Isolation of Low Endotoxin Content Extracellular Vesicles Derived from Cancer Cell Lines

Summary

The proposed protocol includes guidelines on how to avoid contamination with endotoxin during the isolation of extracellular vesicles from cell culture supernatants, and how to properly evaluate them.

Abstract

Extracellular vesicles (EVs) are a heterogeneous population of membrane vesicles released by cells in vitro and in vivo. Their omnipresence and significant role as carriers of biological information make them intriguing study objects, requiring reliable and repetitive protocols for their isolation. However, realizing their full potential is difficult as there are still many technical obstacles related to their research (like proper acquisition). This study presents a protocol for the isolation of small EVs (according to the MISEV 2018 nomenclature) from the culture supernatant of tumor cell lines based on differential centrifugation. The protocol includes guidelines on how to avoid contamination with endotoxins during the isolation of EVs and how to properly evaluate them. Endotoxin contamination of EVs can significantly hinder subsequent experiments or even mask their true biological effects. On the other hand, the overlooked presence of endotoxins may lead to incorrect conclusions. This is of particular importance when referring to cells of the immune system, including monocytes, because monocytes constitute a population that is especially sensitive to endotoxin residues. Therefore, it is highly recommended to screen EVs for endotoxin contamination, especially when working with endotoxin-sensitive cells such as monocytes, macrophages, myeloid-derived suppressor cells, or dendritic cells.

Introduction

Extracellular vesicles (EVs), according to the MISEV 2018 nomenclature, are a collective term describing various subtypes of cell-secreted membranous vesicles that play crucial roles in numerous physiological and pathological processes^1,2. Moreover, EVs show promise as novel biomarkers for various diseases, as well as therapeutic agents and drug delivery vehicles. However, realizing their full potential is difficult as there are still many technical obstacles related to their acquisition³. One such challenge is the isolation of endotoxin-free EVs, which has been neglected in many cases.....

Protocol

1. Preparation of ultracentrifuge tubes

1. Use sterile, single-use tubes. If this is not possible, reuse the ultracentrifuge tubes after washing them with a detergent using a sterile Pasteur pipette or other single-use applicators. Remember that ultracentrifuge tubes should be dedicated to one type of centrifuged material (cell culture supernatant/serum/plasma) and species (human/mouse/etc.).
2. After a detergent wash, rinse the ultracentrifuge tubes with deionized, LPS-free water 3x.

Discussion

In the last few years, methods for proper EVs isolation have become increasingly important, enabling their further reliable analyses, for example, in the context of obtaining reliable omics and functional data²⁴. Based on previous research experience, it seems that not only the type of isolation method, but also other conditions during this procedure may be important. The use of EV-depleted FBS is widely recognized as a necessity^25,26; how.......

Materials

Name	Company	Catalog Number	Comments
Alix (3A9) Mouse mAb	Cell Signaling Technology	2171
1250ul Filter Universal Pipette Tips, Clear, Polypropylene, Non-Pyrogenic	GoogLab Scientific	GBFT1250-R-NS
BD FACSCanto II Flow Cytometr	BD Biosciences
CBA Human Th1/Th2 Cytokine Kit II	BD Biosciences	551809
CD9 (D8O1A) Rabbit mAb	Cell Signaling Technology	13174
ChemiDoc Imaging System	Bio-Rad Laboratories, Inc.	17001401
DMEM (Dulbecco’s Modified Eagle’s Medium)	Corning	10-013-CV
ELX800NB, Universal Microplate Reader	BIO-TEK INSTRUMENTS, INC
Fetal Bovine Serum	Gibco	16000044
Fetal Bovine Serum South America Ultra Low Endotoxin	Biowest	S1860-500
Gentamicin, 50 mg/mL	PAN – Biotech	P06-13100
Goat anti-Mouse IgG- HRP	Santa Cruz Biotechnology	sc-2004
Goat anti-Rabbit IgG- HRP	Santa Cruz Biotechnology	sc-2005
Immun-Blot PVDF Membrane	Bio-Rad Laboratories, Inc.	1620177
LPS from Salmonella abortus equi S-form (TLRGRADE)	Enzo Life Sciences, Inc.	ALX-581-009-L002
Mini Trans-Blot Electrophoretic Transfer Cell	Bio-Rad Laboratories, Inc.	1703930
Nanoparticle Tracking Analysis	Malvern Instruments Ltd
NuPAGE LDS Sample Buffer (4X)	Invitrogen	NP0007
NuPAGE Sample Reducing Agent (10x)	Invitrogen	NP0004
Parafilm	Sigma Aldrich	P7793	transparent film
Perfect 100-1000 bp DNA Ladder	EURx	E3141-01
PierceTM Chromogenic Endotoxin Quant Kit	Thermo Scientific	A39552
PP Oak Ridge Tube with sealing caps	Thermo Scientific	3929, 03613
RPMI 1640	RPMI-1640 (Gibco)	11875093
SimpliAmp Thermal Cycler	Applied Biosystem	A24811
Sorvall wX+ ULTRA SERIES Centrifuge with T-1270 rotor	Thermo Scientific	75000100
Sub-Cell GT Horizontal Electrophoresis System	Bio-Rad Laboratories, Inc.	1704401
SuperSignal West Pico PLUS Chemiluminescent Substrate	Thermo Scientific	34577
SW480 cell line	American Type Culture Collection(ATCC)
SW480 cell line	American Type Culture Collection (ATCC)
Syringe filter 0.22 um	TPP	99722
Trans-Blot SD Semi-Dry Transfer Cell	Bio-Rad Laboratories, Inc.	1703940	Transfer machine
Transfer pipette, 3.5 mL	SARSTEDT	86.1171.001