
RNA in Exosomes and
Extracellular-Vesicles (EVs)
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| The EV and exosomal RNA content
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Obstacles
and opportunities in the functional
analysis of extracellular vesicle RNA
- an ISEV position paper
Mateescu
B, Kowal EJ, van Balkom BW, Bartel S,
Bhattacharyya SN, Buzás EI, Buck AH, de
Candia P, Chow FW, Das S, Driedonks TA,
Fernández-Messina L, Haderk F, Hill AF,
Jones JC, Van Keuren-Jensen KR, Lai CP,
Lässer C, Liegro ID, Lunavat TR, Lorenowicz
MJ, Maas SL, Mäger I, Mittelbrunn M, Momma
S, Mukherjee K, Nawaz M, Pegtel DM, Pfaffl
MW, Schiffelers RM, Tahara H, Théry C, Tosar
JP, Wauben MH, Witwer KW, Nolte-'t Hoen EN
J Extracell Vesicles. 2017 6(1): 1286095
-- eCollection 2017
The
release of RNA-containing extracellular
vesicles (EV) into the extracellular milieu
has been demonstrated in a multitude of
different in vitro cell systems and in a
variety of body fluids. RNA-containing EV
are in the limelight for their capacity to
communicate genetically encoded messages to
other cells, their suitability as candidate
biomarkers for diseases, and their use as
therapeutic agents. Although EV-RNA has
attracted enormous interest from basic
researchers, clinicians, and industry, we
currently have limited knowledge on which
mechanisms drive and regulate RNA
incorporation into EV and on how RNA-encoded
messages affect signalling processes in
EV-targeted cells. Moreover, EV-RNA research
faces various technical challenges, such as
standardisation of EV isolation methods,
optimisation of methodologies to isolate and
characterise minute quantities of RNA found
in EV, and development of approaches to
demonstrate functional transfer of EV-RNA in
vivo. These topics were discussed at the
2015 EV-RNA workshop of the International
Society for Extracellular Vesicles. This
position paper was written by the
participants of the workshop not only to
give an overview of the current state of
knowledge in the field, but also to clarify
that our incomplete knowledge - of the
nature of EV(-RNA)s and of how to
effectively and reliably study them -
currently prohibits the implementation of
gold standards in EV-RNA research. In
addition, this paper creates awareness of
possibilities and limitations of currently
used strategies to investigate EV-RNA and
calls for caution in interpretation of the
obtained data.
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Summary of the
ISEV workshop on extracellular vesicles as
disease biomarkers
Meeting
Report -- held in
Birmingham, UK, during December 2017
Aled
Clayton, Dominik Buschmann, J. Brian Byrd,
David R. F. Carter, Lesley Cheng, Carolyn
Compton, George Daaboul, Andrew Devitt, Juan
Manuel Falcon-Perez, Chris Gardiner, Dakota
Gustafson, Paul Harrison, Clemens
Helmbrecht, An Hendrix, Andrew Hill, Andrew
Hoffman, Jennifer C. Jones, Raghu Kalluri,
Ji Yoon Kang, Benedikt Kirchner, Cecilia
Lässer, Charlotte Lawson, Metka Lenassi,
Carina Levin, Alicia Llorente, Elena S.
Martens-Uzunova, Andreas Möller, Luca
Musante, Takahiro Ochiya, Ryan C Pink,
Hidetoshi Tahara, Marca H. M. Wauben, Jason
P. Webber, Joshua A. Welsh, Kenneth W.
Witwer, Hang Yin & Rienk Nieuwland
Journal of Extracellular Vesicles 2018
(7)1
This
report summarises the presentations and
activities of the ISEV Workshop on
extracellular vesicle biomarkers held in
Birmingham, UK during December 2017. Among
the key messages was broad agreement about
the importance of biospecimen science. Much
greater attention needs to be paid towards
the provenance of collected samples. The
workshop also highlighted clear gaps in our
knowledge about pre-analytical factors that
alter extracellular vesicles (EVs). The
future utility of certified standards for
credentialing of instruments and software,
to analyse EV and for tracking the influence
of isolation steps on the structure and
content of EVs were also discussed. Several
example studies were presented,
demonstrating the potential utility for EVs
in disease diagnosis, prognosis,
longitudinal serial testing and
stratification of patients. The conclusion
of the workshop was that more effort focused
on pre-analytical issues and benchmarking of
isolation methods is needed to strengthen
collaborations and advance more effective
biomarkers.
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A pipeline for the
development and analysis of extracellular
vesicle-based transcriptomic biomarkers in
molecular diagnostics
Christian Grätz, Martina Schuster, Florian
Brandes, Agnes S Meidert, Benedikt Kirchner,
Marlene Reithmair, Gustav Schelling, Michael W
Pfaffl
Mol Aspects Med 2024 (97): 101269
Extracellular
vesicles are shed by every cell type and can
be found in any biofluid. They contain
different molecules that can be utilized as
biomarkers, including several RNA species
which they protect from degradation. Here,
we present a pipeline for the development
and analysis of extracellular
vesicle-associated transcriptomic biomarkers
that our group has successfully applied
multiple times. We highlight the key steps
of the pipeline and give particular emphasis
to the necessary quality control
checkpoints, which are linked to numerous
available guidelines that should be
considered along the workflow. Our pipeline
starts with patient recruitment and
continues with blood sampling and
processing. The purification and
characterization of extracellular vesicles
is explained in detail, as well as the
isolation and quality control of
extracellular vesicle-associated RNA. We
point out the possible pitfalls during
library preparation and RNA sequencing and
present multiple bioinformatic tools to
pinpoint biomarker signature candidates from
the sequencing data. Finally, considerations
and pitfalls during the validation of the
biomarker signature using RT-qPCR will be
elaborated.
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Two distinct
extracellular RNA signatures released by a
single cell type identified by microarray
and next-generation sequencing.
Lässer C, Shelke GV, Yeri A, Kim DK,
Crescitelli R, Raimondo S, Sjöstrand M, Gho
YS, Van Keuren Jensen K, Lötvall J
RNA Biol. 2017 14(1): 58-72
Cells
secrete extracellular RNA (exRNA) to their
surrounding environment and exRNA has been
found in many body fluids such as blood,
breast milk and cerebrospinal fluid.
However, there are conflicting results
regarding the nature of exRNA. Here, we have
separated 2 distinct exRNA profiles released
by mast cells, here termed high-density (HD)
and low-density (LD) exRNA. The exRNA in
both fractions was characterized by
microarray and next-generation sequencing.
Both exRNA fractions contained mRNA and
miRNA, and the mRNAs in the LD exRNA
correlated closely with the cellular mRNA,
whereas the HD mRNA did not. Furthermore,
the HD exRNA was enriched in lincRNA,
antisense RNA, vault RNA, snoRNA, and snRNA
with little or no evidence of full-length
18S and 28S rRNA. The LD exRNA was enriched
in mitochondrial rRNA, mitochondrial tRNA,
tRNA, piRNA, Y RNA, and full-length 18S and
28S rRNA. The proteomes of the HD and LD
exRNA-containing fractions were determined
with LC-MS/MS and analyzed with Gene
Ontology term finder, which showed that both
proteomes were associated with the term
extracellular vesicles and electron
microscopy suggests that at least a part of
the exRNA is associated with exosome-like
extracellular vesicles. Additionally, the
proteins in the HD fractions tended to be
associated with the nucleus and ribosomes,
whereas the LD fraction proteome tended to
be associated with the mitochondrion. We
show that the 2 exRNA signatures released by
a single cell type can be separated by
floatation on a density gradient. These
results show that cells can release multiple
types of exRNA with substantial differences
in RNA species content. This is important
for any future studies determining the
nature and function of exRNA released from
different cells under different conditions.
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Evaluation of
serum extracellular vesicle isolation
methods for profiling miRNAs by
next-generation sequencing.
Buschmann
D, Kirchner B, Hermann S, Märte M, Wurmser
C, Brandes F, Kotschote S, Bonin M,
Steinlein OK, Pfaffl MW, Schelling G,
Reithmair M
J Extracell Vesicles. 2018 7(1): 1481321
-- eCollection 2018
Extracellular
vesicles
(EVs) are intercellular communicators with
key functions in physiological and
pathological processes and have recently
garnered interest because of their
diagnostic and therapeutic potential. The
past decade has brought about the
development and commercialization of a wide
array of methods to isolate EVs from serum.
Which subpopulations of EVs are captured
strongly depends on the isolation method,
which in turn determines how suitable
resulting samples are for various downstream
applications. To help clinicians and
scientists choose the most appropriate
approach for their experiments, isolation
methods need to be comparatively
characterized. Few attempts have been made
to comprehensively analyse vesicular
microRNAs (miRNAs) in patient biofluids for
biomarker studies. To address this
discrepancy, we set out to benchmark the
performance of several isolation principles
for serum EVs in healthy individuals and
critically ill patients. Here, we compared
five different methods of EV isolation in
combination with two RNA extraction methods
regarding their suitability for biomarker
discovery-focused miRNA sequencing as well
as biological characteristics of captured
vesicles. Our findings reveal striking
method-specific differences in both the
properties of isolated vesicles and the
ability of associated miRNAs to serve in
biomarker research. While isolation by
precipitation and membrane affinity was
highly suitable for miRNA-based biomarker
discovery, methods based on size-exclusion
chromatography failed to separate patients
from healthy volunteers. Isolated vesicles
differed in size, quantity, purity and
composition, indicating that each method
captured distinctive populations of EVs as
well as additional contaminants. Even though
the focus of this work was on transcriptomic
profiling of EV-miRNAs, our insights also
apply to additional areas of research. We
provide guidance for navigating the
multitude of EV isolation methods available
today and help researchers and clinicians
make an informed choice about which strategy
to use for experiments involving critically
ill patients.
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The impact of
disparate isolation methods for
extracellular vesicles on downstream RNA
profiling.
Van Deun J, Mestdagh P, Sormunen R, Cocquyt V,
Vermaelen K, Vandesompele J, Bracke M, De
Wever O, Hendrix A.
J Extracell Vesicles. 2014 Sep 18;3 --
eCollection 2014.
Despite
an enormous interest in the role of
extracellular vesicles, including exosomes,
in cancer and their use as biomarkers for
diagnosis, prognosis, drug response and
recurrence, there is no consensus on
dependable isolation protocols. We provide a
comparative evaluation of 4 exosome
isolation protocols for their usability,
yield and purity, and their impact on
downstream omics approaches for biomarker
discovery. OptiPrep density gradient
centrifugation outperforms
ultracentrifugation and ExoQuick and Total
Exosome Isolation precipitation in terms of
purity, as illustrated by the highest number
of CD63-positive nanovesicles, the highest
enrichment in exosomal marker proteins and a
lack of contaminating proteins such as
extracellular Argonaute-2 complexes. The
purest exosome fractions reveal a unique
mRNA profile enriched for translation,
ribosome, mitochondrion and nuclear lumen
function. Our results demonstrate that
implementation of high purification
techniques is a prerequisite to obtain
reliable omics data and identify
exosome-specific functions and biomarkers.
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Importance of
RNA isolation methods for analysis of
exosomal RNA -- evaluation of different
methods.
Eldh M, Lötvall J, Malmhäll C, Ekström K.
Mol Immunol. 2012 Apr;50(4): 278-86.
Exosomes
are small RNA containing vesicles of
endocytic origin, which can take part in
cell-to-cell communication partly by the
transfer of exosomal RNA between cells.
Exosomes are released by many cells and can
also be found in several biological fluids
including blood plasma and breast milk.
Exosomes differ compared to their donor
cells not only in size but also in RNA,
protein and lipid composition. The aim of
the current study was to determine the
optimal RNA extraction method for analysis
of exosomal RNA, to support future studies
determining the biological roles of the
exosomal RNA. Different methods were used to
extract exosomal and cellular RNA. All
methods evaluated extracted high quality and
purity RNA as determined by RNA integrity
number (RIN) and OD values for cellular RNA
using capillary electrophoresis and
spectrophotometer. Interestingly, the
exosomal RNA yield differed substantially
between the different RNA isolation methods.
There was also a difference in the exosomal
RNA patterns in the electropherograms,
indicating that the tested methods extract
exosomal RNA with different size
distribution. A pure column based approach
resulted in the highest RNA yield and the
broadest RNA size distribution, whereas
phenol and combined phenol and column based
approaches lost primarily large RNAs.
Moreover, the use of phenol and combined
techniques resulted in reduced yield of
exosomal RNA, with a more narrow size
distribution pattern resulting in an
enrichment of small RNA including microRNA.
In conclusion, the current study presents a
unique comparison of seven different methods
for extraction of exosomal RNA. As the
different isolation methods give extensive
variation in exosomal RNA yield and
patterns, it is crucial to select an
isolation approach depending on the research
question at hand.
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Selective
release of circRNAs in platelet-derived
extracellular vesicles.
Preußer C, Hung LH, Schneider T, Schreiner S,
Hardt M, Moebus A, Santoso S, Bindereif A
J Extracell Vesicles. 2018 Jan 15;7(1):1424473
Circular
RNAs (circRNAs) are a novel class of
noncoding RNAs present in all eukaryotic
cells investigated so far and generated by a
special mode of alternative splicing of
pre-mRNAs. Thereby, single exons, or
multiple adjacent and spliced exons, are
released in a circular form. CircRNAs are
cell-type specifically expressed, are
unusually stable, and can be found in
various body fluids such as blood and
saliva. Here we analysed circRNAs and the
corresponding linear splice isoforms from
human platelets, where circRNAs are
particularly abundant, compared with other
hematopoietic cell types. In addition, we
isolated extracellular vesicles from
purified and in vitro activated human
platelets, using density-gradient
centrifugation, followed by RNA-seq analysis
for circRNA detection. We could demonstrate
that circRNAs are packaged and released
within both types of vesicles (microvesicles
and exosomes) derived from platelets.
Interestingly, we observed a selective
release of circRNAs into the vesicles,
suggesting a specific sorting mechanism. In
sum, circRNAs represent yet another class of
extracellular RNAs that circulate in the
body and may be involved in signalling
pathways. Since platelets are essential for
central physiological processes such as
haemostasis, wound healing, inflammation and
cancer metastasis, these findings should
greatly extend the potential of circRNAs as
prognostic and diagnostic biomarkers.
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A comprehensive
method for identification of suitable
reference genes in extracellular vesicles.
Gouin K, Peck K, Antes T, Johnson JL, Li C,
Vaturi SD, Middleton R, de Couto G, Walravens
AS, Rodriguez-Borlado L, Smith RR, Marbán L,
Marbán E, Ibrahim AG
J Extracell Vesicles. 2017 6(1): 1347019 --
eCollection 2017
Reverse
transcription-quantitative polymerase chain
reaction (RT-qPCR) is one of the most
sensitive, economical and widely used
methods for evaluating gene expression.
However, the utility of this method
continues to be undermined by a number of
challenges including normalization using
appropriate reference genes. The need to
develop tailored and effective strategies is
further underscored by the burgeoning field
of extracellular vesicle (EV) biology. EVs
contain unique signatures of small RNAs
including microRNAs (miRs). In this study we
develop and validate a comprehensive
strategy for identifying highly stable
reference genes in a therapeutically
relevant cell type, cardiosphere-derived
cells. Data were analysed using the four
major approaches for reference gene
evaluation: NormFinder, GeNorm, BestKeeper
and the Delta Ct method. The weighted
geometric mean of all of these methods was
obtained for the final ranking. Analysis of
RNA sequencing identified miR-101-3p,
miR-23a-3p and a previously identified EV
reference gene, miR-26a-5p. Analysis of a
chip-based method (NanoString) identified
miR-23a, miR-217 and miR-379 as stable
candidates. RT-qPCR validation revealed that
the mean of miR-23a-3p, miR-101-3p and
miR-26a-5p was the most stable normalization
strategy. Here, we demonstrate that a
comprehensive approach of a diverse data set
of conditions using multiple algorithms
reliably identifies stable reference genes
which will increase the utility of gene
expression evaluation of therapeutically
relevant EVs.
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Exosomes
provide
a protective and enriched source
of miRNA for biomarker profiling
compared to intracellular and
cell-free blood.
Cheng L, Sharples RA, Scicluna BJ,
Hill AF
J Extracell Vesicles. 2014 Mar 26;3 --
eCollection 2014
INTRODUCTION:
microRNA (miRNA) are small non-coding
RNA species that are transcriptionally
processed in the host cell and
released extracellularly into the
bloodstream. Normally involved in
post-transcriptional gene silencing,
the deregulation of miRNA has been
shown to influence pathogenesis of a
number of diseases.
BACKGROUND:
Next-generation deep sequencing
(NGS) has provided the ability to
profile miRNA in biological fluids
making this approach a viable
screening tool to detect miRNA
biomarkers. However, collection and
handling procedures of blood needs to
be greatly improved for miRNA analysis
in order to reliably detect
differences between healthy and
disease patients. Furthermore,
ribonucleases present in blood can
degrade RNA upon collection rendering
extracellular miRNA at risk of
degradation. These factors have
consequently decreased sensitivity and
specificity of miRNA biomarker assays.
METHODS:
Here, we use NGS to profile
miRNA in various blood components and
identify differences in profiles
within peripheral blood compared to
cell-free plasma or serum and
extracellular vesicles known as
exosomes. We also analyse and compare
the miRNA content in exosomes prepared
by ultracentrifugation methods and
commercial exosome isolation kits
including treating samples with
RNaseA.
CONCLUSION:
This study demonstrates that exosomal
RNA is protected by RNaseA treatment
and that exosomes provide a consistent
source of miRNA for disease biomarker
detection. |
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Cellular and
extracellular miRNAs are
blood-compartment-specific diagnostic
targets in sepsis.
Reithmair M, Buschmann D, Märte M, Kirchner B,
Hagl D, Kaufmann I, Pfob M, Chouker A,
Steinlein OK, Pfaffl MW, Schelling G
J Cell Mol Med. 2017 21(10): 2403-2411
Septic
shock is a common medical condition with a
mortality approaching 50% where early
diagnosis and treatment are of particular
importance for patient survival. Novel
biomarkers that serve as prompt indicators
of sepsis are urgently needed.
High-throughput technologies assessing
circulating microRNAs represent an important
tool for biomarker identification, but the
blood-compartment specificity of these
miRNAs has not yet been investigated. We
characterized miRNA profiles from serum
exosomes, total serum and blood cells
(leukocytes, erythrocytes, platelets) of
sepsis patients by next-generation
sequencing and RT-qPCR (n = 3 × 22) and
established differences in miRNA expression
between blood compartments. In silico
analysis was used to identify
compartment-specific signalling functions of
differentially regulated miRNAs in
sepsis-relevant pathways. In septic shock, a
total of 77 and 103 miRNAs were down- and
up-regulated, respectively. A majority of
these regulated miRNAs (14 in serum, 32 in
exosomes and 73 in blood cells) had not been
previously associated with sepsis. We found
a distinctly compartment-specific regulation
of miRNAs between sepsis patients and
healthy volunteers. Blood cellular
miR-199b-5p was identified as a potential
early indicator for sepsis and septic shock.
miR-125b-5p and miR-26b-5p were uniquely
regulated in exosomes and serum,
respectively, while one miRNA (miR-27b-3p)
was present in all three compartments. The
expression of sepsis-associated miRNAs is
compartment-specific. Exosome-derived miRNAs
contribute significant information regarding
sepsis diagnosis and survival prediction and
could serve as newly identified targets for
the development of novel sepsis biomarkers.
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Toward reliable
biomarker signatures in the age of liquid
biopsies - how to standardize the small
RNA-Seq workflow.
Buschmann D, Haberberger A, Kirchner B,
Spornraft M, Riedmaier I, Schelling G, Pfaffl
MW
Nucleic Acids Res. 2016 44(13): 5995-6018
Small
RNA-Seq has emerged as a powerful tool in
transcriptomics, gene expression profiling
and biomarker discovery. Sequencing
cell-free nucleic acids, particularly
microRNA (miRNA), from liquid biopsies
additionally provides exciting possibilities
for molecular diagnostics, and might help
establish disease-specific biomarker
signatures. The complexity of the small
RNA-Seq workflow, however, bears challenges
and biases that researchers need to be aware
of in order to generate high-quality data.
Rigorous standardization and extensive
validation are required to guarantee
reliability, reproducibility and
comparability of research findings.
Hypotheses based on flawed experimental
conditions can be inconsistent and even
misleading. Comparable to the
well-established MIQE guidelines for qPCR
experiments, this work aims at establishing
guidelines for experimental design and
pre-analytical sample processing,
standardization of library preparation and
sequencing reactions, as well as
facilitating data analysis. We highlight
bottlenecks in small RNA-Seq experiments,
point out the importance of stringent
quality control and validation, and provide
a primer for differential expression
analysis and biomarker discovery. Following
our recommendations will encourage better
sequencing practice, increase experimental
transparency and lead to more reproducible
small RNA-Seq results. This will ultimately
enhance the validity of biomarker
signatures, and allow reliable and robust
clinical predictions.
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Exosomes -- A
Rising Star in Failing Hearts.
Jun-Yan Xu, Gui-Hao Chen and Yue-Jin Yang
Front Physiol. 2017 (8): 494
Although
exosomes were previously recognized as a
mechanism for discharging useless cellular
components, growing evidence has elucidated
their roles in conveying information between
cells. They contribute to cell–cell
communication by carrying nucleic acids,
proteins and lipids that can, in turn,
regulate behavior of the target cells.
Recent research suggested that exosomes
extensively participate in progression of
diverse cardiovascular diseases (CVDs), such
as myocardial infarction, cardiomyopathy,
pulmonary arterial hypertension and others.
Here, we summarize effects of
exosome-derived molecules (mainly microRNAs
and proteins) on cardiac function, to
examine their potential applications as
biomarkers or therapeutics in CVDs.
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The majority of
microRNAs detectable in serum and saliva
is concentrated in exosomes.
Gallo A, Tandon M, Alevizos I, Illei GG
PLoS One. 2012; 7(3): e30679
There
is an increasing interest in using microRNAs
(miRNA) as biomarkers in autoimmune
diseases. They are easily accessible in many
body fluids but it is controversial if they
are circulating freely or are encapsulated
in microvesicles, particularly exosomes. We
investigated if the majority of miRNas in
serum and saliva are free-circulating or
concentrated in exosomes. Exosomes were
isolated by ultracentrifugation from fresh
and frozen human serum and saliva. The
amount of selected miRNAs extracted from the
exosomal pellet and the exosome-depleted
serum and saliva was compared by
quantitative RT-PCR. Some miRNAs tested are
ubiquitously expressed, others were
previously reported as biomarkers. We
included miRNAs previously reported to be
free circulating and some thought to be
exosome specific. The purity of exosome
fraction was confirmed by electronmicroscopy
and western blot. The concentration of
miRNAs was consistently higher in the
exosome pellet compared to the
exosome-depleted supernatant. We obtained
the same results using an equal volume or
equal amount of total RNA as input of the
RT-qPCR. The concentration of miRNA in
whole, unfractionated serum, was between the
exosomal pellet and the exosome-depleted
supernatant. Selected miRNAs, which were
detectable in exosomes, were undetectable in
whole serum and the exosome-depleted
supernantant. Exosome isolation improves the
sensitivity of miRNA amplification from
human biologic fluids. Exosomal miRNA should
be the starting point for early biomarker
studies to reduce the probability of false
negative results involving low abundance
miRNAs that may be missed by using
unfractionated serum or saliva.
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http://evtrack.org
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EV-TRACK
-- transparent reporting and
centralizing knowledge in
extracellular vesicle research.
EV-TRACK Consortium, Van Deun J,
Mestdagh P, Agostinis P, ... and much
more, Vandesompele J, Hendrix A
Nat Methods. 2017 14(3): 228-232
We
argue that the field of
extracellular vesicle (EV) biology
needs more transparent reporting to
facilitate interpretation and
replication of experiments. To
achieve this, we describe EV-TRACK,
a crowdsourcing knowledgebase (http://evtrack.org)
that centralizes EV biology and
methodology with the goal of
stimulating authors, reviewers,
editors and funders to put
experimental guidelines into
practice.
Is
your article EV-TRACKed?
Van Deun J, Hendrix A, and the
EV-TRACK consortium
J Extracell Vesicles. 2017 Nov
10;6(1): 1379835 -- eCollection 2017
The EV-TRACK knowledgebase is
developed to cope with the need for
transparency and rigour to increase
reproducibility and facilitate
standardization of extracellular
vesicle (EV) research. The
knowledgebase includes a checklist
for authors and editors intended to
improve the transparency of
methodological aspects of EV
experiments, allows queries and
meta-analysis of EV experiments and
keeps track of the current state of
the art. Widespread implementation
by the EV research community is key
to its success.
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Distinct RNA
profiles in subpopulations of
extracellular vesicles -- apoptotic
bodies, microvesicles and exosomes.
Crescitelli R, Lässer C, Szabó TG, Kittel A,
Eldh M, Dianzani I, Buzás EI, Lötvall J
J Extracell Vesicles. 2013 2 -- eCollection
2013.
INTRODUCTION:
In recent years, there has been an
exponential increase in the number of
studies aiming to understand the biology of
exosomes, as well as other extracellular
vesicles. However, classification of
membrane vesicles and the appropriate
protocols for their isolation are still
under intense discussion and investigation.
When isolating vesicles, it is crucial to
use systems that are able to separate them,
to avoid cross-contamination.
METHOD: EVS RELEASED FROM THREE
DIFFERENT KINDS OF CELL LINES: HMC-1, TF-1
and BV-2 were isolated using two
centrifugation-based protocols. In protocol
1, apoptotic bodies were collected at
2,000×g, followed by filtering the
supernatant through 0.8 µm pores and
pelleting of microvesicles at 12,200×g. In
protocol 2, apoptotic bodies and
microvesicles were collected together at
16,500×g, followed by filtering of the
supernatant through 0.2 µm pores and
pelleting of exosomes at 120,000×g.
Extracellular vesicles were analyzed by
transmission electron microscopy, flow
cytometry and the RNA profiles were
investigated using a Bioanalyzer(®).
RESULTS: RNA profiles showed that
ribosomal RNA was primary detectable in
apoptotic bodies and smaller RNAs without
prominent ribosomal RNA peaks in exosomes.
In contrast, microvesicles contained little
or no RNA except for microvesicles collected
from TF-1 cell cultures. The different
vesicle pellets showed highly different
distribution of size, shape and electron
density with typical apoptotic body,
microvesicle and exosome characteristics
when analyzed by transmission electron
microscopy. Flow cytometry revealed the
presence of CD63 and CD81 in all vesicles
investigated, as well as CD9 except in the
TF-1-derived vesicles, as these cells do not
express CD9.
CONCLUSIONS: Our results demonstrate
that centrifugation-based protocols are
simple and fast systems to distinguish
subpopulations of extracellular vesicles.
Different vesicles show different RNA
profiles and morphological characteristics,
but they are indistinguishable using
CD63-coated beads for flow cytometry
analysis.
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Quantitative
and stoichiometric analysis of the
microRNA content of exosomes.
Chevillet JR, Kang Q, Ruf IK, Briggs HA,
Vojtech LN, Hughes SM, Cheng HH, Arroyo JD,
Meredith EK, Gallichotte EN,
Pogosova-Agadjanyan EL, Morrissey C, Stirewalt
DL, Hladik F, Yu EY, Higano CS, Tewari M
Proc Natl Acad Sci U S A. 2014 111(41):
14888-14893
Exosomes
have been proposed as vehicles for microRNA
(miRNA) -based intercellular communication
and a source of miRNA biomarkers in bodily
fluids. Although exosome preparations
contain miRNAs, a quantitative analysis of
their abundance and stoichiometry is
lacking. In the course of studying
cancer-associated extracellular miRNAs in
patient blood samples, we found that exosome
fractions contained a small minority of the
miRNA content of plasma. This low yield
prompted us to perform a more quantitative
assessment of the relationship between
miRNAs and exosomes using a stoichiometric
approach. We quantified both the number of
exosomes and the number of miRNA molecules
in replicate samples that were isolated from
five diverse sources (i.e., plasma, seminal
fluid, dendritic cells, mast cells, and
ovarian cancer cells). Regardless of the
source, on average, there was far less than
one molecule of a given miRNA per exosome,
even for the most abundant miRNAs in exosome
preparations (mean ± SD across six exosome
sources: 0.00825 ± 0.02 miRNA
molecules/exosome). Thus, if miRNAs were
distributed homogenously across the exosome
population, on average, over 100 exosomes
would need to be examined to observe one
copy of a given abundant miRNA. This
stoichiometry of miRNAs and exosomes
suggests that most individual exosomes in
standard preparations do not carry
biologically significant numbers of miRNAs
and are, therefore, individually unlikely to
be functional as vehicles for miRNA-based
communication. We propose revised models to
reconcile the exosome-mediated, miRNA-based
intercellular communication hypothesis with
the observed stoichiometry of miRNAs
associated with exosomes.
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The microRNA
spectrum in 12 body fluids.
Weber JA, Baxter DH, Zhang S, Huang DY, Huang
KH, Lee MJ, Galas DJ, Wang K.
Clin Chem. 2010 56(11): 1733-1741
BACKGROUND:
MicroRNAs
(miRNAs) are small, noncoding RNAs that play
an important role in regulating various
biological processes through their
interaction with cellular messenger RNAs.
Extracellular miRNAs in serum, plasma,
saliva, and urine have recently been shown
to be associated with various pathological
conditions including cancer.
METHODS: With the goal of assessing the
distribution of miRNAs and demonstrating the
potential use of miRNAs as biomarkers, we
examined the presence of miRNAs in 12 human
body fluids and urine samples from women in
different stages of pregnancy or patients
with different urothelial cancers. Using
quantitative PCR, we conducted a global
survey of the miRNA distribution in these
fluids.
RESULTS: miRNAs were present in all
fluids tested and showed distinct
compositions in different fluid types.
Several of the highly abundant miRNAs in
these fluids were common among multiple
fluid types, and some of the miRNAs were
enriched in specific fluids. We also
observed distinct miRNA patterns in the
urine samples obtained from individuals with
different physiopathological conditions.
CONCLUSIONS: MicroRNAs are ubiquitous
in all the body fluid types tested. Fluid
type-specific miRNAs may have functional
roles associated with the surrounding
tissues. In addition, the changes in miRNA
spectra observed in the urine samples from
patients with different urothelial
conditions demonstrates the potential for
using concentrations of specific miRNAs in
body fluids as biomarkers for detecting and
monitoring various physiopathological
conditions.
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Analysis of
extracellular RNA in cerebrospinal fluid.
Saugstad JA, Lusardi TA, Van Keuren-Jensen KR,
Phillips JI, Lind B, Harrington CA, McFarland
TJ, Courtright AL, Reiman RA, Yeri AS, Kalani
MYS, Adelson PD, Arango J, Nolan JP, Duggan E,
Messer K, Akers JC, Galasko DR, Quinn JF,
Carter BS, Hochberg FH
J Extracell Vesicles. 2017 6(1): 1317577
We
examined the extracellular vesicle (EV) and
RNA composition of pooled normal
cerebrospinal fluid (CSF) samples and CSF
from five major neurological disorders:
Alzheimer's disease (AD), Parkinson's
disease (PD), low-grade glioma (LGG),
glioblastoma multiforme (GBM), and
subarachnoid haemorrhage (SAH), representing
neurodegenerative disease, cancer, and
severe acute brain injury. We evaluated: (I)
size and quantity of EVs by nanoparticle
tracking analysis (NTA) and vesicle flow
cytometry (VFC), (II) RNA yield and purity
using four RNA isolation kits, (III)
replication of RNA yields within and between
laboratories, and (IV) composition of total
and EV RNAs by reverse
transcription-quantitative polymerase chain
reaction (RT-qPCR) and RNA sequencing
(RNASeq). The CSF contained ~106 EVs/μL by
NTA and VFC. Brain tumour and SAH CSF
contained more EVs and RNA relative to
normal, AD, and PD. RT-qPCR and RNASeq
identified disease-related populations of
microRNAs and messenger RNAs (mRNAs)
relative to normal CSF, in both total and EV
fractions. This work presents relevant
measures selected to inform the design of
subsequent replicative CSF studies. The
range of neurological diseases highlights
variations in total and EV RNA content due
to disease or collection site, revealing
critical considerations guiding the
selection of appropriate approaches and
controls for CSF studies.
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Deep sequencing
of RNA from three different extracellular
vesicle (EV) subtypes released from the
human LIM1863 colon cancer cell line
uncovers distinct miRNA-enrichment
signatures.
Ji H, Chen M, Greening DW, He W, Rai A, Zhang
W, Simpson RJ
PLoS One. 2014 9(10): e110314 -- eCollection
2014.
Secreted
microRNAs (miRNAs) enclosed within
extracellular vesicles (EVs) play a pivotal
role in intercellular communication by
regulating recipient cell gene expression
and affecting target cell function. Here, we
report the isolation of three distinct EV
subtypes from the human colon carcinoma cell
line LIM1863--shed microvesicles (sMVs) and
two exosome populations (immunoaffinity
isolated A33-exosomes and EpCAM-exosomes).
Deep sequencing of miRNA libraries prepared
from parental LIM1863 cells/derived EV
subtype RNA yielded 254 miRNA
identifications, of which 63 are selectively
enriched in the EVs--miR-19a/b-3p,
miR-378a/c/d, and miR-577 and members of the
let-7 and miR-8 families being the most
prominent. Let-7a-3p*, let-7f-1-3p*,
miR-451a, miR-574-5p*, miR-4454 and miR-7641
are common to all EV subtypes, and 6 miRNAs
(miR-320a/b/c/d, miR-221-3p, and
miR-200c-3p) discern LIM1863 exosomes from
sMVs; miR-98-5p was selectively represented
only in sMVs. Notably, A33-Exos contained
the largest number (32) of
exclusively-enriched miRNAs; 14 of these
miRNAs have not been reported in the context
of CRC tissue/biofluid analyses and warrant
further examination as potential diagnostic
markers of CRC. Surprisingly, miRNA
passenger strands (star miRNAs) for
miR-3613-3p*, -362-3p*, -625-3p*, -6842-3p*
were the dominant strand in A33-Exos, the
converse to that observed in parental cells.
This finding suggests miRNA biogenesis may
be interlinked with endosomal/exosomal
processing.
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Secreted
microRNAs -- a new form of intercellular
communication.
Chen X, Liang H, Zhang J, Zen K, Zhang CY.
Trends Cell Biol. 2012 22(3):125-32
In
multicellular organisms, cell-to-cell
communication is of particular importance
for the proper development and function of
the organism as a whole. Intensive studies
over the past three years suggesting
horizontal transfer of secreted microRNAs
(miRNAs) between cells point to a
potentially novel role for these molecules
in intercellular communication. Using a
microvesicle-dependent, or RNA-binding
protein-associated, active trafficking
system, secreted miRNAs can be delivered
into recipient cells where they function as
endogenous miRNAs, simultaneously regulating
multiple target genes or signaling events.
In this Opinion, we summarize recent
literature on the biogenesis and uptake of
secreted miRNAs, propose a possible working
model for how secreted miRNAs might be
sorted and transferred between cells and
speculate on their biological significance.
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Characterization
of mRNA and microRNA in human mast
cell-derived exosomes and their transfer
to other mast cells and blood CD34
progenitor cells.
Ekström K, Valadi H, Sjöstrand M, Malmhäll C,
Bossios A, Eldh M, Lötvall J.
J Extracell Vesicles. 2012; 1 -- eCollection
2012
BACKGROUND: Exosomes
are
nanosized vesicles of endocytic origin that
are released into the extracellular
environment by many different cells. It has
been shown that exosomes from various
cellular origins contain a substantial
amount of RNA (mainly mRNA and microRNA).
More importantly, exosomes are capable of
delivering their RNA content to target
cells, which is a novel way of cell-to-cell
communication. The aim of this study was to
evaluate whether exosomal shuttle RNA could
play a role in the communication between
human mast cells and between human mast
cells and human CD34(+) progenitor cells.
METHODS:
The mRNA and microRNA content of
exosomes from a human mast cell line, HMC-1,
was analysed by using microarray technology.
Co-culture experiments followed by flow
cytometry analysis and confocal microscopy
as well as radioactive labeling experiments
were performed to examine the uptake of
these exosomes and the shuttle of the RNA to
other mast cells and CD34(+) progenitor
cells.
RESULTS:
In this study, we show that human mast cells
release RNA-containing exosomes, with the
capacity to shuttle RNA between cells.
Interestingly, by using microRNA microarray
analysis, 116 microRNAs could be identified
in the exosomes and 134 microRNAs in the
donor mast cells. Furthermore, DNA
microarray experiments revealed the presence
of approximately 1800 mRNAs in the exosomes,
which represent 15% of the donor cell mRNA
content. In addition, transfer experiments
revealed that exosomes can shuttle RNA
between human mast cells and to CD34(+)
hematopoietic progenitor cells.
CONCLUSION:
These findings suggest that exosomal
shuttle RNA (esRNA) can play a role in the
communication between cells, including mast
cells and CD34(+) progenitor cells, implying
a role in cells maturation process.
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... more papers in the next months
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