwa | I/ III/ III/ III/ III | −/ 1-2/ 1-1, 1-2/ 1-1, 1-2/ 1-1, 1-2/ | 1, 3, 5/ 1, 3, 5/ −/ 1, 3/ 1, 3, 5/ | 7, 10, 12/ 7, 10, 12/ −/ −/ 7, 10, 12/ | Northern blot | [66] | ||
Jijoye | III | 3, 4, 5, 6, 15, 17 | 7, 8, 9, 10, 11, 12, 13, 14, 19, 20 | Northern blot, microarray | [67] | |||
BL-5, Savl, KemI, Akata, Dante, Daudi/ OkuI, GG68, Raji, MutuIII | I/ III | −/ + | 3, 4, 1-5p, 15 | 7, 10, 12, 20-5p | qPCR | [54] | ||
2A8.1, RaeI | + | qPCR | [52] | |||||
B95.8-transformed cells/ Daudi/ Namalwa B | I/ I/ III | 15/ 15, 16/ 16 | −/ 22/ 22 | qPCR | [33] | |||
HL | RPMI6666 | II | + | 1 | + | Northern blot | [35] | |
NPC | C666-1 | II | − | 3, 4, 1-5p, 15 | 7, 10, 12, 20-5p | qPCR | [54] | |
C666 | II | − | 1, 3, 5 | 7, 10, 12 | Northern blot | [66] | ||
C666-1 | II | 1-1, 1-2, 1-3 | + | + | + | qPCR | [52] | |
C666-1 | II | + | + | + | qPCR | [70] | ||
C-15 | − | 1, 3, 5 | 7, 10, 12 | Northern blot | [66] | |||
clinical tissue; C666; NP460hTERT + EBV | 1-3p, 5, 6-5p, 6-3p,17-5p | 7, 8, 9, 14,18-5p, 19-3p | + | Microarray, qPCR | [38] | |||
clinical tissue/ HK1-EBV, C666-1 | − | +/ 15, 16 | +/ 22 | + | qPCR, Deep sequencing | [33] | ||
clinical tissue | − | + | + | + | qPCR, Deep sequencing | [52] | ||
clinical tissue | − | + | + | Northern blot, Deep sequencing | [53] | |||
GC | SNU-719 | I | − | 3, 4, 1-5p, 15 | 7, 10, 12, 20-5p | qPCR | [54] | |
SNU-719 | I | − | + | + | + | qPCR | [69] | |
AGS-EBV | I | 3, 1-3p, 5, 17-5p | 7, 9 | qPCR | [68] | |||
clinical tissue, SNU-719 | + | + | + | qPCR | [70] | |||
clinical tissue | − | + | + | + | qPCR | [69] | ||
YCCEL1 | I | − | 1-3p, 15-3p | 9-3p, 5-5p, 7-3p, 22-3p, 19-3p | Northern blot, qPCR | [71] | ||
SNU-719, AGS-EBV/ Animal model/ clinical tissue | I/ / / | −/ −/ −/ | 1, 3, 5/ 1, 5/ 1 | 7, 10, 12/ 7, 10, 12/ / | +/ / + | Northern blot | [44] | |
NKTL | Lymphoma clinical tissue | − | + | + | + | Deep sequencing | [65] | |
LCL | 721, B958IID6 | III | + | 3, 4, 1-5p, 15 | − | qPCR | [54] | |
IM-9 | III | 1-1, 1-2 | 1, 3, 5/ | 7, 10, 12/ | Northern blot | [66] | ||
IM-9 | III | + | + | + | qPCR | [70] | ||
AT | + | qPCR | [52] | |||||
DLBCL | clinical tissue | − | + | + | + | Deep sequencing | [64] | |
PTLD | PTLD1 | III | + | 3, 4, 1-5p, 15 | 7, 10, 12, 20-5p | qPCR | [54] |
Method | Sample Volume | Yield | Purity | Cost | Advantage | Disadvantage |
---|---|---|---|---|---|---|
UC | 1–100 mL | ++ | ++ | + | No chemical additives | Time and labor intensive; Low throughput; EVs/protein aggregates |
UF | Variety | ++ | + | ++ | Flexible volume; No chemical additives | Low purity; Low throughput; Efficiency dependent on the type of ultra-membrane |
Precipitation | Variety | +++ | + | + | Flexible volume; Time and labor saving; No expensive equipment needed | Low purity; Sample contamination by polymer particles; Co-isolation of nonspecific proteins; EV/protein aggregates |
SEC | <10 mL | ++ | +++ | + | High purity; Time saving; No chemical additives; Physiological buffer | Sample volume limited; Low throughput; Sample diluted |
Immunoaffinity | <5 mL | + | +++ | +++ | High purity; Physiological buffer; Integration with downstream biological analysis | Sample volume limited; Low throughput; Very selective; Dependent on antibody/protein; Contaminated with antibody/protein; Pre-enrichment needed |
AIEX | Variety | ++ | ++ | ++ | Label free; Flexible volume | Low throughput; Sample diluted |
Microfluidic | <1 mL | ++ | N.A. | +++ | Label free; Integration with downstream biological analysis | Sample volume extremely limited; Low throughput |
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Sun, L.; Meckes, D.G., Jr. Methodological Approaches to Study Extracellular Vesicle miRNAs in Epstein–Barr Virus-Associated Cancers. Int. J. Mol. Sci. 2018, 19, 2810. https://doi.org/10.3390/ijms19092810
Sun L, Meckes DG Jr. Methodological Approaches to Study Extracellular Vesicle miRNAs in Epstein–Barr Virus-Associated Cancers. International Journal of Molecular Sciences. 2018; 19(9):2810. https://doi.org/10.3390/ijms19092810
Chicago/Turabian StyleSun, Li, and David G. Meckes, Jr. 2018. "Methodological Approaches to Study Extracellular Vesicle miRNAs in Epstein–Barr Virus-Associated Cancers" International Journal of Molecular Sciences 19, no. 9: 2810. https://doi.org/10.3390/ijms19092810