U.S. patent application number 17/458958 was filed with the patent office on 2022-04-21 for cell-free biofragment compositions and related systems, devices, and methods.
This patent application is currently assigned to The University of Queensland. The applicant listed for this patent is Seattle Children's Hospital dba Seattle Children's Research Institute, The University of Queensland. Invention is credited to Gerard A. Cangelosi, Yadveer Grewal, Muhammad J.A. Shiddiky, Matt Trau.
Application Number | 20220120745 17/458958 |
Document ID | / |
Family ID | 1000006062256 |
Filed Date | 2022-04-21 |
United States Patent
Application |
20220120745 |
Kind Code |
A1 |
Grewal; Yadveer ; et
al. |
April 21, 2022 |
CELL-FREE BIOFRAGMENT COMPOSITIONS AND RELATED SYSTEMS, DEVICES,
AND METHODS
Abstract
The present disclosure relates to biofragment compositions that
comprise bioparticle fragments and at least one heterologous
antigen-binding molecule. In some embodiments, the biofragment is
typically derived from a larger, intact bioparticle that express
the at least one heterologous antigen-binding molecule at the
surface, and the biofragment has increased solubility to facilitate
assays for antigen detection. The disclosure also relates the
related methods of using and making the biofragment compositions,
as well as systems and devices implementing the biofragment
compositions. In some embodiments, the related methods, systems and
devices do not require additional detection reagents, such as
animal derived detection antibodies.
Inventors: |
Grewal; Yadveer; (Logan
City, AU) ; Cangelosi; Gerard A.; (Seattle, WA)
; Shiddiky; Muhammad J.A.; (Saint Lucia, AU) ;
Trau; Matt; (Balmoral, AU) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
The University of Queensland
Seattle Children's Hospital dba Seattle Children's Research
Institute |
St.Lucia
Seattle |
WA |
AU
US |
|
|
Assignee: |
The University of
Queensland
St. Lucia, Queensland
WA
Seattle Children's Hospital dba Seattle Children's Research
Institute
818 Stewart Street, Suite 603
|
Family ID: |
1000006062256 |
Appl. No.: |
17/458958 |
Filed: |
August 27, 2021 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
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14650851 |
Jun 9, 2015 |
11105802 |
|
|
PCT/US2013/074149 |
Dec 10, 2013 |
|
|
|
17458958 |
|
|
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|
61735180 |
Dec 10, 2012 |
|
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
G01N 33/5438 20130101;
G01N 33/56961 20130101; G01N 33/5432 20130101; G01N 33/56911
20130101; G01N 33/56966 20130101; G01N 33/566 20130101; G01N
33/56983 20130101 |
International
Class: |
G01N 33/566 20060101
G01N033/566; G01N 33/543 20060101 G01N033/543; G01N 33/569 20060101
G01N033/569 |
Goverment Interests
STATEMENT OF GOVERNMENT LICENSE RIGHTS
[0002] This invention was made with Government support under
AI082186 awarded by the National Institutes of Health. The
Government has certain rights in the invention.
Claims
1-12. (canceled)
13. A method of detecting the presence of an antigen of interest in
a biological sample, comprising: 1) contacting a biological sample
with a biofragment composition under conditions sufficient to
permit the binding of the composition with an antigen of interest,
wherein the biofragment composition comprises a surface fragment of
a ruptured cell or cellular organelle, wherein the surface fragment
displays at least one antigen-binding molecule heterologous to the
cell or cellular organelle, and wherein the antigen-binding
molecule selectively binds the antigen of interest; and 2)
detecting the binding of the biofragment composition to the antigen
of interest.
14. The method of claim 13, wherein the biofragment composition is
immobilized to a surface.
15. The method of claim 13, further comprising contacting the
biological sample with a detection reagent that binds to the
antigen of interest.
16. The method of claim 15, further comprising contacting the
biological sample with a detectably-labeled reporter reagent and
separating the unbound reporter from the biofragment
composition.
17. The method of claim 13, wherein binding of the antigen of
interest to the biofragment composition is detected using an
antibody sandwich flow cytometric assay, cell bioprobe
immunofluorescence microscopy, an ELISA-like assay, or a
competitive inhibition assay.
18. The method of claim 14, wherein the biofragment composition is
immobilized, directly or indirectly, to a conductive or
semi-conductive electrode surface.
19. The method of claim 18, further comprising providing an
electroactive molecule and measuring the electron transfer
resistance at the electrode surface, wherein binding of the antigen
of interest to the biofragment composition is detected by a change
in the electron transfer resistance as compared to the electron
transfer resistance when the antigen of interest is not
present.
20. The method of claim 13, wherein the biological sample is
selected from the group consisting of blood, urine, sputum, mucus,
saliva, cerebral spinal fluid, tissues, stool, nutrient sources,
environmental sample, or a processed derivative thereof.
21. The method of claim 13, further comprising: 1) contacting the
biological sample with a capture reagent that binds to the antigen
of interest; and 2) contacting the biological sample with the
biofragment composition configured as a detection reagent.
22. The method of claim 21, wherein the detection reagent further
comprises a detectable label.
23. The method of claim 21, further comprising contacting the
biological sample with a detectably-labeled reporter agent that
specifically binds to the detection reagent, and removing the
unbound reporter agent.
24. (canceled)
25. The method of claim 19, wherein the electroactive molecule is a
redox probe.
26. The method of claim 25, wherein the redox probe is
[Fe(CN).sub.6].sup.3-/4-.
27. The method of claim 14, wherein the biofragment composition is
immobilized indirectly to the surface by one or more intervening
tether constructs.
28-33. (canceled)
34. The method of claim 19, wherein binding of the antigen of
interest to the biofragment composition is detected by an increase
in the electron transfer resistance as compared to the electron
transfer resistance when the antigen of interest is not
present.
35-40. (canceled)
41. The method of claim 13, wherein the cell is selected from the
group consisting of a yeast, bacterium, plant, or animal cell.
42. The method of claim 41, wherein the yeast is from the genus
Saccharomyces or Pichia.
43. The method of claim 13, wherein the surface fragment is less
than 200 nm at its greatest dimension.
44. The method of claim 13, wherein the antigen-binding molecule is
an antibody, an antigen-binding antibody fragment, or a T-cell
receptor (TCR).
45. The method of claim 44, wherein the antibody-like molecule is a
single-chain antibody, a bispecific antibody, an Fab fragment, or
an F(ab).sub.2 fragment.
46. The method of claim 45, wherein the single-chain antibody is a
single-chain variable fragment (scFv), single-chain Fab fragment
(scFab), V.sub.HH fragment, V.sub.NAR, or nanobody.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application is a continuation of U.S. patent
application Ser. No. 14/650,851, filed Jun. 9, 2015, which is a
U.S. National Stage of PCT/US2013/074149, filed Dec. 10, 2013,
which claims the benefit of U.S. Provisional Application No.
61/735,180, filed Dec. 10, 2012, the entire disclosures of said
applications are hereby incorporated by reference.
BACKGROUND
[0003] Affinity reagents that bind to specific antigens of interest
are critical tools in biomedical research, biomarker discovery, and
diagnostic testing. Generation of monoclonal antibodies (MAbs) by
traditional methods, typically by the mouse hybridoma route, is a
significant bottleneck in biomedical research and development. MAbs
in diagnostic tests often require significant optimization before
being usable for diagnostic assays, and licensing costs can exceed
all other test costs combined. Cheaper and more available affinity
reagents would greatly facilitate biomedical research, empower
developers of new diagnostic tests, and facilitate development and
use of inexpensive and sensitive assays, testing devices and
testing systems.
[0004] Recombinant antibody-like molecules such as single-chain
Fragment variable (scFv) and fragment antigen binding (Fab) are
potentially appealing alternatives to MAbs. Libraries of these
molecules have been displayed on the surfaces of organisms
including Escherichia coli, phages, yeast, and on ribosomes.
Although these methods have existed for many years, few such
fragments have proven useful as molecular probes in diagnostic
tests. Methods for rapidly selecting antigen-binding
yeast-displayed scFv clones were described nearly ten years ago.
For example, yeast display libraries can be made to express scFv on
the surface of Saccharomyces cerevisiae cells. Using a combination
of magnetic bead enrichment and fluorescent-activated cell sorting
(FACS), yeast clones that bind specifically to antigens of interest
can be selected from naive libraries in 2-3 weeks. This selection
process is much faster and less expensive than the mouse hybridoma
route. However, scFv selected by this method rarely perform well
when secreted into solution. Like natural antibodies,
yeast-displayed scFv are products of selection, in this case for
activity in the environment of a yeast cell surface. Hence,
yeast-displayed scFv tend to perform poorly in other environments,
especially when secreted. Although functional soluble scFv have
been reported, in practice the great majority of scFv culled from
yeast display libraries have exhibited unsatisfactory activity in
standard immunoassay formats, thus requiring additional rounds of
optimization. Therefore, the reliable and efficient production of
scFv for use as effective affinity reagents remains
unpredictable.
[0005] Despite the advances in the art regarding production of
affinity reagents, such as monoclonal antibodies and antibody-like
molecules, a need remains for fast and cost-effective production of
versatile reagents useful for reliable detection of antigens of
interest. The invention set forth in this disclosure addresses this
need and provides further related advantages.
SUMMARY
[0006] This summary is provided to introduce a selection of
concepts in a simplified form that are further described below in
the Detailed Description. This summary is not intended to identify
key features of the claimed subject matter, nor is it intended to
be used as an aid in determining the scope of the claimed subject
matter.
[0007] In one aspect, the present invention provides a biofragment
composition for selectively binding an antigen of interest in a
sample. The biofragment composition comprises a bioparticle
fragment displaying at least one heterologous antigen-binding
molecule, wherein the at least one heterologous antigen-binding
molecule is capable of specifically binding the antigen of
interest.
[0008] In some embodiments, the bioparticle of the composition is a
cell, a cellular organelle, or a virus. In some embodiments, the
cell is selected from the group consisting of a yeast, bacterium,
plant, or animal cell. In some embodiments, the yeast is from the
genus Saccharomyces or Pichia.
[0009] In some embodiments, the heterologous antigen-binding
molecule of the biofragment composition is an antibody-like
molecule or a T cell receptor (TCR). In some embodiments, the
antigen-binding molecule comprises an antigen-binding fragment of
an antibody or TCR. In some embodiments, the antibody-like molecule
is a single-chain antibody, a bispecific antibody, an Fab fragment,
or an F(ab).sub.2 fragment. In some embodiments, the single-chain
antibody is a single-chain variable fragment (scFv), single-chain
Fab fragment (scFab), V.sub.HH fragment, V.sub.NAR, or
nanobody.
[0010] In some embodiments, the bioparticle fragment displaying at
least one heterologous antigen-binding molecule is substantially
isolated from bioparticle fragments not displaying the at least one
heterologous antigen-binding molecule. In some embodiments, the
bioparticle fragment is less than about 1 .mu.m at its greatest
dimension. In some embodiments, the bioparticle fragment is
produced by disruption of the bioparticle surface. In some
embodiments, the bioparticle fragment is derived from a larger
bioparticle, wherein the bioparticle fragment has increased
solubility in aqueous assay conditions. In some embodiments, the at
least one heterologous antigen-binding molecule is attached to the
bioparticle surface prior to disruption of the surface by inducing
expression and translocation of the molecule to, or assembly of the
molecule on, the interior or exterior bioparticle surface.
[0011] In another aspect, the disclosure provides a method of
detecting the presence of an antigen of interest in a biological
sample. The method comprises contacting a biological sample with
the biofragment composition as described herein under conditions
sufficient to permit the binding of the composition with an antigen
of interest, and detecting the binding of the biofragment
composition to the antigen of interest.
[0012] In some embodiments, the method further comprises
immobilizing the biofragment composition. In some embodiments, the
method further comprises contacting the biological sample with a
detection reagent that binds to the antigen of interest. In some
embodiments, the method further comprises contacting the biological
sample with a detectably-labeled reporter reagent and separating
the unbound reporter from the biofragment composition. In some
embodiments, binding of the antigen of interest to the biofragment
composition is detected using an antibody sandwich flow cytometric
assay, cell bioprobe immunofluorescence microscopy, an ELISA-like
assay, or a competitive inhibition assay. In some embodiments, the
biofragment composition is immobilized, directly or indirectly, to
a conductive or semi-conductive electrode surface. In some
embodiments, the method further comprises providing an
electroactive molecule and measuring the electron transfer
resistance at the electrode surface, wherein binding of the antigen
of interest to the biofragment composition is detected by a change
in the electron transfer resistance as compared to the electron
transfer resistance when the antigen of interest is not present. In
some embodiments, the biological sample is selected from the group
consisting of blood, urine, sputum, mucus, saliva, cerebral spinal
fluid, tissues, stool, nutrient sources, or processed derivatives
thereof.
[0013] In another aspect, the disclosure provides a method of
detecting the presence of an antigen of interest in a biological
sample. The method comprises 1) contacting a biological sample with
a capture reagent that binds to the antigen of interest; and 2)
contacting the biological sample with a detection reagent under
conditions sufficient to permit the binding of the detection
reagent with an antigen of interest, wherein the detection reagent
comprises the biofragment composition described herein. In some
embodiments, the detection reagent further comprises a detectable
label. In some embodiments, the method further comprises contacting
the biological sample with a detectably-labeled reporter agent that
specifically binds to the detection reagent, and removing the
unbound reporter agent.
[0014] In another aspect, the disclosure provides a method of
detecting the presence of an antigen of interest in a biological
sample. The method comprises 1) contacting a biological sample to
the biofragment composition described herein under conditions
sufficient to permit the binding of the antigen of interest to the
biofragment composition, wherein the biofragment composition is
immobilized, directly or indirectly, to a conductive or
semi-conductive electrode surface; and 2) measuring the electron
transfer resistance at the electrode surface in the presence of an
electroactive molecule, wherein binding of the antigen of interest
to the biofragment composition is detected by a change in the
electron transfer resistance as compared to the electron transfer
resistance when the antigen of interest is not present.
[0015] In some embodiments, the electroactive molecule is a redox
probe. In some embodiments, the redox probe is
[Fe(CN).sub.6].sup.3-/4-.
[0016] In some embodiments, the biofragment composition is
immobilized indirectly to the electrode surface by one or more
intervening tether constructs. In some embodiments, the method
further comprises the step of immobilizing the biofragment
composition to the electrode surface. In some embodiments, the
immobilizing step comprises: a) attaching an anchor construct to
the electrode, b) immobilizing an epitope-tag binding molecule to
the anchor construct, and c) contacting the epitope-tag binding
molecule with the biofragment composition, wherein the biofragment
composition comprises heterologous antigen-binding molecule with an
epitope tag. In some embodiments, step "c)" comprises: i)
disrupting the surface of one or more bioparticles that have at
least one attached heterologous antigen-binding molecule attached
thereto to produce a plurality of bioparticle surface fragments,
ii) contacting the epitope-tag binding molecule with the plurality
of bioparticle fragments to the epitope-tag binding molecule, and
iii) removing the bioparticle surface fragments that remain unbound
to the immobilized epitope-tag binding molecule. In some
embodiments, the method further comprises optionally rinsing the
electrode surface after one or more of steps a), b), and c).
[0017] In some embodiments, the anchor construct is a protein,
organic or inorganic molecule. In some embodiments, the epitope tag
is any epitope, such as c-myc, HA, FLAG-tag, GST, 6HIS, VSVg, V5,
HSV, AU1, and the like.
[0018] In some embodiments, binding of the antigen of interest to
the biofragment composition is detected by an increase in the
electron transfer resistance as compared to the electron transfer
resistance when the antigen of interest is not present.
[0019] In another aspect, the disclosure provides an antigen
detection system. The system comprises the biofragment composition
as described herein immobilized directly or indirectly to a
conductive or semi-conductive electrode surface, also described
herein. The system also comprises an electroactive molecule, and a
device to monitor electric current, electric potential, and/or
electric impedance, such as a potentiostat or a galvanostat, and
the like. In some embodiments, the biofragment composition is
immobilized indirectly to the electrode surface by one or more
intervening tether constructs. In some embodiments, the one
intervening tether construct is an epitope-tag binding molecule
that binds to an epitope tag present in the heterologous
antigen-binding molecule of the biofragment composition.
[0020] In another aspect, the disclosure provides a device that
implements the system and/or incorporates the biofragment
composition, as described herein, which can be useful, for example,
for the point of care detection of antigens of interest from a
biological sample.
DESCRIPTION OF THE DRAWINGS
[0021] The foregoing aspects and many of the attendant advantages
of this invention will become more readily appreciated as the same
become better understood by reference to the following detailed
description, when taken in conjunction with the accompanying
drawings, wherein:
[0022] FIG. 1A is a general schematic illustration of a label-free
protein detection system based on faradaic electrochemical
impedance spectroscopy (F-EIS). Illustrated in the scheme are E.
histolytica proteins complexed with surface-attached yeast-scFv
biofragments, which hinder the interfacial electron transfer
reaction of [Fe(CN).sub.6].sup.3-/4-.
[0023] FIG. 1B and FIG. 1C are graphical representations of
hypothetical sensor responses representing the presence and absence
of E. histolytica proteins during the label-free impedance and
voltammetric measurements, respectively.
[0024] FIG. 2 graphically illustrates the dynamic light scattering
(DLS) of yeast-scFv biofragments after application filtration
through a 100 nm filter. Analysis performed on Malvern Zetasizer
3000 HSa using multimodal algorithm.
[0025] FIG. 3A illustrates Nyquist plots for (i) bare and sensing
surfaces on gold electrodes, (ii) bio-BSA/streptavidin, (iii)
bio-BSA/streptavidin/bio-anti-HA, (iv)
bio-BSA/streptavidin/bio-anti-HA/yeast-scFv, and (v)
bi-BSA/streptavidin/bio anti-HA/yeast-scFv/`350` antigen, each in
10 mM phosphate buffer solution (pH 7.4) containing 2.5 mM
K.sub.3[Fe(CN).sub.6], 2.5 mM K.sub.2[Fe(CN).sub.6], and 0.1 M
KCl.
[0026] FIG. 3B graphically illustrates the differential pulse
voltammetry (DVP) responses corresponding to complexes (i)-(v), as
described above for FIG. 3A.
[0027] FIG. 4A illustrates Nyquist plots for immunosensing layer on
gold electrodes for detecting (i)
bio-BSA/streptavidin/bio-anti-HA/yeast-scFv/Jacob, (ii)
bio-BSA/streptavidin/bio-anti-HA/yeast-scFv biofragment-2/'350',
(iii) bio-BSA/streptavidin/bio-anti-HA/`350`, and (iv)
bio-BSA/streptavidin/bio-anti-HA/yeast-scFv biofragment/`350`
immunocomplex formation, each in 10 mM phosphate buffer solution
(pH 7.4) containing 2.5 mM K.sub.3[Fe(CN).sub.6], 2.5 mM
K.sub.2[Fe(CN).sub.6], and 0.1 M KCl. Target protein concentrations
for (i), (ii), (iii) and (iv) were 500, 500, 500, and 10 pg/mL,
respectively. Dotted line spectrum represents impedance at
bio-BSA/streptavidin/bio-anti-HA/yeast-scFv sensing layer in the
same electrolyte solution. (B) Corresponding DPV current
responses.
[0028] FIG. 4B graphically illustrates the differential pulse
voltammetry (DVP) responses corresponding to complexes (i)-(v), as
described above for FIG. 4A.
[0029] FIG. 5 graphically illustrates the change of the DPV peak
currents at the immunosensing surface after incubation with
designated concentrations of target E. histolytica `350`
antigen.
[0030] FIG. 6 is a Nyquist plot for (i) bio-BSA, (ii)
bio-BSA/streptavidin, (iii) bio-BSA/streptavidin/bio-anti-HA, (iv)
bio-BSA/streptavidin/bio-anti-HA/yeast-scFv biofragment, and (v)
bio-BSA/streptavidin/bio-anti-HA/yeast-scFv biofragment/`350`
immunocomplex, each determined using F-EIS-based assay with a gold
coated screen-printed electrode and in 10 mM phosphate buffer
solution (pH 7.4) containing 2.5 mM K.sub.3[Fe(CN).sub.6], 2.5 mM
K.sub.2[Fe(CN).sub.6], and 0.1 M KCl.
[0031] FIG. 7 is a Nyquist plot for (i) bio-BSA/streptavidin/bio
anti-HA/`350` at 500 pg/mL (i.e., no yeast-scFv biofragment
reagent), (ii) bio-BSA/streptavidin/bio anti-HA/yeast-scFv
biofragment (i.e., no antigen), (iii) bio-BSA/streptavidin/bio
anti-HA/yeast-scFv biofragment/`Jacob` antigen at 1000 pg/mL, and
(iv) bio-BSA/streptavidin/bio anti-HA/yeast-scFv biofragment/`350`
antigen at 500 pg/mL complex formation, each determined with a gold
coated screen-printed electrode and in 10 mM phosphate buffer
solution (pH 7.4) containing 2.5 mM K.sub.3[Fe(CN).sub.6], 2.5 mM
K.sub.2[Fe(CN).sub.6], and 0.1 M KCl.
[0032] FIG. 8A is a Nyquist plot of the F-EIS responses at the
immunosensing surface of a gold coated screen-printed electrode and
after incubation with designated concentrations of E. histolytica
`350` antigen: (i) 0 (ii) 1 pg/mL (iii) 10 pg/mL (iv) 50 pg/mL (v)
500 pg/mL (vi) 1000 pg/mL.
[0033] FIG. 8B graphically illustrates the relative change of the
charge transfer resistance (R.sub.ct) responses, normalized to the
`zero-antigen` signal, at the immunosensing surface of a gold
coated screen-printed electrode after incubation with designated
concentrations of E. histolytica `350` antigen. Each data point
represents the average of three separate trials (n=3) and error
bars represent standard error of measurements within each
experiment.
[0034] FIG. 9A and FIG. 9B are Nyquist plots for (A) (i) assay with
no antigen, (ii) cognate `350` antigen, and (B) (i) assay with no
antigen, (ii) cognate `030` antigen in stool, each determined with
a gold coated screen-printed electrode and in 10 mM phosphate
buffer solution (pH 7.4) containing 2.5 mM K.sub.3[Fe(CN).sub.6],
2.5 mM K.sub.2[Fe(CN).sub.6], and 0.1 M KCl. Antigens `350` and
`030` concentrations were 500 pg/mL. Stool was diluted 1/5 in
PBS.
[0035] FIG. 9C and FIG. 9D are the DPV responses corresponding to
antigen `350` and antigen `030`, respectively.
DETAILED DESCRIPTION
[0036] Disclosed are materials, compositions, and components that
can be used for, can be used in conjunction with, can be used in
preparation for, or are products of the disclosed methods,
compositions, and related systems and devices. It is understood
that, when combinations, subsets, interactions, groups, etc., of
these materials are disclosed, each of various individual and
collective combinations is specifically contemplated, even though
specific reference to each and every single combination and
permutation of these compounds may not be explicitly disclosed.
This concept applies to all aspects of this disclosure including,
but not limited to, steps in the described methods. Thus, specific
elements of any foregoing embodiments can be combined or
substituted for elements in other embodiments. For example, if
there are a variety of additional steps that can be performed, it
is understood that each of these additional steps can be performed
with any specific method steps or combination of method steps of
the disclosed methods, and that each such combination or subset of
combinations is specifically contemplated and should be considered
disclosed. Additionally, it is understood that the embodiments
described herein can be implemented using any suitable material
such as those described elsewhere herein or as known in the
art.
[0037] Publications cited herein and the subject matter for which
they are cited are hereby specifically incorporated by reference in
their entireties.
[0038] As used in this specification and the appended claims, the
singular forms "a," "an," and "the" include plural references
unless the context clearly dictates otherwise. Thus, for example,
references to "the method" includes one or more methods, and/or
steps of the type described herein and/or which will become
apparent to those persons skilled in the art upon reading this
disclosure and so forth. The use of the term "or" in the claims is
used to mean "and/or" unless explicitly indicated to refer to
alternatives only or the alternatives are mutually exclusive,
although the disclosure supports a definition that refers to only
alternatives and "and/or." As used in this specification, the term
"about" refers to a range of slight variation, such as 10%, above
or below the stated figure.
[0039] Unless the context clearly requires otherwise, throughout
the description and the claims, the words "comprise," "comprising,"
and the like are to be construed in an inclusive sense as opposed
to an exclusive or exhaustive sense; that is to say, in the sense
of "including, but not limited to." Words using the singular or
plural number also include the plural and singular number,
respectively. Additionally, the words "herein," "above," and
"below," and words of similar import, when used in this
application, shall refer to this application as a whole and not to
any particular portions of the application.
[0040] Unless specifically defined herein, all terms used herein
have the same meaning as they would to one skilled in the art of
the present invention. Practitioners are particularly directed to
Sambrook, et al., Molecular Cloning: A Laboratory Manual, 3d ed.,
Cold Spring Harbor Press, Plainsview, N.Y. (2000) and Ausubel, et
al., Current Protocols in Molecular Biology (Supplement 47), John
Wiley & Sons, New York (1999), which are incorporated herein by
reference, for definitions and terms of the art. Additionally, all
other references cited herein are hereby expressly incorporated by
reference in their entireties.
[0041] One solution to problems associated with the generation of
monoclonal antibodies and antibody-like molecules for affinity
reagents is to forgo the attempt to generate soluble scFv and
instead use the yeast-displayed scFv (whole-cell yeast-scFv)
directly as detection reagents. Affinity reagents composed of
lyophilized whole yeast cells with displayed scFv (whole-cell yeast
scFv) have been shown to be viable, cheap and quick alternatives to
generating mAbs or soluble scFv for use in Immunoassays (Gray, S.
A., et al, "Toward Low-Cost Affinity Reagents: Lyophilized
Yeast-scFv Probes Specific for Pathogen Antigens," PLoS ONE 7:
e32042 (2012); see also WO 2012/159075; each of which are hereby
incorporated by reference in their entireties). Whole-cell yeast
scFv are robust and renewable reagents that can be produced in vast
quantities at low cost. However, these whole-cell reagents are
insoluble and too large for many diagnostic applications. Moreover,
they require the use of labeled polyclonal antibodies to detect
antigen binding to the yeast scFv particles (Gray et al, 2012).
[0042] The present invention, which overcomes the limitations of
the art as described above, not only provides sensitive cell-free
scFv affinity reagents, but also provides an affinity reagent
system that does not require labeled, animal derived detection
antibodies. As described in more detail below, the inventors
generated cell-free scFv affinity reagents using fragmentation of
whole-cell yeast scFv cells, followed by mechanical and affinity
based purification of smaller, soluble cell wall fragments bearing
displayed scFv. Moreover, an electrochemical (EC) approach was used
to detect antigen binding to cell free yeast scFv, without the need
for animal derived detection antibodies.
[0043] In accordance with the foregoing, in one aspect, the present
disclosure provides a biofragment composition for selectively
binding an antigen of interest in a sample. The biofragment
composition comprises a bioparticle fragment displaying at least
one heterologous antigen-binding molecule, wherein the at least one
heterologous antigen-binding molecule is capable of specifically
binding the antigen of interest.
[0044] As used herein, the term "biofragment" is used to refer to
any fragment of a bioparticle that contains or displays on its
internal or external surface at least one heterologous antigen
binding molecule, where the heterologous antigen binding molecule
is capable of specifically binding the antigen of interest. In some
embodiments, the biofragment is a surface portion of the original
bioparticle. Thus, the biofragment is not an intact bioparticle
(see below), but rather a bioparticle or portion thereof where the
bioparticle surface has been disrupted. In some embodiments, the
bioparticle surface is disrupted sufficiently to lose its initial
shape or integrity, but remains in a single piece. In other
embodiments, the bioparticle surface has been disrupted into
multiple, independent pieces such that each resulting biofragment
contains less than all of the surface area than the initial intact
bioparticle.
[0045] As used herein, the term "bioparticle" is used to refer to
any particle derived from a biological system while retaining the
integrity of heterologous antigen-binding molecules contained or
displayed (internally or externally) on the surface structure of
the bioparticle. Thus, the term "bioparticle" can encompass intact
cells, cellular organelles, viruses, or other biological constructs
that can be assembled, propagated, or generated to display on the
inner or outer surface at least one heterologous antigen-binding
molecule. For any embodiment, there is no requirement that the
bioparticle be living or demonstrate metabolic integrity
post-lyophilization. However, the bioparticle surface must be
amenable to disruption or fragmentation that allows the retention
of heterologous antigen-binding molecules contained in, attached
to, or displayed on, the resulting surface fragments. In this
context, the term "functional" is used to indicate that the
heterologous antigen-binding molecule(s) retain the capacity to
selectively bind the antigen of interest, while also remaining
attached to any bioparticle fragment (i.e., biofragment; see
below).
[0046] In some embodiments, the bioparticle is a cell. As will be
apparent to persons of ordinary skill in the art, the bioparticle
can be any cell that can be made to express, attach and/or display
a heterologous antigen-binding molecule on its surface and that can
retain its attachment and structural integrity upon fragmentation
of the bioparticle. In some embodiments, the cell is a microbial
cell, such as a yeast or bacterial cell. In alternative
embodiments, the cell is a plant or animal cell. In some
embodiments, the cells that contain rigid cell walls are selected
for use as bioparticles because the rigid cell wall can enhance the
fragment integrity after the fragmentation process.
[0047] In some embodiments, the bioparticle cell is a yeast cell.
Exemplary yeasts include yeast selected from the genera
Saccharomyces or Pichia, for example, Saccharomyces cerevisiae or
Pichia pastoralis. For example, yeast bioparticles have generated
by screening libraries of Saccharomyces cerevisiae displaying
human-derived single-chain variable antibody fragments (scFv) on
their surface. However, persons of skill in the art will recognize
that the present compositions are not limited to such embodiments,
but rather encompass any yeast amenable to display of heterologous
antigen-binding molecule on its surface using common recombinant
DNA techniques. See, e.g., Sambrook, et al. (2000) or Ausubel, et
al. (1999).
[0048] In other embodiments, the bioparticle cell is a bacterium.
The bacterium can be Gram positive or Gram negative. Exemplary
bacteria are selected from the genera Bacillus (Gram positive) and
Escherichia (Gram negative). Specific examples include Bacillus
megaterium and Escherichia coli. Transgenic bacteria have been used
to display a library of heterologous polypeptides, including scFv
antibodies, which are retained on the surface for subsequent cell
sorting. See, e.g., Georgiou, G., et al., "Display of Heterologous
Proteins on the Surface of Microorganisms: From the Screening of
Combinatorial Libraries to Live Recombinant Vaccines," Nat.
Biotechnol. 15:29-34, 1997. As above, persons of skill in the art
will recognize that the present compositions are not limited to
such embodiments, but rather encompass any bacterium amenable to
attachment or display of heterologous antigen-binding molecule to
its surface using common recombinant DNA techniques. See, e.g.,
Sambrook, et al. (2000) or Ausubel, et al. (1999).
[0049] In yet other embodiments, the bioparticle is a non-microbial
cell, such as an animal cell or a plant cell. For example, scFvs
have been displayed and isolated from human embryonic kidney 293T
(HEK-293T) cells (see, e.g., Ho, M. et al., "Isolation of Anti-CD22
Fv With High Affinity by Fv Display on Human Cells," Proc. Natl.
Acad. Sci. USA 103:9637-9642, 2006).
[0050] In other embodiments, the bioparticle is a cellular
organelle. An exemplary organelle is the ribosome, which has been
previously used to display large repertoires of antibodies and
antibody-like molecules. See, e.g., He, M. and Khan, F., "Ribosome
Display: Next-Generation Display Technologies of Antibodies In
Vitro," Expert Rev. Proteomics 2:421-430, 2005.
[0051] In other embodiments, the bioparticle is a virus. An
illustrative example is a bacteriophage. Use of bacteriophages to
display libraries of exogenous polypeptides has been established.
For example, using filamentous M13-derived bacteriophages, many
display libraries have been made by expressing the exogenous
polypeptides as fusions with the bacteriophage coat protein pIII.
As the virus is assembled within the host bacterium, the fusion
protein is transported to the bacterial periplasm and incorporated
into the phage particle. Additional M13 filamentous proteins that
have been utilized for fusion with the exogenous polypeptides
include pVI, pVII, pVIII, and pIX. In the context of antibody-like
polypeptides, the result is a library of diverse antibody-like
polypeptides with intact binding properties linked to the DNA that
encodes them, which enables the subsequent selection and
propagation of polypeptides exhibiting particular binding
properties.
[0052] The bioparticle fragment (i.e., biofragment) can be produced
by any method commonly known in the art. For example, the
bioparticle can be fragmented mechanically, such as with simple
mortar and pestle techniques, as described below. Based on the
bioparticle, a preliminary treatment step, such as lyophilization
or freezing, can be advantageous. Other fragmentation techniques
can include sonication, electroporation, and the like. In yet other
embodiments, fragmentation can be accomplished chemically, such as
by introduction of agents that disrupt external membranes of the
bioparticle.
[0053] The resulting biofragment is typically smaller than the size
of the initial bioparticle. For example, if the initial bioparticle
is a cell, for most embodiments the biofragment will likely be less
than 3 .mu.m, and in some embodiments less than 1 .mu.m, at the
greatest dimension of the biofragment. In some embodiments, the
biofragments are between about 1 .mu.m to about 500 .mu.m. In some
embodiments, the biofragments are between about 20 .mu.m to about
200 .mu.m. In some embodiments, the biofragments are between about
50 .mu.m to about 100 .mu.m. In yet other embodiments, such as
embodiments that are derived from cellular organelles or viruses,
the fragments are less than 0.5 .mu.m, less than 0.2 .mu.m, or less
than 0.1 .mu.m.
[0054] In some embodiments, the biofragments have increased
solubility in aqueous assay conditions over the initial bioparticle
from which they are derived. For example, as described above,
whole-cell yeast-scFv affinity reagents can have low solubility,
thus limiting their applicability in various assay conditions.
However, as described below in more detail, when the whole-cell
yeast-scFv are fragmented, the resulting yeast-scFv biofragments
are very soluble and are highly functional in antigen-detection
assays. Thus, in some embodiments, the biofragments are soluble or
semi-soluble in aqueous solutions. As indicated by the term
"semi-soluble", the biofragments do not necessarily have to be
completely soluble. However, the biofragments must be able to
sufficiently disperse so as to be useful in an affinity binding
assay. This characteristic can be readily observed and/or
established by routine methods. In some embodiments, the
biofragments are derived from larger bioparticles that are
insoluble or less soluble in equivalent solution conditions.
[0055] In some embodiments, the bioparticle fragment is isolated,
purified, or removed from bioparticle fragments (and potentially
other cellular or bioparticle debris) that do not contain a
heterologous antigen-bonding molecule, and/or bioparticles that
have not been disrupted or fragmented (e.g., whole-cell
bioparticles). In some embodiments, the isolation, purification, or
removal is merely partial, such that some debris remains. In some
embodiments, the isolation, purification, or removal is
substantial, such that the majority (e.g., 50% or more) of the
debris, or fragments not containing a heterologous antigen-bonding
molecule, are removed. In some embodiments, the bioparticle
fragments with at least one heterologous antigen-bonding molecule
can be removed from the other components of the solution or mixture
by affinity purification based on a particular antigen or epitope
tag contained in the heterologous antigen-bonding molecule.
Illustrative, non-limiting examples of suitable epitope tags
include c-myc, HA, FLAG-tag, GST, 6HIS, VSVg, V5, HSV, AU1, and
others that are well known in the art. As will be recognized by
persons of ordinary skill in the art, such epitope tags can be
optionally multimerized to create repeating units of the epitope
tag. As described below, the affinity-based isolation or
purification process can be performed during the assembly of an
antigen-detection assay system, where an immobilized epitope-tag
binding molecule binds to the epitope tag present in the
heterologous antigen-binding molecule. Other techniques to separate
the biofragments containing at least one heterologous
antigen-bonding molecule, from debris and/or biofragments that do
not contain at least one heterologous antigen-bonding molecule
include filtration, centrifugation, sedimentation, and other
techniques known in the art.
[0056] As used herein, the term "heterologous antigen-binding
molecule" is used to refer to any molecule that binds to an
antigen. The term "heterologous" specifically refers to the
characteristic that the antigen-binding molecule is not naturally
occurring in or on the bioparticle (or biofragment thereof), but
rather is caused to be expressed in and/or displayed on the
bioparticle by experimental manipulation. In preferred embodiments,
the heterologous antigen-binding molecule selectively binds to its
cognate antigen (e.g., the antigen of interest) as compared to a
non-cognate antigen. The term "selectively binds" is used to refer
to the enhanced affinity and avidity binding characteristics of the
heterologous antigen-binding molecule for the cognate antigen as
compared to the non-cognate antigen. For example, in some
embodiments, the heterologous antigen-binding molecule can bind to
its cognate antigen with 5%, 10%, 25%, 50%, 75% or greater
efficiency as compared to any non-cognate antigen. In preferred
embodiments, the heterologous antigen-binding molecule can bind to
its cognate antigen with an efficiency that is more than 2, 5, 10,
20 times or more as compared to binding to its non-cognate
antigen.
[0057] In some embodiments, the heterologous antigen-binding
molecule is an antibody-like molecule. As used herein, the term
"antibody-like molecule" encompasses antibodies or fragments
thereof, derived from any antibody-producing animal (e.g., fish,
reptiles, birds, and mammals, including mice, rats, rabbits,
camelids, and primates, including human) Unless otherwise stated,
exemplary antibody-like molecule can include antibodies such as
monoclonal, multispecific antibodies (e.g., bispecific antibodies),
chimeric antibodies, anti-idiotype antibodies, and may be any
intact molecule or fragment thereof, and of any isotype. Also, the
antibody-like molecule encompasses molecules that comprise any of
the foregoing, such as fusion proteins.
[0058] As used herein, the term "antibody fragment" refers to a
portion derived from or related to a full-length antibody,
generally including the antigen-binding or variable region thereof.
Illustrative examples of antibody fragments include Fab, Fab',
F(ab).sub.2, F(ab').sub.2 and Fv fragments, scFv fragments,
diabodies, linear antibodies, single-chain antibody molecules and
multispecific antibodies formed from antibody fragments.
[0059] As used herein, the term "single-chain antibody" refers to
an antibody fragment that contains at least one antigen-binding
region in a single polypeptide molecule. For example, as used
herein, the term "single-chain Fv" or "scFv" specifically refers to
an antibody fragment that comprises the V.sub.H and V.sub.L domains
of an antibody, wherein these domains are present in a single
polypeptide chain. Additionally, the Fv polypeptide further
comprises a polypeptide linker between the V.sub.H and V.sub.L
domains, which enables the scFv to form the desired structure for
antigen binding. An scFv can also be generated to be multivalent,
namely to contain multiple pairings of V.sub.H and V.sub.L domains
in a single polypeptide chain, where each pairing can bind to the
same or different antigen. Other exemplary single-chain antibodies
include single-chain Fab fragments (scFab) and nanobodies. The term
single-chain Fab fragments (scFab) refers to an antibody fragment
that comprises a single fragment antigen-binding region (Fab) of an
antibody in a single polypeptide chain, typically with a peptide
linker between the H and L chain fragments. The term "nanobody"
refers to an antibody fragment that consists of a single
polypeptide monomeric variable antibody domain that is able to
specifically bind antigens. Nanobodies can include V.sub.HH
fragments, which refers to fragments of heavy chain antibodies from
camelids, and V.sub.NAR fragments, which refers to fragments of
heavy-chain antibodies derived from cartilaginous fish.
[0060] In other embodiments, the heterologous antigen-binding
molecule is a T-cell receptor. Like antibodies, T-cell receptors
(TCR) are members of the immunoglobulin superfamily of proteins and
function to recognize and/or bind to antigens. In vertebrate immune
system, TCRs recognize antigens presented on the MHC. Native TCRs
exist in .alpha..beta. and .gamma..delta. dimeric forms, which are
structurally similar. When dimerized, the .alpha..beta. and
.gamma..delta. forms appear very similar to an Fab fragment of a
typical antibody. Accordingly, in the present embodiments, the
heterologous antigen-binding molecule comprises antigen-binding
portions of a TCR. As with antibodies, the antigen-binding portions
of a TCR include engineered single-chain TCRs and TCR fragments
comprising the variable regions of .alpha., .beta., .gamma. and
.delta. chains, alone or paired in various combinations. Display of
TCRs in single-chain and dimeric form on ribosomes, bacteriophage,
cell, or proteinaceous particle is described in International
Publication No. WO 2004/044004, incorporated herein by reference
for this purpose and in its entirety.
[0061] In the fragmented state, the biofragment displays on its
surface at least one heterologous antigen-binding molecule. As used
herein, the term "display" refers to the position of the
antigen-binding molecules in the surrounding aqueous environment
immediately around the biofragment. The antigen-binding domains of
the molecules are in communication with the surrounding environment
and are, thus, capable of coming into physical contact with and
binding their cognate antigens. However, as implied by the term
"display," the antigen-binding molecules remain anchored or
connected to the biofragment. In some embodiments, the heterologous
antigen-binding protein is a fusion with a domain of a protein that
is endogenous to the initial bioparticle and that spans the outer
surface (e.g., plasma membrane, cell wall, capsid, and the like).
Such domains are known in the art for various bioparticles. For
example, as described above, the display of exogenous proteins on
M13 filamentous bacteriophages can utilize fusions with coat
proteins pIII, pVI, pVII, pVIII, and pIX. Additionally, as
described below, libraries of yeast cells displaying human scFv
utilized Aga1-Aga2 to tether the human scFv to the yeast cell
walls. However, there is no requirement that the heterologous
antigen-binding molecule be displayed on the exterior side of the
bioparticle surface. Instead, in the original, non-fragmented
bioparticle the at least one heterologous antigen binding molecule
can be attached to or displayed on the internal or external side of
the bioparticle surface. Upon fragmentation, even previously
internal, surface-bound heterologous antigen binding molecules are
accessible to the external environment due to the fragmentation of
the bioparticle surface.
[0062] As used herein, the term "antigen of interest" refers to any
antigen that serves as a cognate antigen to the heterologous
antigen-binding molecule. It will be apparent to persons of
ordinary skill in the art that there is no limitation on the
character, type, or source of antigen in the practice of the
present invention. For example, embodiments of antigens can include
toxins, biomarkers for microbial or parasitic infection, biomarkers
for the presence of transformed cells, such as cancer cells,
biomarkers for a biological state, such as a disease state, and
endogenous biomarkers indicating a particular genotype or
phenotype. Antigens can be peptides, polypeptides, and non-protein
antigens. In some embodiments, the antigens are non-protein small
molecule compounds, such as drugs, metabolites, environmental
pollutants, and the like.
[0063] In another aspect, the described biofragment compositions
can be employed in methods for detecting and/or selectively binding
an antigen of interest in a sample, such as a biological sample. In
some embodiments, the biofragment compositions can be used as a
capture reagent that selectively binds to the antigen of interest
(i.e., molecules comprising the cognate antigen for the displayed
heterologous antigen-binding protein) and does not bind the other
non-cognate antigens present in the sample. Thus, any antigen of
interest that is bound to the biofragment composition can be
selectively removed from the other components of the sample.
Detection of binding can be accomplished according to various assay
formats known in the art. Illustrative examples are described in
more detail below. In other embodiments, the described biofragment
compositions can be used as part of a detection reagent that
selectively binds to the antigen of interest (i.e., molecules
comprising the cognate antigen for the displayed heterologous
antigen-binding protein) that have been previously captured, and
does not bind the other non-cognate antigens present in the
captured sub-sample.
[0064] Accordingly, in one embodiment, the method comprises
contacting a sample with a biofragment composition as described
herein under conditions sufficient to permit the binding of the
biofragment compositions (via the heterologous antigen-binding
protein) to the antigen of interest, and detecting the binding of
the biofragment compositions to the antigen of interest.
[0065] In some embodiments, the method comprises immobilizing the
biofragment composition. As will be recognized in the art, the
biofragment compositions can be immobilized via attachment directly
or indirectly to an appropriate solid support. This can be
performed through use of an immobilized epitope-binding molecule,
such as described in more detail below. By virtue of
immobilization, the biofragment compositions can serve as an
antigen-specific capture reagent to facilitate detection,
isolation, and/or purification of the antigen.
[0066] In some embodiments, the method further comprises contacting
the sample with a detection reagent that also binds to the antigen
of interest. While it is preferred that the detection reagent
specifically binds to the antigen of interest, it is not critical
that it demonstrates a high degree of specificity because the
specificity is provided in the assay by the biofragment
composition. However, it will be apparent that the detection
reagent should not compete with the binding of the biofragment
composition to the antigen of interest. Nonlimiting examples of the
detection reagent include polyclonal antibodies (e.g., as included
in a polyclonal antiserum), monoclonal antibodies, TCRs, lectin,
and any known natural binding partner to the antigen.
[0067] In a further embodiment, the detection reagent is detectably
labeled. Detectable labels can include, but are not limited to,
functional enzymes, chemiluminescent molecules, fluorescent
molecules, phosphorescent molecules, radioactive labels, spin
labels, redox labels, and the like, specific examples of which are
well known in the art.
[0068] In some embodiments, the detection reagent provides a
detectable signal with the further participation of a reporter
reagent, which is also provided in the method. The reporter reagent
performs as a secondary detection reagent, wherein the reporter
reagent binds to a component common to the (primary) detection
reagents.
[0069] In preferred embodiments, the method contains a step wherein
the biofragment/antigen/detection reagent complex is separated from
any unbound detectable label. In a standard ELISA context, the
complex is typically immobilized on a solid substrate, such as the
bottom of a well. The unbound reagent with a detectable label is
removed by one or more rinse procedures. In some methods of the
present invention, no immobilization is required by virtue of the
size of the biofragment, which facilitates the separation of the
labeled biofragment/antigen complex from unbound detectably-labeled
reagent and/or unbound antigen. In other methods, the biofragment
can be immobilized to solid surfaces such as a biofragment plate or
electrode. Simple wash protocols can be used. In some embodiments,
centrifugation can be employed to generate pellets followed by
resuspension in a wash buffer. This can be performed once or in a
series to selectively isolate the labeled biofragment/antigen
complex from unbound detectably label reagent and/or unbound
antigen.
[0070] In some embodiments, the labeled biofragment/antigen complex
is separated from unbound detection reagent, followed by detection
and/or quantification by use of various assays known in the art.
For example, an antibody sandwich flow cytometric assay (ASFC) can
be used to quantify antigen binding by the biofragment. In another
embodiment, the labeled biofragment/antigen complex is detected
and/or quantified by use of an ELISA-like enzymatic assay, which
does not necessarily require immobilization of the antigen/capture
reagent complex. The labeled biofragment/antigen complex is
quantified by use of a detection reagent bound to an enzyme with
detectable activity, such as horseradish peroxidase (HRP). Upon
separation of the labeled biofragment/antigen complex from unbound
detection reagent, the activity of the enzyme is quantified by
virtue of a characteristic of the product of enzyme activity, such
as a color change, or light absorbance at a specific
wavelength.
[0071] In yet another embodiment, binding of the biofragment
composition to the antigen complex is detected and quantified
without the use of a labeled reporter, but rather is detected and
quantified using a competitive inhibition assay. In a
representative example, the assay comprises further contacting the
sample with a detectably-labeled antigen of interest, wherein
binding of the biofragment to any unlabeled antigen of interest
from the sample blocks binding of the biofragment to the
detectably-labeled antigen of interest. By virtue of the
competitive binding with the biofragment, binding of the antigen of
interest results in a detectable reduction of labeled antigen of
interest bound to the biofragment compared to a control sample not
containing any antigen of interest. See, e.g., Gray, S. A., et al.,
Biotechnol Bioeng 105:973-981 (2010).
[0072] In yet another embodiment, a separate detection reagent is
not required. Instead, the successful "capture" of a cognate
antigen by the biofragment composition can be detected
electrochemically. For example, in one embodiment, the binding of
the biofragment composition to the cognate antigen can be detected
with techniques such as by faradaic electrochemical impedance
spectroscopy, which is described below in more detail. Briefly, in
faradaic electrochemical impedance spectroscopy a conductive or
semi-conductive substrate, such as an electrode, is used as a solid
support. The biofragment composition is immobilized directly or
indirectly to the conductive or semi-conductive surface of the
substrate, through conventional methods. By using an electroactive
molecule, the binding of the cognate antigen is detected by sensing
the differences in electrical (or current) transfer resistance when
an antigen binds to the biofragment composition, as compared to
when the antigen is not present. The additional chemical bulk of
the antigen, in combination with the heterologous antigen-binding
agent and its connected bioparticle fragment, and potentially other
tether constructs, contributes to a barrier to the interfacial
electron transfer among the electroactive molecules, which is
detected through the electrode via any commonly known device that
can monitor electrical current, potential, or impedance.
[0073] The foregoing presentation of the method embodiments are
generally in the context of the biofragment composition serving as
a capture reagent, permitting subsequent detection (through
affinity or electrochemical techniques). However, the invention is
not limited to this aspect. Persons of ordinary skill in the art
will recognize that alternative capture reagents can be used that
incorporate antigen-specific binding molecules. Non-limiting
examples include magnetic beads conjugated to polyclonal antibodies
(antiserum), immobilized antibodies, antibody-like molecules, or
fragments thereof, lectins, TCRs, or any naturally occurring
binding partner. After capturing the cognate antigen from the
sample, the biofragment compositions of the present invention can
be used as part of a detection reagent. Detection/quantification of
binding of the biofragment composition (or detection reagent
comprising the biofragment) to the captured antigen can be
performed by incorporating any well-known detectable label, or by
use of a detectably-labeled secondary detection reagent specific
for a component of the biofragment composition.
[0074] In some embodiments, the sample is a biological sample.
Non-limiting examples of biological samples include blood, urine,
sputum, mucus, saliva, cerebral spinal fluid, tissues, stool, or
processed derivatives thereof. Use of such samples can facilitate
the use of the methods of the present invention for purposes of
detecting particular biological states, the presence of pathogens,
parasites, or to determine particular phenotypes, depending on the
antigen of interest. In additional embodiments, the sample is an
environmental sample, such as a water sample. In additional
embodiments, the sample is from a nutrient source, such as from the
food or potable water supply, for example, milk, juice, meat, crop
samples, animal feed, and the like, or any processed derivatives
thereof. The methods of the present invention can be applied to the
monitoring of these samples to monitor for toxins and contaminants,
or, for example, in efforts to monitor against agents used in acts
of bioterrorism.
[0075] In another aspect, the disclosure provides a method of
detecting the presence of an antigen of interest in a biological
sample. The method comprises contacting a sample, such as a
biological sample, to the biofragment composition described herein
under conditions sufficient to permit the binding of the antigen of
interest to the biofragment composition. The biofragment
composition is immobilized, directly or indirectly, to a conductive
or semi-conductive electrode surface. The method also comprises
measuring the electron transfer resistance at the electrode surface
in the presence of an electroactive molecule, wherein binding of
the antigen of interest to the biofragment composition is detected
by a change in the electron transfer resistance as compared to the
electron transfer resistance when the antigen of interest is not
present.
[0076] As used herein, the term "electroactive molecule" is any
molecule that can participate in or facilitate the transfer of
electrons (e.g., electrical current) in an aqueous solution. Such
electroactive molecule can be any appropriate electrolyte, as known
in the art of electrochemical impedance spectroscopy. For example,
the electroactive molecule can be a redox probe, such as
[Fe(CN).sub.6].sup.3-/4-, and the like.
[0077] The electrode surface can be any surface that is conductive
or semi-conductive, such that it is appropriate for detection of
electrical potential, current, or impedance. An example is a
gold-surface electrode, including Gold (AU) marcrodisk working
electrodes or screen-printed gold electrodes, each of which are
described in more detail below.
[0078] In some embodiments, the biofragment composition is
immobilized directly to the conductive or semi-conductive electrode
surface. There are numerous known and commonly used methods to
immobilize affinity agents, such as the biofragment compositions
described herein, to electrode surfaces. For example, the
biofragment composition can be immobilized to the conductive or
semi-conductive electrode surface through known methods, including
chemisorbant or physiosorbant crosslinking.
[0079] In some embodiments, the biofragment composition is
immobilized indirectly to the conductive or semi-conductive
electrode surface via one or more intervening tether constructs.
The term "intervening tether constructs" can include a layer that
directly anchors the complex to the electrode surface. The anchor
layer can be a protein, such as BSA, an organic molecule, or an
inorganic molecule. The anchoring construct can be attached
directly to the electrode surface by, for example, chemisorbant or
physiosorbant crosslinking. The biofragment composition can be
linked to the anchoring construct directly, using known approaches,
such as the appropriate use of biotin/streptavidin interaction,
click chemistry, or epitope binding reagent binding to an affinity
tag in the biofragment composition. In some embodiments, there are
additional intervening tether constructs, which link the
biofragment composition to the anchoring construct (and thus the
electrode surface). For example, as described below, a biotinylated
BSA layer on the electrode is linked to a multivalent streptavidin
molecule. The streptavidin molecule is linked to a biotinylated
epitope tag-binding antibody, which specifically binds to an
epitope tag (e.g., HA) incorporated into the scFv of the
biofragment composition. See also FIG. 1A.
[0080] Accordingly, in some embodiments, the present method
includes the step of immobilizing the biofragment composition to
the electrode surface (directly or indirectly with tether
constructs). In some embodiments, the immobilizing step comprises
attaching an anchor construct to the electrode, immobilizing an
affinity-tag binding molecule to the anchor construct, and
contacting the affinity-tag binding molecule with the biofragment
composition. In these embodiments, the heterologous antigen-binding
molecule of the biofragment composition comprises an affinity tag,
such as described above. As described below, the scFv component of
the biofragment included an HA epitope tag, which was bound by an
anti-HA antibody, which in turn was linked via biotin/streptavidin
interactions with the BSA anchor on the electrode.
[0081] In some embodiments, this immobilizing step serves to
isolate, purify, or remove the biofragment compositions with the at
least one heterologous antigen-binding molecule from fragments of
the bioparticle that do not have at least one heterologous
antigen-binding molecule (and/or other debris or unfragmented
bioparticles). Accordingly, some embodiments of the method include
rinsing steps after any of the assembly steps addressing the
anchor, additional intermediate tether components, and/or the
biofragment composition.
[0082] In another aspect, the disclosure provides a method for
making the biofragment composition. The method can include the
initial step of generating a bioparticle that contains a
heterologous antigen-binding molecule. As described above, this can
be accomplished by causing the expression of the heterologous
molecule in a cell or other particle of interest. The expressed
heterologous protein is caused to attach to, or assemble upon the
outer surface (either internally or externally on the surface) of
the bioparticle. The bioparticle is then fragmented according to
any appropriate techniques, such as mechanical disruption of the
particle surface using a mortar and pestle. In some embodiments,
the biofragments are isolated or purified from the other components
of the solution resulting from the mechanical disruption.
[0083] The disclosed method can be incorporated into methods of
detecting the antigen. For example, in one embodiment, the step of
immobilizing the biofragment compound to the electrode surface (or
other solid support) can coincide with the step of isolating,
removing, or purifying the biofragments with at least one
heterologous antigen-binding molecule in part, substantially, or
completely, from other biofragments in the mixture. Thus, the
immobilizing step described above can comprise additional steps,
such as contacting the affinity-tag binding molecule with the
plurality of bioparticle fragments to the affinity-tag binding
molecule, and removing the bioparticle surface fragments that
remain unbound to the immobilized affinity-tag binding molecule.
Furthermore, the immobilizing step described above can also
comprise (or be preceded by) the initial step of disrupting the
surface of one or more bioparticles that have at least one attached
heterologous antigen-binding molecule attached thereto to produce a
plurality of bioparticle surface fragments.
[0084] In another aspect, the present disclosure provides an
antigen detection system. The system comprises the biofragment
composition described herein. The biofragment composition is
immobilized directly or indirectly to a conductive or
semi-conductive electrode surface, as described herein. The system
also comprises an electroactive molecule, as described herein, and
a device to monitor electric current, electric potential, and/or
electric impedance. Such devices are regularly used and commonly
available. Illustrative devices useful for implementation in the
system include a potentiostat and a galvanostat. Such devices can
be battery operated, thus facilitating the implementation of the
system into simple and convenient point of care devices and set-ups
that can be operated in the field where consistent access to
electricity may not be available. The electrode surface can be any
conductive or semi-conductive electrode, for example, a
screen-printed gold electrode, as described herein.
[0085] In another aspect, the present disclosure provides a device
for detecting an antigen of interest, wherein the device implements
the system and biofragment probes described herein.
[0086] In another aspect, the present disclosure provides methods
for validating a candidate antigen as a biomarker for a biological
state, as described in WO 2012/159075, incorporated herein by
reference. Briefly, an antigen of interest can be contacted to a
library of bioparticles or biofragments derived from bioparticles
with heterologous antigen-binding molecules. In other embodiments,
the library can be contacted with one or more antigens obtained
from target and control samples (such as disease state and healthy
state). The binding of the antigen or antigens is determined, and
the bioparticles that bind to the candidate biomarker antigens (or
the bioparticles from which the binding biofragments were derived)
are propagated to produce a clonal or near clonal population of
bioparticles that can serve as a source of biofragments affinity
reagents. The bioparticles or biofragments thereof can be stored,
such as through lyophilization, as described in WO 2012/159075,
incorporated herein by reference.
[0087] The following is a description of the initial development of
a cell-free affinity reagent comprising a yeast-scFv biofragment
probe that can selectively bind an antigen of interest.
Furthermore, the description provides a representative method for
using the affinity reagent in an electrochemical detection assay
that incorporates a gold electrode and does not require labels or
an additional set of antigen-specific detection or capture
reagents. This is also described in Grewal, Y. S., et al.,
"Label-free electrochemical detection of an Entamoeba histolytica
antigen using cell-free yeast-scFv probes," Chem. Commun.
49:1551-1553 (2013), hereby expressly incorporated by reference in
its entirety.
[0088] Abstract: Inexpensive, simple and quick detection of
pathogen antigens in human samples is a key global health
objective. Limiting factors include the cost and complexity of
diagnostic tests that utilize antibody probes. Herein, we present a
method for label-free electrochemical detection of a protein from
the enteric pathogen Entamoeba histolytica using cell-free
yeast-embedded antibody-like fragments (yeast-scFv) as novel
affinity reagents.
[0089] Description: The waterborne pathogen E. histolytica is a
prevalent but treatable disease that is estimated to cause 100,000
deaths annually in developing countries. Prior detection techniques
relied on microscopy and serology. Microscopy tests cannot
distinguish between E. histolytica and closely related
non-pathogenic commensals that also occur in stool, most notably E.
dispar. Serological tests, which detect serum antibodies against E.
histolytica, cannot distinguish between past and current infection.
For these reasons molecular tests, such as ELISA, have become
preferred diagnostics to identify E. histolytica infection, due to
their specificity and sensitivity.
[0090] ELISA-based methods have the limitation of being reliant on
highly specific affinity reagents, typically monoclonal antibodies
(mAbs). The considerable time and resources required for the
generation of mAbs is a bottleneck in biomedical research and the
development of new diagnostic tests. Potential alternatives to mAbs
are fragments of antibodies known as single-chain variable
fragments (scFv). In contrast to traditional mAbs derived from
vertebrate animals, scFv reagents can be cheaply and rapidly
selected from yeast-display and other libraries. In yeast display,
libraries of genetically engineered Saccharomyces cerevisiae cells
display on their surfaces diverse scFv molecules derived from human
mRNA. By using fluorescence-activated cell sorting (FACS), it is
possible in a 2-3 week process to screen yeast display libraries
for clones that bind specifically to antigens. If needed, affinity
enhancement can be completed in another 3-4 weeks. Biosensors
incorporating scFvs for specific antigen detection have been
described.
[0091] Although many useful scFvs have been reported, most scFvs
derived from display libraries perform unsatisfactorily in
solution. Like natural antibodies, antibody-like fragments culled
from display libraries are products of selection. Yeast-displayed
scFv are selected by FACS for affinity and stability when bound via
Aga1-Aga2 linkages to yeast cell walls. Unfortunately, scFv that
have excellent activity on yeast surfaces usually lose their
activity in solution, an environment for which they were not
selected. This problem has limited the penetration of scFv into
diagnostic practice.
[0092] Affinity reagents composed of lyophilized whole yeast cells
with displayed scFv (yeast-scFv) have been shown to be viable,
cheap and quick alternatives to generating mAbs or soluble scFv for
use in immunoassays. Yeast-scFv are robust and renewable reagents
that can be produced in vast quantities at low cost. However these
whole-cell reagents are insoluble and too large for many diagnostic
applications. Moreover, they required the use of labeled polyclonal
antibodies to detect antigen binding to the yeast-scFv particles.
Although it was not necessary that the detection antibodies be
highly specific to the antigen (monoclonal specificity was
conferred by the yeast-scFv reagent), the requirement for a
traditional animal-derived detection antibody diluted the benefits
of using yeast-scFv.
[0093] To enable the use of yeast-scFv affinity reagents as full
and practical alternatives to traditional antibodies, the current
report describes two new approaches. First, cell-free yeast-scFv
reagents, also referred to herein as "yeast-scFv biofragments",
were generated by mechanical fragmentation of whole yeast-scFv
cells, followed by combined mechanical and affinity-based
purification of semi-soluble cell wall fragments bearing displayed
scFv. Second an electrochemical (EC) approach was used to detect
antigen binding to cell-free yeast-scFv, without the need for
animal-derived detection antibodies. These approaches were combined
to generate a specific, sensitive sensor for a candidate E.
histolytica cyst protein.
[0094] The principle of faradaic electrochemical impedance
spectroscopy (F-EIS) was used for label-free EC detection. This is
one of the most effective methods for the label-free detection of
biomolecules and for probing the build-up of the biomaterials
sensing film on the electrodes. In F-EIS, the successful capture
and detection of the biomolecule of interest, here an E.
histolytica protein, is observed as a change in the capacitance and
interfacial electron transfer resistance of a conductive or
semiconductive electrode modified with the scFv capture probe. A
typical shape for a F-EIS spectrum at a disk macroelectrode,
presented in the form of a Nyquist plot (e.g., Z' versus Z'' at
variable frequencies, where Z' and Z'' are the real and imaginary
components), includes a semicircle region lying on the Z' axis
followed by a straight line The semicircle portion, is observed at
higher frequencies and corresponds to the electron-transfer-limited
process. See, e.g., E. Katz and I. Willner, Electroanalysis, 15:
913-947 (2003) and A. J. Bard and L. R. Faulkner, Electrochemical
Methods: Fundamentals and Applications, John Wiley & Sons,
2000. The diameter of the semicircle corresponds to the
charge-transfer resistance at the electrode surface, R.sub.ct (also
referred to in the art as the electron transfer resistance, or
R.sub.ct). Therefore, the build-up of an immunosensing layer and
scFv-antigen complex formation can be followed by F-EIS, where the
change in impedance of the electrode surface and its interface to
the electrolyte solution containing a redox probe (e.g.,
[Fe(CN).sub.6].sup.3-/4-) at different stages of the immunosensor
fabrication is measured in the form of its R.sub.ct.
[0095] FIG. 1A outlines this approach for using a cell-free
yeast-scFv biofragment reagent in the label-free detection of an E.
histolytica antigen. Briefly, a biolayer on a gold (Au) surface is
formed with biotinylated BSA (bio-BSA). Multivalent streptavidin is
used to link the bio-BSA to a biotinylated anti-human influenza
hemagglutinin tag antibody (bio anti-HA). This complex is used to
capture cell-free yeast-scFv biofragments by virtue of an HA
antigen tag cloned into the recombinant scFv construct. The bound
yeast-scFv fragment is then used to capture the target E.
histolytica antigen (in this study, specifically protein EHI
115350, called `350` herein). To assure that the fragments were
small enough to be useable in the bioassay, dynamic light
scattering (DLS) measurements of the yeast-scFv fragments after
filtration through a 0.1 .mu.m filter was performed. The DLS data
confirmed that fragments existed in the sub-100 nm size range (see
FIG. 2), allowing for attachment of yeast-scFv fragments to bio
anti-HA.
[0096] The attachment of the bio-BSA, streptavidin, yeast-scFv
biofragment, and E. histolytica antigens on the gold electrode was
followed by the F-EIS and differential pulse voltammetry (DPV)
(see, e.g., representative plots in FIGS. 1A and 1B). The BSA
layer, in combination with subsequent attachment of streptavidin
and antibody, act as a barrier for the interfacial electron
transfer reaction of the [Fe(CN).sub.6].sup.3-/4- process,
resulting in an increase in R.sub.ct. When we monitored R.sub.ct
generated by the [Fe(CN).sub.6].sup.3-/4- process before and after
protein binding, there was a clear correlation between the presence
of the target E. histolytica antigen and the increases of the
R.sub.ct (FIG. 3). The presence of the E. histolytica antigen
appears to further block the [Fe(CN).sub.6].sup.3-/4- process from
accessing the electrode surface effectively. The bare gold
electrode (i) gave rise to the lowest semicircle domain indicating
the fastest electron transfer (e.g., the lowest R.sub.ct) followed
by the bio-BSA/streptavidin-coated gold electrode (ii), bio-anti-HA
(iii), yeast-scFv antibody immobilized electrode (iv), and target
antigen (100 pg/mL) (v). These results indicate the successful
stepwise binding of the biomolecules on the sensor surface.
[0097] The risk of false-positive responses for targets at low
concentrations is well-known when using a detection technique based
on attenuation of the interfacial electron transfer reaction of a
redox process. To assess the risk of achieving false-positive
responses in F-EIS, a series of parallel independent DPV
measurements were conducted. FIG. 3B shows the differential pulse
profiles, where the peak current decreases in response to
increasing the hindrance of the interfacial electron transfer
reaction of the [Fe(CN).sub.6].sup.3-/4- process. This is in line
with the results observed in Faradaic EIS by the same
electrode.
[0098] The specificity of the immunosensor towards `350` antigen
was examined by attempting to capture an antigen that was
nonspecific to the immobilized yeast-scFv probes. The Jacob protein
of E. histolytica was previously shown not to bind with
350-specific yeast-scFv. Non-specific binding of the Jacob protein
to the cell-free yeast-scFv probes was evaluated by using F-EIS and
DPV measurements. A relatively high concentration of the Jacob
protein (500 pg/mL) was used to maximize detection of background
binding. A slight increase in the impedance (e.g., R.sub.ct value)
and decrease in the DPV peak current (FIGS. 4A (i) and 4B (i)) were
seen for the
bio-BSA/streptavidin/bio-anti-HA/yeast-scFv/Jacob-coated electrode
compared to that of the
bio-BSA/streptavidin/bio-anti-HA/yeast-scFv-coated electrode
(dotted line in FIG. 4A). A likely explanation for this observation
was that the traditional BSA blocking method used in this approach
could allow some degree of non-specific adsorption of the Jacob
antigen. However, the signal changes for 500 pg/mL Jacob antigen
were smaller than that produced by the target `350` antigen even
when the latter was present at 50-fold lower concentration (10
pg/mL). This indicates that label-free immunosensing with a
cell-free yeast-scFv reagent has specificity toward the target
antigen.
[0099] To further assess whether the yeast cell wall fragment may
contribute to non-specific adsorption of antigens, a second yeast
scFv fragment that is specific to an orthogonal E. histolytica
antigen (named `780`) (hereafter referred to as yeast-scFv-2) was
used as a control. FIGS. 4A(ii) and 4B(ii) show the impedance and
DPV responses obtained for 500 pg/mL `350` antigen at yeast-scFv-2
coated electrode. Compared to the response for 10 pg/mL `350`
antigen at cognate yeast-scFv coated sensing layer (FIGS. 4A (iv)
and 4B (iv), the use of yeast-scFv-2 significantly decreased the
sensor impedance (e.g., lower R.sub.ct) and increased the DPV peak
current, even when a 50-fold higher concentration of `350` antigen
was used. Thus, the non-cognate yeast-scFv-2 reagent failed to
capture `350` antigen with the same efficiency as the cognate
yeast-scFv reagent. It was also noted that a similar R.sub.ct and
peak current values to Jacob antigen were observed, which might
indicate a low level of nonspecific adsorption of antigen on yeast
cell wall.
[0100] To assess the background noise, an assay was performed which
excluded the yeast-scFv layer (FIGS. 4A (iii) and 4B (iii)). This
assay detected non-specific interaction and adsorption of the `350`
antigen on the bio BSA/streptavidin/bio anti-HA electrode. The
R.sub.ct and DPV peak currents without yeast-scFv are comparable to
the R.sub.ct and peak currents to the bio anti-HA surface (see FIG.
3(iii) versus FIG. 4(iii)). These results demonstrate that
detection of `350` antigen by the label-free assay is a function of
specific interactions between the cell-free yeast-scFv reagent and
the antigen, and not to non-specific interactions between the
antigen and other components of the assay.
[0101] To assess the dynamic range for detection of `350` antigen,
the percent changes in DPV current responses (see below Example for
illustrative calculation details) were measured before and after
incubation of the yeast-scFv-modified electrode with designated
concentration of `350` antigens (10 pg/mL to 10 ng/mL). Signals
increased quantitatively with antigen concentration (FIG. 5).
Saturation of the Au surface begins to occur at 2500 pg/mL (3.5
.mu.M) of 350 antigen. Detection of the antigen above background
was confirmed down to 100 pg/mL (558 pM). This concentration of
antigen was similar to the limit of detection of the same antigen
by a whole yeast-scFv probe used in combination with fluorescently
labeled polyclonal signal antibody, as described previously. A
precise lower limit of detection was not determined in this
experiment.
[0102] Conclusion: It is demonstrated herein that a label- and
cell-free electrochemical immunoassay towards an E. histolytica
antigen using antibody fragments embedded in yeast cell wall
fragments function as capture probes. The principle of this
cell-free yeast-scFv based assay is not limited to E. histolytica
350 antigen, because the immunosensor could be fabricated towards
any protein-based disease marker by selecting new yeast-scFv
biofragments against any such antigen. Moreover due to the high
sensitivity, technological simplicity, and quantitative output of
label-free detection using yeast-scFv capture probes, as compared
to flow cytometer based assay, this immunoassay has excellent
potential to translate into a diagnostic application.
[0103] The following is a description of a subsequent, expanded
study including the generation of additional cell-free affinity
reagents comprising yeast-scFv biofragments that can selectively
bind other antigens of interest. Furthermore, the described
yeast-scFv biofragments were applied in an electrochemical
detection assay that, as above, does not require labels or an
additional set of detection reagents. However, the electrochemical
detection assay described below incorporates the use of disposable
(screen-printed) electrodes that have the advantage of very low
cost. Finally, the study described below establishes that the
yeast-scFv biofragments can specifically bind and allow detection
of E. histolytica antigen in human stool samples, demonstrating the
utility of the reagents and detection method in point of care
situations.
[0104] Abstract: The time and costs associated with monoclonal
antibody production limit the potential for portable diagnostic
devices to penetrate the market. Replacing the antibody with a
low-cost alternate affinity reagent would reduce the costs of
diagnostic development and use, and lead to new portable diagnostic
devices towards many diseases. Herein, low-cost affinity reagents,
yeast-scFv biofragments, are described. These biofragment affinity
reagents can be integrated into more traditional detection assay
system, or used in a novel, label-free electrochemical based
detection of antigens. As demonstrated herein, the label-free
electrochemical-based detection can incorporate commercially
available, inexpensive, and portable screen-printed electrodes to
detect antigens of interest, such as E. histolytica cyst antigens.
As described, the biosensor was able to detect antigen at
concentrations of antigen down to 10 pg/mL in buffer with an
inter-assay reproducibility of (% RSD, n=3) 4.1%. The ability of
two differently engineered yeast-scFv biofragments to each
specifically detect their cognate E. histolytica cyst antigens was
demonstrated in a biological matrix derived from human stool.
Because of the simple, inexpensive, and sensitive nature of this
methodology, it provides a sensitive and low-cost alternative to
immunosensors based on antibody-target recognition.
[0105] Introduction: Developing countries and remote areas require
diagnostics that are portable, low-cost, quick, and easy to use, to
ensure patients are expeditiously and accurately treated to control
the spread of infectious disease. In these regions, laboratory
tests are often not viable for reasons of cost and logistics.
Screen-printed electrodes are inexpensive single-use electrodes
that are produced by printing various inks, such as gold and
carbon, on different types of plastics or ceramics. Due to their
relative low cost compared to traditional electrode materials,
screen-printed electrodes can be suitable components in future
point-of-care devices. Electrochemical biosensors utilizing
screen-printing technology have found commercial success for
diabetes management, and have been demonstrated for the detection
of various waterborne pathogens.
[0106] Entamoeba histolytica (E. histolytica) is waterborne
pathogen which causes up to 100,000 deaths annually in developing
countries, and as such, it has been the focus of diagnostic
development to accurately detect E. histolytica infection at point
of care. Microscopy and serology are common diagnostic techniques,
however, these are (respectively) inadequate in accurately
identifying E. histolytica from closely related non-pathogenic
commensals in stool and discriminating from past and current
infection. Additionally, PCR tests towards E. histolytica are
increasingly common, but they are too expensive for most settings
where E. histolytica disease is endemic. New specific and sensitive
detection tests are required to overcome these limitations.
Molecular tests, such as enzyme-linked immunosorbent assay (ELISA),
are able to fulfill these criteria, and are now favored tests to
identify E. histolytica infection.
[0107] However, ELISA-based methods are limited by their dependence
on highly specific affinity reagents, typically monoclonal
antibodies (mAbs). The generation of mAbs necessitates considerable
costs in time and resources. This has constrained advancements in
biomedical research and diagnostic development. Single-chain
variable fragments (scFv) are affinity reagents which have the
potential to overcome the limitations imposed by mAbs. Unlike
traditional vertebrae animal-derived mAbs, scFv reagents can be
inexpensively and quickly selected from a yeast- (or phage-)
display library.
[0108] There are numerous demonstrations of biosensors
incorporating scFv affinity reagents, however, many scFvs derived
from display libraries perform unsatisfactorily in solution. ScFv
reagents culled from a display library are productions of
selection. Unfortunately, selected scFv fragments, which have
excellent activity on yeast surfaces, often lose their activity
once in solution, an environment for which they were not selected.
This decrease in activity has hindered adaption of scFv into
diagnostic practice. To address this limitation, lyophilized whole
yeast cells with displayed scFv (yeast-scFv) have been shown to
function directly as affinity reagents and have been developed as
low-cost, renewable alternatives to mAbs. Yeast-scFv can be quickly
produced in vast quantities at a much lower cost than mAbs.
However, yeast-scFvs are insoluble and too large for the adaption
into many diagnostic applications. Yeast-scFv also require labeled
secondary polyclonal antibodies to detect antigen binding to the
yeast-scFv particles, hence complicating assay development and
performance.
[0109] To address yeast-scFv limitations, cell-free yeast-scFv
biofragment affinity reagents were developed by mechanical
fragmentation of yeast-scFv cells. Cell wall fragments bearing
displayed scFv were enriched by binding to surface-attached
antibodies specific to the scFv's epitope tags. These reagents,
also referred to herein as yeast-scFv biofragments, were developed
as a replacement for monoclonal antibodies. See Grewal, Y. S., et
al., Chem. Commun. 49:1551-1553 (2013), and the above description.
This concept demonstrated the ability of the yeast-scFv
biofragments to detect antibody/antigen capture combinations in a
defined buffer medium, using laboratory-dependent gold disc
macroelectrodes.
[0110] Faradaic electrochemical impedance spectroscopy (F-EIS) is a
highly effective method for the label-free detection of
biomolecules. Successful capture and detection of the biomolecule
of interest using a yeast-scFv biofragment capture probe causes an
observable change in the capacitance and interfacial electron
transfer resistance of a conductive electrode. An F-EIS spectrum on
an electrode (e.g., screen-printed electrode) is commonly presented
in the form of a Nyquist plot with Z' versus Z'' at variable
frequencies, and where Z' and Z'' are the real and imaginary
components. At higher frequencies, the semicircle portion of the
Nyquist plot is observed, which corresponds to the
electron-transfer-limited process. The semicircle diameter is
directly related to the electron-transfer resistance at the
electrode surface, R.sub.ct. Consequently, stepwise construction of
the immunosensing layer and capture of antigen by the yeast-scFv
biofragment complex can be observed by F-EIS, where the impedance
change of the interface between the electrode surface and
electrolyte solution, containing a redox probe (e.g.,
[Fe(CN).sub.6].sup.3-/4-), is measured in the form of its
R.sub.ct.
[0111] To develop and demonstrate yeast-scFv biofragments as
alternative affinity reagents in diagnostics, these inexpensive
affinity reagents were combined with commercially available
disposable screen-printed gold electrodes, in place of the more
expensive gold disk electrodes used for the initial proof of
concept (described above and in Grewal et al., 2013). The system
was validated by its use to detect recombinant E. histolytica
antigens spiked into a complex biological matrix derived from human
stool. Furthermore, a second set of yeast-scFv biofragments
detecting an alternative E. histolytica antigen was examined with
this system. This new combination indicates that yeast-scFv
biofragments, like mAbs, can routinely be engineered to
specifically capture any antigen of interest. The combination of
yeast-scFv biofragments, the screen-printed electrode platform, and
the ease of label-free electrochemical detection allows for simple,
quick, and cheap analysis of antigens, such as antigens from such
pathogens as E. histolytica.
[0112] Results and Discussion: FIG. 1A outlines the approach for
the label-free detection of E. histolytica antigens using
yeast-scFv biofragment affinity reagents on electrodes (e.g.,
screen-printed electrodes). Briefly, the gold electrode (AU) is
coated with a biolayer of biotinylated BSA (Bio-BSA). Streptavidin
is then used to link the bio-BSA to a biotinylated anti-human
influenza hemagglutinin tag antibody (Bio anti-HA). A yeast-scFv
biofragment (prepared from yeast-scFv clone `350-E2` or `030-L`) is
then captured by the use of a HA antigen tag cloned into the
recombinant scFv construct. The bound yeast-scFv biofragment is
then used to capture the target E. histolytica antigens (E. his
antigen, e.g., `350` or `030). The utilized yeast-display library
was constructed with the scFv already fused to HA and c-myc tags.
Thus, beyond the 2-4 weeks required to isolate the yeast-scFvs,
only a single, commercially available ("off-the-shelf")
biotinylated anti-HA mAb was required to build the assay. This
approach is far more cost effective than making monoclonal
detection antibodies for every different antigen of interest.
[0113] The attachment of the bio-BSA, streptavidin, bio-anti-HA,
yeast-scFv biofragments and E. histolytica antigens on the gold
coated screen-printed electrode was measured by F-EIS (FIG. 6). The
assay complex blocks the interfacial electron transfer reaction of
[Fe(CN).sub.6].sup.3-/4-, subsequently increasing the R.sub.ct. An
increase in R.sub.ct is observed from the successive blocking of
the electrode surface with the stepwise attachment of the
streptavidin, the bio-anti-HA, and the yeast-scFv biofragment onto
the bio-BSA modified screen-printed electrode (FIG. 6).
Furthermore, there was a clear and drastic increase of the R.sub.ct
generated from the [Fe(CN).sub.6].sup.3-/4- process in the presence
of E. histolytica antigen (FIG. 6, curve (v)). The bio-BSA modified
screen-printed electrode (FIG. 6 (i)) gave rise to the lowest
semicircle domain, followed by bio-BSA modified/streptavidin (FIG.
6 (ii)), bio-anti-HA (FIG. 6 (iii)), yeast-scFv biofragment (FIG. 6
(iv)), and target antigen (500 pg/mL) (FIG. 6 (v)). These results
indicate successful stepwise construction of the biosensor. The
biosensor was also highly reproducible with less than 5% relative
standard deviation (RSD) between the inter-assay signals, at each
step of the assay: (i) 1.2%, (ii) 2.13%, (iii) 4.76%, (iv) 3.00%,
(v) 4.01%, n=3. To validate the assay construction as well as to
assess the risk of possible false positive impedimetric responses
in this assay, a series of control DPV measurements were conducted
(data not shown) using biomolecule functionalized electrodes. The
peak current decreases in response to an increase in the hindrance
(i.e., via successive biomolecules attachment) of the electron
transfer reaction of [Fe(CN).sub.6].sup.3-/4- process.
[0114] The specificity of the immunosensor towards the `350`
antigen on the gold coated screen-printed electrode was examined by
attempting to capture an antigen that was non-specific to the
yeast-scFv biofragment affinity reagent. The `Jacob` protein was
previously shown not to bind with the `350-E2` yeast-scFv clone or
with `350-E2`-derived yeast-scFv biofragment. Non-specific binding
of the `Jacob` protein was evaluated by using F-EIS measurements. A
high concentration of the `Jacob` protein (1 ng/mL) was used to
determine the detection of background binding (FIG. 7 (ii)). The
signals observed for with `no antigen` case were essentially
identical with the `Jacob` antigen (FIG. 7 (ii) and FIG. 7 (iii)).
This indicates that the assay system detects the bulky
anti-HA-yeast-scFv biofragment complex, but without significant
cross-reaction with the `Jacob` protein. Comparatively, the
R.sub.ct increase produced by the target `350` antigen at 500 pg/mL
(FIG. 7 (iv)) was much greater. This indicates that yeast-scFv
biofragments retain their specificity towards target antigen, which
is in accordance with the initial results described above and in
Grewal et al., 2013. To assess background noise an assay was
performed which excluded the yeast-scFv biofragment layer (FIG. 7
(i)). Non-specific absorption and interaction of the `350` antigen
on the bio-BSA/streptavidin/bio-anti-HA screen-printed electrode
was examined (FIG. 6 (iii) vs. FIG. 7 (i)), however the R.sub.ct
signal increase was small, which indicates that non-specific
absorption was minimal. The reproducibility of F-EIS measurements
for `350` antigen was determined to have a RSD of 4.51% (n=3),
while reproducibility of `Jacob` protein measurements was found to
have a RSD of 3.88% (n=3) and reproducibility of `no antigen`
assays was determined to have a RSD of 3.00% (n=3).
[0115] The dynamic range of detection for antigen `350` using
yeast-scFv biofragments on the screen-printed electrode was
measured before and after the yeast-scFv biofragment modified
electrode was incubated with designated concentrations of `350`
antigens (1 pg/mL to 1 ng/mL). The R.sub.ct signal increased with
increasing amounts of antigen concentration (FIG. 8A and FIG. 8B).
The presence of antigen detected is accounted by faradaic current
generated by
K.sub.3[Fe(CN).sub.6].sup.3-/K.sub.2[Fe(CN).sub.6].sup.4- probe.
The relative R.sub.ct changes corresponding to antigen binding to
the yeast-scFv biofragment (FIG. 8B) was calculated as follows:
% change of
R.sub.ct=.DELTA.R.sub.ct=(R.sub.ct,after-R.sub.ct,before)/R.sub.ct,before-
.times.100 (1)
[0116] where R.sub.ct, before was the mean R.sub.ct at zero
concentration (R.sub.ct for bio-BSA/streptavidin/bio anti-HA) and
R.sub.ct, after was the mean R.sub.ct at any concentration of the
`350` antigen.
[0117] The lower limit of detection was confirmed down to 10 pg/mL
(588 fM). This concentration of antigen detected is 10 times more
sensitive than the lowest detected concentration of `350` antigen
on a gold disk electrode, as described above and in Grewal et al.,
2013, and about 550 times more sensitive than detecting E.
histolytica antigen using whole-cell yeast-scFv with fluorescently
labeled signal antibodies (Gray, S. A., et al, "Toward Low-Cost
Affinity Reagents: Lyophilized Yeast-scFv Probes Specific for
Pathogen Antigens," PLoS ONE 7: e32042 (2012)). This lower limit of
detection is also comparable to the detection of antigen using
ELISA and a typical IgG mAb. This increased sensitivity may be
attributed in part to the presence of gold particles on the
screen-printed electrode surface (the commercially obtained screen
printed electrodes uses a gold ink that is cured at 120.degree. C.,
which forms a rough working surface of gold particles). Gold
particles are known for their high electrocatalytic activity
allowing for increased sensitivity of biomolecule detection using
impedance and other electrochemical measurements. The linear
dynamic range of the assay was determined to be from 10 pg/mL (588
fM) to 500 pg/mL (29.4 pM). Reproducibility of the concentrations
was each examined on three separate electrodes, resulting in a RSD
of <4.1% between the electrodes at each concentration.
[0118] Reproducibility of the concentrations was each examined on
three separate electrodes, resulting in a RSD of <4.1% between
the electrodes at each concentration.
[0119] E. histolytica cysts are detected in patient stool samples
for diagnosis of E. histolytica infection. Therefore, the ability
to detect cyst antigens in stool matrix is a crucial requirement
when designing a clinical diagnostic. Antigens `350` and `030`
(each 500 pg/mL) were spiked into a biological matrix comprised of
disinfected (for occupational safety) stool diluted 1/5 in PBS. The
R.sub.ct signal of the assay complex containing the `030-L`
yeast-scFv biofragment sensing layer in stool (FIG. 9B (i)), showed
a slight increase compared to the `350-E2` yeast-scFv biofragment
complex in PBS (FIG. 7 (ii)) and stool (FIGURE A (i)). This signal
increase may be attributed to low levels of non-specific adsorption
of stool biomolecules on the immunosensor. For both antigens, a
clear increase in signal was observed when antigen was spiked into
the sample compared to the `no antigen control` (FIG. 9A and FIG.
9B). The F-EIS measurements were found to have a RSD of 9.88% and
8.45% (n=3) was found for inter-assay signals for antigens `350`
and `030`, respectively. FIG. 9C and FIG. 9D show the differential
pulse profiles, where the current decreases due to increase
hindrance of [Fe(CN).sub.6].sup.3-/4- process. DPV peak current
decreased when antigen was captured, compared to the assay complex
without antigen (FIG. 9C and FIG. 9D). This is in line with the
F-EIS responses (FIG. 9A and FIG. 9B). This indicates that this
current diagnostic platform has sufficient specificity to
successfully detect antigens, such as from the E. histolytica
pathogen, in a complex biological matrix. Thus, the biosensor
system has demonstrated the potential of yeast-scFv biofragment
affinity reagents to detect antigens in clinical samples. A
commercial ELISA kit is currently available for E. histolytica
detection in stool (TechLab E. histolytica II test). This
diagnostic detects the trophozoite protein Gal/GalNAc lectin, which
is different from the presently described target cyst antigens. The
commercial TechLab kit uses highly optimized antibodies and has
been reported to detect its target antigen at concentrations of
.about.1000 pg/mL in stool. Thus, the analytical sensitivity of the
present system compares favorably to a commercial ELISA functioning
in a similar biological matrix, but can be developed and performed
much more economically.
[0120] Conclusion: In conclusion, it is demonstrated yeast-scFv
biofragment affinity reagents can specifically bind to antigens of
interest, and can be included into detection assays, including a
novel, low-cost system incorporating commercial gold screen-printed
electrode for the sensitive detection of antigens in complex
samples (e.g., E. histolytica antigens in human stool samples).
This work is the first demonstration of yeast-scFv biofragments on
a portable low-cost platform and the first demonstration of using
yeast-scFv biofragment affinity reagents to detect antigens in a
complex biological matrix. A new antibody/antigen recognition
combination was also demonstrated, consistent with the expectation
that new yeast-scFv biofragment affinity reagents can be routinely
engineered towards diverse target antigens. Coupling a commercially
available battery operated portable potentiostat with the described
yeast-scFv biofragment coated screen-printed would allow for field
testing of pathogen antigens, such as E. histolytica antigens and
other antigens that are of clinical interest. Accordingly, the
biofragment affinity reagents have the ability to replace mAbs in
point of care diagnostics.
[0121] The following examples are provided for the purpose of
illustrating, not limiting, the invention.
EXAMPLES
Example 1
[0122] This Example describes the materials and methods used to
generate the illustrative reagents and assays described above for
the initial development of a yeast-scFv biofragment probe and
related EC bioassay.
[0123] Chemicals
[0124] All chemicals purchased from the Australian supplier's
branch, unless otherwise stated. Lyophilized yeast-scFv, `350`, and
Jacob antigens were generated at Seattle Biomedical Research
Institute, USA. Biotinylated anti-HA obtained from Sapphire
Bioscience. Biotinylated BSA was obtained from Thermo Scientific.
Streptavidin was obtained from Invitrogen. PBS tablets were
obtained from Astral Scientific. Potassium ferrocyanide, potassium
ferricyanide, and potassium chloride were obtained from Sigma
Aldrich. Protease Inhibitor EDTA-free cocktail tables were obtained
from Roche. Glycerol was obtained from Ajax Finechem.
[0125] Determination of the Surface Area of the Electrodes
[0126] Gold (AU) marcrodisk (diameter=3 mm) working electrodes were
purchased from CH Instrument (Austin, USA). Prior to
electrochemical experiment, the electrodes were cleaned physically
with 0.1 micron alumina, sonicated in acetone for 20 minutes, and
chemically with piranha solution (H.sub.2SO.sub.4:H.sub.2O.sub.2;
3:1) for 30 seconds to remove any organic impurities and finally
electrochemically in 0.5 M H.sub.2SO.sub.4 until characteristic
gold electrode profiles were achieved. The effective working area
of the electrodes were determined under linear sweep voltammetric
conditions for the one-electron reduction of K.sub.3[Fe(CN).sub.6]
[1.0 mM in water (0.5 M KCl)] and use of the Randles-Sevcik
relationship (see A. J. Bard and L. R. Faulkner, Electrochemical
Methods: Fundamentals and Applications, John Wiley & Sons,
2000):
i.sub.p=0.4463nF(nF/RT).sup.1/2AD.sup.1/2v.sup.1/2C (1)
where i.sub.p is the peak current (A), n (=1) is the number of
electrons transferred, A is the effective area of the electrode
(cm.sup.2), D is the diffusion coefficient of [Fe(CN).sub.6].sup.3-
(taken to be 7.60.times.10.sup.-6 cm.sup.2s.sup.-1), C is the
concentration (mol cm.sup.-3), v is the scan rate (Vs.sup.-1), and
other symbols have their usual meanings.
[0127] Generation of Cell-Free Yeast-scFv Biofragments
[0128] Whole yeast cells expressing scFv on their surface (whole
yeast-scFv), were selected for their binding towards the E.
histolytica antigen EHI 115350 (Gray, S. A., et al., PLoS ONE,
7:e32042 (2012)) called `350` in this report. After confirmation of
specific antigen binding, the cells were lyophilized for long-term
storage (Gray, S. A., et al., PLoS ONE, 7:e32042 (2012)).
Lyophilized yeast were disrupted with a mortar and pestle into a
fine powder, then 10 mL of PBS, 5% glycerol and protease inhibitor
cocktail were added. The sample was centrifuged at 500 rpm for 2
minutes at 15.degree. C. to remove whole yeast. The processed
lysates (supernatant) were stored at 4.degree. C. until used.
[0129] Dynamic Light Scattering Sizing of Biofragments
[0130] To assure that the yeast-scFv fragments were small enough to
be useable in the bioassay, DLS measurements (FIG. 2) (Malvern
Zetasizer series) were taken of the yeast-scFv biofragments after
filtration through a 0.1 .mu.m filter (Millipore). The DLS data
confirmed that biofragments existed in the sub 100 nm size range,
and lacked detectable whole-cell yeast-scFv.
[0131] Assay Protocol
[0132] Gold disk electrodes were functionalized with BSA by
incubating them for 45 min in biotinylated BSA solution (100
.mu.g/ml) and incubated on a thermoshaker set to 25.degree. C. at
300 rpm. The thermoshaker and these settings (time and temperature)
were used in all subsequent steps. The electrodes were washed with
1.times.PBS (pH 7.4, 137 mM sodium chloride, 2 mM potassium
chloride, 10 mM phosphate buffer) after each incubation step. The
electrode was incubated in 400 .mu.l of streptavidin (100 ug/ml)
solution for 45 minutes. These electrodes were treated with 100
ug/ml of biotinylated HA antibody solution at room temperature for
another 45 min, leading to immobilization of the anti-HA on the
electrode surface. Finally, the cell-free yeast-scFv biofragment
reagent diluted 1/10 in PBS was allowed to react for 45 minutes
before washing with PBS. The sensing electrodes were then incubated
in 400 .mu.l of antigen solution at varying concentrations to
complete the immunoreactions.
[0133] Electrochemical Procedure
[0134] All electrochemical experiments were conducted at room
temperature (25.+-.1.degree. C.) in a standard three-electrode
electrochemical cell arrangement using an electrochemical analyzer
CHI 650D (CH Instruments, Austin, Tex.), where the electrochemical
cell consisted of an Au sensor as a working electrode, a Pt wire
counter electrode, and a Ag/AgCl (3 M NaCl) reference electrode.
Electrochemical signals were measured in a 10 mM phosphate buffer
solution (pH 7.4) containing 2.5 mM
[Fe(CN).sub.6].sup.3-/[Fe(CN).sub.6].sup.4- (1:1) and 0.1 M KCl.
Differential pulse voltammetric (DPV) signals were obtained with a
potential step of 5 mV, pulse amplitude of 50 mV, pulse with 50 ms,
and a pulse period of 100 ms. The EIS spectra were recorded in 10
mM phosphate buffer solution (pH 7.4) containing 2.5 mM
[Fe(CN).sub.6].sup.3-/[Fe(CN).sub.6].sup.4- (1:1) and 0.1 M KCl
using an alternating current voltage of 10 mV, with the frequency
range of 0.1 Hz-100 kHz.
[0135] The faradaic current generated by the
K.sub.3[Fe(CN).sub.6]/K.sub.2[Fe(CN).sub.6] probe accounts on the
presence of a protein. The current changes corresponding to target
antigen binding to the antibody was calculated as follows:
% Decrease of peak
current=(I.sub.before-I.sub.after)/I.sub.before.times.100 (2)
where I.sub.before=mean current at zero target concentration (e.g.,
current generated by the
bio-BSA/streptavidin/bio-anti-HA/yeast-scFv layer),
I.sub.after=mean current at any concentration of target
antigen.
Example 2
[0136] This Example describes the materials and methods used to
generate the illustrative reagents and assays described above for
the subsequent development of yeast-scFv biofragment probes and the
related EC bioassay incorporating screen-printed electrodes.
[0137] Chemicals and Materials
[0138] All chemicals purchased from the Australian supplier's
branch, unless otherwise stated. Stool samples, lyophilized
yeast-scFv, and E. histolytica antigens EHI 115350, EHI 182030, and
EHI 044550 (called `350`, `030`, and `Jacob` respectively) in this
report were produced by The University of Washington, USA and
Seattle Structural Genomics Center for Infectious Disease (SSGCID).
Biotinylated anti-HA antibody (Bio-anti-HA) was purchased from
Sapphire Bioscience. Biotinylated bovine serum albumin (BSA) was
obtained from Thermo Scientific. Streptavidin was procured from
Invitrogen. Phosphate buffered saline (PBS) tablets were purchased
from Astral Scientific. Potassium ferrocyanide, potassium
ferricyanide, and potassium chloride were all purchased from Sigma
Aldrich. Protease Inhibitor EDTA-free cocktail tablets were
obtained from Roche. Glycerol was procured from Ajax Finechem.
Screen-printed gold electrodes, DRP-C220BT (geometric area=0.126
cm.sup.2), were acquired from Dropsens, Spain. Millex-VV 0.1 .mu.m,
Durapore PVDF (diameter 33 mm), low protein binding syringe filters
were purchased from Millipore. The effective working area (=0.180
cm.sup.2) of the screen-printed gold electrodes were determined
under linear sweep voltammetric conditions for the one-electron
reduction of K.sub.3[Fe(CN).sub.6] [1.0 mM in water (0.5 M KCl)]
and use of the Randles-Sevcik relationship (Bard and Faulkner,
2000; Grewal et al., 2013).
[0139] Residues 135-271 of antigen EHI 115350 ('350) were expressed
recombinantly in E. coli in a modified, N-terminal 6.times.His
pET11b vector and purified by Ni-NTA IMAC. Residues 159-481 of EHI
044550 (`Jacob`) were expressed in a pE-SUMO vector (Life Sensors),
also purified by Ni-NTA IMAC, and cleaved from the His-SUMO tag by
SUMO protease digestion. Full-length EHI 182030 (`030`) was
expressed in E. coli and purified in Tier 1 of SSGCID (Bryan et
al., "High-throughput protein production and purification at the
Seattle Structural Genomics Center for Infectious Disease," Acta
Crystallograph. Sect. F Struct. Biol. Cryst. Commun. 67:1010-1014
(2011); Stacy et al., "Structural genomics of infectious disease
drug targets: the SSGCID," Acta Crystallograph. Sect. F Struct.
Biol. Cryst. Commun. 6:979-984. (2011)).
[0140] The yeast-scFv library was a generous gift from K. Dane
Wittrup. Antigens 350 and 030 were biotinylated with EZ-Link
NHS-PEG4 biotin (Thermo Pierce), respectively. Yeast selections
were conducted as before (Chao et al., "Isolating and engineering
human antibodies using yeast surface display," Nat. Protoc.
1:755-768 (2006); Gray et al., 2012). In brief, two rounds of
magnetic selection were conducted on the induced library with 100
nM of a biotinylated antigen and streptavidin (R1)- or
.alpha.-biotin(R2)-conjugated beads (Milentyi). The resultant
output was further enriched for bio-antigen/SA-PE and
.alpha.-myc-FITC double-positive cells through two rounds on a
Beckman Aria II cell sorter. After plating, individual clones were
confirmed to be antigen specific by flow cytometry analysis, and
clone diversity was determined by scFv PCR amplification and BstNI
digest (New England Biosciences, USA).
[0141] The stool matrix was derived from human samples collected by
the International Centre for Diarrheal Disease Research, Bangladesh
(ICDDR,B) with institutional review board approval from the
University of Washington and the ICDDR,B. Five 1-2 mL E.
histolytica-negative samples were combined, diluted 1:1 in PBS, and
spun at high speed for 5 minutes. The supernatant was collected and
disinfected by boiling for 10 minutes at 90.degree. C. Before use,
disinfection was confirmed by 3 days absence of microbial growth on
tryptic soy and nutrient agar plates.
[0142] Generation of Yeast-scFv Biofragments
[0143] After confirmation of specific antigen binding, the cells
were lyophilized for long-term storage as described (Gray et al.,
2012), following a modified protocol that added 10% dextran and 5%
sodium glutamate to yeast. Yeast-scFv biofragments were created as
described above and in Grewal et al., 2013, with a modified
protocol that added sodium azide. Briefly, lyophilized yeast was
disrupted with a mortar and pestle into a fine powder, then 10 mL
of PBS, 5% glycerol and protease inhibitor cocktail were added. The
sample was centrifuged at 500 RCF for 2 minutes at 15.degree. C. to
remove whole yeast. To prevent microbial growth, sodium azide 0.05%
was added. The processed lysates (supernatant) were stored at
4.degree. C. until use and filtered using a 0.1 .mu.m filter.
[0144] Assay Protocol
[0145] Screen-printed gold electrodes were functionalized with BSA
by incubating them in 700 .mu.l of biotinylated BSA solution (500
.mu.g/mL) for 1 hour at 25.degree. C. on an intelli-mixer (PCOD
Scientific) with gentle agitation. These intelli-mixer settings
were used in all subsequent steps. The electrodes were then stored
overnight at 4.degree. C. The electrodes were then washed with
1.times.PBS (pH 7.4, 137 mM sodium chloride, 2 mM potassium
chloride, 10 mM phosphate buffer) after each incubation step. The
electrode was incubated in 700 .mu.L of streptavidin (500
.mu.g/mL). These functionalized electrodes were then treated with
100 .mu.g/mL of biotinylated HA antibody solution at room
temperature for another hour, leading to immobilization of the
anti-HA antibody on the electrode surface. Finally, the yeast-scFv
biofragment reagent diluted 1/5 in PBS was allowed to bind (by
virtue of the interaction between anti-HA and the HA affinity tag
cloned into the yeast-display scFv) for 1 hour before washing with
PBS. This step tethered the yeast-scFv biofragment to the electrode
surface while at the same time removing yeast fragments that do not
bear displayed scFv. The electrodes were then incubated in 700
.mu.L of antigen solution (spiked in either PBS or stool) at
varying concentrations to complete the immunoreactions.
[0146] Electrochemical Procedure
[0147] All electrochemical experiments were conducted at room
temperature (25.+-.1.degree. C.) using screen-printed gold
electrodes which comprised of an Ag reference, gold counter, and a
4 mm diameter gold working electrode using an electrochemical
analyser CHI 650D (CH Instruments, Austin, Tex.). Electrochemical
measurements were measured in a 10 mM phosphate buffer solution (pH
7.4) containing 2.5 mM [Fe(CN).sub.6].sup.3-/[Fe(CN).sub.6].sup.4-
(1:1) and 0.1 M KCl. Differential pulse voltammetric (DPV) signals
were obtained with a potential step of 5 mV, pulse amplitude of 50
mV, pulse width 50 ms, and a pulse period of 100 ms. The EIS
spectra were recorded using an alternating current voltage of 10
mV, with the frequency range of 1 Hz-100 kHz.
[0148] While illustrative embodiments have been illustrated and
described, it will be appreciated that various changes can be made
therein without departing from the spirit and scope of the
invention.
* * * * *