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Methods in
Molecular Biology 2504
Maurizio Federico
Barbara Ridolfi Editors
Extracellular
Vesicles in Diagnosis
and Therapy
METHODS IN MOLECULAR BIOLOGY
Series Editor
John M. Walker
School of Life and Medical Sciences
University of Hertfordshire
Hatfield, Hertfordshire, UK
Edited by
This Humana imprint is published by the registered company Springer Science+Business Media, LLC, part of Springer
Nature.
The registered company address is: 1 New York Plaza, New York, NY 10004, U.S.A.
Dedication
v
Preface
vii
viii Preface
EVs are provided. This section is opened by a review from Chiozzini and colleagues offering
a comparative analysis of EV-based versus other nanovesicle-based methods in terms of
antigen delivery to induce immunity. Dieterich and colleagues then describe a protocol for
fluorescently labeling the membrane of tumor EVs, whereas Manfredi and colleagues
propose a way to incorporate fluorescent proteins into the EV lumen. Finally, two different
methods to upload miRNAs and other nucleic acids are provided by Pomatto and colleagues
and Jeyaram and colleagues, respectively.
Overall, this book provides an exhaustive picture of current methods to detect, isolate,
and analyze EVs from diverse sources. In addition, the methods of EV labeling and
macromolecule uploading would be of outmost utility for the study of still incompletely
known EV processes (i.e., cell attachment, cell entry, fate of EV cargo) as well as for the use
of EVs as immunogens/therapeutics.
Clearly, EVs have been proven to have great potentialities as disease biomarkers as well as
delivery tools of therapeutic/immunogenic molecules. Recent advances pave the way for a
wide use of EVs in both diagnosis and therapy. Protocols included in the present volume are
expected to be of great utility to further enlarge the number of scientists interested in EV
research.
Dedication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xi
ix
x Contents
PART IV EV ENGINEERING
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 241
Contributors
xi
xii Contributors
Abstract
Cancerous exosomes that carry multiple biomarkers are attractive targets for the early diagnosis and therapy
of cancer. As one of the powerful molecular recognition tools, aptamers with excellent binding affinity and
specificity toward biomarkers have been exploited to construct various aptamer-based biosensors (aptasen-
sors) for exosome detection. Here, we review recent advances in aptasensors for the detection of cancerous
exosomes. We first discuss the importance and potential of cancerous exosomes in cancer diagnosis and then
summarize some conventional aptasensors from the perspective of biomarker recognition and signal
collection strategies. Finally, we comment on the outlook for aptasensor research and new directions for
cancerous exosome detection.
Key words Cancerous exosome, Aptamer, Early diagnosis, Aptasensor, Exosome detection
Maurizio Federico and Barbara Ridolfi (eds.), Extracellular Vesicles in Diagnosis and Therapy,
Methods in Molecular Biology, vol. 2504, https://doi.org/10.1007/978-1-0716-2341-1_1,
© The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2022
3
4 Jin Li et al.
Table 1
Summary of cancerous protein target and corresponding aptamers
Protein
target Aptamer Cell type References
CD24 CD24A_2 HT29 [26]
CD63 LL4A, CD63-1 Melanoma cells, MDA-MB-231, HT29, [27–30]
MCF-7, HepG2
PD-L1 aptPD-L1, XQ-P3 A549, MDA-MB-231 [31]
EGFR CL4, GR200, TuTu22 A549, A431, U87, U251 [32, 33]
HER2 Aptamers 2-2, Heraptamer N87, SKOV3 [34, 35]
EpCAM 19-nt RNA aptamer, Ep1 Breast, colorectal, gastric cancer cells [36]
aptamer
PSMA xPSM aptamer PSMA-expressing LNCaP cells [37]
PTK7 sgc8 CCRF-CEM cells [23]
CEA YJ-1 CEA-positive cell lines [38]
MUC1 S1.3, 5TR1, GalNAc3 MUC1-positive cell lines [39]
aptamers
AFP AP273 HepG2 [40]
HSP70 A8 Breast, lung, ovarian cancer cells [41]
3.1 Fluorescent Fluorescence imaging has the advantages of high sensitivity and
Aptasensor-Based reliability, noninvasiveness, and short-term analysis and is, there-
Methods fore, the most commonly used method in exosome detection
[50, 51]. Fluorescent aptasensors can be easily constructed by
integrating aptamers with fluorescent dyes, quantum dots, upcon-
version nanoparticles, or other fluorescent materials. For example,
Zhang et al. designed an “on-off”-type aptasensor for detecting
cancer exosomes (Fig. 1a) [52]. A TAMRA fluorophore and a
Dabcyl quencher were labeled at the two ends of the hairpin-like
aptamer, respectively. In the absence of tumor exosomes (TEX), the
fluorescence generated by TAMRA was quenched by the
6 Jin Li et al.
Fig. 1 Aptasensor-based fluorescent platform for exosome detection. (a) Fluorescence resonance energy
transfer (FRET)-based aptasensor for exosome detection, reproduced from Zhang 2018 with permission from
Elsevier [52]. (b) HCR-based signal amplification and detection of exosomes [53]. (c) Exosome detection based
on nuclease-assisted signal amplification, reproduced from Wang 2018 with permission from Elsevier [54]. (d)
Identifying exosomes with a FP-based aptasensor, reproduced from Zhang 2019 with permission from Royal
Society of Chemistry [55]
Fig. 2 Aptasensor-based electrochemical platform for exosome detection. (a) NTH-assisted aptasensor for
exosome detection, reproduced from Wang 2017 with permission from American Chemical Society [61]. (b)
HCR-based signal amplification and detection of exosomes, reproduced from An 2019 with permission from
Elsevier [62]. (c) RCA-based signal amplification and detection of exosomes [63]. (d) Dual-amplified-based
aptasensor for exosome detection, reproduced from Zhao 2019 with permission from American Chemical
Society [64]
exosomes derived from MCF-7 cells (Fig. 2b) [62]. In this design,
CD63 aptamers were immobilized onto glassy carbon electrodes to
capture exosomes. Then, a DNA initiator was anchored to the
captured exosomes to initiate HCR between two biotin-labeled
DNA monomers. Finally, horseradish peroxidase (HRP) was com-
bined with the HCR products through interactions between biotin
and streptavidin. HRP could catalyze the oxidation of
o-phenylenediamine (OPD) to obtain detectable electrical signals,
thus identifying exosomes. By using this HCR-based amplification
strategy, exosomes could be detected with a LOD of 9.6 101
particles μL1. The ability of this HCR-based electrochemical apta-
sensor to detect exosomes in serum samples has also been proved.
In another work, Huang et al. constructed an RCA-based
electrochemical aptasensor for detecting gastric cancer exosomes
(Fig. 2c) [63]. In this work, anti-CD63 antibodies were immobi-
lized onto gold electrodes to capture exosomes. MUC1 aptamers
bound to the captured exosomes and subsequently triggered RCA
to generate a range of G-quadruplex-hemin complexes. The G-
quadruplex-hemin complexes catalyzed the reduction of H2O2 to
10 Jin Li et al.
3.3 Colorimetric Colorimetric sensors have been widely used in bioanalysis for their
Aptasensor-Based simplicity and ability to convert sample data into a signal readable
Methods by the naked eye. Thus far, several colorimetric aptasensors have
been constructed for exosome detection [49, 65]. Xia et al. con-
structed a single-walled carbon nanotubes (s-SWCNTs)-based col-
orimetric aptasensor to detect exosomes derived from MCF-7 cells
(Fig. 3a) [66]. In this design, CD63 aptamers able to improve the
peroxidase activity of s-SWCNTs were first absorbed onto
s-SWCNTs. The absorbed s-SWCNTs could then efficiently cata-
lyze the oxidation of 3,30 ,5,50 -tetramethylbenzidine (TMB) to
generate a large number of products with blue color. In the pres-
ence of exosomes, CD63 aptamers specifically bound to exosomes,
and their release from s-SWCNTs led to a decrease in peroxidase
activity of s-SWCNTs. As a consequence, fewer products with blue
Aptasensors for Cancerous Exosome Detection 11
Fig. 3 Aptasensor-based colorimetric platform for exosome detection. (a) s-SWCNTs-based aptasensor for
exosome detection, reproduced from Xia 2017 with permission from Elsevier [66]. (b) Multicolor detection
platform for visual detection of exosomes, reproduced from Zhang 2019 with permission from American
Chemical Society [67]. (c) Profiling the membrane proteins of exosomes with Aptamer/AuNP sensing platform,
reproduced from Jiang 2017 with permission from Wiley [68]
Fig. 4 (a) SPR-based, dual-amplification aptasensor for exosome detection, reproduced from Wang 2019 with
permission from Elsevier [27]. (b) Identifying exosomes with a SERS-based aptasensor, reproduced from
Wang 2018 with permission from Royal Society of Chemistry [72]. (c) Exosome detection based on AuNPs-
MXenes-Apt nanoprobes, reproduced from Zhang 2020 with permission from American Chemical Society [73]
Fig. 5 (a) Thermophoresis-based aptasensor for cancer diagnosis [74]. (b) Aptasensor-based nanoplatform for
cancer diagnosis, reproduced from Li 2019 with permission from American Chemical Society [75]. (c)
Thermophoretic aptasensor for cancer screening and classification, reproduced from Liu 2019 with permis-
sion from Springer Nature [76]
the diluted serum sample and the mixture was then locally heated
with an infrared laser to accumulate extracellular vesicles and
obtained a detectable fluorescence signal. Then, the surface pro-
teins of extracellular vesicles could be profiled by detecting the
fluorescence signal. Importantly, this isolation-free, small-volume
(<1 μL serum sample), low-cost, and noninvasive extracellular
vesicle detection strategy had been used to detect and classify
6 types of cancers, and to distinguish prostate cancer from benign
disease. These results indicate that this thermophoretic aptasensor
has great potential in the early screening and classification of
cancers.
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Chapter 2
Abstract
Exosomes are a type of extracellular vesicles that contain constituents including proteins, DNAs, and RNAs
of the cells that secrete them. Cancerous exosomes are potential biomarkers for cancer diagnosis. Biosensors
are useful analytical tools for quantification of biomarkers and targeted molecules. An aptasensor uses the
aptamer as the biorecognition element to bind to the target and is one main type of biosensors that is
promising for exosomes analysis and clinical cancer detection. The assay described in this chapter allows for
reliable, sensitive, and specific detection of cancer-derived exosomes using a colorimetric aptasensor that is
promising for point-of-care testing.
1 Introduction
Maurizio Federico and Barbara Ridolfi (eds.), Extracellular Vesicles in Diagnosis and Therapy,
Methods in Molecular Biology, vol. 2504, https://doi.org/10.1007/978-1-0716-2341-1_2,
© The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2022
21
22 Lizhou Xu and Khuloud T. Al-Jamal
Fig. 1 Schematic illustration of the principle of a colorimetric aptasensor for the sensitive detection of cancer-
derived exosomes
2 Materials
Prepare all solutions used in this work using the deionized water
(18 MΩ-cm at 25 C) and analytical grade reagents. Store all
reagents and as-prepared solutions in the fridge at 4 C (unless
indicated otherwise). When disposing off waste materials, please
follow all waste disposal regulations.
2.1 Preparation of Prepare exosomes samples from tissue culture according to Xu et al.
Exosomes Stock [12, 19, 20] or Faruqu et al. [21], or use a commercial exosomes
Solution isolation kit. Prepare the exosomes samples in PBS solution (see
below) at a certain concentration as the stock (see Note 1). Store
the exosomes stock at 80 C for long term or 4 C for short term.
3 Methods
3. Add sterile PBS to top up to 1 mL. Mix gently using the pipette
and incubate for 60 min at room temperature with mild
agitation.
3. Gently transfer the solution to a 5 mL Falcon® Round-Bottom
Polystyrene Tubes using an appropriate pipette, e.g., p1000
(see Note 8).
4. Pellet the beads with centrifugation at 4 C for 5 min at
580 g.
5. Carefully remove the supernatant using an appropriate pipette,
e.g., p200 (see Note 9).
6. Add 1 mL of 100 mM glycine buffer in PBS to the sample tube,
mix gently using the pipette, and incubate for 30 min at room
temperature with mild agitation.
3.3 Quantification of 1. When incubation period finishes, observe the final color of the
Color Intensity samples directly by naked eye and make reasonable comparison
to estimate the CD63 expression level on exosomes (see
Note 12).
2. To obtain the absorbance spectra and quantitative data, transfer
100 μL of the sample using an appropriate pipette, e.g., p200,
26 Lizhou Xu and Khuloud T. Al-Jamal
3.4 Data Analysis The final signal intensity for a sample should be the absorbance
reading subtracted by the background noise. This resulting (rela-
3.4.1 Analyze the Final
tive) signal intensity represents the exosomes marker (CD63 in this
Result of a Sample
case) expression level in the correlating sample tested (Fig. 2). The
final detection result can also be visualized qualitatively by naked
eye for each sample (Fig. 3).
3.4.2 Establish a 1. Detect a serial samples with different exosomes stock concen-
Calibration Curve trations (which means different surface marker amount) using
the proposed aptasensor method.
2. Record the final absorbance signal for all the samples (see
Subheading 3.4.1).
3. Then plot the data between the log value of known exosomes
concentration (X-axis) and the final absorbance signal intensity
of the correlating exosomes samples (Y-axis). Build a calibra-
tion curve using the fitting function in the software.
Fig. 2 Detection of CD63 amount on exosomes from P04.03 cancer cells using
the aptasensor. The calibration curve was obtained by plotting the color signal
intensity over a serial concentrations of exosomes samples tested (4.3 103,
4.3 105, 4.3 107, 4.3 109, 4.3 1011 particles/mL). The limit of
detection (LOD, dashed line) was established at 1.583, which were expressed
as mean 3 SD (n ¼ 3) of the blank control sample (without exosomes) (see
Note 14)
Colorimetric Aptasensor for Sensitive Exosome Detection 27
3.4.3 Detect an Unknown 1. Test an unknown sample by using the sample protocol.
Sample 2. Analyze the final absorbance signal results of the unknown
testing sample as described in Subheading 3.4.1.
3. Fit the final absorbance signal into the calibration curve
(Y-axis) and obtain the corresponding exosomes concentration
of the tested samples. This result suggests the surface CD63
expression level in this tested sample.
4. In the case of clinical testing, first measure the exosomes
marker expression level by using this aptasensor assay. Then
obtain the final result for each sample. At last, compare the
results between healthy control samples and patient samples.
4 Notes
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Chapter 3
Abstract
Circulating extracellular vesicles (EVs) are gaining increased attention as carriers of proteins, nucleic acids,
and lipids. Blood contains EVs from different cell sources that constitute an attractive target for biomarker
studies. However, there is no consensus on the best approach to isolate EVs from blood. Non-EV proteins
and lipoproteins in plasma/serum tend to contaminate isolated EVs and confound functional experiments.
Here we describe a single-step, high-performance size-exclusion chromatography procedure for separation
of EVs from most lipoproteins and non-EV proteins, and compare it to ultracentrifugation, still the most
commonly used method for EV isolation.
Key words Extracellular vesicles, Exosomes, Size-exclusion chromatography, HPLC, Plasma, Lipo-
proteins, Proteomics
1 Introduction
Maurizio Federico and Barbara Ridolfi (eds.), Extracellular Vesicles in Diagnosis and Therapy,
Methods in Molecular Biology, vol. 2504, https://doi.org/10.1007/978-1-0716-2341-1_3,
© The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2022
31
32 Kaloyan Takov et al.
(C - 0.01)t = K
where C is the concentration observed for a given time
t
. K has the approximate value of 1.7, where
t
varies between 7.5 and 480 minutes.
Vesicant Action
In addition to its toxicity mustard gas is highly important because of
its peculiar irritating effect upon the skin. Its value is seen when we
realize that one part in 14,000,000 is capable of causing conjunctivitis
of the eye and that one part in 3,000,000 and possibly one part in
5,000,000 will cause a skin burn in a sensitive person on prolonged
exposure. According to Warthin, the lesions produced by mustard gas
are those of a chemical, not unlike hydrochloric acid, but of much
greater intensity. The pathology of these lesions has been carefully
studied and fully described by Warthin and Weller in their book on The
Pathology of Mustard Gas. Our observations will therefore be confined
to certain striking features of the vesicant action of this substance.
Diphenylchloroarsine
The best known of the arsenicals, however, is
diphenylchloroarsine or sneezing gas. Although this is an old
compound (having been prepared by German chemists in 1885),
there was no method for its preparation on a large scale when, first
introduced into chemical warfare. It was finally discovered that the
interaction of triphenyl arsine with arsenic trichloride was fairly
satisfactory and a plant was erected for its manufacture.
When pure, diphenylchloroarsine is a colorless solid, melting at
44°. Because of this, it was always used in solution in a toxic gas or
in a shell which contained a large amount of explosive so that on the
opening of the shell the material would be finely divided and
scattered over a wide territory.
Its value lay in the fact that the fine particles readily penetrated
the ordinary mask and caused the irritation of the nose and throat,
which resulted in sneezing. This necessitated the perfection of
special smoke filters to remove the particles, after which the other
toxic materials were removed by the absorbent in the canister.
It causes sneezing and severe burning sensations in the nose,
throat and lungs in concentrations as slight as 1 part in 10 million. In
higher concentrations, say 1 in 200 to 500 thousand it causes severe
vomiting. While neither of these effects are dangerous or very
lasting, still higher concentrations are serious, as in equal
concentrations diphenylchloroarsine is more poisonous than
phosgene.
Various other arsenical chemicals were developed in the
laboratory, but with one or two exceptions they were not as valuable
as diphenylchloroarsine and methyldichloroarsine and were
therefore discarded.
Diphenylchloroarsine
C₆H₅N₂Cl + C₆H₅AsO₃Na₂ +
=
Na₃AsO₃ NaCl + N₂
C₆H₅AsO₃Na₂ + C₆H₅AsO₃H₂ +
=
2HCl 2NaCl
C₆H₅AsO₃H₂ + C₆H₅AsO₂H₂ +
=
SO₂+H₂O H₂SO₄
C₆H₅N₂Cl + (C₆H₅)₂AsO₂Na +
=
C₆H₅AsO₂Na₂ NaCl + N₂
(C₆H₅)₂AsO₂Na + (C₆H₅)₂AsO₂H +
=
HCl NaCl
2(C₆H₅)₂AsO₂H + [(C₆H₅)₂As]₂O +
=
2SO₂ + H₂O 2H₂SO₄
[(C₆H₅)₂As]₂O + 2(C₆H₅)₂AsCl +
=
2HCl H₂O.
“The entire process was carried out at Höchst.
The method used at Höchst was as follows: In
preparing the diazonium solution, 3 kg.-mols of
aniline were dissolved in 3000 liters of water and the
theoretical quantity of hydrochloric acid. The
temperature of the solution was reduced to between
0° and 5° and the theoretical amount of sodium
nitrite added. The reaction was carried out in a
wooden tank of the usual form for the preparation of
diazonium compounds. A solution of sodium
arsenite was prepared which contained 20 per cent
excess of oxide over that required to react with the
aniline used. The arsenous oxide was dissolved in
sodium carbonate, care being taken to have enough
of the alkali present to neutralize all of the acid
present in the solution of the diazonium salt. To the
solution of the sodium arsenite were added 20 kg. of
copper sulfate dissolved in water, this being the
amount required when 3 kg.-mols of aniline are
used. The solution of the diazonium compound was
allowed to flow slowly into the solution of the
arsenite while the temperature was maintained at
15°. The mixture was constantly stirred during the
addition which requires about 3 hrs. After the
reaction was complete, the material was passed
through a filter press in order to remove the coupling
agent and the tar which had been formed.
Hydrochloric acid was next added to the clear
solution to precipitate phenylarsenic acid, the last
portions of which were removed by the addition of
salt.
“The phenylarsenic acid was next reduced to
phenylarsenous acid by means of a solution of
sodium bisulfite, about 20 per cent excess of the
latter over the theoretical amount being used. For
100 parts of arsenic acid, 400 parts of solution were
used. The reaction was carried out in a wooden
vessel and the mixture stirred during the entire
operation. A temperature of 80° was maintained by
means of a steam coil. Phenylarsenous acid
separated as an oil. The aqueous solution was
decanted from the oil, which was dissolved in a
solution of sodium hydroxide, 40° Bé. The solution
of the sodium salt of phenylarsenous acid was
treated with water so that the resulting solution had
a volume of 6 cu. m. when 3 kg.-mols of the salt
were present. Ice was next added to reduce the
temperature to 15° and a solution of benzene
diazonium chloride, prepared in the manner
described for the first operation, was slowly added.
After the coupling, diphenylarsenic acid was
precipitated by means of hydrochloric acid. The acid
was removed by means of a filter press and
dissolved in hydrochloric acid, 20° Bé. For one part
of diphenylarsenic acid, 3 parts of hydrochloric acid
were used. Into this solution was passed 5 per cent
excess of sulfur dioxide over that required for the
reduction. The sulfur dioxide used was obtained
from cylinders which contained it in liquid condition.
“The reduction was carried out in an iron tank
lined with tiles and a temperature of 80° was
maintained. About 8 hrs. were required for the
reaction. The diphenylarsenic acid on reduction by
the sulfur dioxide was converted into
diphenylarsenous oxide which, in the presence of
the hydrochloric acid, was converted into
diphenylchloroarsine, which separated as an oil.
The oil was next removed and heated in the best
vacuum obtainable until it was dry and free from
hydrochloric acid. The compound melted at 34°. It
was placed in iron tanks for shipment. The yield of
diphenylchloroarsine calculated from the aniline
used was from 25 to 30 per cent of the theoretical.
No marked trouble was observed in handling the
materials and no serious poisoning cases were
reported.
Diphenylcyanoarsine
Ethyldichloroarsine