Antibody microarrays: the crucial impact of mass transport on assay kinetics and sensitivity

Enhancement of Convection and Molecular Transport into Film Stacked Structures by Introduction of Notch Shape for Micro-Immunoassay

A 3D-stack microfluidic device that can be used in combination with 96-well plates for micro-immunoassay was developed by the authors. ELISA for detecting IgA by the 3D-stack can be performed in one-ninth of the time of the conventional method by using only 96-well plates. In this study, a notched-shape film was designed and utilized for the 3D-stack to promote circulation by enhancing and utilizing the axial flow and circumferential flow in order to further reduce the reaction time. A finite element analysis was performed to evaluate the axial flow and circumferential flow while using the 3D-stack in a well and design the optimal shape. The 3D-stack with the notched-shape film was fabricated and utilized for the binding rate test of the antibody and antigen and ELISA. As a result, by promoting circulation using 3D-stack with notched-shape film, the reaction time for each process of ELISA was reduced to 1 min, which is 1/60 for 96 wells at low concentrations.

A prototype of ultrasensitive time-resolved fluoroimmunoassay for the quantitation of lead in plasma using a fluorescence-enhanced europium chelate label for the detection system

This study describes the prototype of a novel ultra-sensitive time-resolved fluoroimmunoassay (TRFIA) for the quantification of lead (Pb) in plasma. The assay procedures were conducted in 96-microwell plates and involved the competitive binding format. The assay used a mouse monoclonal antibody, designated as 2C33, that specifically recognized the diethylenetriamine pentaacetic acid chelate of Pb (Pb-DTPA) but did not recognize Pb-free DTPA chelator. The antigen used for coating onto the inner surfaces of assay plate microwells was Pb-DTPA conjugated with bovine serum albumin protein (Pb-DTPA-BSA). The competitive binding reaction occurred between Pb-DTPA chelates, formed in the sample solutions by treating the samples with an excess DTPA, and the coated Pb-DTPA-BSA for a limited quantity of 2C33 antibody binding sites. The antigen-antibody complex formed in the plate wells was quantified by a europium-DTPA-labeled secondary antibody and a fluorescence enhancement solution. The conditions of the assay were refined, and its optimum procedures were established. The TRFIA was validated following the immunoassay validation guidelines, and all of the validation criteria were acceptable. The working range of the assay was 20-300 pg mL-1 and its limit of quantitation was 20 pg mL-1. Metals that are commonly encountered in blood plasma did not interfere with Pb in the analysis by the proposed TRFIA. The assay was applied to the quantitation of Pb in plasma samples with satisfactory accuracy and precision. The results were compared favorably with those obtained by atomic emission spectroscopy. In conclusion, the present study represents the first TRFIA for the quantitation of Pb in plasma. The assay is superior to the existing atomic spectrometric methods and other immunoassays for Pb in terms of sensitivity, convenience, and analysis throughputs. The proposed TRFIA is anticipated to effectively contribute to assessing Pb concentrations and controlling the exposure of humans to its potential toxicity.

Development of a highly sensitive chemiluminescence immunoassay using a novel signal-enhanced detection system for quantitation of durvalumab, an immune-checkpoint inhibitor monoclonal antibody used for immunotherapy of lung cancer

Durvalumab (DUR) is a human monoclonal antibody used for the immunotherapy of lung cancer. It is a novel immune-checkpoint inhibitor, which blocks the programmed death 1 (PD-1) and programmed death-ligand 1 (PD-L1) proteins and works to promote the normal immune responses that attack the tumour cells. To support the pharmacokinetic (PK) studies, therapeutic drug monitoring (TDM) and refining the safety profile of DUR, an efficient assay is required, preferably immunoassay. This study describes, for the first time, the development of a highly sensitive chemiluminescence immunoassay (CLIA) for the quantitation of DUR in plasma samples with enhanced chemiluminescence detection system. The CLIA protocol was conducted in 96-microwell plates and involved the non-competitive binding reaction of DUR to its specific antigen (PD-L1 protein). The immune complex of DUR with PD-L1 formed onto the inner surface of the assay plate wells was quantified by a chemiluminescence (CL)-producing horseradish peroxidase (HRP) reaction. The reaction employed 4-(1,2,4-triazol-1-yl)phenol (TRP) as an efficient enhancer of the HRP-luminol-hydrogen peroxide (H2O2) CL reaction. The optimum protocol of the proposed CLIA was established, and its validation parameters were assessed as per the guidelines for the validation of immunoassays for bioanalysis. The working dynamic range of the assay was 10-800 pg mL-1 with a limit of detection (LOD) of 10.3 pg mL-1. The assay enables the accurate and precise quantitation of DUR in human plasma at a concentration as low as 30.8 pg mL-1. The CLIA protocol is simple and convenient; an analyst can analyse several hundreds of samples per working day. This high throughput property enables the processing of many samples in clinical settings. The proposed CLIA has a significant benefit in the quantitation of DUR in clinical settings for assessment of its PK, TDM and refining the safety profile.

Enhancement of Molecular Transport into Film Stacked Structures for Micro-Immunoassay by Unsteady Rotation

A film-stacked structure consisting of polyethylene terephthalate (PET) films stacked in a gap of 20 µm that can be combined with 96-well microplates used in biochemical analysis has been developed by the authors. When this structure is inserted into a well and rotated, convection flow is generated in the narrow gaps between the films to enhance the chemical/bio reaction between the molecules. However, since the main component of the flow is a swirling flow, only a part of the solution circulates into the gaps, and reaction efficiency is not achieved as designed. In this study, an unsteady rotation is applied to promote the analyte transport into the gaps using the secondary flow generated on the surface of the rotating disk. Finite element analysis is used to evaluate the changes in flow and concentration distribution for each rotation operation and to optimize the rotation conditions. In addition, the molecular binding ratio for each rotation condition is evaluated. It is shown that the unsteady rotation accelerates the binding reaction of proteins in an ELISA (Enzyme Linked Immunosorbent Assay), a type of immunoassay.

What Digital Immunoassays Can Learn from Ambient Analyte Theory: A Perspective

Immunoassays are important tools for clinical diagnosis as well as environmental and food analysis because they enable highly sensitive and quantitative measurements of analyte concentrations. In the 1980s, Roger Ekins suggested to improve the sensitivity of immunoassays by employing microspot assays, which are carried out under ambient analyte conditions and do not change the bulk analyte concentration of a sample during a measurement. More recently, the measurement of single analyte molecules has additionally attracted wide research interest. Although the ability to detect a single analyte molecule is not synonymous with the highest analytical sensitivity, single-molecule detection makes new routes accessible to avoiding background noise. This perspective follows the development of solid-phase immunoassays from the design of label techniques to single-molecule (digital) assays against the backdrop of Ekins's fundamental work on immunoassay theory. The essential aspects of both ambient analyte and digital assay approaches are presented as a guideline to finding a balance between the speed, sensitivity, and precision of immunoassays.

A 3D Microfluidic ELISA for the Detection of Severe Dengue: Sensitivity Improvement and Vroman Effect Amelioration by EDC-NHS Surface Modification

Serum is commonly used as a specimen in immunoassays but the presence of heterophilic antibodies can potentially interfere with the test results. Previously, we have developed a microfluidic device called: 3D Stack for enzyme-linked immunosorbent assay (ELISA). However, its evaluation was limited to detection from a single protein solution. Here, we investigated the sensitivity of the 3D Stack in detecting a severe dengue biomarker—soluble CD163 (sCD163)—within the serum matrix. To determine potential interactions with serum matrix, a spike-and-recovery assay was performed, using 3D Stacks with and without surface modification by an EDC–NHS (N-ethyl-N′-(3-(dimethylamino)propyl)carbodiimide/N-hydroxysuccinimide) coupling. Without surface modification, a reduced analyte recovery in proportion to serum concentration was observed because of the Vroman effect, which resulted in competitive displacement of coated capture antibodies by serum proteins with stronger binding affinities. However, EDC–NHS coupling prevented antibody desorption and improved the sensitivity. Subsequent comparison of sCD163 detection using a 3D Stack with EDC–NHS coupling and conventional ELISA in dengue patients’ sera revealed a high correlation (R = 0.9298, p < 0.0001) between the two detection platforms. Bland–Altman analysis further revealed insignificant systematic error between the mean differences of the two methods. These data suggest the potentials of the 3D Stack for further development as a detection platform.

Quantitative detection of aflatoxin B1 using quantum dots-based immunoassay in a recyclable gravity-driven microfluidic chip

To achieve rapid and sensitive detection of aflatoxin B₁ (AFB₁), we developed a polydimethylsiloxane gravity-driven cyclic microfluidic chip using the two-signal mode strategy. The structural design of the chip, together with the two-wavelength quantum dot ratio fluorescence, effectively eliminates the influence of environmental factors, improves the signal stability, and ensures that the final detection result positively correlates with the target concentration. Moreover, the theoretical analysis performed for the established physical model of the three-dimensional reaction interface inside the chip confirmed the improved reaction rate of immune adsorption in the microfluidic strategy. Overall, the method exhibited a wide analytic range (0.2-500 ng mL^-1), low detection limit (0.06 ng mL^-1), high specificity, good precision (coefficient of variation < 5%), excellent reusability (20 times, 89.1%) and satisfactory practical sample analysis capacity. Furthermore, the reusability and designability of this chip provide a reliable scheme for field detection of AFB₁, analysis of other small molecules, and establishment of high-throughput detection systems under different conditions.

Production of high-complexity frameshift neoantigen peptide microarrays

Parallel measurement of large numbers of antigen-antibody interactions are increasingly enabled by peptide microarray technologies. Our group has developed an in situ synthesized peptide microarray of >400 000 frameshift neoantigens using mask-based photolithographic peptide synthesis, to profile patient specific neoantigen reactive antibodies in a single assay. The system produces 208 replicate mircoarrays per wafer and is capable of producing multiple wafers per synthetic lot to routinely synthesize over 300 million peptides simultaneously. In this report, we demonstrate the feasibility of the system for detecting peripheral-blood antibody binding to frameshift neoantigens across multiple synthetic lots.

Development of a highly sensitive ELISA for determination of darunavir in plasma samples using a polyclonal antibody with high affinity and specificity

Aim: To support pharmacokinetic studies and therapeutic monitoring of darunavir (DRV), a highly sensitive ELISA was developed for the determination of DRV in plasma samples at picogram levels. Results: The assay LOD and LOQ were 15 and 30 pg ml-1, respectively. The working range of the assay was 20–2000 pg ml-1. Analytical recoveries of DRV from spiked plasma were in the ranges of 98.4–113.0 and 86.0–99.1% for intra-assay and inter-assay runs, respectively. The precision of the assay was satisfactory. Conclusion: The ELISA is characterized by high throughput and it is expected to significantly contribute to routine analysis of DRV in its pharmacokinetic studies and therapeutic monitoring.

An aptamer based thermofluorimetric assay for ethanolamine

There is a great need for fast, simple and precise diagnostic assays capable of direct quantification of biomarkers in complex biological matrices. Yet, the commonly used techniques such as ELISA/Immunoassays are tedious and involve various steps e.g. blocking, washing and signal development. Moreover, most of these assays have very limited ability of detecting small molecules and have hardly any multiplexing capabilities. The gold standard and alternative, mass-spectrometry, however, depends upon expensive hardware and is incompatible with point of care (POC) diagnostics. As opposed to POC assays for proteins or larger targets where variable formats are readily available. Here, we present a simple, versatile and fast one-step assay for detecting a small molecule, ethanolamine as example. The assay makes use of commonly available qPCR machines to detect target-concentration dependent shifts in the melting temperatures of aptamer beacons. The method allows detection of ethanolamine in the low nM range without requiring tedious elaboration of assay conditions as required for molecular beacons at room temperature. If generalizable, it may change the situation of small molecule assays significantly.

Development and validation of an ELISA with high sensitivity for therapeutic monitoring of afatinib

AIM

To support the therapeutic drug monitoring of afatinib (AFT), an ELISA was required.

RESULTS

A hapten for AFT was prepared and linked to each of BSA and KLH proteins by diazotization/coupling reaction. A polyclonal antibody recognizing AFT with high affinity (IC₅₀ = 40 ng ml^-1) was generated and used in the development of a competitive ELISA for quantitation of AFT in plasma samples. The assay limit of detection was 2 ng ml^-1. The assay accuracy and precision were proved.

CONCLUSION

The assay is an appropriate alternative to the existing LC-MS/MS assays for AFT and it is anticipated to effectively contribute to the therapeutic drug monitoring of AFT in clinical settings.

Improving Lateral Flow Assay Performance Using Computational Modeling

The performance, field utility, and low cost of lateral flow assays (LFAs) have driven a tremendous shift in global health care practices by enabling diagnostic testing in previously unserved settings. This success has motivated the continued improvement of LFAs through increasingly sophisticated materials and reagents. However, our mechanistic understanding of the underlying processes that drive the informed design of these systems has not received commensurate attention. Here, we review the principles underpinning LFAs and the historical evolution of theory to predict their performance. As this theory is integrated into computational models and becomes testable, the criteria for quantifying performance and validating predictive power are critical. The integration of computational design with LFA development offers a promising and coherent framework to choose from an increasing number of novel materials, techniques, and reagents to deliver the low-cost, high-fidelity assays of the future.

Towards an Electrochemical Immunosensor System with Temperature Control for Cytokine Detection

The cytokine interleukin-13 (IL-13) plays a major role in airway inflammation and is a target of new anti-asthmatic drugs. Hence, IL-13 determination could be interesting in assessing therapy success. Thus, in this work an electrochemical immunosensor for IL-13 was developed and integrated into a fluidic system with temperature control for read-out. Therefore, two sets of results are presented. First, the sensor was set up in sandwich format on single-walled carbon nanotube electrodes and was read out by applying the hydrogen peroxide–hydroquinone–horseradish peroxidase (HRP) system. Second, a fluidic system was built up with an integrated heating function realized by Peltier elements that allowed a temperature-controlled read-out of the immunosensor in order to study the influence of temperature on the amperometric read-out. The sensor was characterized at the temperature optimum of HRP at 30 °C and at 12 °C as a reference for lower performance. These results were compared to a measurement without temperature control. At the optimum operation temperature of 30 °C, the highest sensitivity (slope) was obtained compared to lower temperatures and a limit of detection of 5.4 ng/mL of IL-13 was calculated. Taken together, this approach is a first step towards an automated electrochemical immunosensor platform and shows the potential of a temperature-controlled read-out.

Enhancement of binding kinetics on affinity substrates by laser point heating induced transport

Binding of analyte to an affinity substrate is significantly enhanced by laser point heating induced transport.

Suspension arrays based on nanoparticle-encoded microspheres for high-throughput multiplexed detection

Spectrometrically or optically encoded microsphere based suspension array technology (SAT) is applicable to the high-throughput, simultaneous detection of multiple analytes within a small, single sample volume. Thanks to the rapid development of nanotechnology, tremendous progress has been made in the multiplexed detecting capability, sensitivity, and photostability of suspension arrays. In this review, we first focus on the current stock of nanoparticle-based barcodes as well as the manufacturing technologies required for their production. We then move on to discuss all existing barcode-based bioanalysis patterns, including the various labels used in suspension arrays, label-free platforms, signal amplification methods, and fluorescence resonance energy transfer (FRET)-based platforms. We then introduce automatic platforms for suspension arrays that use superparamagnetic nanoparticle-based microspheres. Finally, we summarize the current challenges and their proposed solutions, which are centered on improving encoding capacities, alternative probe possibilities, nonspecificity suppression, directional immobilization, and "point of care" platforms. Throughout this review, we aim to provide a comprehensive guide for the design of suspension arrays, with the goal of improving their performance in areas such as multiplexing capacity, throughput, sensitivity, and cost effectiveness. We hope that our summary on the state-of-the-art development of these arrays, our commentary on future challenges, and some proposed avenues for further advances will help drive the development of suspension array technology and its related fields.

Miniaturization of multiplexed planar recombinant antibody arrays for serum protein profiling

BACKGROUND

Antibody-based microarrays are a developing tool for high-throughput proteomics in health and disease. However, in order to enable global proteome profiling, novel miniaturized high-density antibody array formats must be developed.

RESULTS

In this proof-of-concept study, we have designed a miniaturized planar recombinant (single-chain Fragment variable). antibody array technology platform for multiplexed profiling of non-fractionated, directly labelled serum samples. The size of the individual spot features was reduced 225-times (78.5 μm(2)/spot) and the array density was increased 19-times (38,000 spots/cm(2)). These miniaturized, multiplexed arrays were produced, using a desktop nanofabrication system based on dip-pen nanolithography technology, and interfaced with a high-resolution fluorescent-based scanner. The reproducibility, sensitivity, specificity, and applicability of the set-up were demonstrated by profiling a set of well-characterized serum samples.

CONCLUSION

The designed antibody array platform opens up new possibilities for large-scale, multiplex profiling of crude proteomes in a miniaturized fashion.

On the Slow Diffusion of Point-of-Care Systems in Therapeutic Drug Monitoring

Recent advancements in point-of-care (PoC) technologies show great transformative promises for personalized preventative and predictive medicine. However, fields like therapeutic drug monitoring (TDM), that first allowed for personalized treatment of patients' disease, still lag behind in the widespread application of PoC devices for monitoring of patients. Surprisingly, very few applications in commonly monitored drugs, such as anti-epileptics, are paving the way for a PoC approach to patient therapy monitoring compared to other fields like intensive care cardiac markers monitoring, glycemic controls in diabetes, or bench-top hematological parameters analysis at the local drug store. Such delay in the development of portable fast clinically effective drug monitoring devices is in our opinion due more to an inertial drag on the pervasiveness of these new devices into the clinical field than a lack of technical capability. At the same time, some very promising technologies failed in the clinical practice for inadequate understanding of the outcome parameters necessary for a relevant technological breakthrough that has superior clinical performance. We hope, by over-viewing both TDM practice and its yet unmet needs and latest advancement in micro- and nanotechnology applications to PoC clinical devices, to help bridging the two communities, the one exploiting analytical technologies and the one mastering the most advanced techniques, into translating existing and forthcoming technologies in effective devices.

High-throughput proteomics using antibody microarrays: an update

Antibody-based microarrays are a rapidly emerging technology that has advanced from the first proof-of-concept studies to demanding serum protein profiling applications during recent years, displaying great promise within disease proteomics. Miniaturized micro- and nanoarrays can be fabricated with an almost infinite number of antibodies carrying the desired specificities. While consuming only minute amounts of reagents, multiplexed and ultrasensitive assays can be performed targeting high- as well as low-abundance analytes in complex nonfractionated proteomes. The microarray images generated can then be converted into protein expression profiles or protein atlases, revealing a detailed composition of the sample. The technology will provide unique opportunities for fields such as disease diagnostics, biomarker discovery, patient stratification, predicting disease recurrence and drug target discovery. This review describes an update of high-throughput proteomics, using antibody-based microarrays, focusing on key technological advances and novel applications that have emerged over the last 3 years.

Microfluidic processor allows rapid HER2 immunohistochemistry of breast carcinomas and significantly reduces ambiguous (2+) read-outs

Biomarker analysis is playing an essential role in cancer diagnosis, prognosis, and prediction. Quantitative assessment of immunohistochemical biomarker expression on tumor tissues is of clinical relevance when deciding targeted treatments for cancer patients. Here, we report a microfluidic tissue processor that permits accurate quantification of the expression of biomarkers on tissue sections, enabled by the ultra-rapid and uniform fluidic exchange of the device. An important clinical biomarker for invasive breast cancer is human epidermal growth factor receptor 2 [(HER2), also known as neu], a transmembrane tyrosine kinase that connotes adverse prognostic information for the patients concerned and serves as a target for personalized treatment using the humanized antibody trastuzumab. Unfortunately, when using state-of-the-art methods, the intensity of an immunohistochemical signal is not proportional to the extent of biomarker expression, causing ambiguous outcomes. Using our device, we performed tests on 76 invasive breast carcinoma cases expressing various levels of HER2. We eliminated more than 90% of the ambiguous results (n = 27), correctly assigning cases to the amplification status as assessed by in situ hybridization controls, whereas the concordance for HER2-negative (n = 31) and -positive (n = 18) cases was 100%. Our results demonstrate the clinical potential of microfluidics for accurate biomarker expression analysis. We anticipate our technique will be a diagnostic tool that will provide better and more reliable data, onto which future treatment regimes can be based.

Microarray Glycoprofiling of CA125 improves differential diagnosis of ovarian cancer

The CA125 biomarker assay plays an important role in the diagnosis and management of primary invasive epithelial ovarian/tubal cancer (iEOC). However, a fundamental problem with CA125 is that it is not cancer-specific and may be elevated in benign gynecological conditions such as benign ovarian neoplasms and endometriosis. Aberrant O-glycosylation is an inherent and specific property of cancer cells and could potentially aid in differentiating cancer from these benign conditions, thereby improving specificity of the assay. We report on the development of a novel microarray-based platform for profiling specific aberrant glycoforms, such as Neu5Acα2,6GalNAc (STn) and GalNAc (Tn), present on CA125 (MUC16) and CA15-3 (MUC1). In a blinded cohort study of patients with an elevated CA125 levels (30-500 kU/L) and a pelvic mass from the UK Ovarian Cancer Population Study (UKOPS), we measured STn-CA125, ST-CA125 and STn-CA15-3. The combined glycoform profile was able to distinguish benign ovarian neoplasms from invasive epithelial ovarian/tubule cancer (iEOCs) with a specificity of 61.1% at 90% sensitivity. The findings suggest that microarray glycoprofiling could improve differential diagnosis and significantly reduce the number of patients elected for further testing. The approach warrants further investigation in other cancers.

Quantification of kinase activity in cell lysates via photopatterned macroporous poly(ethylene glycol) hydrogel arrays in microfluidic channels

The efficacy of tyrosine kinase inhibitors (TKIs) as cancer therapeutics varies amongst individual patients as a result of patient-specific differences in molecular regulation of cancer development and progression, and acquisition of resistance to TKIs during therapy. A sensitive assay that can quantify kinase activity and predict inhibition of that activity from minimally invasive patient tissue samples may aid design of efficacious individualized TKI treatments. A microfluidic format can be useful in reducing limitations in standard protein kinase assays, including sensitivity required and low sample volume available. We present photopatterned macroporous poly(ethylene glycol) diacrylate hydrogel pillars functionalized with kinase substrates within microchannels for quantifying kinase activity in complex cellular lysates. We determined the effect of using a porogen to induce macroporosity in hydrogel pillars and showed that hydrogel poration enhanced the sensitivity of detecting Bcr-Abl activity in cell lysates by an order of magnitude. Bcr-Abl tyrosine kinase activity in K562 cell lysates could be detected from 0.01 μg/μL of cell lysate, corresponding to approximately 500 cells, using GST-Crkl immobilized in macroporous hydrogels. This device was also capable of quantifying inhibition of Bcr-Abl activity by imatinib mesylate, which demonstrates the potential to predict the biochemical response to drug inhibitors. These results indicate that microfluidic devices containing macroporous hydrogels functionalized with kinase substrates provide a promising platform for sensitive and specific quantification of kinase activity and efficacy of kinase inhibitors in cancer cell lysates.

Impact of substrates for probe immobilization

Protein chips are becoming a key technology in proteomic research and medical diagnostics. Surface chemistry for immobilization of proteins forms the basis for assay design and determines the properties of protein microarrays. Optimal substrates provide a homogeneous environment for probes, preventing loss of biological activity and unspecific adsorption. Numerous immobilization approaches, based on covalent binding, affinity, or adsorption, have been proposed thus far, and these represent the toolbox for choosing optimized strategies for each individual application.

Fast detection of biomolecules in diffusion-limited regime using micromechanical pillars

We have developed a micromechanical sensor based on vertically oriented oscillating beams, in which contrary to what is normally done (for example with oscillating cantilevers) the sensitive area is located at the free end of the oscillator. In the micropillar geometry used here, analyte adsorption is confined only to the tip of the micropillar, thus reducing the volume from which the analyte molecules must diffuse to saturate the surface to a sphere of radius more than 2 orders of magnitude smaller than the corresponding linear distance valid for adsorption on a macroscopic surface. Hence the absorption rate is 3 orders of magnitude faster than on a typical 200 × 20 square micrometer cantilever. Pillar oscillations are detected by means of an optical lever method, but the geometry is suitable for multiplexing with compact integrated detection. We demonstrate our technology by investigating the formation of a single-strand DNA self-assembled monolayer (SAM) consisting of less than 10(6) DNA molecules and by measuring their hybridization efficiency. We show that the binding rate is 1000 times faster than on a "macroscopic" surface. We also show that the hybridization of a SAM of maximum density DNA is 40% or 4 times the value reported in the literature. These results suggest that the lower values previously reported in the literature can be attributed to incomplete saturation of the surface due to the slower adsorption rate on the "macroscopic" surfaces used.

Development of macroporous poly(ethylene glycol) hydrogel arrays within microfluidic channels

The mass transport of solutes through hydrogels is an important design consideration in materials used for tissue engineering, drug delivery, and protein arrays used to quantify protein concentration and activity. We investigated the use of poly(ethylene glycol) (PEG) as a porogen to enhance diffusion of macromolecules into the interior of polyacrylamide and PEG hydrogel posts photopatterned within microfluidic channels. The diffusion of GST-GFP and dextran-FITC into hydrogels was monitored and effective diffusion coefficients were determined by fitting to the Fickian diffusion equations. PEG-diacrylate (M(r) 700) with porogen formed a macroporous structure and permitted significant penetration of 250 kDa dextran. Proteins copolymerized in these macroporous hydrogels retained activity and were more accessible to antibody binding than proteins copolymerized in nonporous gels. These results suggest that hydrogel macroporosity can be tuned to regulate macromolecular transport in applications such as tissue engineering and protein arrays.

Oriented immobilization of prion protein demonstrated via precise interfacial nanostructure measurements

Nanopatterning of biomolecules on functionalized surfaces offers an excellent route for ultrasensitive protein immobilization, for interaction measurements, and for the fabrication of devices such as protein nanoarrays. An improved understanding of the physics and chemistry underlying the device properties and the recognition process is necessary for performance optimization. This is especially important for the recognition and immobilization of intrinsically disordered proteins (IDPs), like the prion protein (PrP), a partial IDP, whose folding and stability may be influenced by local environment and confinement. Atomic force microscopy allows for both highly controllable nanolithography and for sensitive and accurate direct detection, via precise topographic measurements on ultraflat surfaces, of protein interactions in a liquid environment, thus different environmental parameters affecting the biorecognition phenomenon can be investigated in situ. Using nanografting, a tip-induced lithographic technique, and an affinity immobilization strategy based on two different histidine tagged antibodies, with high nM affinity for two different regions of PrP, we successfully demonstrated the immobilization of recombinant mouse PrP onto nanostructured surfaces, in two different orientations. Clear discrimination of the two molecular orientations was shown by differential height (i.e., topographic) measurements, allowing for the estimation of binding parameters and the full characterization of the nanoscale biorecognition process. Our work opens the way to several high sensitivity diagnostic applications and, by controlling PrP orientation, allows for the investigation of unconventional interactions with partially folded proteins, and may serve as a platform for protein misfolding and refolding studies on PrP and other thermodynamically unstable, fibril forming, proteins.

Mass-transport limitations in spot-based microarrays

Mass transport of analyte to surface-immobilized affinity reagents is the fundamental bottleneck for sensitive detection in solid-support microarrays and biosensors. Analyte depletion in the volume adjacent to the sensor causes deviation from ideal association, significantly slows down reaction kinetics, and causes inhomogeneous binding across the sensor surface. In this paper we use high-resolution molecular interferometric imaging (MI2), a label-free optical interferometry technique for direct detection of molecular films, to study the inhomogeneous distribution of intra-spot binding across 100 micron-diameter protein spots. By measuring intra-spot binding inhomogeneity, reaction kinetics can be determined accurately when combined with a numerical three-dimensional finite element model. To ensure homogeneous binding across a spot, a critical flow rate is identified in terms of the association rate k(a) and the spot diameter. The binding inhomogeneity across a spot can be used to distinguish high-affinity low-concentration specific reactions from low-affinity high-concentration non-specific binding of background proteins.

High sensitivity protein assays on microarray silicon slides

In this work, we report on the improvement of microarray sensitivity provided by a crystalline silicon substrate coated with thermal silicon oxide functionalized by a polymeric coating. The improvement is intended for experimental procedures and instrumentations typically involved in microarray technology, such as fluorescence labeling and a confocal laser scanning apparatus. The optimized layer of thermally grown silicon oxide (SiO(2)) of a highly reproducible thickness, low roughness, and fluorescence background provides fluorescence intensification due to the constructive interference between the incident and reflected waves of the fluorescence radiation. The oxide surface is coated by a copolymer of N,N-dimethylacrylamide, N-acryloyloxysuccinimide, and 3-(trimethoxysilyl)propyl methacrylate, copoly(DMA-NAS-MAPS), which forms, by a simple and robust procedure, a functional nanometric film. The polymeric coating with a thickness that does not appreciably alter the optical properties of the silicon oxide confers to the slides optimal binding specificity leading to a high signal-to-noise ratio. The present work aims to demonstrate the great potential that exists by combining an optimized reflective substrate with a high performance surface chemistry. Moreover, the techniques chosen for both the substrate and surface chemistry are simple, inexpensive, and amenable to mass production. The present application highlights their potential use for diagnostic applications of real clinical relevance. The coated silicon slides, tested in protein and peptide microarrays for detection of specific antibodies, lead to a 5-10-fold enhancement of the fluorescence signals in comparison to glass slides.

Tracking humoral responses using self assembling protein microarrays

The humoral immune response is a highly specific and adaptive sensor for changes in the body's protein milieu, which responds to novel structures of both foreign and self antigens. Although Igs represent a major component of human serum and are vital to survival, little is known about the response specificity and determinants that govern the human immunome. Historically, antigen-specific humoral immunity has been investigated using individually produced and purified target proteins, a labor-intensive process that has limited the number of antigens that have been studied. Here, we present the development of methods for applying self-assembling protein microarrays and a related method for producing 96-well formatted macroarrays for monitoring the humoral response at the proteome scale. Using plasmids encoding full-length cDNAs for over 850 human proteins and 1700 pathogen proteins, we demonstrate that these microarrays are highly sensitive, specific, reproducible, and can simultaneously measure immunity to thousands of proteins without a priori protein purification. Using this approach, we demonstrate the detection of humoral immunity to known and novel self-antigens, cancer antigens, autoimmune antigens, as well as pathogen-derived antigens. This represents a powerful and versatile tool for monitoring the immunome in health and disease.

Arrayed primer extension on in situ synthesized 5'-->3' oligonucleotides in microchannels

Arrays of oligonucleotides synthesized in the 5'-->3' direction have potential benefit in several areas of life sciences research because the free 3'-end can be modified by enzymatic reactions. A Geniom One instrument (febit biomed GmbH, Germany), with integrated chip fabrication, multiplex primer extension, fluorescence imaging, and data analysis, was evaluated for studies of genomic variations. Microchannels used for the array synthesis in Geniom One were not optimized before for the APEX method and, as preliminary experiments demonstrated in this study, the signals were strongly affected by the speed of the process inside reaction channels. Using the two-compartment model (TCM), target binding to feature were quantitatively analyzed, revealing profound mass-transport limitations in the observed kinetics and enabling us to draw a series of physicochemical conclusions of the optimal set-up for the APEX reaction. Some kinetically relevant parameters such as target concentration, reaction time, and temperature were comprehensively analyzed. Finally, we applied the arrays and methods in a proof-of-principle experiment where 36 individuals were typed with 900 oligonucleotide probes (sense and antisense primers for 450 markers), using the ABCR gene as a test system. A new DNA analysis method for studies of genomic variation was developed using this all-in-one platform.

Why 3-D? Gel-based microarrays in proteomics

Gel-based microarrays (biochips) consisting of nanoliter and sub-nanoliter gel drops on hydrophobic substrate are a versatile technology platform for immobilization of proteins and other biopolymers. Biochips provide a highly hydrophilic environment, which stabilizes immobilized molecules and facilitates their interactions with analytes. The probes are immobilized simultaneously with gel polymerization, evenly distributed throughout individual elements, and are easily accessible because of large pores. Each element is an isolated nanotube. Applications of biochips in the studies of protein interactions with other proteins, nucleic acids, and glycans are described. In particular, biochips are compatible with MALDI-MS. Biochip-based assay of prostate-specific antigen became the first protein microarray approved for clinical use by a national regulatory agency. In this review, 3-D immobilization is compared with mainstream technologies based on surface immobilization.

Generation of hydroxyapatite patterns by electrophoretic deposition

Hydroxyapatite (HAp) patterns with distinct boundaries were generated by electrophoretic deposition (EPD) utilizing an insulating mask that partially blocks the electric field. For the EPD process, we selected two types of mask: a polytetrafluoroethylene (PTFE) board with holes and a resist pattern. A porous PTFE film, which differed from the mask PTFE, was employed as a substrate and attached to the mask. EPD was performed with a suspension of wollastonite particles in acetone, which were deposited on the substrate in the form of the patterned mask. The deposited wollastonite particles induced HAp patterns during a soak in simulated body fluid (SBF). As a result, minute HAp patterns, such as dots, lines, and corners were fabricated on the porous PTFE substrate with a minimum line width of about 100 microm.

Layer-by-layer coated digitally encoded microcarriers for quantification of proteins in serum and plasma

The "layer-by-layer" (LbL) technology has been widely investigated for the coating of flat substrates and capsules with polyelectrolytes. In this study, LbL polyelectrolyte coatings applied at the surface of digitally encoded microcarriers were evaluated for the quantitative, sensitive, and simultaneous detection of proteins in complex biological samples like serum, plasma, and blood. LbL coated microcarriers were therefore coupled to capture antibodies, which were used as capture agents for the detection of tumor necrosis factor (TNF-alpha), P24, and follicle stimulating hormone (FSH). It was found that the LbL coatings did not disassemble upon incubating the microcarriers in serum and plasma. Also, nonspecific binding of target analytes to the LbL coating was not observed. We showed that the LbL coated microcarriers can reproducibly detect TNF-alpha, P24, and FSH down to the picogram per milliliter level, not only in buffer but also in serum and plasma samples. Microcarrier-to-microcarrier intratube variations were less then 30%, and interassay variations less than 8% were observed. This paper also shows evidence that the LbL coated digitally encoded microcarriers are ideally suited for assaying proteins in "whole" blood in microfluidic chips, which are of high interest for "point-of-care" diagnostics.

Evaluation of surface chemistries for antibody microarrays

Antibody microarrays are an emerging technology that promises to be a powerful tool for the detection of disease biomarkers. The current technology for protein microarrays has been derived primarily from DNA microarrays and is not fully characterized for use with proteins. For example, there are a myriad of surface chemistries that are commercially available for antibody microarrays, but there are no rigorous studies that compare these different surfaces. Therefore, we have used a sandwich enzyme-linked immunosorbent assay (ELISA) microarray platform to analyze 17 different commercially available slide types. Full standard curves were generated for 23 different assays. We found that this approach provides a rigorous and quantitative system for comparing the different slide types based on spot size and morphology, slide noise, spot background, lower limit of detection, and reproducibility. These studies demonstrate that the properties of the slide surface affect the activity of immobilized antibodies and the quality of data produced. Although many slide types produce useful data, glass slides coated with aldehyde silane, poly-l-lysine, or aminosilane (with or without activation with a crosslinker) consistently produce superior results in the sandwich ELISA microarray analyses we performed.

Reverse-phase protein microarrays: application to biomarker discovery and translational medicine

Mapping of protein signaling networks within tumors can identify new targets for therapy and provide a means to stratify patients for individualized therapy. Kinases are important drug targets, as such kinase network information could become the basis for development of therapeutic strategies for improving treatment outcome. An urgent clinical goal is to identify functionally important molecular networks associated with subpopulations of patients that may not respond to conventional combination chemotherapy. Reverse-phase protein microarrays are a technology platform designed for quantitative, multiplexed analysis of specific phosphorylated, cleaved, or total (phosphorylated and nonphosphorylated) forms of cellular proteins from a limited amount of sample. This class of microarray can be used to interrogate cellular samples, serum or body fluids. This review focuses on the application of reverse-phase protein microarrays for translational research and therapeutic drug target discovery.

High-throughput antibody microarrays for quantitative proteomic analysis

The antibody microarray is an intrinsically robust and quantitative system that delivers high-throughput and parallel measurements on particular sets of known proteins. It has become an important proteomics research tool, complementary to the conventional unbiased separation-based and mass spectrometry-based approaches. This review summarizes the technical aspects of production and the application for quantitative proteomic analysis with an emphasis on disease proteomics, especially the identification of biomarkers. Quality control, data analysis methods and the challenges for quantitative assays are also discussed.

Comparison of surface and hydrogel-based protein microchips

Protein microchips are designed for high-throughput evaluation of the concentrations and activities of various proteins. The rapid advance in microchip technology and a wide variety of existing techniques pose the problem of unified approach to the assessment and comparison of different platforms. Here we compare the characteristics of protein microchips developed for quantitative immunoassay with those of antibodies immobilized on glass surfaces and in hemispherical gel pads. Spotting concentrations of antibodies used for manufacturing of microchips of both types and concentrations of antigen in analyte solution were identical. We compared the efficiency of antibody immobilization, the intensity of fluorescence signals for both direct and sandwich-type immunoassays, and the reaction-diffusion kinetics of the formation of antibody-antigen complexes for surface and gel-based microchips. Our results demonstrate higher capacity and sensitivity for the hydrogel-based protein microchips, while fluorescence saturation kinetics for the two types of microarrays was comparable.

Antibody microarray-based profiling of complex specimens: systematic evaluation of labeling strategies

Antibody microarrays have often had limited success in detection of low abundant proteins in complex specimens. Signal amplification systems improve this situation, but still are quite laborious and expensive. However, the issue of sensitivity is more likely a matter of kinetically appropriate microarray design as demonstrated previously. Hence, we re-examined in this study the suitability of simple and inexpensive detection approaches for highly sensitive antibody microarray analysis. N-hydroxysuccinimidyl ester (NHS)- and Universal Linkage System (ULS)-based fluorescein and biotin labels used as tags for subsequent detection with anti-fluorescein and extravidin, respectively, as well as fluorescent dyes were applied for analysis of blood plasma. Parameters modifying strongly the performance of microarray detection such as labeling conditions, incubation time, concentrations of anti-fluorescein and extravidin and extent of protein labeling were analyzed and optimized in this study. Indirect detection strategies whether based on NHS- or ULS-chemistries strongly outperformed direct fluorescent labeling and enabled detection of low abundant cytokines with many dozen-fold signal-to-noise ratios. Finally, particularly sensitive detection chemistry was applied to monitoring cytokine production of stimulated peripheral T cells. Microarray data were in accord with quantitative cytokine levels measured by ELISA and Luminex, demonstrating comparable reliability and femtomolar range sensitivity of the established microarray approach.

High-Throughput Screening of Single-Chain Antibodies Using Multiplexed Flow Cytometry

We have developed a screening method that has the potential to streamline the high-throughput analysis of affinity reagents for proteomic projects. By using multiplexed flow cytometry, we can simultaneously determine the relative expression levels, the identification of nonspecific binding, and the discrimination of fine specificities to generate a complete functional profile for each clone. The quality and quantity of data, combined with significant reductions in analysis time and antigen consumption, provide notable advantages over standard ELISA methods and yield much information in the primary screen which is usually only obtained in later screens. By combining high-throughput screening capabilities with multiplex technology, we have redefined the parameters for the initial identification of affinity reagents recovered from combinatorial libraries and removed a significant bottleneck in the generation of affinity reagents on a proteomic scale.

Antibody microarrays: current status and key technological advances

Antibody-based microarrays are among the novel classes of rapidly evolving proteomic technologies that holds great promise in biomedicine. Miniaturized microarrays (< 1 cm2) can be printed with thousands of individual antibodies carrying the desired specificities, and with biological sample (e.g., an entire proteome) added, virtually any specifically bound analytes can be detected. While consuming only minute amounts (< microL scale) of reagents, ultra- sensitive assays (zeptomol range) can readily be performed in a highly multiplexed manner. The microarray patterns generated can then be transformed into proteomic maps, or detailed molecular fingerprints, revealing the composition of the proteome. Thus, protein expression profiling and global proteome analysis using this tool will offer new opportunities for drug target and biomarker discovery, disease diagnostics, and insights into disease biology. Adopting the antibody microarray technology platform, several biomedical applications, ranging from focused assays to proteome-scale analysis will be rapidly emerging in the coming years. This review will discuss the current status of the antibody microarray technology focusing on recent technological advances and key issues in the process of evolving the methodology into a high-performing proteomic research tool.

Optimal design of microarray immunoassays to compensate for kinetic limitations: theory and experiment

In this report we examine the limitations of existing microarray immunoassays and investigate how best to optimize them using theoretical and experimental approaches. Derived from DNA technology, microarray immunoassays present a major technological challenge with much greater physicochemical complexity. A key physicochemical limitation of the current generation of microarray immunoassays is a strong dependence of antibody microspot kinetics on the mass flux to the spot as was reported by us previously. In this report we analyze, theoretically and experimentally, the effects of microarray design parameters (incubation vessel geometry, incubation time, stirring, spot size, antibody-binding site density, etc.) on microspot reaction kinetics and sensitivity. Using a two-compartment model, the quantitative descriptors of the microspot reaction were determined for different incubation and microarray design conditions. This analysis revealed profound mass transport limitations in the observed kinetics, which may be slowed down as much as hundreds of times compared with the solution kinetics. The data obtained were considered with relevance to microspot assay diffusional and adsorptive processes, enabling us to validate some of the underlying principles of the antibody microspot reaction mechanism and provide guidelines for optimal microspot immunoassay design. For an assay optimized to maximize the reaction velocity on a spot, we demonstrate sensitivities in the am and low fm ranges for a system containing a representative sample of antigen-antibody pairs. In addition, a separate panel of low abundance cytokines in blood plasma was detected with remarkably high signal-to-noise ratios.

Microarray technology: beyond transcript profiling and genotype analysis

Understanding complex functional mechanisms requires the global and parallel analysis of different cellular processes. DNA microarrays have become synonymous with this kind of study and, in many cases, are the obvious platform to achieve this aim. They have already made important contributions, most notably to gene-expression studies, although the true potential of this technology is far greater. Whereas some assays, such as transcript profiling and genotyping, are becoming routine, others are still in the early phases of development, and new areas of application, such as genome-wide epigenetic analysis and on-chip synthesis, continue to emerge.