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Преимущества и недостатки широко используемых методов изучения внеклеточных везикул

https://doi.org/10.18705/2311-4495-2025-12-1-51-66

EDN: XJCLEP

Аннотация

Внеклеточные везикулы (ВВ) представляют собой гетерогенную группу везикул, имеющих размер от нескольких десятков до нескольких сотен нанометров. ВВ способны проникать через гистогематические барьеры и обнаруживаются во всех биологических жидкостях. Состав ВВ в значительной степени отражает состав секретировавших их клеток. В настоящее время ВВ широко используются для поиска диагностических и терапевтических маркеров, в связи с чем исследования состава и свойств ВВ сегодня становятся все более востребованными. Несмотря на очевидный потенциал ВВ в биомедицинских приложениях, отсутствие единых методов их выделения, анализа и количественного измерения значительно ограничивает научный прогресс в данной области. В научной литературе встречаются описания десятков методов выделения и изучения ВВ, причем зачастую исследователи не представляют сравнительных преимуществ и недостатков используемых методов. В связи с этим становится актуальным обзор методов исследования ВВ. В данном обзоре представлен всесторонний анализ современных методов исследования ВВ. Каждый метод обладает своими преимуществами и ограничениями, влияющими на выход, чистоту и характеристики выделенных везикул, а также на точность получаемых результатов. Метод выделения и анализа ВВ необходимо выбирать с учетом цели и специфики исследования, поскольку универсального подхода в настоящее время не существует. Только глубокое понимание особенностей различных методик позволит подобрать оптимальный протокол для решения конкретных задач исследования, обеспечивая надежность и воспроизводимость результатов.

Об авторах

В. В. Костина
Федеральное государственное бюджетное учреждение науки «Институт высшей нервной деятельности и нейрофизиологии Российской академии наук»; Федеральное государственное автономное образовательное учреждение высшего образования «Российский национальный исследовательский медицинский университет имени Н. И. Пирогова» Министерства здравоохранения Российской Федерации
Россия

Костина Василиса Васильевна, бакалавр 

 Москва 


Конфликт интересов:

Авторы заявили об отсутствии потенциального конфликта интересов 



А. А. Яковлев
Федеральное государственное бюджетное учреждение науки «Институт высшей нервной деятельности и нейрофизиологии Российской академии наук»; Государственное бюджетное учреждение здравоохранения города Москвы «Научно-практический психоневрологический центр имени З. П. Соловьева Департамента здравоохранения Москвы»
Россия

Яковлев Александр Александрович, д.б.н., внештатный научный сотрудник лаборатории функциональной биохимии нервной системы 

 ул. Бутлерова, д. 5А, Москва, 117485 


Конфликт интересов:

Авторы заявили об отсутствии потенциального конфликта интересов 



Список литературы

1. Welsh JA, Goberdhan DCI, O’Driscoll L, Buzas EI, Blenkiron C, Bussolati B, et al. Minimal information for studies of extracellular vesicles (MISEV2023): From basic to advanced approaches. Journal of Extracellular Vesicles. 2024;13(2):e12404.

2. van Niel G, Carter DRF, Clayton A, Lambert DW, Raposo G, Vader P. Challenges and directions in studying cell–cell communication by extracellular vesicles. Nature Reviews Molecular Cell Biology. 2022;23(5):369–82.

3. Mohammadipoor A, Hershfield MR, Linsenbardt HR, Smith J, Mack J, Natesan S, et al. Biological function of Extracellular Vesicles (EVs): a review of the field. Mol Biol Rep. 2023 Oct;50(10):8639–51.

4. Margolis L, Sadovsky Y. The biology of extracellular vesicles: The known unknowns. PLoS Biol. 2019 Jul 18;17(7):e3000363.

5. Panneerselvam S, Muthukumaran NS, Ghosh D, Chatterjee S, Langford D, Natarajaseenivasan K. Extracellular Vesicles in Cell–Cell Communications and Potential in Clinical Interventions. In: Ghosh AR, editor. Extracellular Vesicles in Human Health and Diseases [Internet]. Singapore: Springer Nature Singapore; 2024 [cited 2024 Nov 11]. p. 73–92. Available from: https://link.springer.com/10.1007/978-981-97-2494-9_4

6. Quiralte M, Barquín A, Yagüe-Fernández M, Navarro P, Grazioso TP, Sevillano-Fernández E, et al. Proteomic profiles of peritoneal fluid-derived small extracellular vesicles correlate with patient outcome in ovarian cancer. Journal of Clinical Investigation. 2024 May 15;134(10):e176161.

7. Delgado-Peraza F, Nogueras-Ortiz C, Simonsen AH, Knight DD, Yao PJ, Goetzl EJ, et al. Neuron-derived extracellular vesicles in blood reveal effects of exercise in Alzheimer’s disease. Alz Res Therapy. 2023 Sep 20;15(1):156.

8. Vreones M, Mustapic M, Moaddel R, Pucha KA, Lovett J, Seals DR, et al. Oral nicotinamide riboside raises NAD + and lowers biomarkers of neurodegenerative pathology in plasma extracellular vesicles enriched for neuronal origin. Aging Cell. 2023 Jan;22(1):e13754.

9. D’Ascenzo F, Femminò S, Ravera F, Angelini F, Caccioppo A, Franchin L, et al. Extracellular vesicles from patients with Acute Coronary Syndrome impact on ischemia-reperfusion injury. Pharmacological Research. 2021 Aug;170:105715.

10. Elsharkasy OM, Nordin JZ, Hagey DW, De Jong OG, Schiffelers RM, Andaloussi SE, et al. Extracellular vesicles as drug delivery systems: Why and how? Advanced Drug Delivery Reviews. 2020;159:332–43.

11. Herrmann IK, Wood MJA, Fuhrmann G. Extracellular vesicles as a next-generation drug delivery platform. Nat Nanotechnol. 2021 Jul;16(7):748–59.

12. Théry C, Amigorena S, Raposo G, Clayton A. Isolation and Characterization of Exosomes from Cell Culture Supernatants and Biological Fluids. CP Cell Biology [Internet]. 2006 Mar [cited 2024 Nov 5];30(1). Available from: https://currentprotocols.onlinelibrary.wiley.com/doi/10.1002/0471143030.cb0322s30

13. Cvjetkovic A, Lötvall J, Lässer C. The influence of rotor type and centrifugation time on the yield and purity of extracellular vesicles. J of Extracellular Vesicle. 2014 Jan;3(1):23111.

14. Bobrie A, Colombo M, Krumeich S, Raposo G, Théry C. Diverse subpopulations of vesicles secreted by different intracellular mechanisms are present in exosome preparations obtained by differential ultracentrifugation. J of Extracellular Vesicle. 2012 Jan;1(1):18397.

15. Jeppesen DK, Hvam ML, Primdahl‐Bengtson B, Boysen AT, Whitehead B, Dyrskjøt L, et al. Comparative analysis of discrete exosome fractions obtained by differential centrifugation. J of Extracellular Vesicle. 2014 Jan;3(1):25011.

16. Nordin JZ, Lee Y, Vader P, Mäger I, Johansson HJ, Heusermann W, et al. Ultrafiltration with size-exclusion liquid chromatography for high yield isolation of extracellular vesicles preserving intact biophysical and functional properties. Nanomedicine: Nanotechnology, Biology and Medicine. 2015 May;11(4):879–83.

17. Mol EA, Goumans MJ, Doevendans PA, Sluijter JPG, Vader P. Higher functionality of extracellular vesicles isolated using size-exclusion chromatography compared to ultracentrifugation. Nanomedicine: Nanotechnology, Biology and Medicine. 2017 Aug;13(6):2061–5.

18. Böing AN, Van Der Pol E, Grootemaat AE, Coumans FAW, Sturk A, Nieuwland R. Single‐step isolation of extracellular vesicles by size‐exclusion chromatography. J of Extracellular Vesicle. 2014 Jan;3(1):23430.

19. Giddings JC, Yang FJF, Myers MN. Flow-Field-Flow Fractionation: A Versatile New Separation Method. Science. 1976 Sep 24;193(4259):1244–5.

20. Willms E, Cabañas C, Mäger I, Wood MJA, Vader P. Extracellular Vesicle Heterogeneity: Subpopulations, Isolation Techniques, and Diverse Functions in Cancer Progression. Front Immunol. 2018 Apr 30;9:738.

21. Zhang H, Lyden D. Asymmetric-flow field-flow fractionation technology for exomere and small extracellular vesicle separation and characterization. Nat Protoc. 2019 Apr;14(4):1027–53.

22. Xu R, Greening DW, Rai A, Ji H, Simpson RJ. Highly-purified exosomes and shed microvesicles isolated from the human colon cancer cell line LIM1863 by sequential centrifugal ultrafiltration are biochemically and functionally distinct. Methods. 2015 Oct;87:11–25.

23. Xu R, Simpson RJ, Greening DW. A Protocol for Isolation and Proteomic Characterization of Distinct Extracellular Vesicle Subtypes by Sequential Centrifugal Ultrafiltration. In: Hill AF, editor. Exosomes and Microvesicles [Internet]. New York, NY: Springer New York; 2017 [cited 2024 Nov 5]. p. 91–116. (Methods in Molecular Biology; vol. 1545). Available from: http://link.springer.com/10.1007/978-1-4939-6728-5_7

24. Singh AD, Patnam S, Manocha A, Bashyam L, Rengan AK, Sasidhar MV. Polyethylene glycol-based isolation of urinary extracellular vesicles, an easily adoptable protocol. MethodsX. 2023 Dec;11:102310.

25. Kamei N, Nishimura H, Matsumoto A, Asano R, Muranaka K, Fujita M, et al. Comparative study of commercial protocols for high recovery of high-purity mesenchymal stem cell-derived extracellular vesicle isolation and their efficient labeling with fluorescent dyes. Nanomedicine: Nanotechnology, Biology and Medicine. 2021 Jul;35:102396.

26. Ströhle G, Gan J, Li H. Affinity-based isolation of extracellular vesicles and the effects on downstream molecular analysis. Anal Bioanal Chem. 2022 Oct;414(24):7051–67.

27. Nakai W, Yoshida T, Diez D, Miyatake Y, Nishibu T, Imawaka N, et al. A novel affinity-based method for the isolation of highly purified extracellular vesicles. Sci Rep. 2016 Sep 23;6(1):33935.

28. Gardiner C, Shaw M, Hole P, Smith J, Tannetta D, Redman CW, et al. Measurement of refractive index by nanoparticle tracking analysis reveals heterogeneity in extracellular vesicles. J of Extracellular Vesicle. 2014 Jan;3(1):25361.

29. Van Der Pol E, Coumans FAW, Sturk A, Nieuwland R, Van Leeuwen TG. Refractive Index Determination of Nanoparticles in Suspension Using Nanoparticle Tracking Analysis. Nano Lett. 2014 Nov 12;14(11):6195–201.

30. Van Der Pol E, Welsh JA, Nieuwland R. Minimum information to report about a flow cytometry experiment on extracellular vesicles: Communication from the ISTH SSC subcommittee on vascular biology. Journal of Thrombosis and Haemostasis. 2022 Jan;20(1):245–51.

31. Cavallaro S, Hååg P, Viktorsson K, Krozer A, Fogel K, Lewensohn R, et al. Comparison and optimization of nanoscale extracellular vesicle imaging by scanning electron microscopy for accurate size-based profiling and morphological analysis. Nanoscale Adv. 2021;3(11):3053–63.

32. Wu Y, Deng W, Klinke Ii DJ. Exosomes: improved methods to characterize their morphology, RNA content, and surface protein biomarkers. Analyst. 2015;140(19):6631–42.

33. Van Der Pol E, Coumans FAW, Grootemaat AE, Gardiner C, Sargent IL, Harrison P, et al. Particle size distribution of exosomes and microvesicles determined by transmission electron microscopy, flow cytometry, nanoparticle tracking analysis, and resistive pulse sensing. Journal of Thrombosis and Haemostasis. 2014 Jul;12(7):1182–92.

34. Höög JL, Lötvall J. Diversity of extracellular vesicles in human ejaculates revealed by cryo‐electron microscopy. J of Extracellular Vesicle. 2015 Jan;4(1):28680.

35. Bordanaba-Florit G, Royo F, Kruglik SG, Falcón-Pérez JM. Using single-vesicle technologies to unravel the heterogeneity of extracellular vesicles. Nat Protoc. 2021 Jul;16(7):3163–85.

36. Obeid S, Sung PS, Le Roy B, Chou ML, Hsieh SL, Elie-Caille C, et al. NanoBioAnalytical characterization of extracellular vesicles in 75-nm nanofiltered human plasma for transfusion: A tool to improve transfusion safety. Nanomedicine: Nanotechnology, Biology and Medicine. 2019 Aug;20:101977.

37. Sharma S, LeClaire M, Gimzewski JK. Ascent of atomic force microscopy as a nanoanalytical tool for exosomes and other extracellular vesicles. Nanotechnology. 2018 Apr 3;29(13):132001.

38. Cavallaro S, Pevere F, Stridfeldt F, Görgens A, Paba C, Sahu SS, et al. Multiparametric Profiling of Single Nanoscale Extracellular Vesicles by Combined Atomic Force and Fluorescence Microscopy: Correlation and Heterogeneity in Their Molecular and Biophysical Features. Small. 2021 Apr;17(14):2008155.

39. Parisse P, Rago I, Ulloa Severino L, Perissinotto F, Ambrosetti E, Paoletti P, et al. Atomic force microscopy analysis of extracellular vesicles. Eur Biophys J. 2017 Dec;46(8):813–20.

40. Piontek MC, Lira RB, Roos WH. Active probing of the mechanical properties of biological and synthetic vesicles. Biochimica et Biophysica Acta (BBA) - General Subjects. 2021 Apr;1865(4):129486.

41. Ridolfi A, Brucale M, Montis C, Caselli L, Paolini L, Borup A, et al. AFM-Based High-Throughput Nanomechanical Screening of Single Extracellular Vesicles. Anal Chem. 2020 Aug 4;92(15):10274–82.

42. Van Der Pol E, Van Gemert MJC, Sturk A, Nieuwland R, Van Leeuwen TG. Single vs. swarm detection of microparticles and exosomes by flow cytometry. Journal of Thrombosis and Haemostasis. 2012 May;10(5):919–30.

43. Koliha N, Wiencek Y, Heider U, Jüngst C, Kladt N, Krauthäuser S, et al. A novel multiplex bead‐based platform highlights the diversity of extracellular vesicles. J of Extracellular Vesicle. 2016 Jan;5(1):29975.

44. Wiklander OPB, Bostancioglu RB, Welsh JA, Zickler AM, Murke F, Corso G, et al. Systematic Methodological Evaluation of a Multiplex Bead-Based Flow Cytometry Assay for Detection of Extracellular Vesicle Surface Signatures. Front Immunol. 2018 Jun 13;9:1326.

45. Zhu S, Ma L, Wang S, Chen C, Zhang W, Yang L, et al. Light-Scattering Detection below the Level of Single Fluorescent Molecules for High-Resolution Characterization of Functional Nanoparticles. ACS Nano. 2014 Oct 28;8(10):10998–1006.

46. Morales‐Kastresana A, Musich TA, Welsh JA, Telford W, Demberg T, Wood JCS, et al. High‐fidelity detection and sorting of nanoscale vesicles in viral disease and cancer. J of Extracellular Vesicle. 2019 Dec;8(1):1597603.

47. Sandau US, Duggan E, Shi X, Smith SJ, Huckans M, Schutzer WE, et al. Methamphetamine use alters human plasma extracellular vesicles and their microRNA cargo: An exploratory study. J of Extracellular Vesicle. 2020 Nov;10(1):e12028.

48. Welsh JA, Killingsworth B, Kepley J, Traynor T, McKinnon K, Savage J, et al. A simple, high-throughput method of protein and label removal from extracellular vesicle samples. Nanoscale. 2021;13(6):3737–45.

49. Kondratov K, Nikitin Y, Fedorov A, Kostareva A, Mikhailovskii V, Isakov D, et al. Heterogeneity of the nucleic acid repertoire of plasma extracellular vesicles demonstrated using high‐sensitivity fluorescence‐activated sorting. J of Extracellular Vesicle. 2020 Sep;9(1):1743139.

50. Stoner SA, Duggan E, Condello D, Guerrero A, Turk JR, Narayanan PK, et al. High sensitivity flow cytometry of membrane vesicles. Cytometry Pt A. 2016 Feb;89(2):196–206.

51. Tian Y, Gong M, Hu Y, Liu H, Zhang W, Zhang M, et al. Quality and efficiency assessment of six extracellular vesicle isolation methods by nano‐flow cytometry. J of Extracellular Vesicle. 2020 Sep;9(1):1697028.

52. Welsh JA, Jones JC, Tang VA. Fluorescence and Light Scatter Calibration Allow Comparisons of Small Particle Data in Standard Units across Different Flow Cytometry Platforms and Detector Settings. Cytometry Pt A. 2020 Jun;97(6):592–601.

53. Welsh JA, Van Der Pol E, Bettin BA, Carter DRF, Hendrix A, Lenassi M, et al. Towards defining reference materials for measuring extracellular vesicle refractive index, epitope abundance, size and concentration. J of Extracellular Vesicle. 2020 Sep;9(1):1816641.

54. Pleet ML, Cook S, Tang VA, Stack E, Ford VJ, Lannigan J, et al. Extracellular Vesicle Refractive Index Derivation Utilizing Orthogonal Characterization. Nano Lett. 2023 Oct 25;23(20):9195–202.

55. Van Der Pol E, De Rond L, Coumans FAW, Gool EL, Böing AN, Sturk A, et al. Absolute sizing and label-free identification of extracellular vesicles by flow cytometry. Nanomedicine: Nanotechnology, Biology and Medicine. 2018 Apr;14(3):801–10.

56. Van Der Pol E, Sturk A, Van Leeuwen T, Nieuwland R, Coumans F, Mobarrez F, et al. Standardization of extracellular vesicle measurements by flow cytometry through vesicle diameter approximation. Journal of Thrombosis and Haemostasis. 2018 Jun;16(6):1236–45.

57. Aebersold R, Mann M. Mass spectrometry-based proteomics. Nature. 2003 Mar;422(6928):198–207.

58. Hoshino A, Kim HS, Bojmar L, Gyan KE, Cioffi M, Hernandez J, et al. Extracellular Vesicle and Particle Biomarkers Define Multiple Human Cancers. Cell. 2020 Aug;182(4):1044-1061.e18.

59. Pocsfalvi G, Stanly C, Vilasi A, Fiume I, Capasso G, Turiák L, et al. Mass spectrometry of extracellular vesicles. Mass Spectrometry Reviews. 2016 Jan;35(1):3–21.

60. Liebler DC, Zimmerman LJ. Targeted Quantitation of Proteins by Mass Spectrometry. Biochemistry. 2013 Jun 4;52(22):3797–806.

61. Nakayasu ES, Gritsenko M, Piehowski PD, Gao Y, Orton DJ, Schepmoes AA, et al. Tutorial: best practices and considerations for mass-spectrometry-based protein biomarker discovery and validation. Nat Protoc. 2021 Aug;16(8):3737–60.

62. Newman LA, Useckaite Z, Rowland A. Addressing MISEV guidance using targeted LC‐MS/MS: A method for the detection and quantification of extracellular vesicle‐enriched and contaminant protein markers from blood. J of Extracellular Bio. 2022 Sep;1(9):e56.

63. Pocsfalvi G, Stanly C, Fiume I, Vékey K. Chromatography and its hyphenation to mass spectrometry for extracellular vesicle analysis. Journal of Chromatography A. 2016 Mar;1439:26–41.

64. Rodrigues AD, Van Dyk M, Sorich MJ, Fahmy A, Useckaite Z, Newman LA, et al. Exploring the Use of Serum‐Derived Small Extracellular Vesicles as Liquid Biopsy to Study the Induction of Hepatic Cytochromes P450 and Organic Anion Transporting Polypeptides. Clin Pharma and Therapeutics. 2021 Jul;110(1):248–58.

65. Stetefeld J, McKenna SA, Patel TR. Dynamic light scattering: a practical guide and applications in biomedical sciences. Biophys Rev. 2016 Dec;8(4):409–27.

66. Bhatt M, Rai V, Kumar A, Kiran, Yadav AK, Rajak KK, et al. SDS-PAGE and Western Blotting: Basic Principles and Protocol. In: Deb R, Yadav AK, Rajkhowa S, Malik YS, editors. Protocols for the Diagnosis of Pig Viral Diseases [Internet]. New York, NY: Springer US; 2022 [cited 2024 Nov 11]. p. 313–28. (Springer Protocols Handbooks). Available from: https://link.springer.com/10.1007/978-1-0716-2043-4_23

67. Kowal EJK, Ter-Ovanesyan D, Regev A, Church GM. Extracellular Vesicle Isolation and Analysis by Western Blotting. In: Kuo WP, Jia S, editors. Extracellular Vesicles [Internet]. New York, NY: Springer New York; 2017 [cited 2024 Nov 5]. p. 143–52. (Methods in Molecular Biology; vol. 1660). Available from: https://link.springer.com/10.1007/978-1-4939-7253-1_12


Рецензия

Для цитирования:


Костина В.В., Яковлев А.А. Преимущества и недостатки широко используемых методов изучения внеклеточных везикул. Трансляционная медицина. 2025;12(1):51-66. https://doi.org/10.18705/2311-4495-2025-12-1-51-66. EDN: XJCLEP

For citation:


Kostina V.V., Yakovlev A.A. Key techniques for studying extracellular vesicles. Translational Medicine. 2025;12(1):51-66. (In Russ.) https://doi.org/10.18705/2311-4495-2025-12-1-51-66. EDN: XJCLEP

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