Tugba Kilic1,2, Young Kwan Cho1,3, Naebong Jeong1, Ik-Soo Shin4, Bob S Carter5, Leonora Balaj5, Ralph Weissleder1,2,6, Hakho Lee1,2. 1. Center for Systems Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States. 2. Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States. 3. Department of Chemistry, Kennedy College of Sciences, University of Massachusetts Lowell, Lowell, Massachusetts 01854, United States. 4. Department of Chemistry, Soongsil University, Seoul 06978, South Korea. 5. Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States. 6. Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States.
Abstract
Detecting protein markers in extracellular vesicles (EVs) is becoming a useful tool for basic research and clinical diagnoses. Most EV protein assays, however, require lengthy processes-conjugating affinity ligands onto sensing substrates and affixing EVs with additional labels to maximize signal generation. Here, we present an iPEX (impedance profiling of extracellular vesicles) system, an all-electrical strategy toward fast, multiplexed EV profiling. iPEX adopts one-step electropolymerization to rapidly functionalize sensor electrodes with antibodies; it then detects EV proteins in a label-free manner through impedance spectroscopy. The approach streamlines the entire EV assay, from sensor preparation to signal measurements. We achieved (i) fast immobilization of antibodies (<3 min) per electrode; (ii) high sensitivity (500 EVs/mL) without secondary labeling; and (iii) parallel detection (quadruple) in a single chip. A potential clinical utility was demonstrated by directly analyzing plasma samples from glioblastoma multiforme patients.
Detecting protein markers in extracellular vesicles (EVs) is becoming a useful tool for basic research and clinical diagnoses. Most EV protein assays, however, require lengthy processes-conjugating affinity ligands onto sensing substrates and affixing EVs with additional labels to maximize signal generation. Here, we present an iPEX (impedance profiling of extracellular vesicles) system, an all-electrical strategy toward fast, multiplexed EV profiling. iPEX adopts one-step electropolymerization to rapidly functionalize sensor electrodes with antibodies; it then detects EV proteins in a label-free manner through impedance spectroscopy. The approach streamlines the entire EV assay, from sensor preparation to signal measurements. We achieved (i) fast immobilization of antibodies (<3 min) per electrode; (ii) high sensitivity (500 EVs/mL) without secondary labeling; and (iii) parallel detection (quadruple) in a single chip. A potential clinical utility was demonstrated by directly analyzing plasma samples from glioblastoma multiforme patients.
Extracellular vesicles
(EVs) have gained traction as a new class
of soluble biomarkers. Present in most bodily fluids (e.g., blood,
cerebrospinal fluid, urine, saliva), EVs carry molecular constituents
of parental tumor and host cells. Analyzing EVs can enable clinicians
to detect and monitor tumors in real time, while minimizing complications
from specimen collection.[1−3] Profiling EV proteins, in particular,
has been shown to achieve high diagnostic accuracy by targeting tumor-specific
antigens,[4−6] identify tumor origins or subtypes based on the EV-protein
signature,[7−10] and distinguish between indolent and high-risk lesions.[11] New assay formats have been developed to facilitate
such EV-protein detection, many of which demonstrated high analytical
sensitivity and throughput (see Table S1 for a comparison of methods).[6,12−20] These new systems, however, still have practical limitations in
clinical environments: (i) Essentially based on immunodetection, test
systems require lengthy preparation steps of immobilizing affinity
ligands on sensing devices. (ii) Secondary labeling is often necessary
to generate an analytical signal (e.g., sandwich-type assay). (iii)
Scaling up assays for parallel multiplexing can be complex.Here, we present an iPEX (impedance profiling of extracellular
vesicles) approach to fast, sensitive, and parallel EV detection.
We hypothesized that electrochemistry can be used to streamline the
entire EV assay, from sensor preparation to signal measurements. Specifically,
we adopted electropolymerization to prime electrodes for target-specific
EV capture and electrochemical impedance spectroscopy for label-free
EV detection. Electropolymerization enables fast, one-step deposition
of polymers on electrodes.[21,22] We applied the method
to rapidly immobilize antibodies on a custom-designed iPEX chip. Furthermore,
through a selective application of electrical potential, multiple
electrodes were individually functionalized, each with antibodies
against a different protein target; the prepared iPEX chip allowed
for parallel detection of multiple markers. For subsequent EV assays,
we used an iPEX chip to capture EVs and measured changes in electrochemical
impedance. The iPEX approach offered the advantages of (i) fast immobilization
of antibodies (<3 min) on electrodes; (ii) high sensitivity (∼500
EVs/mL) without the need for a secondary labeling; and (iii) multimarker
detection in a single chip. As a pilot clinical application, we used
iPEX to directly analyze plasma samples from healthy donors (n = 10) and glioblastoma (GBM) patients (n = 10).
Results and Discussion
iPEX Strategy
Figure summarizes the iPEX workflow. To prepare
sensors for
EV detection, we immobilized capture antibodies on the electrode surface
through simple electropolymerization (Figure A). A mixture of antibodies and pyrrole (Py)
monomers was added to a given electrode, and an electrical potential
was applied to induce a polymerization reaction (see the Experimental Section for details).[22] During Py polymerization into polypyrrole (PPy), antibodies
were entrapped in the polymer matrix. For EV profiling, we flood-loaded
samples over an electrode array to target-specifically capture EVs
on individual electrodes (Figure B). Captured EVs changed the charge transfer resistance
of the electrochemical reaction, which was measured via impedance
spectroscopy. To further increase the resistance signal, antibodies
against tetraspanins (e.g., CD63, CD9, or CD81), which are overexpressed
in EVs, could be introduced as an optional, secondary label.
Figure 1
iPEX strategy.
(A) Surface functionalization. A mixture of antibodies
and pyrrole was drop-cast onto electrodes. Performing cyclic voltammetry
coated a select electrode with antibodies through electrochemical
polymerization. The process was repeated for other electrodes with
new pyrrole–antibody mixtures. (B) Label-free detection of
extracellular vesicles (EVs). An EV sample was loaded over functionalized
electrodes, and the electrochemical impedance of each electrode was
measured using a ferri- and ferrocyanide couple as a redox probe.
(C) An iPEX chip for quadruple measurements was custom-designed. Four
working electrodes (carbon) were individually addressed during measurements,
whereas the reference electrode (Ag/AgCl) and the counter electrode
(carbon) were shared.
iPEX strategy.
(A) Surface functionalization. A mixture of antibodies
and pyrrole was drop-cast onto electrodes. Performing cyclic voltammetry
coated a select electrode with antibodies through electrochemical
polymerization. The process was repeated for other electrodes with
new pyrrole–antibody mixtures. (B) Label-free detection of
extracellular vesicles (EVs). An EV sample was loaded over functionalized
electrodes, and the electrochemical impedance of each electrode was
measured using a ferri- and ferrocyanide couple as a redox probe.
(C) An iPEX chip for quadruple measurements was custom-designed. Four
working electrodes (carbon) were individually addressed during measurements,
whereas the reference electrode (Ag/AgCl) and the counter electrode
(carbon) were shared.The iPEX approach simplified
the sensor preparation for immunoassays.
We could rapidly (3 min) functionalize electrodes with antibodies
in one simple step rather than relying on chemical conjugation. Importantly,
antibodies against different protein targets can be selectively immobilized
on designated electrodes. The polymerization occurs only in an electrode
connected to a potentiostat while other unconnected electrodes remain
unmodified. The following EV assays were also facilitated with samples
applied to all electrodes in a single drop fashion. To take these
advantages, we custom-designed an iPEX chip for parallel processing
(Figure C). Four detection
spots (working electrodes) were arranged as a circular array, and
they shared common reference and counter electrodes that were placed
in a symmetrical way. This arrangement made the chip compact and minimized
the number of required electrical contacts. The iPEX chip was fabricated
on a flexible substrate with electrodes patterned through screening
printing (Experimental Section).
Surface Characterization
We first characterized the
formation of PPy and antibody entrapment on electrodes. The topography
of electrode surfaces, measured by atomic force microscopy, indicated
that surface roughness increased with cycles of electropolymerization
(Figure A,B). Py-polymerization
with antibodies further increased surface roughness (Figure B), suggesting antibody embedding.
Figure 2
Characterization
of sensor electrodes. (A) Atomic force microscopy
was used to investigate the surface of bare and polypyrrole (PPy)-coated
electrodes. (B) The surface roughness increased, as the polymerization
was repeated and antibodies were incorporated. PPy3 and
PPy11, 3 and 11 polymerization cycles, respectively; PPy11/Ab, 11 polymerization in the presence of antibody (Ab).
(C) Cyclic voltammograms of different electrode conditions were recorded
at the presence of ferri- and ferrocyanide. The non-Faradaic current
increased with repeated polymerization, indicating the gradual thickening
of the PPy layer. (D) The peak current was measured, while the potential
scan rate was varied in cyclic voltammetry. From the measured data,
the effective reaction area was estimated for the ferri- and ferrocyanide
redox process (inset). Note the increase of reaction area with polymerization
and antibody embedding.
Characterization
of sensor electrodes. (A) Atomic force microscopy
was used to investigate the surface of bare and polypyrrole (PPy)-coated
electrodes. (B) The surface roughness increased, as the polymerization
was repeated and antibodies were incorporated. PPy3 and
PPy11, 3 and 11 polymerization cycles, respectively; PPy11/Ab, 11 polymerization in the presence of antibody (Ab).
(C) Cyclic voltammograms of different electrode conditions were recorded
at the presence of ferri- and ferrocyanide. The non-Faradaic current
increased with repeated polymerization, indicating the gradual thickening
of the PPy layer. (D) The peak current was measured, while the potential
scan rate was varied in cyclic voltammetry. From the measured data,
the effective reaction area was estimated for the ferri- and ferrocyanide
redox process (inset). Note the increase of reaction area with polymerization
and antibody embedding.Cyclic voltammetry confirmed
the change in polymer thickness as
well as antibody entrapment in the polymer matrix (Figure C and Figure S1). Using electrodes that had different polymerization conditions,
we measured electrochemical redox behavior of 10 mM K3(FeCN)6 in 100 mM KCl aqueous solution, at the scan rate of 10 mV/s.
Ferricyanide is a typical redox species exhibiting one-electron, quasireversible
oxidation. A bare carbon electrode showed an oxidation anodic peak
at the applied voltage of Epa = 103 mV
and a reversal cathodic peak at Epc =
−109 mV (against the reference electrode). The peak current
ratio was ∼0.8 indicating quasireversible redox conversion
between [Fe(CN)6]3– and [Fe(CN)6]4– at E1/2 = −3
mV (= [Epa + Epc]/2). As PPy progressively covered the electrode surface, the non-Faradaic
current increased, indicating the capacitive charging/discharging
through the PPy layer. We set the Py-polymerization cycle to 11. Further
increasing the cycle number led to no appreciable changes in voltammograms,
suggesting a limiting behavior.We further estimated the effective
surface area of PPy-coated electrodes
by measuring voltammograms at different scan rates (v = 10, 25, 50, 100, 150, and 250 mV/s). The oxidation peak current
(ip) was then fitted to the Randles–Sevcik
equation (Figure D):where S is the surface area
(cm2), D is the diffusion coefficient
(7.66 × 10–6 cm2/s for [Fe(CN)6]3–),[23]n is the number of electrons transferred (n = 1), and C is the total concentration of electroactive
species (mol/cm3). The effective surface area of the electrode
increased with PPy coating and antibody entrapment (Figure D, inset); the results qualitatively
matched with roughness measurements and with a previous report.[24]
Assay Optimization
We next optimized
the iPEX assay
for EV detection. We measured electrochemical impedance (Z) of three assay steps (Figure A, Figure S2), before EV
capture on an electrode, after EV capture, and postlabeling for signal
amplification. The impedance spectra had three general features: (i)
At high frequency (>104 Hz), the Z value
converged to electrolyte resistance, as the electrochemical reaction
became diffusion limited. (ii) Between 10 and 104 Hz, impedance
differences emerged, driven by the electrical resistance at the electrode–electrolyte
interface. (iii) Below 10 Hz, the double-layer capacitance became
dominant, and impedance differences disappeared. The impedance change
after EV capture was maximal near 10 Hz (Figure B) which was set as the iPEX detection frequency.
Figure 3
iPEX assay
optimization. (A) Bode impedance plots during assay
steps. As EVs were captured and further labeled with additional antibodies,
electrochemical impedance values gradually increased between 10 and
1000 Hz. (B) Relative impedance changes against background (no EVs)
had their maxima around 10 Hz which was set as the iPEX detection
frequency. (C) Impedance values were measured from different assay
conditions. Significant signal changes occurred only when electrodes
were configured for target-specific EV capture. Data were obtained
at 10 Hz and displayed as mean ± SD from quadruplicate measurements.
iPEX assay
optimization. (A) Bode impedance plots during assay
steps. As EVs were captured and further labeled with additional antibodies,
electrochemical impedance values gradually increased between 10 and
1000 Hz. (B) Relative impedance changes against background (no EVs)
had their maxima around 10 Hz which was set as the iPEX detection
frequency. (C) Impedance values were measured from different assay
conditions. Significant signal changes occurred only when electrodes
were configured for target-specific EV capture. Data were obtained
at 10 Hz and displayed as mean ± SD from quadruplicate measurements.We further compared EV-specific and background
signals (Figure C).
When electrodes
were not configured for EV capture (i.e., PPy matrices without capture
antibodies or with nonspecific IgG control antibodies), iPEX reported
low impedance upon incubation with EV samples (GLI36 EVs; 105 EVs/mL, 200 μL). The measured Z values were
slightly higher with PPy-IgG electrodes than with PPy-only electrodes,
which can be attributed to antibody entrapment in the polymer. With
electrodes functionalized with CD63 antibodies, the impedance rose
significantly from the background (P < 0.001;
two-sided t-test) and could be further increased
through the secondary labeling. These results demonstrated target-specific
EV capture with iPEX electrodes, indicating that antibodies embedded
in PPy retained their affinity.For EV detection, we measured
two Z values, one
from a capture electrode (ZM) and the
other from an IgG control electrode (ZIgG). As an analytical metric, we used the net difference (ΔZM = ZM – ZIgG). This differential metric allowed us to
compensate for signals coming from nonspecific EV binding. We also
placed the IgG control site per chip to monitor potential chip-to-chip
variations (Figure S3).
iPEX Performance
Applying the optimized protocol, we
next characterized iPEX’s performance for EV detection. To
examine selectivity in multiplexed detection, we prepared a set of
iPEX chips with varying assignments of EV targets (i.e., CD63, CD9,
EGFR, or EGFRvIII) among electrodes (Figure A, left); each chip was functionalized to
detect at least two different protein markers. EV samples (from 104 EVs/mL; GLI36 cell line) were drop-loaded to cover electrodes,
and electrochemical impedance was measured. For a given protein target,
we observed consistent Z values (coefficient of variation <7%)
regardless of electrode assignment (Figure A, right). The results confirmed (i) the
immobilization of target antibodies only on intended electrodes during
Py polymerization and (ii) negligible electrical crosstalk between
electrodes.
Figure 4
iPEX assay performance. (A) Potential cross-talk between electrodes
was assessed. Three different iPEX chips were configured to detect
CD63, CD9, EGFR, or EGFRvIII (color-coded in the left schematic).
The bar graph on the right shows measured impedance values. Electrode
positions are color-coded and numbered. (B) Comparison of detection
sensitivity. Samples containing varying amounts of EVs in phosphate-buffered
saline (PBS) were analyzed by iPEX and enzyme-linked immunosorbent
assay (ELISA). EVs were probed for CD63 expression. For iPEX, the
limit of detection was close to 500 EV/mL, and the dynamic range spanned
up to 5 orders of magnitude. For ELISA, the limit of detection was
about 108 EV/mL. Data are shown as mean ± SD from
technical duplicates. (C) Cancer EVs (GLI36vIII cells) were spiked
in PBS and human serum and assayed by iPEX for EGFRvIII. The analytical
resolution of iPEX was comparable in both media. Data are shown as
mean ± SD from quadruplicate measurements.
iPEX assay performance. (A) Potential cross-talk between electrodes
was assessed. Three different iPEX chips were configured to detect
CD63, CD9, EGFR, or EGFRvIII (color-coded in the left schematic).
The bar graph on the right shows measured impedance values. Electrode
positions are color-coded and numbered. (B) Comparison of detection
sensitivity. Samples containing varying amounts of EVs in phosphate-buffered
saline (PBS) were analyzed by iPEX and enzyme-linked immunosorbent
assay (ELISA). EVs were probed for CD63 expression. For iPEX, the
limit of detection was close to 500 EV/mL, and the dynamic range spanned
up to 5 orders of magnitude. For ELISA, the limit of detection was
about 108 EV/mL. Data are shown as mean ± SD from
technical duplicates. (C) Cancer EVs (GLI36vIII cells) were spiked
in PBS and human serum and assayed by iPEX for EGFRvIII. The analytical
resolution of iPEX was comparable in both media. Data are shown as
mean ± SD from quadruplicate measurements.We next determined iPEX’s detection sensitivity. Samples
with varying EV concentrations were prepared and detected via CD63-specific
iPEX chips. The label-free iPEX achieved a limit of detection (LOD)
of ∼500 EVs/mL and a dynamic range of 5 orders of magnitude
(Figure B). The observed
LOD was much lower than those of ELISA (∼108 EV/mL)
and was comparable to or better than those by other EV profiling technologies
(see Table S1 for comparison). We further
tested whether plasma samples could be directly used without purification.
Samples were prepared by spiking EVs (from GLI36vIII cells) into PBS
or plasma. We then detected EGFRvIII to exclude the endogenous signal
from plasma EVs. Plasma samples showed Z values that
were slightly higher than those for samples in buffer (Figure C). Abundant plasma proteins
apparently adsorbed on electrodes to raise the background level. In
both media, however, the net signal changes were similar between different
EV concentrations (Figure S4), which indicated
that iPEX retained analytical resolution.
Profiling of Clinical GBM
Samples
To demonstrate its
clinical utility, we tuned iPEX to detect GBM-derived EVs (see Figure S5 for the study design). We first used
a panel of GBM cell lines (GLI36, GLI36vIII, U87, U87vIII, GBM 11/5,
GBM R132H) for marker validation.[5,25,26] Flow cytometry (Figure A) on these cells revealed differential expression
of EGFR, EGFRvIII, and PDGFRα. These markers have been shown
to be unregulated in GBM. EGFR gene overexpression
has been reported in up to 57% of GBM cases, followed by PDGFRα (13%).[27] EGFRvIII is highly GBM-specific
and the most common EGFR mutation in GBM.[28,29] Using iPEX, we next screened cell-derived EVs for these GBM markers.
The marker profiles of EVs positively correlated with those of parent
cells (Pearson r = 0.78; Figure B), which supported EV’s utility as
a tumor surrogate.
Figure 5
GBM EV detection. (A) A panel of GBM cell lines were profiled
via
flow cytometry to validate the expression of key GBM protein markers
(EGFR, EGFRvIII, PDGFRα). a.u., arbitrary unit. (B) iPEX was
applied to detect GBM markers in cell-line-derived EVs. Expression
profiles correlated between EVs and cells (Pearson correlation coefficient, r = 0.78), supporting EVs’ use as a cellular surrogate.
(C) Plasma EVs from GBM patients (n = 10) and healthy
controls (n = 10) were profiled for EV-specific tetraspanins
(CD63, CD9, CD81) and GBM markers (EGFR, EGFRvIII, PDGFRα).
The inset (right) shows the marker assignment for tetraspanin and
GBM chips. Impedance values from tetraspanin measurements (ΔZM, M = CD63, CD9, CD81) were nondiagnostic with
no significant difference between patient and control groups. (D)
GBM markers, when normalized against EV load (Znorm = ΔZGBM/ΔZCD63), were elevated in the patient cohort.
(E) Expressions of three GBM markers were combined through logistic
regression, and a receiver operation characteristic curve was constructed
for GBM diagnostics. The area under the curve (AUC) via iPEX EV profiling
was 0.94.
GBM EV detection. (A) A panel of GBM cell lines were profiled
via
flow cytometry to validate the expression of key GBM protein markers
(EGFR, EGFRvIII, PDGFRα). a.u., arbitrary unit. (B) iPEX was
applied to detect GBM markers in cell-line-derived EVs. Expression
profiles correlated between EVs and cells (Pearson correlation coefficient, r = 0.78), supporting EVs’ use as a cellular surrogate.
(C) Plasma EVs from GBM patients (n = 10) and healthy
controls (n = 10) were profiled for EV-specific tetraspanins
(CD63, CD9, CD81) and GBM markers (EGFR, EGFRvIII, PDGFRα).
The inset (right) shows the marker assignment for tetraspanin and
GBM chips. Impedance values from tetraspanin measurements (ΔZM, M = CD63, CD9, CD81) were nondiagnostic with
no significant difference between patient and control groups. (D)
GBM markers, when normalized against EV load (Znorm = ΔZGBM/ΔZCD63), were elevated in the patient cohort.
(E) Expressions of three GBM markers were combined through logistic
regression, and a receiver operation characteristic curve was constructed
for GBM diagnostics. The area under the curve (AUC) via iPEX EV profiling
was 0.94.We next pilot-tested iPEX with
human plasma samples. Clinical samples
(n = 20) were collected from healthy controls (n = 10) and GBM patients (n = 10; see Table S2 for patient information). We used a
pair of iPEX chips for a given plasma sample: a tetraspanin chip whose
four electrodes were functionalized for CD63, CD9, CD81, and IgG (control),
respectively; and a GBM chip whose four electrodes were functionalized
for known GBM markers (EGFR, EGFRvIII, PDGFRα) and IgG (control).
The tetraspanin chip was used to estimate EV loading for signal normalization.
For GBM markers, we normalized the measured impedance values (ΔZGBM) against ΔZCD63 (from the tetraspanin chip), defining Znorm = ΔZGBM/ΔZCD63; this metric was used to account for different EV concentrations
among samples.Figure C summarizes
the profiling results. The top heatmap (Figure C, top) shows impedance values (ΔZ) from the tetraspanin (CD63, CD81, CD9) measurements.
Tetraspanin levels showed high variations with no significant difference
between controls and GBM patients (Figure S6). On the other hand, the normalized expression (Znorm) of GBM markers (Figure C, bottom) was observed as higher in GBM
patients (Figure D).
We further estimated the diagnostic power of each GBM marker by constructing
receiver operating characteristic (ROC) curves (Figure S7). The areas under the curve (AUCs) were 88% (EGFR),
90% (EGFRvIII), and 92% (PDGFR). Combining three markers improved
the AUC to 94% (Figure E).
Conclusions
The iPEX approach simplified and sped up
EV protein assays. By
codepositing affinity ligands through electropolymerization, iPEX
rapidly and selectively primed sensors specific to target proteins.
The following EV assays measured electrochemical impedance that is
highly responsive to the sensor surface, which allowed iPEX to achieve
excellent sensitivity (∼500 EVs/mL). The assay was performed
in a label-free manner. No additional antibody binding was necessary
to generate an analytical signal; this advantage simplified and sped
up the assay procedure, contrasting with conventional sandwich-type
assays (e.g., ELISA). We prototyped a quadruplex iPEX chip and tuned
it to detect key GBM markers (i.e., EGFR, EGFRvIII, PDFGRa). With
one-drop loading of a plasma sample, iPEX detected multiple EV protein
markers, which led to high diagnostic accuracy in classifying GBM
from noncancer cases. Further validation, however, would be necessary
to test the specificity of these markers in differentiating GBM from
other tumor types. iPEX can facilitate such studies by allowing for
high-throughput, multiple-marker assays.We expect that the
iPEX assay would be more sensitive in detecting
small EVs and other smaller targets such as exomeres, cytokines, and
serum proteins. These targets can bind to electrodes at a high density,
which would lead to large changes in charge transfer impedance (ΔZ). More importantly, small targets can shorten the assay
time due to favorable kinetics. The required time (τ) to capture
the detection target on an electrode scales as τ ∼ 1/(Da), where D is the diffusivity of the
target, and a is the diameter of an electrode.[30] Because D is inversely promotional
to the hydrodynamic size (dh) of the target,
we estimate that τ ∼ dh/a. For typical EVs (dh ∼
150 nm), our assay time was τEV ∼ 60 min.
With smaller targets, for example, antibodies (dh ∼ 10 nm), this time would be in the order of a few
minutes (60 min ×10/150).We also envision other technical
developments to improve iPEX’s
analytical capabilities. First, one could enhance the throughput by
implementing an array of microelectrodes. Each electrode would still
be functionalized via selective electropolymerization, obviating the
need for external microprinting of reagents. Using such arrays would
reduce the sample volume (to cover electrodes) while increasing the
number of markers analyzed. Second, a new measurement device could
be designed for electrode arrays. An appealing approach is to use
a common potentiostat but configure it to sequentially access individual
electrodes. Because measuring impedance at a single frequency is fast
(<0.1 s), this configuration will effectively realize a parallel
detection in a compact device. With these improvements, iPEX would
be a powerful, microarray-type platform, facilitating comprehensive
EV-protein profiling for clinical diagnoses.
Experimental Section
Multielectrode
Design and Fabrication
The quadruple
iPEX chip was designed to have four individual working electrodes,
one counter electrode, and one reference electrode. Electrodes were
fabricated via screen printing (QSTAG, Korea). A carbon ink and a
Ag/AgCl paste were screen-printed for working/counter and reference
electrodes, respectively, on a flexible poly(ethylene terephthalate)
substrate (thickness, 1 mm). The chip was then partly covered with
an insulating layer and heat-treated for 1 h. The final fabricated
chip had a cross-shaped Ag/AgCl reference electrode (area, 5.3 mm2) in the center, four circular working electrodes (diameter,
3 mm), and a ring-shaped counter electrode.
Electrode Functionalization
Pyrrole (reagent grade,
98%, Sigma-Aldrich) solution (0.1 M) was prepared in 0.1 M NaCl supporting
electrolyte. The antibody (Ab) of interest (see Table S3) was diluted in pyrrole solution to a final concentration
of 6 μg/mL. Electropolymerization of pyrrole to polypyrrole
(PPy) was performed via cyclic voltammetry between 0.0 and +0.95 V
with respect to the Ag/AgCl reference electrode at the scan rate of
50 mV/s. After polymerization, electrodes were washed with phosphate-buffered
saline (PBS) buffer and kept in PBS until use. The surface topography
of electrodes was measured using an atomic force microscope (NX-10,
Park Systems) equipped with CONTSCR cantilevers (NanoWorld). Topography
images were generated using XEI software (Park Systems).
iPEX Detection
EV samples (200 μL) were drop-cast
on PPy-Ab functionalized electrodes and incubated for 1 h at 20 °C.
For optional signal amplification, CD63 antibody (2 μg/mL) was
drop-cast on captured EVs and incubated for 1 h at 20 °C. A potentiostat
with an impedance analyzer (Sp-200, Bio-Logic) was used to perform
electrochemical impedance spectroscopy. The electrolyte was a mixture
of K4[Fe(CN)6] (10 mM) and K3[Fe(CN)6] (10 mM) in a phosphate (50 mM)-buffered K2SO4 (100 mM) solution (pH 7). The impedance spectrum was measured
over a frequency range from 100 mHz to 100 kHz with a 10 mV alternative
current voltage superimposed on a constant bias of −0.195 V.
Enzyme-Linked Immunosorbent Assay (ELISA)
CD63 antibody
and IgG antibody were diluted in PBS (5 μg/mL) and added to
the Maxisorp 96-well plate (Nunc) for overnight incubation at 4 °C.
After washing with PBS, 2% bovine serum albumin (BSA) in PBS was added
to the plate (2 h incubation at 20 °C). For EV detection, samples
(in 100 μL of PBS) were added to each well for 1 h of incubation
at 20 °C. After discarding samples, biotinylated CD63 antibody
(1 μg/mL) was added to each well and incubated for another 2
h at room temperature (RT). Unbounded antibodies were removed via
triple-washing with PBS. Streptavidin-HRP molecules then were added
to each well, and the mixture was incubated for 1 h at 20 °C.
After washout with PBS, a solution of chromogenic electron mediator
(3,3′,5,5′-tetramethylbenzidine) was added. After 20-min
incubation, a stop solution (2 M, H2SO4) was
added. The optical density at 450 nm was then read by a plate reader
(Tecan).
GBM Cell Culture
GLI36 and U87-EGFR cell lines were
purchased from ATTC. GLI36vIII and U87vIII cell lines were generated
from GLI36 and U87-EGFR cell lines, respectively, through lentivirus
transduction.[26] GBM 11/5 and GBM R132H
primary cell lines were obtained from Dr. Breakefield’s laboratory
(Massachusetts General Hospital). All cell lines were cultured in
Dulbecco’s modified essential medium (DMEM, Life Technologies)
that contained 10% fetal bovine serum (FBS; Thermo Fischer Scientific)
and 1% penicillin/streptomycin (10 IU/mL and 10 μg/mL, respectively;
Thermo Fischer Scientific).
EV Isolation from Cell Culture
Cells
at passage 1–20
were cultured until 80% confluency in their complete medium and then
in DMEM containing 5% depleted FBS for 48 h. Next, the conditioned
media from ∼107 cells were collected, filtered through
a 0.2 μm filter (Millipore), and centrifuged at 300g for 10 min. The supernatant was concentrated to 0.5 mL via a centrifugal
filter (Centricon Plus-70 centrifugal filter 10 kDa cutoff) and added
to a qEV 70 nm column (iZon). As the supernatant passed through the
column, 4 mL of PBS was added in 100–200 μL aliquots.
First, 3 mL was discarded, and a subsequent 1.5 mL was collected as
an EV fraction. As a final step, EVs were concentrated with an Amicon
Ultra-2 centrifugal filter unit with an Ultracel-100 membrane. The
size and concentration of prepared EVs were measured via nanoparticle-tracking
analysis (LM10, Melvern).
Flow Cytometry
About 105 cells were used
per marker for flow cytometry. Cells were fixed with 4% formaldehyde
(ThermoFisher) in PBS for 15 min at room temperature on a nutating
mixer. Fixed cells were then washed twice in PBS–BSA (1×
PBS with 0.5% BSA) and incubated with primary antibodies (10 μg/mL)
in PBS–BSA for 1 h at room temperature. Labeled cells were
washed twice in PBS–BSA, incubated with fluorophore-conjugated
secondary antibodies (1:1000 dilution) for 30 min at room temperature,
and washed again. Control samples were similarly labeled using isotype-matched
IgG and secondary antibodies. The fluorescence signal was measured
using a CytoFlex flow cytometer (Beckman Coulter) with 96-well plate
handling. A total of 10 000 events were collected. The expression
level of a target marker was calculated as the signal difference between
targeted and control samples.
Clinical Samples
The study population included patients
18 years or older with pathology confirmed gliomas who underwent surgery
at the Massachusetts General Hospital and age-matched healthy controls.
For glioma cohorts, exclusion criteria consisted of a history of other
primary or metastatic cancers, active infectious disease, current
or previous enrollment in clinical trials, and hemolyzed plasma samples.
All healthy control subjects were screened for pertinent oncologic
and neurologic medical histories. Individuals with a history of cancer,
neurological disorders, and infectious diseases were excluded from
the study. All samples were collected with written informed consent
after the patient was advised of the potential risks and benefits,
as well as the investigational nature of the study. Our studies were
conducted in accordance with principles for human experimentation
as defined in the U.S. Common Rule and were approved by the Human
Investigational Review Board of each study center under Partners institutional
review board (IRB)-approved protocol number 2017P001581. Caution!
Clinical samples should be handled following Biosafety Level (BSL)
2 protocols. PPy-Ab functionalized electrodes were directly incubated
with plasma samples (100 μL) for 1 h at room temperature, and
the iPEX signal was measured after washing the electrodes with PBS
twice.
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