Impact of isolation methods on the biophysical heterogeneity of single extracellular vesicles

Shivani Sharma,Michael Leclaire,James Gimzewski,James Wohlschlegel

doi:10.1038/s41598-020-70245-1

Abstract

Extracellular vesicles (EVs) have raised high expectations as a novel class of diagnostics and therapeutics. However, variabilities in EV isolation methods and the unresolved structural complexity of these biological-nanoparticles (sub-100 nm) necessitate rigorous biophysical characterization of single EVs. Here, using atomic force microscopy (AFM) in conjunction with direct stochastic optical reconstruction microscopy (dSTORM), micro-fluidic resistive pore sizing (MRPS), and multi-angle light scattering (MALS) techniques, we compared the size, structure and unique surface properties of breast cancer cell-derived small EVs (sEV) obtained using four different isolation methods. AFM and dSTORM particle size distributions showed coherent unimodal and bimodal particle size populations isolated via centrifugation and immune-affinity methods respectively. More importantly, AFM imaging revealed striking differences in sEV nanoscale morphology, surface nano-roughness, and relative abundance of non-vesicles among different isolation methods. Precipitation-based isolation method exhibited the highest particle counts, yet nanoscale imaging revealed the additional presence of aggregates and polymeric residues. Together, our findings demonstrate the significance of orthogonal label-free surface characteristics of single sEVs, not discernable via conventional particle sizing and counts alone. Quantifying key nanoscale structural characteristics of sEVs, collectively termed ‘EV-nano-metrics’ enhances the understanding of the complexity and heterogeneity of sEV isolates, with broad implications for EV-analyte based research and clinical use.

Highlights

Extracellular vesicles (EVs) have raised high expectations as a novel class of diagnostics and therapeutics
Our findings reveal that the quantification of key biophysical parameters within small EVs (sEV) isolates collectively termed ‘EV-nano-metrics’ provides novel orthogonal markers to precisely quantify the nanoscale effects of isolation strategies at the single particle level
We visualized sEVs from four different isolation methods (UC, UCg, IA, and PT as outlined in Fig. 1) from well-established breast cancer cell lines[29] at the single-particle level using atomic force microscopy (AFM) imaging under ambient conditions

Summary

Introduction

Extracellular vesicles (EVs) have raised high expectations as a novel class of diagnostics and therapeutics. Variabilities in EV isolation methods and the unresolved structural complexity of these biological-nanoparticles (sub-100 nm) necessitate rigorous biophysical characterization of single EVs. Here, using atomic force microscopy (AFM) in conjunction with direct stochastic optical reconstruction microscopy (dSTORM), micro-fluidic resistive pore sizing (MRPS), and multi-angle light scattering (MALS) techniques, we compared the size, structure and unique surface properties of breast cancer cell-derived small EVs (sEV) obtained using four different isolation methods. Using atomic force microscopy (AFM) in conjunction with direct stochastic optical reconstruction microscopy (dSTORM), micro-fluidic resistive pore sizing (MRPS), and multi-angle light scattering (MALS) techniques, we compared the size, structure and unique surface properties of breast cancer cell-derived sEVs obtained using different isolation methods. Our findings reveal that the quantification of key biophysical parameters within sEV isolates collectively termed ‘EV-nano-metrics’ provides novel orthogonal markers to precisely quantify the nanoscale effects of isolation strategies at the single particle level. The findings hold significant potential implications for EV-based downstream applications where molecular markers of sEVs are not established or not available

Methods

Results

Discussion

Conclusion