Quantitative measurement of serum allergen-specific IgE on protein chip

Electrochemical Cell-Based Sensor for Detection of Food Hazards

People’s health has been threatened by several common food hazards. Thus, it is very important to establish rapid and accurate methods to detect food hazards. In recent years, biosensors have inspired developments because of their specificity and sensitivity, short reaction time, low cost, small size and easy operation. Owing to their high precision and non-destructive characteristics, cell-based electrochemical detection methods can reflect the damage of food hazards to organisms better. In this review, the characteristics of electrochemical cell-based biosensors and their applications in the detection of common hazards in food are reviewed. The strategies of cell immobilization and 3D culture on electrodes are discussed. The current limitations and further development prospects of cell-based electrochemical biosensors are also evaluated.

Allergen Microarrays for In Vitro Diagnostics of Allergies: Comparison with ImmunoCAP and AdvanSure

BACKGROUND

In vitro detection of the allergen-specific IgE antibody (sIgE) is a useful tool for the diagnosis and treatment of allergies. Although multiple simultaneous allergen tests offer simple and low-cost screening methods, these platforms also have limitations with respect to multiplexibility and analytical performance. As an alternative assay platform, we developed and validated a microarray using allergen extracts that we termed "GOLD" chip.

METHODS

Serum samples of 150 allergic rhinitis patients were used in the study, and the diagnostic performance of the microarray was compared with that of AdvanSure (LG Life Sciences, Daejun, Korea) and ImmunoCAP (Phadia, Uppsala, Sweden). Standard IgE samples were used for the quantitative measurement of sIgEs.

RESULTS

The microarray-based assay showed excellent performance in the quantitative measurement of sIgEs, demonstrating a linear correlation within the range of sIgE concentrations tested. The limit of detection (LOD) was lower than 0.35 IU/mL, which is the current standard for the LOD cut-off. The assay also provided highly reproducible sets of data. The total agreement percentage of positive and negative calls was 92.2% compared with ImmunoCAP. Moreover, an outstanding correlation was observed between the microarray and the ImmunoCAP results, with Cohen's kappa and Pearson correlation coefficient values of 0.80 and 0.79, respectively.

CONCLUSIONS

The microarray-based in vitro diagnostic platform offers a sensitive, reproducible, and highly quantitative method to detect sIgEs. The results showed strong correlations with that of ImmunoCAP. These results suggest that the new allergen microarray can serve as a useful alternative to current screening platforms, ultimately becoming a first-line screening method.

Quantification of bovine β-casein allergen in baked foodstuffs based on ultra-performance liquid chromatography with tandem mass spectrometry

The quantification of allergens in food including baked food matrices is of great interest. The aim of the present study was to describe a non-immunologic method to quantify bovine β-casein using ultra-performance liquid chromatography tandem triple quadrupole mass spectrometry (UPLC-TQ-MS/MS) in multiple reaction monitoring (MRM) mode. Eight of 10 theoretical peptides from β-casein after tryptic digestion were compared and MRM methods were developed to determine five signature peptides. The peptide VLPVPQK was selected as the signature peptide for bovine β-casein because of the high sensitivity. A stable isotope-labelled internal standard was designed to adjust the instability of sample pre-treatment and ionisation caused by matrix effect. Using the present suspension digestion method, the native and denatured β-casein could be digested to release the signature peptide at the maximum extent. The UPLC-TQ-MS/MS method developed based on a tryptic signature peptide led to a reliable determination of bovine β-casein allergen in baked food matrices at a low quantitation level down to 500 μg kg(-1) with a satisfactory accuracy (< 8.9%) and recovery (98.8% ± 2.6% to 106.7% ± 3.0%).

Development of hydrogel biochip for in vitro allergy diagnostics

A hydrogel biochip was developed for the simultaneous quantitative determination of sIgE for 21 allergens and total IgE in human serum. The biochips are manufactured by photoinduced copolymerization of different molecules (allergens and antibodies) with gel-forming monomers resulting in the formation of three-dimensional hydrogel elements (1nl gel drops). After incubation of the biochip with the serum, the results are visualized using fluorescently labeled anti-IgE antibodies. Using biochips, serum samples from allergic patients and healthy donors were analyzed and good correlation with the results obtained using commercial EIA test systems of generally recognized quality (Dr. Fooke Laboratorien GmbH, Germany) was observed.

Multiplex approaches in protein microarray technology

The success of genome sequencing projects has provided the basis for systematic analysis of protein function and has led to a shift from the description of single molecules to the characterization of complex samples. Such a task would not be possible without the provision of appropriate high-throughput technologies, such as protein microarray technology. In addition, the increasing number of samples necessitates the adaptation of such technologies to a multiplex format. This review will discuss protein microarray technology in the context of multiplex analysis and highlight its current prospects and limitations.

Cow's milk allergy: from allergens to new forms of diagnosis, therapy and prevention

The first adverse reactions to cow's milk were already described 2,000 years ago. However, it was only 50 years ago that several groups started with the analysis of cow's milk allergens. Meanwhile the spectrum of allergy eliciting proteins within cow's milk is identified and several cow's milk allergens have been characterized regarding their biochemical properties, fold and IgE binding epitopes. The diagnosis of cow's milk allergy is diverse ranging from fast and cheap in vitro assays to elaborate in vivo assays. Considerable effort was spent to improve the diagnosis from an extract-based into a component resolved concept. There is still no suitable therapy available against cow's milk allergy except avoidance. Therefore research needs to focus on the development of suitable and safe immunotherapies that do not elicit severe side effect.

IgE-mediated cow's milk allergy in children

The age at which the majority of children outgrow cow's milk allergy now appears to be later than previously reported. Recent studies have attempted to elucidate factors that may help prevent cow's milk allergy, assess markers of persistence, and evaluate the usefulness of new diagnostic methods. Strict avoidance of cow's milk has been the mainstay of treatment. However, given the potential nutritional, social, and immunologic ramifications of cow's milk elimination from a child's diet, there has been a focus on reevaluating this therapeutic approach.

The added value of allergen microarray technique to the management of poly-sensitized allergic patients

PURPOSE OF REVIEW

To evaluate the relevance of results obtained using allergen microarray technique for the description of the IgE repertoire in allergic patients.

RECENT FINDINGS

Allergen microarray was introduced at the beginning of the last decade. Since then, an increasing number of allergens have been identified, correspondingly increasing the accuracy of the description of immunoglobulin (Ig)E repertoire. In the last 2 years, a large number of articles were published that accurately described not only the general features of this technique, but also the use of allergen microarray in specific situations.

SUMMARY

The recent availability of highly purified or recombinant allergen components has deeply modified the laboratory approach to allergy diagnosis that, now, it cannot be limited to the detection of IgE specific to extractive allergens. Indeed, these contain both specific components (i.e. molecules strictly associated to that allergen source) and pan-allergen or cross-reacting allergens (i.e. molecules that are present in different similar allergen sources or that are present in highly homologous structures in different species). Newer techniques such as recombinant allergen testing and allergen microarray allow a more detailed evaluation of IgE responses. Future research is needed to more clearly define their role in clinical practice.

Detection of Allergen-Specific IgE Antibody Responses

Allergen-specific IgE production is the central event in the pathogenesis of atopic disorders and increases in specific IgE serum antibodies are an indicator of immediate hypersensitivity responses in humans and in animal models of allergy. Consequently, accurate and user-friendly methods are needed to measure serum levels of allergen-specific IgE. This review examines historical and recent developments in in vivo and in vitro methods for the detection of allergen-specific IgE in humans and in animal models. Routinely, in vitro methods such as enzyme-linked immunosorbant assays or radioallergosorbant tests and in vivo methods such as the skin prick test (SPT) for humans and the passive cutaneous anaphylaxis assay (PCA) used in animals are utilized to detect allergen-specific IgE. While in vivo assays are usually more accurate than in vitro assays since they provide a functional readout of IgE activity, they are relatively costly and require considerable expertise. On the other hand in vitro assays are limited by the fact that the amount of allergen-specific serum IgG exceeds IgE antibody by several orders of magnitude, resulting in competition for allergen binding. Consequently, methods that use allergen as a direct capture step are limited by the availability of free allergen binding sites for IgE. In order to circumvent this problem, in vitro methods usually require prior depletion of IgG or use high amounts of allergen in order to facilitate availability of free binding sites for IgE detection. Clearly, these approaches are limited for small sample volumes and allergens that are in short supply. New methods such as protein microarray could potentially overcome this problem by providing high allergen concentrations in a relatively small reaction volume. Currently, in vitro methods are rarely used in isolation for prognosis but are used primarily to complement the information obtained from in vivo assays. With the emergence of new technologies it is conceivable that in vitro assays may in the future replace in vivo assays, however until then in vivo assays remain the gold standard of allergen-specific IgE detection.

[Microarray technique for component resolved diagnosis (CRD) in type-I allergies. An innovative technology at the border between research tool and routine diagnostics]

Approximately 25% of the population in industrialized countries suffer from IgE-associated Type-1 allergies. Multiple allergens can be tested simultaneously in one assay by using the protein microarray. Moreover, it is possible to measure more than one analytical parameter (e.g. allergen specific IgEs and IgGs) in one assay by combining different fluorescent markers with specific secondary antibodies. The different allergen components that are of interest are immobilized on a planar surface. By adding the patient's serum (a smaller amount of serum is needed compared to an immunoassay) the inherent IgE antibodies are captured by the corresponding allergens. Secondary fluorescing anti-IgE antibodies are added subsequently, thus the intensity of each spot on the microarray can be measured by using a biochipscanner. The detected signal is then transformed into quantitative data, which allows the classification of the patient's serum IgE level for the tested allergens. There are different approaches to reduce the complexity of the original extracts used for the production of the solid microarray phase to a smaller number of relevant pathogenic molecules. The component-resolved diagnosis still needs to be clinically validated, but initial studies show positive results concerning the sensitivity and specificity of the protein microarray. Protein microarrays are promising tools for screening diagnoses in allergic diseases as well as for the improvement of allergen-specific immunotherapy.

Expression of the major mugwort pollen allergen Art v 1 in tobacco plants and cell cultures: problems and perspectives for allergen production in plants

An economic and cheap production of large amounts of recombinant allergenic proteins might become a prerequisite for the common use of microarray-based diagnostic allergy assays which allow a component-specific diagnosis. A molecular pharming strategy was applied to express the major allergen of Artemisia vulgaris pollen, Art v 1, in tobacco plants and tobacco cell cultures. The original Art v 1 with its endogenous signal peptide which directs Art v 1 to the secretory pathway, was expressed in transiently transformed tobacco leaves but was lost in stable transformed tobacco plants during the alternation of generations. Using a light-regulated promoter and "hiding" the recombinant Art v 1 in the ER succeeded in expression of Art v 1 over three generations of tobacco plants and in cell cultures generated from stable transformed plants. However, the amounts of the recombinant allergen were sufficient for analysis but not high enough to allow an economic production. Although molecular pharming has been shown to work well for the production of non-plant therapeutic proteins, it might be less efficient for closely related plant proteins.

Microarray of allergenic component-based diagnosis in food allergy

PURPOSE OF REVIEW

The determination of specific IgE (sIgE) against allergenic components fixed in a solid support that is provided as a microarray of high capacity and allows a more precise evaluation in the food allergy diagnosis. In this review, we will analyze the results obtained to date with this technology applied to the component-based diagnosis of food allergy.

RECENT FINDINGS

Microarrays of proteins or glycoproteins allow us to know the profile of sensitization of a patient with food allergy. At present, a commercially available technique exists which allows sIgE to be detected against 103 allergenic molecules. Several laboratories worldwide have explored and optimized this technique for few allergen extracts and the results have been promising with high reliabilities and sensitivities and above all, good correlations with previous existing conventional assays.

SUMMARY

In recent years, as a result of advances in molecular biology, together with the development of new technologies of producing high-capacity solid-phase matrices such as microarrays, the diagnosis of food allergy has improved and the basic situation of analyzing sIgE against an allergenic source has now become real the possibility of analyzing sIgE against an allergenic protein or glycoprotein. This change has not only led to a more precise diagnosis of sensitization, but can also be used to explain the different hazards of certain molecular sensitizations, crossreactivity phenomena in many cases and can even change the clinical management according to the information provided. Further studies are clearly needed to evaluate more precisely the scope of this new technique.

Microarrayed allergen molecules for the diagnosis of allergic diseases

IgE-mediated allergic diseases are among the most prevalent diseases worldwide. The use of extracts in the skin test and the additional use of IgE testing still represent the current basis for the diagnostic work-up. During the past 30 years, knowledge of the molecular structure of allergens has increased dramatically, and the characterization and production of allergenic molecules, as natural purified compounds or recombinant products, is allowing us to approach the allergy diagnostic work-up differently. Much of this is based on the adoption of microtechnology since the first release of a biochip for IgE detection. Its use has prompted the development of new concepts linked to the diagnosis of allergic diseases. This review describes the background of allergy diagnosis and the tools currently used for specific IgE detection. It gives insight into the most recent advancement in the field of biotechnology leading to allergenic molecule availability, microtechnology leading to the routine use of protein biochips for IgE detection, and how they should be combined with information technology.

Multiple protein extract microarray for profiling human food-specific immunoglobulins A, M, G and E

Existing food immunoglobulin (Ig) tests require large volumes of serum, are limited to one immunoglobulin class, are not amenable to high throughput analysis and only give a limited picture of the immunological response to food antigens. Conversely a new generation of Component Resolved Diagnostic systems using pure proteins is highly specific and totally dependent on the availability of the protein in its recombinant or natural origin form. Here we demonstrate a proof-of-concept of a microarray test based on protein extracts of food components. Our approach relies on innovations on three different fronts: the novelty of using arrayed food samples sequentially extracted with detergent and chaotropic agents, the ability to measure four different Ig classes simultaneously and the ability to analyse the generated data via a suitable bioinformatics/statistical analysis interface. This approach combines high numerical power of microarrays with automation, high throughput analysis and enables detailed investigation of the Ig profiles to food antigens. The prototype shown contains extracts of approximately 350 food ingredients that cover most of the food products found in the UK. Here we showed that the use of a sequential extraction technique to solubilise and then denature food samples has its benefits in the assessment of variations in antigenicity when tested with human sera. A patient dependent degree of class specificity was observed with human sera (IgG specificity correlates well with IgA>IgM>>>>>IgE). Besides generating a simultaneous profile for IgA, IgM, IgG and IgE the array system has shown good discrimination between challenge responders in atopic and non-atopic individuals. Poly- and mono-specific IgE responders were easily identified. The mathematical modelling of specific IgE content showed good correlations when compared with established IgE antibody testing assay (UniCAP). Although in its proof-of-principle stages, the immune profiling technique described here has the potential to provide unique insights into exposure/sensitization and establish relationships between specific immunoglobulin classes and subclasses against food protein antigens. In further developments, the immune profiling technique could also be extended to other related areas such as parasite and bacterial gut infection. Full analyses of large longitudinal and retrospective clinical trials are on going to determine the positive and negative predictive values of the technique.

Determination of multiple allergen-specific IgE by microfluidic immunoassay cartridge in clinical settings

Our aims were to evaluate the performance of an automated microfluidic immunoassay system for measuring allergen-specific IgE (sIgE) in sera against an established in vitro assay and to assess the system's diagnostic accuracy against objective clinical criteria for identifying sensitization to specific allergens in daily practice of allergy clinics. Using both the automated microfluidic-based immunoassay system (BioIC and ImmunoCAP, we measured sIgE in serum samples from 212 children who visited allergic clinics in two medical centers. Outcomes of skin prick tests (SPT) served as the clinical comparison method. The assay results of targeted allergen of BioIC have a good correlation with ImmunoCAP in the diagnosis of allergen sensitivity by patients' clinical history. When comparing the test results of the sIgE against overall allergens, in either two tests among the three assays performed showed high percentage of agreement between BioIC and ImmunoCAP (77.8%, 95% CI: 72-83.3%) but not with SPT (BioIC 64.9%, 95% CI: 58-72%; ImmunoCAP 67.5%, 95% CI: 61-74%). Using ROC analysis and SPT as quasi-standard, BioIC and ImmunoCAP have nearly the same performance of sensitivity and specificity in the confirmation of SPT results. The total and within one-class agreements of each allergen test result between BioIC and ImmunoCAP ranged between 55.2% and 99.5% with an overall average of 80.9%. Laboratory testing for sIgE can be performed on a fully automated, microfluidic cartridge system with advantages of low sample volume, simultaneously tested allergens, and with diagnostic accuracy for representative allergens equivalent to the semi-automated CAP technology.

Microarrays: molecular allergology and nanotechnology for personalised medicine (I)

The diagnosis of antibody-mediated allergic disorders is based on the clinical findings and the detection of allergen-specific IgE based on in vitro and in vivo techniques, together with allergen provocation tests. In vitro diagnostic techniques have progressed enormously following the introduction of the advances made in proteomics and nanotechnology--offering tools for the diagnosis and investigation of allergy at molecular level. The most advanced developments are the microarray techniques, which in genomics allowed rapid description of the human genetic code, and which now have been applied to proteomics, broadening the field for research and clinical use. Together with these technological advances, the characterisation of most of the different proteins generating specific IgE and which conform each natural allergen, as well as their purification or genetic engineering-based synthesis, have been crucial elements--offering the possibility of identifying disease-causing allergens at molecular level, establishing a component-resolved diagnosis (CRD), using them to study the natural course of the disease, and applying them to improvements in specific immunotherapy. Microarrays of allergic components offer results relating to hundreds of these allergenic components in a single test, and use a small amount of serum that can be obtained from capillary blood. The availability of new molecules will allow the development of panels including new allergenic components and sources, which will require evaluation for clinical use. The present study reviews these new developments, component-resolved diagnosis, and the development of microarray techniques as a critical element for furthering our knowledge of allergic disease.

A protein allergen microarray detects specific IgE to pollen surface, cytoplasmic, and commercial allergen extracts

Background

Current diagnostics for allergies, such as skin prick and radioallergosorbent tests, do not allow for inexpensive, high-throughput screening of patients. Additionally, extracts used in these methods are made from washed pollen that lacks pollen surface materials that may contain allergens.

Methodology/Principal Findings

We sought to develop a high-throughput assay to rapidly measure allergen-specific IgE in sera and to explore the relative allergenicity of different pollen fractions (i.e. surface, cytoplasmic, commercial extracts). To do this, we generated a protein microarray containing surface, cytoplasmic, and commercial extracts from 22 pollen species, commercial extracts from nine non-pollen allergens, and five recombinant allergenic proteins. Pollen surface and cytoplasmic fractions were prepared by extraction into organic solvents and aqueous buffers, respectively. Arrays were incubated with <25 uL of serum from 176 individuals and bound IgE was detected by indirect immunofluorescence, providing a high-throughput measurement of IgE. We demonstrated that the allergen microarray is a reproducible method to measure allergen-specific IgE in small amounts of sera. Using this tool, we demonstrated that specific IgE clusters according to the phylogeny of the allergen source. We also showed that the pollen surface, which has been largely overlooked in the past, contained potent allergens. Although, as a class, cytoplasmic fractions obtained by our pulverization/precipitation method were comparable to commercial extracts, many individual allergens showed significant differences.

Conclusions/Significance

These results support the hypothesis that protein microarray technology is a useful tool for both research and in the clinic. It could provide a more efficient and less painful alternative to traditionally used skin prick tests, making it economically feasible to compare allergen sensitivity of different populations, monitor individual responses over time, and facilitate genetic studies on pollen allergy.

The importance of in vitro component-resolved diagnosis in paediatric patients

In recent years, thanks to advances in molecular biology, allergological diagnosis has improved and specific IgE (sIgE) against an allergenic source has been transformed into sIgE against an allergenic protein or glycoprotein. This change, which has resulted in a more precise diagnosis of sensitisation, could explain the different dangers of certain molecular sensitisations and in many cases cross-reactivity phenomena, and could change indications for immunotherapy or clinical management. Here, we present two cases of children where the indication for immunotherapy and management of the disorder changed due to component-resolved diagnosis. However, the clinical history and skin prick tests should complement molecular in vitro diagnosis to improve routine clinical practice.

Development of a novel peptide microarray for large-scale epitope mapping of food allergens

BACKGROUND

The peptide microarray is a novel assay that facilitates high-throughput screening of peptides with a small quantity of sample.

OBJECTIVE

We sought to use overlapping peptides of milk allergenic proteins as a model system to establish a reliable and sensitive peptide microarray-based immunoassay for large-scale epitope mapping of food allergens.

METHODS

A milk peptide microarray was developed by using commercially synthesized peptides (20-mers, 3 offset) covering the primary sequences of alpha(s1)-casein, alpha(s2)-casein, beta-casein, kappa-casein, and beta-lactoglobulin. Conditions for printing and immunolabeling were optimized using a serum pool of 5 patients with milk allergy. Reproducibility of the milk peptide microarray was evaluated using replicate arrays immunolabeled with the serum pool, whereas specificity and sensitivity were assessed by using serial dilution of the serum pool and a peptide inhibition assay.

RESULTS

Our results show that epitopes identified by the peptide microarray were mostly consistent with those identified previously by SPOT membrane technology, but with specific binding to a few newly identified epitopes of milk allergens. Data from replicate arrays were reproducible (r > or = 0.92) regardless of printing lots, immunolabeling, and serum pool batches. Using the serially diluted serum pool, we confirmed that IgE antibody binding detected in the array was specific. Peptide inhibition of IgE binding to the same peptide and overlapping peptides further confirmed the specificity of the array.

CONCLUSION

A reliable peptide microarray was established for large-scale IgE epitope mapping of milk allergens, and this robust technology could be applied for epitope mapping of other food allergens.

Assessment of the immunoglobulin E-mediated immune response to milk-specific proteins in allergic patients using microarrays

BACKGROUND

Cow's milk allergy (CMA) is one of the most widespread human allergies, especially in young children. Although CMA is intensively studied, little is known about the recognition patterns of milk allergens in allergic patients, and the determination these patterns is a prerequisite for the development of efficient diagnostic and prognostic tools. Several factors present difficulties for such a determination, because (i) milk contains a large number of potential allergens; (ii) the majority of these allergens consist of complex suspensions rather than solutions; (iii) the major allergens, such as caseins, cannot be highly purified in large amounts; and (iv) most of the time, very small amount of young patients' sera are readily available.

METHODS

To overcome these difficulties, we developed a sensitive microarray assay that, in combination with near-infrared fluorescence detection, was used to study the immune response to milk and purified native milk proteins.

RESULTS

This new assay allowed us to assess the binding ability of IgE to milk allergens from a large number of young patients using reduced amounts of clinical material. The data show that bovine lactoferrin can be classed as a strong milk allergen. We confirmed that bovine caseins are the main allergens in milk and that alpha(S1)-casein is more allergenic than alpha(S2)-, beta- and kappa-caseins, which were recognized with almost a similar frequency by the sera of patients.

CONCLUSION

Microarray methods, in combination with near-infrared fluorescence detection, can be useful for the in vitro diagnosis of food allergies.

Biotechnology-based allergy diagnosis and vaccination

The diagnosis and immunotherapy currently applied to allergic diseases involve the use of crude extracts of the allergen source without defining the allergy-eliciting molecule(s). Advances in recombinant DNA technology have made identification, cloning, expression and epitope mapping of clinically significant allergens possible. Recombinant allergens that retain the immunological features of natural allergens form the basis of accurate protein-chip-based methods for diagnosing allergic conditions. The ability to produce rationally designed hypoallergenic forms of allergens is leading to the development of novel and safe forms of allergy vaccines with improved efficacy. The initial clinical tests on recombinant-allergen-based vaccine preparations have provided positive results, and ongoing developments in areas such as alternative routes of vaccine delivery will enhance patient compliance.

Protein microchips in biomedicine and biomarker discovery

Protein microarray technology is of high recent interest, especially for generating confirmatory and complementary information for transcriptomic studies. In this paper, the advantages, technical limitations, main application fields, and some early results of protein microarrays are reviewed. Today protein microchip technology is mostly available in the form of printed glass slides, bioaffinity surfaces, and tissue microarray (TMA)-based techniques. The advantages of glass slide-based microchips are the simplicity of their application and their relatively low cost. Affinity surface-based protein chip techniques are applicable to minute amounts of starting material (< 1 microg), but interrogation of these chips requires expensive instrumentation, such as mass spectrometers. TMAs are useful for parallel testing of antibody specificities on a broad range of histological specimens in a single slide. Protein microarrays have been successfully implemented for serum tumor marker profiling, cell physiology studies, and mRNA expression study verification. Some of the bottlenecks of the technology are protein instability, problems with nonspecific interactions, and the lack of amplification techniques to generate sufficient amounts of the lower abundance proteins. In spite of the current difficulties, protein microchips are envisioned to be available for routine biomedical and diagnostic applications provided that the ongoing technological developments are successful in improving sensitivity, specificity, and reducing costs.

[Protein arrays and perspectives of medical applications]

Protein microarrays make it possible to detect molecular interactions with various partners (proteins, peptides, nucleic acids, sugars, etc.). Their advantages are crucial for high-throughput analysis of proteomes of different organisms. Moreover, the recent data reveal the performance of microarrays over current immunological methods. Therefore, the antigen and antibody microarrays become indispensable for medical applications, in particular, for diagnosis and prognosis of microbial infections, autoimmune and allergic diseases. The further technological progress might provide the extension of the miniaturized assays for multiparametric monitoring of human pathologies in practical medicine.

Proteomic approaches for identifying new allergens and diagnosing allergic diseases

BACKGROUND

Allergic diseases are (IgE)-mediated hypersensitivity reactions affecting more than 25% of the world's population. Proteomic technologies have been increasingly used in the field of allergy and include the use of protein microarrays and two-dimensional gel electrophoresis coupled with immunoblotting.

METHODS

The literature relevant to proteomic approaches to allergic diseases was searched using MEDLINE database. We reviewed proteomics approaches and applications, focusing specifically on two-dimensional immunoblotting techniques and allergen microarrays.

RESULTS

The results obtained show that proteomic approaches using two-dimensional immunoblotting appear to be a powerful strategy for the identification of allergenic proteins. Likewise, the use of allergen microarrays allows a large number of IgE antibodies to be simultaneously identified.

CONCLUSIONS

Proteomic approaches are only beginning to be applied to the study of allergy. In the field of in vitro diagnosis, allergen microarrays provide a promising tool not routinely used in the allergy laboratory. In the near future this powerful technique will be used as a standard technique for in vitro diagnosis of allergy.

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.

The clinical significance of food specific IgE/IgG4 in food specific atopic dermatitis

Food is closely associated with the pathogenesis of atopic dermatitis. Food allergy is usually mediated by IgE antibody to specific food proteins and determination of specific IgE antibody is the basis of the common diagnostic test for food allergy. IgG4 have been reported as blocking antibody and the protective effects of blocking antibody may be clear in inhalant allergy. However, the role of IgG4 in food allergy is still a matter of debate. In this study, the clinical significance of food allergen-specific IgE/IgG4 in atopic dermatitis was investigated and compared with that of IgE. A total of 97 patients who fulfilled the diagnostic criteria for atopic dermatitis participated in this study. Skin prick test and allergy patch test were performed. Specific IgE and IgG4 concentration were measured using allergy protein chip, 'AllergyChip'. Double blinded placebo controlled food challenge test (DBPCFC) was performed for the diagnosis of allergy to milk, egg white, wheat, and soybean. DBPCFCs for milk, egg white, soybean, and wheat were performed. The positive rates were 31.7% (19/60) in milk, 36.7% (18/49) in egg white, 30.4% (7/23) in soybean, and 34.8% (8/23) in wheat. Mean IgE/IgG4 levels in DBPCFC (+) subjects is higher than those in DBPCFC (-) subjects in all food items studied. Of them, there were significantly different between two groups in egg white and wheat (Egg white in DBPCFC (+) vs. (-): 0.4 +/- 0.3 vs. 0.2 +/- 0.2, wheat in DBPCFC (+) vs. (-): 1.2 +/- 1.2 vs. 0.3 +/- 0.3, p < 0.05). Allergen-specific IgE/IgG4 may provide one of the clues to understand the mechanism of food allergy in atopic dermatitis. The present study suggests that protein microarray can be one of the useful methods to assess ongoing status of allergic diseases.

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.

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.

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.

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.

Systematic comparison of surface coatings for protein microarrays

To process large numbers of samples in parallel is one potential of protein microarrays for research and diagnostics. However, the application of protein arrays is currently hampered by the lack of comprehensive technological knowledge about the suitability of 2-D and 3-D slide surface coatings. We have performed a systematic study to analyze how both surface types perform in combination with different fluorescent dyes to generate significant and reproducible data. In total, we analyzed more than 100 slides containing 1152 spots each. Slides were probed against different monoclonal antibodies (mAbs) and recombinant fusion proteins. We found two surface coatings to be most suitable for protein and antibody (Ab) immobilization. These were further subjected to quantitative analyses by evaluating intraslide and slide-to-slide reproducibilities, and the linear range of target detection. In summary, we demonstrate that only suitable combinations of surface and fluorescent dyes allow the generation of highly reproducible data.

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.

Seafood allergy: lessons from clinical symptoms, immunological mechanisms and molecular biology

Food allergy consists of a wide range of disorders that result from adverse immune responses to dietary antigens. Manifestations of allergic response includes acute, potentially fatal anaphylactic reactions and a variety of chronic diseases that mainly affect the gastrointestinal tract, skin, and respiratory tract. Tools for clinical diagnosis and management, which have not changed much in the past two decades, include the clinical history, tests for specific IgE antibody to suspected foods, elimination diets, oral food challenges, and provision of medications such as epinephrine for emergency treatment. On the other hand, recent immunological and molecular biological research have enhanced our understanding of the mechanisms of these disorders and revealed the identities of many food allergens. Here, we will discuss seafood allergies with respect to the clinical manifestations, diagnosis, immunological mechanisms, and molecular biology of seafood allergens. Furthermore, potential applications and future directions in the clinical management of seafood allergies are discussed.

Amplification of circularizable probes for the detection of target nucleic acids and proteins

BACKGROUND

Circularizable oligonucleotide probe (C-probe) is a unique molecule that offers significant advantages over conventional probes.

METHODS

Closed circular structure can be formed through ligation of the juxtaposed ends of the C-probe after hybridization with a target, and subsequently locked onto its target through the helical turns formed between the complementary sequences of the target and the C-probe (padlock probe). Under isothermal condition, C-probe can be amplified by rolling circle amplification (RCA) to generate multimeric single-stranded DNA (ssDNA). This multimeric ssDNA can be further amplified by a ramification mechanism (RAM) through primer extension and downstream DNA displacement, resulting in an exponential amplification. Usually, an unbiased product is generated by either RCA or ramification amplification method (or RAM) due to the generic primers of C-probe and its localization onto DNA targets.

CONCLUSIONS

These advantages make C-probe amplification very useful for research and molecular diagnosis, especially in areas where other techniques were proved to be inadequate. The development of C-probe-based technologies offers a promising prospect for molecular diagnosis. The applications of C-probe, RCA, RAM, in situ detection, microarray, immunoassay, single nucleotide polymorphism, and whole genome amplification, etc. are discussed in this review.