Imaging of Extracellular Vesicles by Atomic Force Microscopy

Summary

A step-by-step procedure is described for label-free immobilization of exosomes and extracellular vesicles from liquid samples and their imaging by atomic force microscopy (AFM). The AFM images are used to estimate the size of the vesicles in the solution and characterize other biophysical properties. 

Abstract

Exosomes and other extracellular vesicles (EVs) are molecular complexes consisting of a lipid membrane vesicle, its surface decoration by membrane proteins and other molecules, and diverse luminal content inherited from a parent cell, which includes RNAs, proteins, and DNAs. The characterization of the hydrodynamic sizes of EVs, which depends on the size of the vesicle and its coronal layer formed by surface decorations, has become routine. For exosomes, the smallest of EVs, the relative difference between the hydrodynamic and vesicles sizes is significant. The characterization of vesicles sizes by the cryogenic transmission electron microscopy (cryo-TEM) imaging, a gold standard technique, remains a challenge due to the cost of the instrument, the expertise required to perform the sample preparation, imaging and data analysis, and a small number of particles often observed in images. A widely available and accessible alternative is the atomic force microscopy (AFM), which can produce versatile data on three-dimensional geometry, size, and other biophysical properties of extracellular vesicles. The developed protocol guides the users in utilizing this analytical tool and outlines the workflow for the analysis of EVs by the AFM, which includes the sample preparation for imaging EVs in hydrated or desiccated form, the electrostatic immobilization of vesicles on a substrate, data acquisition, its analysis, and interpretation. The representative results demonstrate that the fixation of EVs on the modified mica surface is predictable, customizable, and allows the user to obtain sizing results for a large number of vesicles. The vesicle sizing based on the AFM data was found to be consistent with the cryo-TEM imaging. 

Introduction

Extracellular vesicles (EVs) are present in all body fluids, including blood, urine, saliva, milk, and the amniotic fluid. Exosomes form a district class of EVs differentiated from other EVs by endosomal biogenesis, the markers of the endosomal pathway, and the smallest size among all EVs. The size of exosomes is often reported with substantial variability between studies. The sizing results were found to be method dependent, reflecting the difference in physical principles employed by different analytical techniques to estimate EV sizes^1,2. For example, the nanoparticle tracking analysis (NTA) ― the mos....

Protocol

1. Isolation of EVs from a biofluid

1. Isolate EVs by one of the established methods, such as the differential ultracentrifugation⁸, precipitation, or size-exclusion chromatography⁹.
2. Confirm the presence of expected surface and luminal biomarkers and the absence of biomarkers indicating cross-contamination of the preparation. Confirm the lipid bilayer morphology of the isolated particles by electron microscopy.
   NOTE: When isolatin.......

Discussion

The immobilization of EVs from a biological fluid, surface scanning, and image analysis are the essential steps of the developed protocol for the AFM characterization of EVs in liquid. The number of vesicles amenable to AFM imaging scales with the imaged surface area and the surface concentration of the vesicles immobilized on the substrate. Given a negative zeta potential of EVs and exosomes¹⁸, we advocate electrostatic fixation of EVs from liquid samples to the AFM substrate. The immobilization .......

Materials

Name	Company	Catalog Number	Comments
AFM/STM Controller	Bruker	Multimode Nanoscope V	This AFM controller supports imaging of biological samples in liquid and air.
AFM/STM metal specimen discs (10 mm)	TedPella	16207	Metal specimen disc on which a mica disk is attached by a double-sided tape or other means.
AFM/STM Mica discs (10 mm)	TedPella	50	Highest quality grade V1 mica, 0.21mm (0.0085”) thick. Interleaved, in packages of 10. Can be mounted on AFM/STM discs. Available in four diameters
AFM probe for imaging in the air	Bruker	TESP-V2	High quality etched silicon probes for tapping mode and non-contact mode for scanning in the air.
AFM probe for soft sample imaging in liquid	Bruker	MLCT	Soft silicon nitride cantilevers with silicon nitride tips, which are well-suited for liquid operation.  The range in force constants enables users to image extremely soft samples in contact mode as well as high load vs distance spectroscopy.
Double sided tape	Spectrum	360-77705	Used to fix the mica disk on the metal specimen disc.
ExoQuick-TC	System Biosciences	EXOTC50A-1	ExoQuick-TC is a proprietary polymer-based kit designed for exosome isolation from tissue culture media.
Glass probe AFM holder for imaging in liquid	Bruker	MTFML-V2	This glass probe holder is designed for scanning in fluid with the MultiMode AFM.  The holder can be used in peak force tapping mode, contact mode, tapping mode, and force modulation.  The probe is acoustically driven by a separate piezo oscillator for larger amplitude modulation.  The holder is supplied with two ports, required fittings, and accessories kit for adding and removing fluids.
Gwyddion	Czech Metrology Institute.	Version 2.52	Open Source software for visualization and analysis of data fields obtained by scanning probe microscopy techniques.
Lint-free blotting paper	GE Healthcare Whatman	Grade GB003 Blotting Paper	Use this blotting paper to remove NiCl2 after the modification of the mica's substrate.
Lint-free cleanroom wipes	Texwipe	AlphaWipe TX1004	Use these polyester wipes for surface cleaning.
Nickel(II) chloride (NiCl2)	Sigma-Aldrich	339350	Powder used to make 10 mM NiCl2 in DI water
Phosphate Buffered Saline (1x)	Gibco	10010023	PBS, pH 7.4