Adaptation of Microarray Assay for Serum Amyloid a Analysis in Human Serum.

Serum amyloid A is an inflammatory biomarker whose concentration changes during infectious and inflammatory diseases. SAA's tendency for aggregation and complex formation makes it difficult to determine its concentration in samples, especially when there is an increased level of it. Immunofluorescence SAA determination on a microarray was adapted for SAA quantification in human serum. Both the procedure and the diluent for the calibrator samples were chosen to obtain a dynamic range between 1 and 100 µg/mL. Mixtures of animal (rabbit, goat, mouse) sera with recombinant antigen diluted in certain concentrations were used for the calibrator samples. The method was tested using serum samples from 15 patients with rheumatoid arthritis or ankylosing spondylitis and 9 healthy donors. The results obtained on the microarray demonstrated a good correlation with the results determined by ELISA (Pearson's correlation coefficient is 0.93). The method developed could be a convenient tool for assessing SAA levels in a number of diseases, such as rheumatoid arthritis or infections of various etiologies, characterized by a significant increase in the level of this protein in the blood. The use of a microarray for the analysis allows the determination of the SAA concentration simultaneously with other inflammatory biomarkers.

[Adaptation of Microarray Assay for Serum Amyloid A Analysis in Human Serum].

Serum amyloid A is an inflammatory biomarker whose concentration changes during infectious and inflammatory diseases. SAA's tendency for aggregation and complex formation makes it difficult to determine its concentration in samples, especially when there is an increased level of it. Immunofluorescence SAA determination on a microarray was adapted for SAA quantification in human serum. Both the procedure and the diluent for the calibrator samples were chosen to obtain a dynamic range between 1 and 100 µg/mL. Mixtures of animal (rabbit, goat, mouse) sera with recombinant antigen diluted in certain concentrations were used for the calibrator samples. The method was tested using serum samples from 15 patients with rheumatoid arthritis or ankylosing spondylitis and 9 healthy donors. The results obtained on the microarray demonstrated a good correlation with the results determined by ELISA (Pearson's correlation coefficient is 0.93). The method developed could be a convenient tool for assessing SAA levels in a number of diseases, such as rheumatoid arthritis or infections of various etiologies, characterized by a significant increase in the level of this protein in the blood. The use of a microarray for the analysis allows the determination of the SAA concentration simultaneously with other inflammatory biomarkers.

Analysis of rheumatoid factor and acute phase proteins using microarrays in patients with rheumatoid arthritis.

One of the biomarkers of biggest clinical importance in rheumatoid arthritis (RA) is rheumatoid factor (IgM RF). The rheumatoid factor has insufficient sensitivity and specificity, therefore, to increase the diagnostic information of the test, acute phase proteins were used as concomitant biomarkers. Using biological microchips, we measured IgM RF, C-reactive protein (CRP) and Serum amyloid protein A (SAA) in patients with RA (n = 60), ankylosing spondylitis (AS) (n=55), systemic lupus erythematosus (SLE) (n=20) and healthy donors (HD) (n=9). It was shown that the medians of IgM RF concentrations are significantly higher (p<0.01) in patients with RA compared to patients suffering from other diseases and healthy donors. CRP and SAA were also significantly increased (p<0.05) in patients with RA and AS compared with SLE and HD. It has been shown that the complex determination of three biomarkers in differentiating RA patients with the comparison group had a higher diagnostic sensitivity than the isolated determination of IgM RF, while the addition of SAA makes the greatest contribution to improving the diagnostic characteristics of the biomarker panel: the use of a logistic regression model based on IgM RF and SAA allowed to increase the diagnostic sensitivity of the analysis from 58.3% to 65%. Thus, the developed microarray-based method can be used to detect and elucidate the diagnostic characteristics of RA biomarkers; however, further use requires validation of the obtained results on an expanded sampling.

[Microarray for Quantitative Determination of Inflammatory Biomarkers in a Culture Medium].

Cytokines and acute phase proteins play an important role in the development of the immune response during inflammatory reactions. Depending on the type of disease, the development of inflammation is accompanied by changes in concentrations (both decrease and increase) of not one, but many inflammatory biomarkers. Here, a quantitative microarray-based method for multiplex immunoassay of eight biomarkers of human inflammation, namely acute phase proteins (C-reactive protein, serum amyloid protein A) and cytokines (IL-6, IL-8, IL-17, IL-18, IP10/CXCL10, TNFα) was developed and the possibility of its use for the detection of inflammatory biomarkers in a culture medium has been demonstrated. The developed method can be used to evaluate changes of the inflammatory biomarker profile induced by different agents or to determine the concentrations of biomarkers after activation of cells while studying different diseases with the help of in vitro models.

Analysis of Anti-Glycan IgG and IgM Antibodies in Colorectal Cancer.

We propose an approach that allows simultaneous determination of the levels of M and G isotypes of antibodies to the panel of glycans using microarrays. The level of IgG antibodies to 3'-O-su-Lea glycan detects patients with colorectal cancer with a sensitivity of 69.77% and specificity of 62.75%. The percentage of correctly classified colorectal cancer patients with the use of a combination of two markers IgM antibodies to glycans 3'-sialyl-TF and 3'-O-su-Lea is as high as 74.23%. The levels of IgM antibodies to 3'-O-su-Lea glycan differ significantly in patients with and without regional metastases. The levels of some of antiglycan IgM or IgG antibodies differed significantly in patients with tumors of different location and differentiation.

[Modification of Anti-Glycan IgG and IgM Profiles in Allergic Inflammation].

Glycans and anti-glycan antibodies (AGAs) are essential for infiltration of inflammatory cells in various allergies. The glycocalyx structure of the cells is modified during disease progression, and this modification is possible to evaluate by assessment of AGAs. A printed glycan array with 55 immobilized glycans and immobilized antibodies to IgG, IgA, and IgM was used to study the changes in AGA profiles in bronchial asthma (BA). Levels of antibodies to certain glycans in BA patients statistically differed from levels in healthy donors (p < 0.0007 by the Mann-Whitney test); the glycan set included 6Su-6`-SiaLec, Sia LeX, Sia6Htype2; Tαα, Manß1-4GlcNAc, and Manα1-4Manß. The obtained results help to better understand the mechanisms of the cell-mediated immune response in bronchial asthma and other types of allergic reactions.

The EIMB Hydrogel Microarray Technology: Thirty Years Later.

 Biological microarrays (biochips) are analytical tools that can be used to implement complex integrative genomic and proteomic approaches to the solution of problems of personalized medicine (e.g., patient examination in order to reveal the disease long before the manifestation of clinical symptoms, assess the severity of pathological or infectious processes, and choose a rational treatment). The efficiency of biochips is predicated on their ability to perform multiple parallel specific reactions and to allow one to study the interactions of biopolymer molecules, such as DNA, proteins, glycans, etc. One of the pioneers of microarray technology was the Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences (EIMB), with its suggestion to immobilize molecular probes in the three-dimensional structure of a hydrophilic gel. Since the first experiments on sequencing by hybridization on oligonucleotide microarrays conducted some 30 years ago, the hydrogel microarrays designed at the EIMB have come a long and successful way from basic research to clinical laboratory diagnostics. This review discusses the key aspects of hydrogel microarray technology and a number of state-ofthe-art approaches for a multiplex analysis of DNA and the protein biomarkers of socially significant diseases, including the molecular genetic, immunological, and epidemiological aspects of pathogenesis.

[Exosomal surface protein markers in diagnosis of colorectal cancer].

Colorectal cancer (CRC) is one of the most common primary malignancies. Early stages of the disease are asymptomatic in the majority of cases, leading to late detection and high mortality. Available noninvasive diagnostic techniques are limited in sensitivity and specificity, and designing new ones is still a pressing problem. Exosomes are membrane-derived microvesicles secreted into human biological fluids and provide a novel way to assess the course of an oncology disease. The review describes the repertoire of exosomal surface biomarkers found in the blood of CRC patients and the prospects of employing multiplexed tests for exosomal markers in early noninvasive diagnosis of cancer.

[Hydrogel microchip as a tool for studying exosomes in human serum].

Exosomes are cell-derived vesicles that are secreted by both normal and cancer cells. Over the last decade, a few studies have revealed that exosomes cross talk and/or influence major tumor-related pathways such as angiogenesis and metastasis involving many cell types within the tumor microenvironment. The protein composition of the membrane of an exosome reflects that of the membrane of the cell of origin. Because of this, tumor-derived exosomes differ from exosomes that are derived from normal cells. The detection of tumor exosomes and analysis of their molecular composition hold promise for diagnosis and prognosis of cancer. Here, we present hydrogel microarrays (biochips), which contain a panel of immobilized antibodies that recognize tetraspanins (CD9, CD63, CD81) and prognostic markers for colorectal cancer (A33, CD147). These biochips make it possible to analyze the surface proteins of either isolated exosomes or exosomes that are present in the serum samples without isolation. These biochips were successfully used to analyze the surface proteins of exosomes from serum that was collected from a colorectal cancer patient and healthy donor. Biochip-guided immunofluorescent analysis of the exosomes has made it possible for us to detect the A33 antigen and CD147 in the serum sample of the colorectal cancer patient with normal levels of CEA and CA19-9.

[Allergy and autoimmunity: Molecular diagnostics, therapy, and presumable pathogenesis].

Allergic and autoimmune diseases represent immunopathological reactions of an organism to antigens. Despite that the allergy is a result of exaggerated immune response to foreign antigens (allergens) and autoimmune diseases are characterized by the pathological response to internal antigens (autoantigens), the underlying mechanisms of these diseases are probably common. Thus, both types of diseases represent variations in the hypersensitivity reaction. A large percentage of both the adult and pediatric population is in need of early diagnostics of these pathologies of the immune system. Considering the diversity of antibodies produced in allergic and autoimmune disease and the difficulties accompanying clinical diagnosing, molecular diagnostics of these pathological processes should be carried out in several stages, including screening and confirmatory studies. In this review, we summarize the available data on the molecular diagnostics and therapy of allergic and autoimmune diseases and discuss the basic similarities and differences in the mechanisms of their development.

[Preparation of recombinant serpins B3 and B4 and investigation of their specific interactions with antibodies using hydrogel-based microarrays].

The objective of this work was to obtain preparations of recombinant squamous-cell carcinoma antigens (serpins B3 and B4) and to investigate their interactions with different monoclonal antibodies using hydrogel-based microarrays (biochips). Two genetic constructs encoding full-length serpin B3 and serpin B4 molecules were created to produce recombinant SPB3 and SPB4 proteins carrying a N-terminal His6-tag. Monoclonal antibodies against serpin B3 (H3, C5, H5, H81, and G9) were also obtained. An experimental gel-based biological microchip was designed to contain gel elements that carry immobilized antibodies against SPB3, immobilized commercial monoclonal SCC107 and SCC140 antibodies against squamous-cell carcinoma antigen (SCCA), and gel elements with immobilized SPB3 or SPB4. Judging by the specificity of recombinant SPB3 and SPB4, which bind to monoclonal antibodies against SCCA and, according to the manufacturer's data, can recognize conformational epitopes of both SPB3 and SPB4, it was concluded that the obtained recombinant serpins had the correct tertiary structure. A biochip-based direct immunoassay showed that SPB4 could bind effectively only to SCC107 and SCC140 antibodies, while SPB3 interacted specifically not only with these antibodies, but also with H3 and C5 monoclonal antibodies. Using biochip-based sandwich immunoassay, a pair of monoclonal antibodies SCC107/C5 that interacted specifically with serpin B3 but did not interact with serpin B4 was identified. Thus, it has been demonstrated that serpin B3 can be selectively determined in the presence of highly homologous serpin B4 using a biochip-based assay.

[Methods for Reducing Laser Speckles to Achieve Even Illumination of the Microscope Field of View in Biophysical Studies].

The aim of this work was to compare different speckle reduction techniques. It was shown that the use of devices based on liquid crystals only leads to partial reduction of speckle contrast. In quantitative luminescent microscopy an application of the mechanical devices when a laser beam is spread within the field of view turned out to be more efficient. Laser speckle noise was virtually eliminated with the developed and manufactured mechanical device comprising a fiber optic ring light guide and the vibrator that permits movement of optical fiber ends towards the laser diode during measurements. The method developed for the analysis of microarrays was successfully applied to the problem of speckle reduction.

[The evaluation of ratio of oncomarkers in search of initial focus of tumor: on the occasion of fiftieth anniversary of discovery of alpha-fetoprotein as an oncomarker].

The article presents research data testifying the dominant value of HAFP behavior in diagnostic of oncological diseases. The importance of study of profile of main oncomarkers in patient is demonstrated. The method of hydrohelium biochips, developed in the institute of molecular biology, was used to determine 9 key oncomarkers. The application of this method made it possible to essentially complete the information map in 8 patients according to clinical interpretation of disease. In economically justified variant, this method is able to shorten period of study of patient, to specify character of pathological process and to transfer examination load of patients to the out-patient level.

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.

Simultaneous detection of seven staphylococcal enterotoxins: development of hydrogel biochips for analytical and practical application.

A method of simultaneous analysis of staphylococcal enterotoxins using hydrogel-based microarrays (biochips) has been developed. The method allows simultaneous quantitative detection of seven enterotoxins: A, B, C1, D, E, G, and I in a single sample. The development of the method included expression and purification of recombinant toxins, production of panels of monoclonal antibodies (mAbs) against the toxins, and design and manufacturing of an experimental biochip for the screening of mAbs and selection of optimal pairs of primary and secondary antibodies for each toxin. The selected mAbs have high affinity toward their targets and no cross-reactivity with unrelated enterotoxins. Finally, a diagnostic biochip was designed for quantitative analysis of the toxins, and the analytical protocols were optimized. The sensitivity of the detection reached 0.1-0.5 ng/mL, depending on the type of enterotoxin. The evaluation of the resulting biochip using spiked food samples demonstrated that the sensitivity, specificity, and reproducibility of the proposed test system fully satisfy the requirements for traditional immunoanalytical systems. The diagnostic biochips manufactured on reflecting metal-coated surfaces shortened the time of analysis from 17 to 2 h without loss of sensitivity. The method was successfully tested on samples of food and biological media.

Biological microchip for a simultaneous quantitative immunoassay of tumor markers in human serum.

The biochip was constructed for simultaneous assay of total and free prostate-specific antigen, alpha-fetoprotein, cancer embryonic antigen, human chorionic gonadotropin, and neuron-specific enolase. These biochips represent an array of gel elements with covalently immobilized proteins. The major analytic characteristics of the developed method were obtained. It was shown that the results of simultaneous assay of six tumor markers in blood serum well correlated with routine measurement of each marker using enzyme immunoassay kits. This approach allowed us to reveal the hook effect of high concentrations during biochip assay, which prevents distortion of the diagnostic picture at high concentration of the analyte in the sample.

Hydrogel-based protein and oligonucleotide microchips on metal-coated surfaces: enhancement of fluorescence and optimization of immunoassay.

Manufacturing of hydrogel-based microchips on metal-coated substrates significantly enhances fluorescent signals upon binding of labeled target molecules. This observation holds true for both oligonucleotide and protein microchips. When Cy5 is used as fluorophore, this enhancement is 8-10-fold in hemispherical gel elements and 4-5-fold in flattened gel pads, as compared with similar microchips manufactured on uncoated glass slides. The effect also depends on the hydrophobicity of metal-coated substrate and on the presence of a layer of liquid over the gel pads. The extent of enhancement is insensitive to the nature of formed complexes and immobilized probes and remains linear within a wide range of fluorescence intensities. Manufacturing of gel-based protein microarrays on metal-coated substrates improves their sensitivity using the same incubation time for immunoassay. Sandwich immunoassay using these microchips allows shortening the incubation time without loss of sensitivity. Unlike microchips with probes immobilized directly on a surface, for which the plasmon mechanism is considered responsible for metal-enhanced fluorescence, the enhancement effect observed using hydrogel-based microchips on metal-coated substrates might be explained within the framework of geometric optics.