Allergen microarray: comparison of microarray using recombinant allergens with conventional diagnostic methods to detect allergen-specific serum immunoglobulin E

Optimization of critical factors affecting the performance of an allergen chip for the analysis of an allergen-specific human IgE in serum

A sensitive and multiplexed assay of allergen-specific human immunoglobulin E (IgE) is of great significance in the precise diagnosis of allergies. We report on the optimization of critical factors for chip-based analysis of IgE in human serum with a high reliability. Extracts of two mite species were used as model allergens, and were spotted onto a glass slide for the construction of an allergen chip. Respective allergen-specific IgE in human serum was analyzed by using biotinylated anti-human IgE and a streptavidin-Cy3 conjugate. Factors affecting the performance of the allergen chip were investigated and optimized. Especially, the effect of additives, the concentrations of biotinylated anti-human IgE and the streptavidin-Cy3 conjugate, the serum dilution factor, and the concentration of allergen extract as a capturing agent were examined in detail. Under the optimized conditions, a chip-based analysis for sera from 43 patients revealed a reliable and reproducible diagnosis of respective allergies, showing a good correlation with a conventional CAP assay.

Allergen microarrays for the diagnosis of specific IgE against components of cow's milk and hen's egg in a multiplex biochip-based immunoassay

Over the last few decades, the prevalence of allergic diseases has increased dramatically in developed nations. The resulting burden on health care systems worldwide has provoked a whole series of research initiatives among allergy experts and commercial companies that aim to develop novel tests to improve the diagnostic risk assessment and early preventive treatment of the disease. The advent of protein microarray technology has inspired the development of miniaturized immunological applications that permit the simultaneous analysis of huge numbers of disease-related parameters. Allergen microarrays have been developed for the monitoring of patient-specific antibody profiles to a previously unknown variety of allergens in a single analytical step. This has been accomplished by the successful adaptation of solid-phase antibody assays for the detection of surface-bound allergens to the microarray format, the development of appropriate assay conditions, and the improvement of software-guided microarray image analysis. Here we report a protocol for the development and analysis of food allergen microarrays.

Measuring allergen-specific IgE: where have we been and where are we going?

About 40 yr ago, two groups of investigators identified a new class of immunoglobulins, IgE. By exchanging their results and reagents, they proved that the immunoglobulin responsible for immediate hypersensitivity was IgE. From that day forward the science of allergy was greatly advanced. Within a few years of the IgE discovery, an assay for IgE was developed. This test was named the radio allergosorbent test. The specific IgE testing methodology has matured in the last four decades. Different means of detecting IgE bound to allergen is the subject of this review. We have included methods for measuring specific IgE using the ImmunoCAP 1000 instrument. The methodology for measuring basophile histamine release is also detailed in this chapter.

[In vitro allergy testing]

Along with the history, skin tests and provocation tests, in vitro test procedures are essential for the adequate care for patients with allergies. While serological investigations of immediate-type allergic reactions primarily detect allergen-specific IgE antibodies, basophil activation tests with different read-out parameters are available for cellular diagnosis of immediate-type reaction patterns. If clinically necessary, further immunological methods (i. e. immunoblots, lymphocyte transformation tests) can be employed. New options are provided by allergen microarray technology, which makes it possible to determine not only the specific antigenic protein but also to analyze different epitopes.

Biotechnologies in new high-throughput food allergy tests: why we need them

The increase in prevalence of food allergies generates a need for more accurate and reliable quantitative allergy testing in order to help diagnosis. In this short review, we briefly outline the history of food allergy testing and extend our comments to current multiplex techniques. Particular emphasis is given to new developments in the protein microarray area, where the use of recent advances in biotechnology has the potential to produce high-throughput devices with improved clinical significance.

Human body fluid proteome analysis

The focus of this article is to review the recent advances in proteome analysis of human body fluids, including plasma/serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, and amniotic fluid, as well as its applications to human disease biomarker discovery. We aim to summarize the proteomics technologies currently used for global identification and quantification of body fluid proteins, and elaborate the putative biomarkers discovered for a variety of human diseases through human body fluid proteome (HBFP) analysis. Some critical concerns and perspectives in this emerging field are also discussed. With the advances made in proteomics technologies, the impact of HBFP analysis in the search for clinically relevant disease biomarkers would be realized in the future.

Expression profiling of proteins inL-threonine biosynthetic pathway ofEscherichia coli by using antibody microarray

We demonstrate the use of an antibody (Ab) microarray for a comparative expression profiling of proteins in an L-threonine biosynthetic pathway of Escherichia coli between a parental strain (W3110) and L-threonine overproducing mutant (TF5015). On the basis of a global comparative transcriptome analysis between the two strains, 28 analytical target proteins were selected and subjected to a production of polyclonal Abs against them. An Ab microarray was constructed by spotting a set of produced antibodies on a glass slide, and was employed for a comparative expression profiling of the proteins between the two strains by a two-color fluorescence assay method. The performance of the Ab microarray was evaluated with respect to cross-reactivity of the antibodies, dye-labeling efficiency, and the nature of antigenic proteins. Of these, the cross-reactivity of the used antibodies was found to mainly cause the deviation of the observed expression ratios from the expected ones. To offset the deviations, correction factors were derived from a statistical analysis and introduced. As a result, ten proteins were categorized to be up-regulated, while one was down-regulated in TF5015. Expression profiling of proteins using the Ab microarray was further verified by comparison with Western blotting and 2-DE.

Diagnostic applications of microarrays

Microarrays were designed to monitor the expression of many genes in parallel, providing substantially more information than Northern blots or reverse transcription polymerase chain reaction analysing one or few genes at a time. The large sequencing projects provided the content for detailed expression studies under a variety of stimuli and conditions. The human genome project identified around 30 000 human genes. Estimated number of protein products is, however, 10-30 times higher, mainly due to the alternative splicing and post-translational modifications. The identification of gene functions requires both genomic and proteomic approaches, including protein microarrays, and numerous current microarray projects focus on deciphering gene expression patterns under a variety of conditions. Establishing the key genes and gene products for particular conditions opens the way for diagnostic applications using multiparameter, high-throughput assays. This format can also accommodate existing blood screening assays, potentially providing a single testing platform. This review considers the progress in diagnostic microarrays in a wider context of in vitro diagnostics field.

Diagnostic challenges for multiplexed protein microarrays

Multiplexed protein analysis using planar microarrays or microbeads is growing in popularity for simultaneous assays of antibodies, cytokines, allergens, drugs and hormones. However, this new assay format presents several new operational issues for the clinical laboratory, such as the quality control of protein-microarray-based assays, the release of unrequested test data and the use of diagnostic algorithms to transform microarray data into diagnostic results.

Multiplexed protein array platforms for analysis of autoimmune diseases

Several proteomics platforms have emerged in the past decade that show great promise for filling in the many gaps that remain from earlier studies of the genome and from the sequencing of the human genome itself. This review describes applications of proteomics technologies to the study of autoimmune diseases. We focus largely on biased technology platforms that are capable of analyzing a large panel of known analytes, as opposed to techniques such as two-dimensional gel electrophoresis (2DIGE) or mass spectroscopy that represent unbiased approaches (as reviewed in 1). At present, the main analytes that can be systematically studied in autoimmunity include autoantibodies, cytokines and chemokines, components of signaling pathways, and cell-surface receptors. We review the most commonly used platforms for such studies, citing important discoveries and limitations that exist. We conclude by reviewing advances in biomedical informatics that will eventually allow the human proteome to be deciphered.

A new time-resolved fluorometric microarray detection system using core–shell-type fluorescent nanosphere and its application to allergen microarray

We have developed a new time-resolved fluorometric (TRF) microarray detection system consisting of fluorescent NH2 nanosphere, TRF microarray detector and gamma-irradiated polystyrene chip. Using the TRF microarray detector, we detected 500 particles of the fluorescent nanosphere in one channel. Cross-talk fluorescence from the adjacent channels was little observed in the TRF microarray detector (<0.0004 %). The TRF microarray detection system was further applied for serum allergen-specific immunoglobulin E (IgE) multi-analyses. As a labeled tag antibody, an anti-human IgE Fab' fragment-conjugated fluorescent nanosphere (Fab' nanosphere) was prepared as described previously. As a chip surface appropriate for allergen immobilization, the polystyrene chip surface was modified by gamma irradiation. The immunoassay reactivity using the gamma-irradiated polystyrene chip was approximately 2.5-times improved compared with that of the non-treated polystyrene chip. Non-specific adsorption of the Fab' nanosphere onto the gamma-irradiated polystyrene chip surface was very low level (<0.0009 %). In only 20 mul of serum, six allergen-specific IgEs could be simultaneously determined in one reaction well in fewer than 90 min. Good correlation curves were obtained between the microarray immunoassay and the CAP RAST fluoro-enzyme immunoassay (CAP/RAST FEIA) method (r > 0.961). Reproducibility (CVs) of the microarray immunoassay was 8.6 % to 19.0 % (n = 5).

The performance of a component-based allergen-microarray in clinical practice

BACKGROUND

Currently, the diagnosis of IgE-mediated allergy is based on allergen-specific history and diagnostic procedures using natural allergen extracts for in vivo and in vitro tests.

OBJECTIVE

The aim of the study was to comparatively analyse a new component-based allergen-microarray and the 'quasi-standard' ImmunoCAP for their clinical relevance in patients with allergic rhinoconjunctivitis to five aeroallergens [house dust mite (HDM), cat dander, birch, grass and mugwort pollen] in a prospective, double-centre study.

METHODS

We enrolled 120 subjects at the two study centres. Allergic patients were defined as having an allergen-specific history plus a concomitant positive skin-prick test (SPT) to natural allergen extracts and specific serum IgE was measured by both methods. Each allergen was analysed separately.

RESULTS

The microarray performed equally well in receiver-operating characteristic curve (ROC) analyses when compared with the CAP in cat (23 allergic vs 97 non-allergic, ROC area under the curve microarray 0.950 vs CAP 0.894, P = 0.211), birch (31/89, 0.908 vs 0.878, P = 0.483) and grass pollen (47/73, 0.923 vs 0.915, P = 0.770). It was slightly less sensitive in HDM-allergic subjects (26 allergic vs 94 non-allergic, ROC area microarray 0.808 vs CAP 0.911, P = 0.053) and displayed a reduced sensitivity in the mugwort pollen-allergic patients (17/103, 0.723 vs 0.879, P = 0.032).

CONCLUSIONS

Component-based testing and the whole-allergen CAP are equally relevant in the diagnosis of grass-, birch- and cat-allergic patients. Although slightly less sensitive, the microarray is sufficient for the diagnosis of HDM-allergic patients, but needs alternative and/or additional components for detecting mugwort allergy.

Multiplexed protein measurement: technologies and applications of protein and antibody arrays

The ability to measure the abundance of many proteins precisely and simultaneously in experimental samples is an important, recent advance for static and dynamic, as well as descriptive and predictive, biological research. The value of multiplexed protein measurement is being established in applications such as comprehensive proteomic surveys, studies of protein networks and pathways, validation of genomic discoveries and clinical biomarker development. As standards do not yet exist that bridge all of these applications, the current recommended best practice for validation of results is to approach study design in an iterative process and to integrate data from several measurement technologies. This review describes current and emerging multiplexed protein measurement technologies and their applications, and discusses the remaining challenges in this field.

Diagnostic and analytical applications of protein microarrays

DNA microarrays have changed the field of biomedical sciences over the past 10 years. For several reasons, antibody and other protein microarrays have not developed at the same rate. However, protein and antibody arrays have emerged as a powerful tool to complement DNA microarrays during the past 5 years. A genome-scale protein microarray has been demonstrated for identifying protein-protein interactions as well as for rapid identification of protein binding to a particular drug. Furthermore, protein microarrays have been shown as an efficient tool in cancer profiling, detection of bacteria and toxins, identification of allergen reactivity and autoantibodies. They have also demonstrated the ability to measure the absolute concentration of small molecules. Besides their capacity for parallel diagnostics, microarrays can be more sensitive than traditional methods such as enzyme-linked immunosorbent assay, mass spectrometry or high-performance liquid chromatography-based assays. However, for protein and antibody arrays to be successfully introduced into diagnostics, the biochemistry of immunomicroarrays must be better characterized and simplified, they must be validated in a clinical setting and be amenable to automation or integrated into easy-to-use systems, such as micrototal analysis systems or point-of-care devices.

Protein and peptide arrays: recent trends and new directions

Microarrays of proteins and peptides make it possible the screening of thousands of binding events in a parallel and high throughput fashion; therefore they are emerging as a powerful tool for proteomics and clinical assays. The complex nature of Proteome, the wide dynamic range of protein concentration in real samples and the critical role of immobilized protein orientation must be taken into account to maximize the utility of protein microarrays. Immobilization strategy and designing of an ideal local chemical environment on the solid surface are both essential for the success of a protein microarray experiment. This review article will focus on protein and peptide arrays highlighting their technical challenges and presenting new directions by means of a set of selected recent applications.

Microarray techniques for more rapid protein quantification: Use of single spot multiplex analysis and a vibration reaction unit

Protein microarray technology is a powerful, popular tool for the high-throughput analysis of protein interactions. One important use for protein microarray technology is protein quantification by immunoassay, which was originally based on enzyme linked immunosorbent assay (ELISA) methods. Recently, new research and diagnostic applications have created a need for a rapid and easily applied high-throughput protein quantification method. Here, we introduce several novel techniques that address these needs. Our improved protein microarray-based sandwich immunoassay techniques allow researchers to: (1) control the size and shape of protein spots on the microarray using a perforated seal; (2) analyze two proteins within a single spot, thus increasing the number of tests run on a single microarray without increasing the number of protein spots; (3) improve the efficiency and speed of the Ag-Ab interaction through vibratory reagent convection, which increased the signal intensity by more than two-fold and decreased the reaction time from 30 to 10 min. These new techniques will facilitate rapid immunoassays for diagnostic purposes and other research areas utilizing protein microarray analysis, such as investigations of ligand-receptor or protein-small molecule interactions.

Versatile protein microarray based on carbohydrate-binding modules

Non-DNA microarrays, such as protein, peptide and small molecule microarrays, can potentially revolutionize the high-throughput screening tools currently used in basic and pharmaceutical research. However, fundamental obstacles remain that limit their rapid and widespread implementation as an alternative bioanalytical approach. These include the prerequisite for numerous proteins in active and purified form, ineffectual immobilization strategies and inadequate means for quality control of the considerable numbers of multiple reagents. This study describes a simple yet efficient strategy for the production of non-DNA microarrays, based on the tenacious affinity of a carbohydrate-binding module (CBM) for its three-dimensional substrate, i.e., cellulose. Various microarray formats are described, e.g., conventional and single-chain antibody microarrays and peptide microarrays for serodiagnosis of human immunodeficiency virus patients. CBM-based microarray technology overcomes many of the previous obstacles that have hindered fabrication of non-DNA microarrays and provides a technically simple but effective alternative to conventional microarray technology.

Molecular design of allergy vaccines

Recombinant-allergen-based diagnostic tests enable the dissection and monitoring of the molecular reactivity profiles of allergic patients, resulting in more specific diagnosis, disease monitoring, prevention and therapy. In vitro experiments, animal studies and clinical trials in patients demonstrate that allergenic molecules can be engineered to induce different immune responses ranging from tolerance to vigorous immunity. The available data thus suggest that molecular engineering of the disease-related antigens is a technology that may be applicable not only for the design of allergy vaccines but also for the design of vaccines against infectious diseases, autoimmunity and cancer.

The future of microarray technology: networking the genome search

In recent years microarray technology has been increasingly used in both basic and clinical research, providing substantial information for a better understanding of genome-environment interactions responsible for diseases, as well as for their diagnosis and treatment. However, in genomic research using microarray technology there are several unresolved issues, including scientific, ethical and legal issues. Networks of excellence like GA(2)LEN may represent the best approach for teaching, cost reduction, data repositories, and functional studies implementation.

Immunobiology of grass pollen allergens

Among pollen allergens, grass pollen allergens are some of the most frequent contributors to allergic symptoms. Substantial progress has been made since the 1960s in the identification and characterization of the grass allergens. Members of this group belong to the Poaceae family, and have been classified into 13 distinct groups based on their structure, and their biological and immunologic properties. The major contributors to allergy and, hence, most studied among the grass allergens, are those belonging to groups 1 and 5. This review is focused on the structure and immunobiology of the grass allergens and highlights how recent advances in the field have contributed to superior diagnosis and immunotherapy for allergy to grass pollens.

Importance of databases in experimental and clinical allergology

Information technology (IT) is leading us to reconsider some of the approaches we have been using in both basic research and clinical work in allergology. Resources mainly coming from the advent of the Internet are further amplified by the parallel development of other new tools, such as molecular biology and nanotechnology. These three powerful tools are now available and are cross-linked to a certain degree to express their power when applied to biomedical fields. Bioinformatics applied to allergy simplifies our way of handling an increasing wealth of knowledge. This review assesses the current status of allergen databases that are mainly dedicated to sequence homology collection for computational purposes. Whether or not they integrate features that are now typical of IT in other biomedical fields is analyzed as well. The results of these analyses are discussed with a view to the critical need of integrating biochemical data with clinical, epidemiological information and how this goal can be reached by the use of proteomic microarrays for IgE detection. Future directions for a more comprehensive use of allergen databases are proposed.

Affinity determinations of purified IgE and IgG antibodies against the major pollen allergens Phl p 5a and Bet v 1a: discrepancy between IgE and IgG binding strength

Allergen-specific IgE and IgG antibodies coexist in allergic individuals, but only IgE has anaphylactogenic capacity. This study aimed to determine the association, dissociation and equilibrium constants for the interaction of allergen-specific IgE and IgG with the major grass and birch pollen allergens Phl p 5a and Bet v 1a. We isolated specific IgE and IgG antibodies from pollen allergic patients' sera by a two-step affinity chromatography protocol and controlled the high purity in a recombinant allergen chip microarray. Surface plasmon resonance measurements of polyclonal IgE and IgG species revealed that their affinities diverge widely, being in the range of 10(-10) and 10(-11) M for IgE, but only 10(-6)-10(-7) M for IgG. Moreover, murine monoclonal IgG1 antibodies against the allergens showed affinities of 10(-7)-10(-8) M. Thus, we conclude from our data that even stringently affinity matured IgG cannot score the superior affinity of IgE antibodies to allergens.

Protein biochips: A new and versatile platform technology for molecular medicine

The human genome has been sequenced and the challenges of understanding the function of the newly discovered genes have been addressed. High-throughput technologies such as DNA microarrays have been developed for the profiling of gene expression patterns in whole organisms or tissues. Protein arrays are emerging to follow DNA chips as possible screening tools. Here, we review the generation and application of microarray technology to obtain more information on the regulation of proteins, their biochemical functions and their potential interaction partners. Already, a large variety of assays based on antibody-antigen interactions exists. In addition, the medical relevance of protein arrays will be discussed.

Development of a sensitive, colorometric microarray assay for allergen-responsive human IgE

With the existence of several thousand unique human allergens, a multiplex format, such as protein microarrays, is an attractive option for allergy screening. To determine the feasibility and sensitivity of using an enzyme-based, colorimetric protein microarray assay, three common allergens (mold, dust-mite, grass) were arrayed and added sera assayed for responsive human IgE. Normal, low positive, and negative control samples were assayed to determine optimal reaction parameters. Sensitivity of the assay (in international units, IU) was determined by constructing a standard curve using World Health Organization (WHO) standards. The system described here can reliably detect allergen-specific IgE below 0.35 IU, the current WHO standard cutoff. By taking advantage of the sensitivity of enzyme-linked immunosorbent assays (ELISAs) and the multiplex format of microarrays, we have achieved a high throughput system, capable of screening patients for allergen-susceptibility with optimal sensitivity.

Protein microarrays for the diagnosis of allergic diseases: state-of-the-art and future development

In the emerging field of

Preparation of Steroid Antibodies and Parallel Detection of Multianabolic Steroid Abuse with Conjugated Hapten Microarray

A conjugated hapten microarray based on miniature immunoassay for fast and multiplex detection of anabolic steroids is reported for the first time. This preliminary study investigated the possibility of using a microarray technology as a multisteroid detection assay. The microarray system used eight monoclonal antibodies raised against three steroid conjugates, 4-androsten-4-chloro-17beta-ol-3-one, 1,5alpha-androsten-1beta-methyl-17beta-ol-3-one, and 5beta-androsten-1-en-17beta-ol-3-one, which were conjugated to BSA by the active ester method. In addition to 4 commercial conjugated haptens, 18 steroid-BSA conjugates were synthesized and from all these a conjugated hapten microarray was fabricated. The analyzed substances included 42 types of anabolic steroid reference materials and 28 positive urine samples. Of these, 24 anabolic steroids and 12 positive urines were successfully detected.

In vitro assays for the diagnosis of IgE-mediated disorders

Advances in technology have provided new laboratory tools for the quantitation of allergen-specific IgE antibodies in serum and on the surface of basophils. This review examines the evolution from qualitative IgE antibody assays of the late 1960s to the present-day, third-generation, automated and quantitative allergen-specific IgE assays. The latest technology trend is toward microarrays in which crude or purified native and recombinant allergens can be spotted in microdot arrays on silica chips to permit extensive panels of specific IgE measurements to be performed with small quantities of serum. Although these technologies hold promise, their diagnostic performance requires further assessment once their technical details have been optimized. Potential abuses of this newer IgE antibody technology include the use of allergosorbent specificities (eg, especially food and drugs) that lack validation, application of IgE antibody measurements in the diagnosis of non-IgE-dependent disorders (eg, aspirin sensitivity), and modification of IgE antibody assays to measure food-specific IgG antibody for which there is no clinical indication. Basophil mediator release assays have evolved to include flow cytometric methods that can quantitatively detect the presence of cell surface-bound allergen-specific IgE antibodies. Assays for histamine and leukotriene C 4 released after in vitro basophil activation are now more accurate and standardized. Current analytic methods for IgE antibodies provide more quantitative and reproducible measurements of IgE than ever before, although still with less sensitivity that traditional skin testing. The current challenge is to translate the quantitative IgE antibody results into a more accurate diagnosis of allergic disease.

Array technology and proteomics in autoimmune diseases

Two new technologies (tissue microarrays (TMAs) and proteomics) have generated a great amount of data in life science. High-density TMAs allow for the simultaneous analysis of proteins and RNA by various methods (immunohistochemistry, in situ hybridization, FISH) on a large scale and under highly standardized conditions. Proteomics includes a variety of techniques that are partly high throughput. These techniques aim at the innovation of proteins, the description of the domain structure, the determination of protein sequences and epitope characterization, and ultimately the definition of protein function and protein reactivities in immunologic processes. Proteins that have been characterized accordingly require validation mostly at the morphologic level of defined tissue, linking proteomics to TMAs. In autoimmune diseases, array-based antigenic fingerprinting of autoantibodies will drive the development and the selection of antigen-specific diagnostic tools and therapies. The powerful combination of genomics and proteomics formed in tissue arrays has the potential to change the way the biology of autoimmunity is studied. Novel targets of drug discovery, based on antigen-specific therapies to induce anergy, or regulatory T-cells using the targeted autoantigens of individual patients could be developed in the coming decades.