Array-based measurements of aero-allergen-specific IgE correlate with skin-prick test reactivity in asthma regardless of specific IgG4 or total IgE measurements

Skin prick testing (SPT) and measurement of serum allergen-specific IgE (sIgE) are used to investigate asthma and other allergic conditions. Measurement of serum total IgE (tIgE) and allergen-specific IgG4 (sIgG4) may also be useful. The aim was to ascertain the correlation between these serological parameters and SPT. Sera from 60 suspected asthmatic patients and 18 healthy controls were assayed for sIgE and sIgG4 reactivity against a panel of 70 SPT allergen preparations, and for tIgE. The patients were also assessed by skin prick tests for reactivity to cat, dog, house dust mite and grass allergens. Over 50% of the patients had tIgE levels above the 75th percentile of the controls. 58% of patients and 39% of controls showed sIgE reactivity to ≥1 allergen. The mean number of allergens detected by sIgE was 3.1 in suspected asthma patients and 0.9 in controls. 58% of patients and 50% of controls showed sIgG4 reactivity to ≥1 allergen. The mean number of allergens detected by sIgG4 was 2.5 in patients and 1.7 in controls. For the patients, a strong correlation was observed between clinical SPT reactivity and serum sIgE levels to cat, dog, house dust mite (HDM) and grass allergens. SPT correlations using sIgE/sIgG4 or sIgE/tIgE ratios were not markedly higher. The measurement of serum sIgE by microarray using SPT allergen preparations showed good correlation with clinical SPT reactivity to cat, dog, HDM and grass allergens. This concordance was not improved by measuring tIgE or sIgG4.

Diagnosis of anaphylactic death in forensics: Review and future perspectives

The diagnosis of anaphylaxis in a pre- or post-mortal phase involves the formulation of problems not yet solved by the international scientific literature, due to the complexity of pathogenic factors and pathophysiological processes that characterizes it. For forensic autopsies, further problems of differential diagnosis arise and often leave the forensic pathologist unable to express an opinion of certainty, as a result of lack of case history, circumstantial and autoptical-histopathological data. Nevertheless, in routine cases the postmortem diagnosis of anaphylactic death continues to be based on exclusion and circumstantial evidence. The author, after an extensive review of the literature relating to deaths from anaphylaxis of forensic pathological interest, and a discussion of the microscopical and biochemical findings, proposes a diagnostic protocol for forensic purposes and evaluates the diagnostic perspectives enabled by the newly available analytic techniques and markers. Maybe, the application of omics methodologies could help in the future for anaphylaxis diagnosis.

Label-free colorimetric aptasensor for IgE using DNA pseudoknot probe

The development of simple and low-cost approaches to the detection of immunoglobulin E (IgE) would provide a method for the early diagnosis and prevention of atopic diseases. The current methods of detection are generally tedious, multi-step processes and are limited by the high cost of the labeled proteins. We describe here a label-free structure-switching colorimetric method for the simple measurement of IgE using DNA pseudoknot probes and gold nanoparticles. In the absence of a target the IgE aptamer probe adopts a pseudoknot conformation that dissociates a capture probe from the unmodified gold nanoparticles. However, when IgE binds to the aptamer probe, the pseudoknot is resolved, leading to a favorable hybridization between the 3' terminal loop of the aptamer probe and the capture probe; this induces the aggregation of the gold nanoparticles. As a result, the colorimetric IgE sensor using this structure-switching mechanism is sensitive, specific and convenient, and the assay works even when challenged with complicated biological matrixes such as vaginal fluids. The proposed method is expected to be of great clinical value for IgE detection and could be used, after appropriate design, for sensing applications of other structured aptamers.

Exploiting fluorescence for multiplex immunoassays on protein microarrays

Protein microarray technology is becoming the method of choice for identifying protein interaction partners, detecting specific proteins, carbohydrates and lipids, or for characterizing protein interactions and serum antibodies in a massively parallel manner. Availability of the well-established instrumentation of DNA arrays and development of new fluorescent detection instruments promoted the spread of this technique. Fluorescent detection has the advantage of high sensitivity, specificity, simplicity and wide dynamic range required by most measurements. Fluorescence through specifically designed probes and an increasing variety of detection modes offers an excellent tool for such microarray platforms. Measuring for example the level of antibodies, their isotypes and/or antigen specificity simultaneously can offer more complex and comprehensive information about the investigated biological phenomenon, especially if we take into consideration that hundreds of samples can be measured in a single assay. Not only body fluids, but also cell lysates, extracted cellular components, and intact living cells can be analyzed on protein arrays for monitoring functional responses to printed samples on the surface. As a rapidly evolving area, protein microarray technology offers a great bulk of information and new depth of knowledge. These are the features that endow protein arrays with wide applicability and robust sample analyzing capability. On the whole, protein arrays are emerging new tools not just in proteomics, but glycomics, lipidomics, and are also important for immunological research. In this review we attempt to summarize the technical aspects of planar fluorescent microarray technology along with the description of its main immunological applications.

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.

Antigen microarrays for the study of autoimmune diseases

BACKGROUND

The immune response involves the activation of heterogeneous populations of T cells and B cells that show different degrees of affinity and specificity for target antigens. Although several techniques have been developed to study the molecular pathways that control immunity, there is a need for high-throughput assays to monitor the specificity of the immune response.

CONTENT

Antigen microarrays provide a new tool to study the immune response. We reviewed the literature on antigen microarrays and their advantages and limitations, and we evaluated their use for the study of autoimmune diseases. Antigen arrays have been successfully used for several purposes in the investigation of autoimmune disorders: for disease diagnosis, to monitor disease progression and response to therapy, to discover mechanisms of pathogenesis, and to tailor antigen-specific therapies to the autoimmune response of individual patients. In this review we discuss the use of antigen microarrays for the study of 4 common autoimmune diseases and their animal models: type 1 diabetes, systemic lupus erythematosus, rheumatoid arthritis, and multiple sclerosis.

CONCLUSIONS

Antigen microarrays constitute a new tool for the investigation of the immune response in autoimmune disorders and also in other conditions such as tumors and allergies. Once current limitations are overcome, antigen microarrays have the potential to revolutionize the investigation and management of autoimmune diseases.

Protein Microarrays and Midtrimester Amniotic Fluids: A Novel Approach for the Diagnosis of Early Intrauterine Inflammation Related to Preterm Delivery

Novel technologies that allow simultaneous assessment of multiple biomarkers provide new and promising diagnostic/prognostic approaches. By protein microarrays, here we analyzed amniotic fluids (AF) from 50 women with preterm delivery (PTD) and 50 control women, who delivered at term. In detail, cytokines, chemokines, matrix metalloproteinases and antigen-specific antibodies were assessed. The AF analysis showed significant differences between women with preterm and term delivery in the levels of IL-1α, IL-1β, IL-4, IL-6, IL-8, MCP-1, IFN-γ and anti-HSV2 IgG. No significant differences were observed in the levels of TNF-α, MMP-2, MMP-9 and specific IgG for seven vertically transmitted pathogens. In conclusion, we demonstrated the feasibility of protein microarrays in the diagnosis of early intrauterine inflammation. The significant association between the increased levels of certain cytokines and preterm delivery argues on their relevance as early pathogenetic markers for identification of risk patients.

Nanoparticles rapidly assess specific IgE in plasma

Allergy is the sixth leading cause of chronic disease in the world. This study demonstrates the feasibility of detecting allergy indicators in human plasma, noninvasively, at the point of care and with a comparable efficiency and reduced turnaround time compared with the gold standard. Peanut allergy was utilized as a model due to its widespread occurrence among the US population and fatality if not treated. The detection procedure utilized magnetic nanoparticles that were coated with an allergen layer (peanut protein extract). Peanut immunoglobulin E (IgE) was detected in concentrations close to the minimum detection range of CAP assay. The results were obtained in minutes compared with the CAP assay which requires more than 3 h.

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.

Serum IgE reactivity profiling in an asthma affected cohort

BACKGROUND

Epidemiological evidence indicates that atopic asthma correlates with high serum IgE levels though the contribution of allergen specific IgE to the pathogenesis and the severity of the disease is still unclear.

METHODS

We developed a microarray immunoassay containing 103 allergens to study the IgE reactivity profiles of 485 asthmatic and 342 non-asthmatic individuals belonging to families whose members have a documented history of asthma and atopy. We employed k-means clustering, to investigate whether a particular IgE reactivity profile correlated with asthma and other atopic conditions such as rhinitis, conjunctivitis and eczema.

RESULTS

Both case-control and parent-to-siblings analyses demonstrated that while the presence of specific IgE against individual allergens correlated poorly with pathological conditions, particular reactivity profiles were significantly associated with asthma (p<10E-09). An artificial neural network (ANN)-based algorithm, calibrated with the profile reactivity data, correctly classified as asthmatic or non-asthmatic 78% of the individual examined. Multivariate statistical analysis demonstrated that the familiar relationships of the study population did not affect the observed correlations.

CONCLUSIONS

These findings indicate that asthma is a higher-order phenomenon related to patterns of IgE reactivity rather than to single antibody reactions. This notion sheds new light on the pathogenesis of the disease and can be readily employed to distinguish asthmatic and non-asthmatic individuals on the basis of their serum reactivity profile.

Detection of follicular fluid and serum antibodies by protein microarrays in women undergoing in vitro fertilization treatment

A protein microarray serological assay was used to assess the antibody profile of 102 women subjected to in vitro fertilization treatment. The studies were conducted on pairs of serum and follicular fluid samples, collected from each woman on the same day at the time of oocyte recovery. The samples, stored as frozen aliquotes, were assessed by both microarray and ELISA. Follicular fluids and sera were screened to detect the presence of specific IgG and IgM antibodies against seven vertically transmitted pathogens. The IgG reactivity of follicular fluids closely mirrored that of serum in all the patients and for all the antigens, with an agreement of more than 85%. IgM antibodies were undetectable in follicular fluids. The antibody patterns were subsequently related to the biological and clinical outcomes of in vitro fertilization cycles. The results showed that varicella zoster virus (VZV) IgG positive women and cytomegalovirus (CMV) IgG negative women had on average a higher number of inseminated, good quality oocytes compared to VZV IgG negative and CMV IgG positive women. In addition, the rate of successful embryo transfers was significantly higher in Toxoplasma gondii IgG negative women than in their positive counterparts. Overall, the microarray was proven to be a suitable tool for detecting analytes in follicular fluids, therefore supporting its application in a wide spectrum of investigations.

Reverse phase protein microarrays: fluorometric and colorimetric detection

The Reverse Phase Protein Microarray (RPMA) is an array platform used to quantitate proteins and their posttranslationally modified forms. RPMAs are applicable for profiling key cellular signaling pathways and protein networks, allowing direct comparison of the activation state of proteins from multiple samples within the same array. The RPMA format consists of proteins immobilized directly on a nitrocellulose substratum. The analyte is subsequently probed with a primary antibody and a series of reagents for signal amplification and detection. Due to the diversity, low concentration, and large dynamic range of protein analytes, RPMAs require stringent signal amplification methods, high quality image acquisition, and software capable of precisely analyzing spot intensities on an array. Microarray detection strategies can be either fluorescent or colorimetric. The choice of a detection system depends on (a) the expected analyte concentration, (b) type of microarray imaging system, and (c) type of sample. The focus of this chapter is to describe RPMA detection and imaging using fluorescent and colorimetric (diaminobenzidine (DAB)) methods.

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.

An antigen microarray immunoassay for multiplex screening of mouse monoclonal antibodies

The mouse monoclonal antibody (mAb) technology still represents a key source of reagents for research and clinical diagnosis, although it is relatively inefficient and expensive and therefore unsuitable for high-throughput production against a vast repertoire of antigens. In this article, we describe a protocol that combines the immunization of individual mice with complex mixtures of influenza virus strains and a microarray-based immunoassay procedure to perform a parallel screening against the viral antigens. The protocol involves testing the supernatants of somatic cell hybrids against a capture substratum containing an array of different antigens. For each fusion experiment, we carried out more than 25,000 antigen-antibody reactivity tests in less than a week, a throughput that is two orders of magnitude higher than that of traditional antibody detection assays such as enzyme-linked immunosorbent assays and immunofluorescence. Using a limited number of mice, we can develop a vast repertoire of mAbs directed against nuclear and surface proteins of several human and avian influenza virus strains.

Current Clinical and Pharmaceutical Applications of Microarrays: From Disease Biomarkers Discovery to Automated Diagnostics

Microarrays used for measuring chromosomal aberrations in genomic DNA and for defining gene expression patterns have become almost routine. A microarray consists of an arrayed series of microscopic spots each containing either DNA or protein molecules known as feature reporters. Advances in microarray fabrication and in feature detection systems, such as high-resolution scanners and their associated software, lead to high-throughput screening of the genome or the transcriptome of a cell or a group of cells in only few days. Despite the potential of high-density microarrays, several problems about data interpretation are still to be solved. In addition, targeted microarrays are shown to be useful tools for rapid and accurate diagnosis of diseases. The aim of this review was to discuss the impact of microarrays on different application levels from the definition of disease biomarkers to pharmaceutical and clinical diagnostics.

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.

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.

A protein microarray immunoassay for the serological evaluation of the antibody response in vertically transmitted infections

The detection of specific serum antibodies is mainly achieved by enzyme-linked immunosorbent assay (ELISA). Here, we describe the setting up of a microarray-based serological assay to screen for IgG and IgM against vertically transmitted pathogens (Toxoplasma gondii, rubella virus, cytomegalovirus, herpes simplex virus types 1 and 2, varicella zoster virus, Chlamydia trachomatis). The test, accommodated onto a restricted area of a microscope slide, consists of: (a) the immobilization of antigens and human IgG and IgM antibody dilution curves, laid down in an orderly manner; (b) addition of serum samples; (c) detection of antigen-serum antibodies complexes by indirect immunofluorescence. The IgG and IgM curves provide an internal calibration system for the interpolation of the signals from the single antigens. The test was optimized in terms of spotting conditions and processing protocol. The detection limit was 400 fg for the IgG assay and 40 fg for the IgM assay; the analytical specificity was >98%. The clinical sensitivity returned an average value of 78%, the clinical specificity was >96%, the predictive values were >73%, and the efficiency was >88%. The results obtained make this test a promising tool, suitable for introduction in the clinical diagnostic routine of vertically transmitted infections, in parallel (and in future as an alternative) to ELISA.

Protein microarrays

With the introduction of DNA microarrays as novel analytical tools, the determination of thousands of binding events in one reaction became possible. The developed technology platforms are not limited to nucleic acids, and, in principle, every ligand-binding assay that works on solid phase can be miniaturized and brought into an array format. This unit explains how protein microarrays can be generated using equipment originally designed for DNA microarrays and how multiplexed assays for the quantification of proteins are set up. A protocol that describes a parallelized system for detecting autoantibodies in human serum is included as an example, and it is shown how existing sandwich immunoassays can be miniaturized and performed in array format. The unit also provides some theoretical background and commentary on the problems associated with this still-novel technology.

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.

Profiling the antibody immune response against blood stage malaria vaccine candidates

BACKGROUND

The complexity and diversity of the antibody immune response to the antigen repertoire of a pathogen has long been appreciated. Although it has been recognized that the detection of antibodies against multiple antigens dramatically improves the clinical sensitivity and specificity of diagnostic assays, the prognostic value of serum reactivity profiles against multiple microbial antigens in protection has not been investigated.

METHODS

Using malaria as a model we investigated whether antigen reactivity profiles in serum of children with different levels of clinical immunity to Plasmodium falciparum malaria correlated with protection. We developed a microarray immunoassay of 18 recombinant antigens derived from 4 leading blood-stage vaccine candidates for P. falciparum [merozoite surface protein 1 (MSP1), MSP2, MSP3, and apical membrane antigen (AMA)-1]. Associations between observed reactivity profiles and clinical status were sought using k-means clustering and phylogenetic networks.

RESULTS

The antibody immune response was unexpectedly complex, with different combinations of antigens recognized in different children. Serum reactivity to individual antigens did not correlate with immune status. By contrast, combined recognition of AMA-1 and allelic variants of MSP2 was significantly associated with protection against clinical malaria. This finding was confirmed independently by k-means clustering and phylogenetic networking.

CONCLUSIONS

The analysis of reactivity profiles provides a wealth of novel information about the immune response against microbial organisms that would pass unnoticed in analysis of reactivity to antigens individually. Extension of this approach to a large fraction of the proteome may expedite the identification of correlates of protection and vaccine development against microbial diseases.

On-chip Complement Activation Adds an Extra Dimension to Antigen Microarrays

Antibody profiling on antigen microarrays helps us in understanding the complexity of responses of the adaptive immune system. The technique, however, neglects another, evolutionarily more ancient apparatus, the complement system, which is capable of both recognizing and eliminating antigen and serves to provide innate defense for the organism while cooperating with antibodies on multiple levels. Complement components interact with both foreign substances and self molecules, including antibodies, and initiate a cascade of proteolytic cleavages that lead to the covalent attachment of complement components to molecules in nanometer proximity. By refining the conditions of antibody profiling on antigen arrays we made use of this molecular tagging to identify antigens that activate the complement system. Antigen arrays were incubated with serum under conditions that favor complement activation, and the deposited complement C3 fragments were detected by fluorescently labeled antibodies. We used genetically C3-deficient mice or inhibition of the complement cascade to prove that the technique requires complement activation for the binding of C3 to features of the array. We demonstrate that antigens on the array can initiate complement activation both by antibody-dependent or -independent ways. Using two-color detection, antibody and complement binding to the relevant spots was measured simultaneously. The effect of adjuvants on the quality of the immune response and binding of autoantibodies to DNA with concomitant complement activation in the serum of mice suffering from systemic autoimmune disease was readily measurable by this new method. We propose that measurement of complement deposition on antigen microarrays supplements information from antibody binding measurements and provides an extra, immune function-related fingerprint of the tested serum.

Microarray profiling of skeletal muscle sarcoplasmic reticulum proteins

Microarrays were developed to profile the level of proteins associated with calcium regulation in sarcoplasmic reticulum (SR) isolated from porcine Longissimus muscle. The microarrays consisted of SR preparations printed onto to glass slides and probed with monoclonal antibodies to 7 target proteins. Proteins investigated included: ryanodine receptor, (RyR), dihydropyridine receptor, (DHPR), triadin (TRI), calsequestrin (CSQ), 90 kDa junctional protein (JSR90), and fast-twitch and slow-twitch SR calcium ATPases (SERCA1 and SERCA2). Signal from a fluorescently-labeled detection antibody was measured and quantitated using a slide reader. The microarray developed was also employed to profile Longissimus muscle SR proteins from halothane genotyped animals. Significant (P<0.05) reductions in levels of several proteins were found including: RyR, CSQ, TRI, DHPR and SERCA2 in SR samples from halothane positive animals. The results illustrate the potential of microarrays as a tool for profiling SR proteins and aiding investigations of calcium regulation.

Profiling cancer stem cells using protein array technology

Since cancer cells and somatic stem cells share the biological characteristics of self-renewal and proliferation, it has been suggested that the principles of stem cell biology can be applied to improve our understanding of cancer biology. Recent studies have shown that the majority of cancers appear to originate from a small subset of cells that have the ability of self-renewal and to proliferate, namely 'cancer stem cells'. The isolation of cancer stem cells has been demonstrated using cell surface markers in haematopoietic and non-haematopoietic malignancies. Advances in protein array technologies have enabled the use of minuscule amounts of biological materials to profile these cells at the molecular level. Using a combination of protein arrays and cancer stem cell isolation techniques, a higher resolution molecular profiling can be performed, which might improve therapies targeting the cancer stem cells.

Optical technologies for the read out and quality control of DNA and protein microarrays

Microarray formats have become an important tool for parallel (or multiplexed) monitoring of biomolecular interactions. Surface-immobilized probes like oligonucleotides, cDNA, proteins, or antibodies can be used for the screening of their complementary targets, covering different applications like gene or protein expression profiling, analysis of point mutations, or immunodiagnostics. Numerous reviews have appeared on this topic in recent years, documenting the intriguing progress of these miniaturized assay formats. Most of them highlight all aspects of microarray preparation, surface chemistry, and patterning, and try to give a systematic survey of the different kinds of applications of this new technique. This review places the emphasis on optical technologies for microarray analysis. As the fluorescent read out of microarrays is dominating the field, this topic will be the focus of the review. Basic principles of labeling and signal amplification techniques will be introduced. Recent developments in total internal reflection fluorescence, resonance energy transfer assays, and time-resolved imaging are addressed, as well as non-fluorescent imaging methods. Finally, some label-free detection modes are discussed, such as surface plasmon microscopy or ellipsometry, since these are particularly interesting for microarray development and quality control purposes.

A comparability study of the emerging protein array platforms with established ELISA procedures

Recent developments in microarray technology have made it possible to perform immunoassays in a multiplexed format. This ability is highly desirable given the potential for greater throughput analysis. In spite of the obvious advantages, a number of issues arise as a result of multiplexing the reactions. In this study, we have assessed the performance characteristics that are associated with the transfer of technology from a uniplexed to a multiplexed format. Two solution phase array platforms were chosen for this study: the commercially available Luminex(100) xMap system (Austin, Texas, USA) and the UltraPlex technology devised by SmartBead Technologies Ltd. (Cambridge, UK). For this comparative study, a test for the presence of six autoantibodies in a selection of human patient serum samples was chosen as a model system. The multiplexed Luminex xMap and SmartBead UltraPlex assays were generally comparable. However, both systems generated some results that were at variance with those obtained by ELISA. The different methods used for the assignment of the cut-off levels for each of the assays within any given platform was identified as the major source of these non-concordant results. The present study demonstrates that array platforms have the potential to be used in immunodiagnostics providing that suitable cut-off levels are established.

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.

Microarrays based on affinity-tagged single-chain Fv antibodies: Sensitive detection of analyte in complex proteomes

Protein-based microarrays are among the novel class of rapidly emerging proteomic technologies that will allow us to efficiently perform global proteome analysis. However, the process of designing adequate protein microarrays is a major inherent problem. In this study, we have evaluated a protein microarray platform based on nonpurified affinity-tagged single-chain (sc) Fv antibody fragments to generate proof-of-principle and to demonstrate the specificity and sensitivity of the array design. To this end, we used our human recombinant scFv antibody library genetically constructed around one framework, the n-CoDeR library containing 2 x 10(10) clones, as a source for our probes. The probes were immobilized via engineered C-terminal affinity tags, his- or myc-tags, to either Ni(2+)-coated slides or anti-tag antibody coated substrates. The results showed that highly functional microarrays were generated and that nonpurified scFvs readily could be applied as probes. Specific and sensitive microarrays were obtained, providing a limit of detection in the pM to fM range, using fluorescence as the mode of detection. Further, the results showed that spotting the analyte on top of the arrayed probes, instead of incubating the array with large sample volumes (333 pL vs. 40 microL), could reduce the amount of analyte required 4000 times, from 1200 attomole to 300 zeptomole. Finally, we showed that a highly complex proteome, such as human sera containing several thousand different proteins, could be directly fluorescently labeled and successfully analyzed without compromising the specificity and sensitivity of the antibody microarrays. This is a prerequisite for the design of high-density antibody arrays applied in high-throughput proteomics.

Protein microarray detection strategies: focus on direct detection technologies

Protein microarrays are being utilized for functional proteomic analysis, providing information not obtainable by gene arrays. Microarray technology is applicable for studying protein-protein, protein-ligand, kinase activity and posttranslational modifications of proteins. A precise and sensitive protein microarray, the direct detection or reverse-phase microarray, has been applied to ongoing clinical trials at the National Cancer Institute for studying phosphorylation events in EGF-receptor-mediated cell signaling pathways. The variety of microarray applications allows for multiple, creative microarray designs and detection strategies. Herein, we discuss detection strategies and challenges for protein microarray technology, focusing on direct detection of protein microarrays.

Use of proteomic analysis to monitor responses to biological therapies

Proteomics has the potential to revolutionise diagnosis and disease management. Serum protein pattern profiling by surface-enhanced laser desorption/ionisation time of flight (SELDI-TOF) mass spectrometry is emerging as a novel approach to discover protein patterns capable of distinguishing disease and disease-free states with high sensitivity and specificity. This method has shown great promise for early diagnosis of ovarian cancer and is being applied to a range of pathological states. Protein microarray technology is being evaluated as a new means to track biological responses to therapy. Through the measurement of key protein phosphorylation sites at different stages of disease progression or before and after treatment, protein signal pathways can be mapped and thus become the starting point for individualised therapy. Laser capture microdissection (LCM) coupled with immunostaining of protein microarrays allows isolation of pure cell populations and relative quantitation of phosphorylated and non-phosphorylated forms of the cell's key signalling proteins. This technology is currently in use at the National Institutes of Health in Phase II clinical trials of metastatic breast and ovarian cancer. Cell survival and apoptotic protein pathways are monitored as biological markers of disease progression in these clinical trials. Proteomic technologies, such as serum protein pattern profiling, combined with protein microarray technologies, constitute a new paradigm for detecting disease and monitoring disease response to therapy. Ultimately, proteomics and genomics will become integrated into cancer patient management through the design and tracking of individualised therapy.

Clinical value and measurement of specific IgE

The diagnosis of human allergic diseases involves the combined use of a careful clinical history, physical examination, and in vitro and in vivo assay methods for the detection of IgE antibodies of defined allergen specificities. In vivo (skin testing) and in vitro (measurement of specific IgE in serum) techniques cannot be considered interchangeable, the former reflecting not only the presence of IgE but also mast cell integrity, vascular and neural responsiveness. Both techniques have similarities and differences, advantages and disadvantages. Recently introduced "second generation" immunoassays have continued to improve the analytical sensitivity and reproducibility thanks to automation and improved reagent quality. Quantitative assays may allow the use of specific clinical thresholds able to differentiate symptomatic from asymptomatic patients. False-negative and false-positive results should derive from lability of some major extracts, and from possible cross-reactivities, respectively. Characterization of allergens at a molecular and submolecular level and, where necessary, the use of recombinant allergens can reduce cross-reactions and further improve the quality of immunoassays.