Comprehensive isolation of extracellular vesicles and nanoparticles

Qin Zhang, Dennis K. Jeppesen, James N. Higginbotham, Jeffrey L. Franklin, Robert J. Coffey

Published: 2023-03-12 DOI: 10.1038/s41596-023-00811-0

['Extracellular Vesicles', 'Nanoparticles', 'Isolation Methods', 'Differential Ultracentrifugation', 'Biomarker Discovery']

AI 解读

Efficient and safe single-cell cloning of human pluripotent stem cells using the CEPT cocktail

Profiling native pulmonary basement membrane stiffness using atomic force microscopy

Genetic circuit design automation with Cello 2.0

Synthesis of siRNA nanoparticles to silence plaque-destabilizing gene in atherosclerotic lesional macrophages

Scalable dual-omics profiling with single-nucleus chromatin accessibility and mRNA expression sequencing 2 (SNARE-seq2)

A practical guide to scanning light-field microscopy with digital adaptive optics

Effective high-throughput isolation of fully human antibodies targeting infectious pathogens

Improved sampling and DNA extraction procedures for microbiome analysis in food-processing environments

MOF-derived nanoporous carbons with diverse tunable nanoarchitectures

Tutorial: a statistical genetics guide to identifying HLA alleles driving complex disease

查看全部

Sections

Figures

References

There is an increasing appreciation for the heterogeneous nature of extracellular vesicles (EVs). In addition, two nonvesicular extracellular nanoparticles (NVEPs), exomeres and supermeres, have been discovered recently that are enriched in many cargo pre
Introduction
Materials
Procedure
Troubleshooting
Timing
Anticipated results
- Reporting summary
- References
References
ACKNOWLEDGMENTS

Yates, A. G. et al. In sickness and in health: the functional role of extracellular vesicles in physiology and pathology in vivo. Part II: pathology. J. Extracell. Vesicles 11, e12190 (2022).
Yates, A. G. et al. In sickness and in health: the functional role of extracellular vesicles in physiology and pathology in vivo. Part I: health and normal physiology. J. Extracell. Vesicles 11, e12151 (2022).
van Niel, G. et al. Challenges and directions in studying cell-cell communication by extracellular vesicles. Nat. Rev. Mol. Cell Biol. 23, 369–382 (2022).
Roefs, M. T., Sluijter, J. P. G. & Vader, P. Extracellular vesicle-associated proteins in tissue repair. Trends Cell Biol. 30, 990–1013 (2020).
Zhang, H. et al. Identification of distinct nanoparticles and subsets of extracellular vesicles by asymmetric flow field-flow fractionation. Nat. Cell Biol. 20, 332–343 (2018).
Kowal, J. et al. Proteomic comparison defines novel markers to characterize heterogeneous populations of extracellular vesicle subtypes. Proc. Natl Acad. Sci. USA 113, E968–E977 (2016).
van Niel, G., D’Angelo, G. & Raposo, G. Shedding light on the cell biology of extracellular vesicles. Nat. Rev. Mol. Cell Biol. 19, 213–228 (2018).
Willms, E., Cabanas, C., Mager, I., Wood, M. J. A. & Vader, P. Extracellular vesicle heterogeneity: subpopulations, isolation techniques, and diverse functions in cancer progression. Front. Immunol. 9, 738 (2018).
Jeppesen, D. K. et al. Reassessment of exosome composition. Cell 177, 428–445.e18 (2019).
Zhang, Q. et al. Transfer of functional cargo in exomeres. Cell Rep. 27, 940–954.e6 (2019).
Mathieu, M., Martin-Jaular, L., Lavieu, G. & Thery, C. Specificities of secretion and uptake of exosomes and other extracellular vesicles for cell-to-cell communication. Nat. Cell Biol. 21, 9–17 (2019).
Cheng, L. & Hill, A. F. Therapeutically harnessing extracellular vesicles. Nat. Rev. Drug Discov. 21, 379–399 (2022).
Jeppesen, D. K., Zhang, Q., Franklin, J. L. & Coffey, R. J. Are supermeres a distinct nanoparticle? J. Extracell. Biol. 1, e44 (2022).
Tosar, J. P., Cayota, A. & Witwer, K. Exomeres and supermeres: monolithic or diverse? J. Extracell. Biol. 1, e45 (2022).
Zhang, Q. et al. Supermeres are functional extracellular nanoparticles replete with disease biomarkers and therapeutic targets. Nat. Cell Biol. 23, 1240–1254 (2021).
Tosar, J. P., Witwer, K. & Cayota, A. Revisiting extracellular RNA release, processing, and function. Trends Biochem. Sci. 46, 438–445 (2021).
Li, K., Wong, D. K., Luk, F. S., Kim, R. Y. & Raffai, R. L. Isolation of plasma lipoproteins as a source of extracellular RNA. Methods Mol. Biol. 1740, 139–153 (2018).
Tulkens, J., De Wever, O. & Hendrix, A. Analyzing bacterial extracellular vesicles in human body fluids by orthogonal biophysical separation and biochemical characterization. Nat. Protoc. 15, 40–67 (2020).
Zhang, X., Borg, E. G. F., Liaci, A. M., Vos, H. R. & Stoorvogel, W. A novel three step protocol to isolate extracellular vesicles from plasma or cell culture medium with both high yield and purity. J. Extracell. Vesicles 9, 1791450 (2020).
Park, J. et al. An integrated magneto-electrochemical device for the rapid profiling of tumour extracellular vesicles from blood plasma. Nat. Biomed. Eng. 5, 678–689 (2021).
Boing, A. N. et al. Single-step isolation of extracellular vesicles by size-exclusion chromatography. J. Extracell. Vesicles http://doi.org/10.3402/jev.v3.23430 (2014).
Sahoo, S. et al. Therapeutic and diagnostic translation of extracellular vesicles in cardiovascular diseases: roadmap to the clinic. Circulation 143, 1426–1449 (2021).
Cheruvanky, A. et al. Rapid isolation of urinary exosomal biomarkers using a nanomembrane ultrafiltration concentrator. Am. J. Physiol. Ren. Physiol. 292, F1657–F1661 (2007).
Clos-Sansalvador, M., Monguio-Tortajada, M., Roura, S., Franquesa, M. & Borras, F. E. Commonly used methods for extracellular vesicles’ enrichment: implications in downstream analyses and use. Eur. J. Cell Biol. 101, 151227 (2022).
Hinger, S. A. et al. Rab13 regulates sEV secretion in mutant KRAS colorectal cancer cells. Sci. Rep. 10, 15804 (2020).
Arroyo, J. D. et al. Argonaute2 complexes carry a population of circulating microRNAs independent of vesicles in human plasma. Proc. Natl Acad. Sci. USA 108, 5003–5008 (2011).
Onodi, Z. et al. Isolation of high-purity extracellular vesicles by the combination of iodixanol density gradient ultracentrifugation and bind-elute chromatography from blood plasma. Front. Physiol. 9, 1479 (2018).
Vergauwen, G. et al. Robust sequential biophysical fractionation of blood plasma to study variations in the biomolecular landscape of systemically circulating extracellular vesicles across clinical conditions. J. Extracell. Vesicles 10, e12122 (2021).
Zhang, Q. et al. Angiotensin-converting enzyme 2-containing small extracellular vesicles and exomeres bind the severe acute respiratory syndrome coronavirus 2 spike protein. Gastroenterology 160, 958–961.e3 (2021).
Cvjetkovic, A., Lotvall, J. & Lasser, C. The influence of rotor type and centrifugation time on the yield and purity of extracellular vesicles. J. Extracell. Vesicles http://doi.org/10.3402/jev.v3.23111 (2014).
Dhondt, B. et al. Unravelling the proteomic landscape of extracellular vesicles in prostate cancer by density-based fractionation of urine. J. Extracell. Vesicles 9, 1736935 (2020).
Dhondt, B., Lumen, N., De Wever, O. & Hendrix, A. Preparation of multi-omics grade extracellular vesicles by density-based fractionation of urine. STAR Protoc. 1, 100073 (2020).
Jeppesen, D. K. et al. Comparative analysis of discrete exosome fractions obtained by differential centrifugation. J. Extracell. Vesicles 3, 25011 (2014).
Karimi, N. et al. Detailed analysis of the plasma extracellular vesicle proteome after separation from lipoproteins. Cell. Mol. Life Sci. 75, 2873–2886 (2018).
Zonneveld, M. I. et al. Recovery of extracellular vesicles from human breast milk is influenced by sample collection and vesicle isolation procedures. J. Extracell. Vesicles http://doi.org/10.3402/jev.v3.24215 (2014).
Zhang, H. & Lyden, D. Asymmetric-flow field-flow fractionation technology for exomere and small extracellular vesicle separation and characterization. Nat. Protoc. 14, 1027–1053 (2019).
Bojmar, L. et al. Extracellular vesicle and particle isolation from human and murine cell lines, tissues, and bodily fluids. STAR Protoc. 2, 100225 (2021).
Hoshino, A. et al. Extracellular vesicle and particle biomarkers define multiple human cancers. Cell 182, 1044–1061.e18 (2020).
Muller, L., Hong, C. S., Stolz, D. B., Watkins, S. C. & Whiteside, T. L. Isolation of biologically-active exosomes from human plasma. J. Immunol. Methods 411, 55–65 (2014).
Ostenfeld, M. S. et al. miRNA profiling of circulating EpCAM+ extracellular vesicles: promising biomarkers of colorectal cancer. J. Extracell. Vesicles 5, 31488 (2016).
Clancy, J. W., Boomgarden, A. C. & D’Souza-Schorey, C. Profiling and promise of supermeres. Nat. Cell Biol. 23, 1217–1219 (2021).
Lucotti, S., Kenific, C. M., Zhang, H. & Lyden, D. Extracellular vesicles and particles impact the systemic landscape of cancer. EMBO J. 41, e109288 (2022).
Mateescu, B. et al. Phase 2 of extracellular RNA communication consortium charts next-generation approaches for extracellular RNA research. iScience 25, 104653 (2022).
Jeppesen, D. K. et al. Quantitative proteomics of fractionated membrane and lumen exosome proteins from isogenic metastatic and nonmetastatic bladder cancer cells reveal differential expression of EMT factors. Proteomics 14, 699–712 (2014).
Mitchell, J. P., Court, J., Mason, M. D., Tabi, Z. & Clayton, A. Increased exosome production from tumour cell cultures using the Integra CELLine Culture System. J. Immunol. Methods 335, 98–105 (2008).
Higginbotham, J. N. et al. Identification and characterization of EGF receptor in individual exosomes by fluorescence-activated vesicle sorting. J. Extracell. Vesicles 5, 29254 (2016).
Thery, C. et al. Minimal information for studies of extracellular vesicles 2018 (MISEV2018): a position statement of the International Society for Extracellular Vesicles and update of the MISEV2014 guidelines. J. Extracell. Vesicles 7, 1535750 (2018).
Skliar, M. & Chernyshev, V. S. Imaging of extracellular vesicles by atomic force microscopy. J. Vis. Exp. http://doi.org/10.3791/59254 (2019).
Rikkert, L. G., Nieuwland, R., Terstappen, L. & Coumans, F. A. W. Quality of extracellular vesicle images by transmission electron microscopy is operator and protocol dependent. J. Extracell. Vesicles 8, 1555419 (2019).
Bachurski, D. et al. Extracellular vesicle measurements with nanoparticle tracking analysis—An accuracy and repeatability comparison between NanoSight NS300 and ZetaView. J. Extracell. Vesicles 8, 1596016 (2019).
Olson, B. J. & Markwell, J. Assays for determination of protein concentration. Curr. Protoc. Protein Sci. Ch. 3, Unit 3.4 (2007).
Pham, C. V. et al. Bovine extracellular vesicles contaminate human extracellular vesicles produced in cell culture conditioned medium when ‘exosome-depleted serum’ is utilised. Arch. Biochem. Biophys. 708, 108963 (2021).
Lehrich, B. M., Liang, Y. & Fiandaca, M. S. Foetal bovine serum influence on in vitro extracellular vesicle analyses. J. Extracell. Vesicles 10, e12061 (2021).

Comprehensive isolation of extracellular vesicles and nanoparticles

Supplementary information

Reporting Summary

推荐阅读