Purification and microRNA Profiling of Exosomes Derived from Blood and Culture Media

Summary

The presence of stable microRNAs (miRNAs) in exosomes has generated immense interest as a novel mode of intercellular communication, for their potential utility as biomarkers and as a route for therapeutic intervention. Here we demonstrate exosome purification from blood and culture media followed by quantitative PCR to identify miRNAs being transported.

Abstract

Stable miRNAs are present in all body fluids and some circulating miRNAs are protected from degradation by sequestration in small vesicles called exosomes. Exosomes can fuse with the plasma membrane resulting in the transfer of RNA and proteins to the target cell. Their biological functions include immune response, antigen presentation, and intracellular communication. Delivery of miRNAs that can regulate gene expression in the recipient cells via blood has opened novel avenues for target intervention. In addition to offering a strategy for delivery of drugs or RNA therapeutic agents, exosomal contents can serve as biomarkers that can aid in diagnosis, determining treatment options and prognosis.

Here we will describe the procedure for quantitatively analyzing miRNAs and messenger RNAs (mRNA) from exosomes secreted in blood and cell culture media. Purified exosomes will be characterized using western blot analysis for exosomal markers and PCR for mRNAs of interest. Transmission electron microscopy (TEM) and immunogold labeling will be used to validate exosomal morphology and integrity. Total RNA will be purified from these exosomes to ensure that we can study both mRNA and miRNA from the same sample. After validating RNA integrity by Bioanalyzer, we will perform a medium throughput quantitative real time PCR (qPCR) to identify the exosomal miRNA using Taqman Low Density Array (TLDA) cards and gene expression studies for transcripts of interest.

These protocols can be used to quantify changes in exosomal miRNAs in patients, rodent models and cell culture media before and after pharmacological intervention. Exosomal contents vary due to the source of origin and the physiological conditions of cells that secrete exosomes. These variations can provide insight on how cells and systems cope with stress or physiological perturbations. Our representative data show variations in miRNAs present in exosomes purified from mouse blood, human blood and human cell culture media.

Here we will describe the procedure for quantitatively analyzing miRNAs and messenger RNAs (mRNA) from exosomes secreted in blood and cell culture media. Purified exosomes will be characterized using western blot analysis for exosomal markers and PCR for mRNAs of interest. Transmission electron microscopy (TEM) and immunogold labeling will be used to validate exosomal morphology and integrity. Total RNA will be purified from these exosomes to ensure that we can study both mRNA and miRNA from the same sample. After validating RNA integrity by Bioanalyzer, we will perform a medium throughput quantitative real time PCR (qPCR) to identify the exosomal miRNA using Taqman Low Density Array (TLDA) cards and gene expression studies for transcripts of interest.

These protocols can be used to quantify changes in exosomal miRNAs in patients, rodent models and cell culture media before and after pharmacological intervention. Exosomal contents vary due to the source of origin and the physiological conditions of cells that secrete exosomes. These variations can provide insight on how cells and systems cope with stress or physiological perturbations. Our representative data show variations in miRNAs present in exosomes purified from mouse blood, human blood and human cell culture media

Introduction

Short noncoding miRNAs modulate gene expression by binding to the target mRNA. Seed sequence complementarity of ~7 base pairs enables miRNA to bind to the target mRNA resulting in the inhibition of translation or in reduction in the stability of the mRNA, both of which can result in decreased expression of the target protein ¹. Research over the last decade has unequivocally proven a fundamental role for miRNAs in mediating cellular functions. There has also been considerable effort directed towards dissecting miRNA mediated molecular changes underlying various diseases ^2,3. Furthermore, recent identification of stable miRNAs in bodily fluids

Protocol

All experiments using blood samples from human and rodents were executed in compliance with all relevant guidelines, regulations and regulatory agencies. Human subjects were enrolled after giving informed consent as approved by the Drexel University College of Medicine Institutional Review Board and all procedures for studies performed using animals were approved by Drexel's Institutional Animal Care and Use Committee.

1. Exosome Purification from Blood (~5.5 hr)

TIPS

• We resuspend exosomes from one tube of blood (~10 ml human blood and ~2 ml mouse blood) in 300 μl RNA lysis buffer....

Results

After isolating exosomes from blood or cell culture media, the purity of the exosomes can be tested by electron microscopy (EM) and western blot (Figures 1A and 1B). We confirmed our exosome preparations from various sources with EM and western blot using multiple antibodies. Figure 1A shows EM images confirming that exosomes are intact with a diameter of ~30 -100 nm and contain CD81 by immunogold labeling. Commonly used exosomal markers are Hsp70 and tetraspannin family.......

Discussion

In this protocol, we show the quantification of miRNAs and mRNAs from exosomes purified by differential centrifugation from blood and culture media. Exosomes have diverse components dependent upon their origin and are involved in a number of biological functions, including immune response, antigen presentation, intracellular communication, and the transfer of RNA and proteins ^{9,11,12,19,20}. While size and shape is a determinant of exosome purity, a number of papers showing EM data of exosomes indicate that the.......

Materials

List of materials used in this article

Name	Company	Catalog Number	Comments
EDTA coated vacutainer (10 ml tubes)	BD Diagnostics	366643	For exosome purification from human blood
EDTA coated vacutainer (2 ml tubes)	BD Diagnostics	367841	For exosome purification from mouse blood
PAXgene Blood RNA Tube	BD Diagnostics	762165	For miRNA isolation from total blood
miRVana microRNA isolation kit	Ambion	AM1561
Acid-Phenol: CHCl3	Ambion	9721G
DNase 1	Qiagen	79254
TaqMan Universal PCR Master Mix, No AmpErase UNG	Applied Biosystems	4326614	For TLDA cards
Megaplex RT rodent Pool Set v3.0	Applied Biosystems	4444746
Megaplex preamp rodent Pool set v3.0	Applied Biosystems	4444747
Taqman Array Rodent MicroRNA A+B set V3.0	Applied Biosystems	4444909
Megaplex RT Human Pool set V3.0	Applied Biosystems	4444745
Megaplex Preamp human pool set v3.0	Applied Biosystems	4444748
Taqman Array Human MicroRNA A+B Cards Set v3.0	Applied Biosystems	4444913
Taqman MicroRNA RT kit	Applied Biosystems	4366596
Taqman fast universal PCR master mix	Applied Biosystems	4366072	For mRNA qRT-PCR
Tumor necrosis factor (primer probe)	Applied Biosystems	Hs01113624_g1
Vascular endothelial growth factor A (primer probe)	Applied Biosystems	Hs00900055_m1
Maxima First Strand cDNA Synthesis Kit for RT-qPCR	Thermo Scientific	K1642	For mRNA
HSP70 antibody	Abcam	ab94368	For western blot
Anti-rabbit IgG-Gold	Sigma	G7402	For electron microscopy
Rabbit-anti CD81	Sigma	SAB3500454
Nickel 300 mesh carbon formvar grids	Electron Microscopy Sciences	FCF300-Ni
Copper 300 mesh carbon formvar grids	Electron Microscopy Sciences	FCF300-Cu
Table 1. Table of specific reagents.