Alla Rubina

Why 3‐D? Gel‐based microarrays in proteomics

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

Gel-based microarrays in clinical diagnostics in Russia

Immobilization of molecular probes in 3D hydrogel elements provides some essential advantages compared with conventional flat surfaces. In this article, an integrated technology based on the use of low-density microarrays comprised of hemispherical gel elements, developed at the Engelhardt Institute of Molecular Biology (Moscow, Russia) for various applications will be reviewed. The structure of the gel can be adapted for immobilization of virtually any biological molecules in a natural hydrophilic environment. The discrimination between matching and mismatching duplexes of nucleic acids in these conditions is more reliable than on conventional flat surfaces, minimizing the number of elements needed to detect specific sequences. Protein molecules immobilized in hydrogel-based biochips better preserve their biological properties. As described in this article, such biochips were successfully applied for laboratory diagnostics in a wide variety of clinical conditions involving the identification of bacterial and viral pathogens, cancer-related mutations and protein tumor markers.

Quantification of target proteins using hydrogel antibody arrays and MALDI time-of-flight mass spectrometry (A2M2S)

Mass spectrometry-based analysis techniques are widely applied in proteomics. This study presents a novel method for quantitative multiplex candidate protein profiling. It applies immunocapture of differentially labeled protein complements on hydrogel antibody arrays and subsequent quantification by MS. To make this approach quantitative a labeling approach was devised. The impact of labeling on the antibody/antigen interaction was assessed in detail by surface plasmon resonance. Owing to there solution by mass more than two protein samples can be compared simultaneously. Direct labeling of crude samples such as sera was developed and so enables the absolute quantification of target proteins straight from crude samples without a protein purification step. It was used to measure the concentration of apolipoprotein A-1 in serum. This method has been termed A2M2S for Affinity Array sand MALDI Mass Spectrometry.

Multiplex determination of serological signatures in the sera of colorectal cancer patients using hydrogel biochips

Colorectal cancer (CRC) is the third most common malignancy in industrialized countries. Despite the advances in diagnostics and development of new drugs, the 5‐year survival remains only 60–65%. Our approach to early diagnostics of CRC is based on the determination of serological signatures with an array of hemispherical hydrogel cells containing immobilized proteins and oligosaccharides (glycochip). The compounds immobilized on the glycochip include tumor‐associated glycans (SiaTn, Tn, TF, LeC, LeY, SiaLeA, and Manβ1‐4GlcNAcβ) and antibodies against human immunoglobulins IgG, IgA, and IgM. The glycochip detects antibodies against tumor‐associated glycans in patients’ sera. The simultaneous measurement of the levels of immunoglobulins enhances the diagnostic impact of the signatures. In this work, we found previously unreported increase in antibodies against oligosaccharide Manβ1‐4GlcNAcβ in patients with CRC. In parallel with these experiments, we determined the levels of oncomarkers carcinoembryonic antigen (CEA), cancer antigen (CA) 19–9, CA 125, CA 15–3, human chorionic gonadotropin (HCG), and alpha‐fetoprotein (AFP) using another gel‐based biochip with immobilized antibodies (oncochip) developed earlier in our laboratory. In total, 69 samples from healthy donors, 33 from patients with colorectal carcinoma, and 27 from patients with inflammatory bowel diseases were studied. The use of combined signatures of antiglycan antibodies and oncomarkers provides much better predictive value than the conventional measurement of oncomarkers CEA and CA 19–9. Positive predictive value of CRC diagnoses using together glycochip and oncochip reached 95% with the sensitivity and specificity 88% and 98%, respectively. Thus, the combination of antibody profiling with detection of conventional oncomarkers proved to be a promising tool in diagnostics of CRC.

UV fluorescence of tryptophan residues effectively measures protein binding to nucleic acid fragments immobilized in gel elements of microarrays.

Microarrays allow for the simultaneous monitoring of protein interactions with different nucleic acid (NA) sequences immobilized in microarray elements. Either fluorescently labeled proteins or specific fluorescently labeled antibodies are used to study protein–NA complexes. We suggest that protein–NA interactions on microarrays can be analyzed by ultraviolet (UV) fluorescence of tryptophan residues in the studied proteins, and this approach may eliminate the protein‐labeling step. A specialized UV microscope was developed to obtain fluorescent images of microarrays in the UV wavelengths and to measure the fluorescence intensity of individual microarray elements. UV fluorescence intensity of BSA immobilized in microarray gel elements increased linearly with increased BSA amount with sensitivity of 0.6 ng. Real‐time interaction curves between the DNA‐binding domain of the NFATc1 transcription factor (NFATc1‐DBD) and synthetic hairpin‐forming oligodeoxyribonucleotides immobilized within 0.2 nL microarray gel elements at a concentration 5 × 10–5 M and higher were obtained. The UV fluorescence intensities of microarray gel elements containing NFATc1‐DBD–DNA complexes at equilibrium allowed the estimation of the equilibrium binding constant for complex formation. The developed method allows the protein–NA binding to be monitored in real time and can be applied to assess the sequence‐specific affinity of NA‐binding proteins in parallel studies involving many NA sequences.

Microarray analyzer based on wide field fluorescent microscopy with laser illumination and a device for speckle suppression

A microarray analyzer was developed to obtain images and measure the fluorescence intensity of microarrays at three wavelengths from 380 nm to 850 nm. The analyzer contains lasers to excite fluorescence, barrier filters, optics to project images on an image detector, and a device for suppressing laser speckles on the microarray support. The speckle suppression device contains a fibre-optic bundle and a rotating mirror positioned in a way to change the distance between the bundle butt and mirror surface during each mirror revolution. The analyzer provides for measurements with accuracy within ± 5%. Obtaining images at several exposure times allowed a significant expansion in the range of measured fluorescence intensities. The analyzer is useful for high throughput analysis of the same type of microarrays.

Patterns of sensitization to inhalant and food allergens among pediatric patients from the Moscow region (Russian Federation)

The immunological profiles of human specific IgE (sIgE) and specific IgG4 (sIgG4) vary by genetic predisposition, living conditions in different geographical locations and patient’s age. The aim of our study was to analyze sIgE and sIgG4 patterns and their age-dependent changes in patients from the Moscow region. For identifying sIgE and sIgG4 profiles the blood samples from 513 patients aged 6 months to 17 years who were showing symptoms of allergic diseases were analyzed using microarrays containing 31 allergens. The highest sIgE prevalence was observed for birch pollen (32%) among pollen allergens, cat dander (24%) among indoor allergens, and egg whites (21%) among food allergens. The most common sIgG4 response was developed toward egg whites (80% of patients). Age-related elevation was identified for patients with increased sIgE to pollen allergens and indoor allergens (cat or dog dander and house dust mites). For each allergen, the proportion of cases with significant levels of sIgG4 appeared to increase with patients’ age. The data on allergen-specific sIgE and sIgG4 prevalence show both general trends and some local special aspects that are indicative for the Moscow region. This information should be useful in terms of epidemiology of allergic diseases.

Differential quantification of SCCA1 and SCCA2 cancer antigens using a hydrogel biochip

Methods employing hydrogel-based microarrays (biochips) allow the simultaneous monitoring of protein interactions with different antibodies immobilized in gel elements. The method was applied for the simultaneous differential quantification of two highly homologous antigens of squamous cell carcinomas (SCCs) SCCA1 and SCCA2 in a single analysis. Two panels of monoclonal antibodies against recombinant SCCA1 and SCCA2 were generated, and two antibodies, C5 (anti-SCCA1) and A11 (anti-SCCA2), were selected for further evaluation based on their ability to specifically interact with their cognate antigens. Using a sandwich analysis, these antibodies were further tested in combination with anti-SCCA antibodies (H31 and SCC107) recognizing both of the SCCA antigens, thus allowing a quantitative independent measurement of both antigens. The intra- and inter-assay coefficients of variation for all resultant tests did not exceed 10% for the range of SCCA concentrations tested and were independent of whether SCCA1 and SCCA2 concentrations were determined simultaneously. The lower limit of detection (LOD) was estimated as 0.006 ng ml−1 for SCCA1 and 0.011 ng ml−1 for SCCA2 using the SCC107-Cy5 developing antibody and 0.014 ng ml−1 and 0.01 ng ml−1 concentrations, respectively, of the H31-Cy5 developing antibody. This assay provides a simple and accurate procedure for the differential quantitation of SCCA1 and SCCA2 using a single analysis of human serum on a biochip.

Correction: Differential quantification of SCCA1 and SCCA2 cancer antigens using a hydrogel biochip

Correction for ‘Differential quantification of SCCA1 and SCCA2 cancer antigens using a hydrogel biochip’ by Aleksei A. Tikhonov et al., Anal. Methods, 2016, DOI: 10.1039/c6ay02216b.