Liquid Bead Array Research Articles

Development and validation of a multi-marker liquid bead array assay for the simultaneous detection of PIK3CA and ESR1 hotspot mutations in single circulating tumor cells (CTCs)

BackgroundPIK3CA and ESR1 mutations are associated with progression and therapy resistance in metastatic breast cancer (MBC). CTCs are highly heterogeneous and their analysis at single cell level can provide unique information for mutational profiling and the existence of different sub-clones related to tumor progression. We have developed a novel multi-marker liquid bead array assay based on combination of an enzymatic mutation enrichment method, multiplex PCR-based assay, and liquid bead array technology for the simultaneous detection of PIK3CA and ESR1 hotspot mutations in liquid biopsy samples. We focus on single CTCs, however the assay can be used for bulk CTC and ctDNA analysis. Materials and methodsSingle CTCs were isolated from an ER+/HER2+ MBC patient from CellSearch® cartridges using the VyCAP Puncher System and subjected to whole genome amplification followed by nuclease-assisted minor-allele enrichment with probe-overlap (NaME-PrO) enrichment. The assay was validated for analytical sensitivity and specificity for the simultaneous detection of PIK3CA (E545K, E542K, H1047R, H1047L) and ESR1 (Y537S, Y537C, Y537N, D538G, L536H) mutations in single CTCs, while its clinical performance was evaluated on 22 single CTCs and three single white blood cells (WBCs). ResultsThe developed multi-marker liquid bead array assay is novel, highly specific and sensitive for both mutation panels. The assay can reliably detect mutation-allelic-frequencies (MAFs) as low as 0.1 %. The presence of PIK3CA and ESR1 mutations was detected in 13.6 % and 72.7 % of single CTCs, respectively. The developed assay is sample-saving since it requires only 2 μL of amplified DNA to check for nine hotspot PIK3CA and ESR1 mutations in a single cell. The developed liquid bead array assay (Luminex, US), based on a 96 microwell plate format, enables the simultaneous analysis of 96 single cells. ConclusionsThe developed novel multi-marker liquid bead array assay for the simultaneous detection of PIK3CA and ESR1 hotspot mutations in single CTCs is highly specific, highly sensitive, high-throughput, and sample-, cost-, and time-saving. This multi-marker liquid bead array assay can be extended to detect up to 100 mutations in many genes at once and can be applied for bulk CTC and ctDNA analysis.

A high-throughput liquid bead array assay confirms strong correlation between SARS-CoV-2 antibody level and COVID-19 severity

SummaryA detailed understanding of the adaptive host response to SARS-CoV-2 infection in humans is urgently needed. We developed a sensitive, high-throughput, and efficient assay using liquid bead array technology. We observed advantages over traditional ELISA for the detection and quantification of binding IgG against the receptor binding domain (RBD) of SARS-CoV-2. To determine whether COVID-19 symptom severity correlates with SARS-CoV-2 IgG, we measured anti-RBD IgG levels from 67 subjects recovered from PCR-confirmed COVID-19. We found that COVID-19 symptom severity strongly correlated with RBD IgG level (p < 0.001). These findings have substantial implications for public policy surrounding assessments of antibody responses and possible immunity, as not all cases of COVID-19 can be assumed to generate a protective antibody response, and mild disease in particular is capable of generating very low-level anti-RBD IgG levels. These findings also have important implications for the selection of donors for convalescent plasma to be used therapeutically.

Use of a Novel Liquid Bead-Array Assay to Determine Correlation between SARS-CoV-2 Binding Antibody Level and COVID-19 Disease Severity

A detailed understanding of the adaptive host response to SARS-CoV-2 infection in humans is urgently needed, as questions abound regarding serologic responses and the development of antibody-mediated immunity against COVID-19. We developed a highly sensitive, high-throughput, and efficient assay using liquid bead array technology. We observed advantages over traditional indirect ELISA for the detection and quantification of binding IgG against the receptor binding domain (RBD) of SARS-CoV-2. Using this sensitive and highly reproducible assay, we sought to determine whether the severity of COVID-19 symptoms is correlated with SARS-CoV-2 binding IgG level. We measured SARS-CoV-2 RBD IgG levels from 67 subjects who had recovered from PCR-confirmed, symptomatic COVID-19. Samples were obtained approximately 6 weeks post-symptom onset. We found that COVID-19 symptom severity, assessed on an 8-point severity scale, strongly correlated with RBD IgG level (p<0.001), with and without adjustment for covariates of age, sex, and time from symptom onset. These findings have substantial implications for public policy surrounding assessments of antibody responses and possible immunity, as not all cases of COVID-19 can be assumed to generate a protective antibody response, and mild disease in particular is capable of generating very low-level anti-RBD IgG levels. These findings also have important implications for the selection of donors for convalescent plasma to be used as a therapeutic, and other scenarios where antibody level, rather than mere presence or absence, is relevant.

Tissue microRNAs in non-small cell lung cancer detected with a new kind of liquid bead array detection system

BackgroundCommonly used miRNA detection methods cannot be applied for high-throughput analyses. However, this study was aimed to performed a liquid bead array detection system (LBAS) to detect tissue 6 miRNAs in non-small cell lung cancer (NSCLC).MethodsIn this study, evaluation of LBAS was performed to observe the precision, specificity, limitation and stability. Then, a total of 52 primary NSCLC patients who received resection operation without preoperative radiotherapy and chemotherapy between June 2013 and March 2014 were selected, and then the total RNA of the tissues were extracted. We prepared six NSCLC-related miRNAs for LBAS. After optimization and evaluation, LBAS was verified by detecting the relative expression levels of 6 microRNAs in the pathological tissues and corresponding normal tissues of 52 NSCLC patients.ResultsThe results of evaluation of LBAS showed that the Mean Fluorescence Intensity (MFI) of the reaction only added with chimeric probes and beads showed no significant change after 180 days (P > 0.05). And the intra-assay Coefficient of Variation (CV) was between 1.57 and 3.5%, while the inter-assay CV was between 4.24 and 11.27%, indicating this system was ideal for diagnostic reagents. In addition, only the beads corresponding to the additional miRNAs showed high MFIs from 8426 to 18,769, whereas the fluorescence values of the other beads were under background levels (MFIs = 20 to 55) in each reaction, indicating no cross reactivity among the miRNAs. The limit of detection of miR-21, miR-210, miR-125b, miR-155, miR-375, and miR-31 were 5.27, 1.39, 1.85, 2.01, 1.34, and 2.73 amol/μL, respectively, showing that the lowest detection limit of miRNA by this system was under pM level. Then, the relative expression levels of miR-21, miR-210, miR-125b, miR-155, miR-375, and miR-31 by using this system were significantly correlated with NSCLC (P < 0.05). And the results of AUC method indicated that specific of the LBAS system was 94.2%.ConclusionsOur findings suggest that LBAS was simple, high-throughput, and freely combined with absolute quantification. Thus, this system could be applied for tumor miRNAs detection.

Development and Validation of Multiplex Liquid Bead Array Assay for the Simultaneous Expression of 14 Genes in Circulating Tumor Cells.

Liquid biopsy, based on the molecular information extracted from circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA), offers the possibility to characterize the evolution of a solid tumor in real time and is highly important for diagnostic and therapeutic purposes. The aim of the present study was the development and validation of a novel liquid bead array methodology for the molecular characterization of CTCs and its application in breast cancer. In the present study we developed and evaluated a multiplex polymerase chain reaction (PCR)-coupled liquid bead array (MLBA) assay for studying simultaneously the expression of 14 genes in CTCs. The 14-gene MLBA assay is characterized by high analytical specificity, sensitivity, and reproducibility. The analytical performance of the 14-gene MLBA assay was compared with a commercially available test (AdnaTest BreastCancer, Qiagen, Germany) and our previously described multiplex quantitative reverse transcription PCR (RT-qPCR) assays. The developed assay has the potential to be further expanded in order to include up to 100 gene targets. The assay is highly specific for each target gene and is not affected by the numerous primers and probes used for multiplexing; hence, it constitutes a sample-, cost-, and time-saving analysis.

Establishment and optimization of a liquid bead array for the simultaneous detection of ten insect-borne pathogens

BackgroundInsect-borne diseases could induce severe symptoms in human and clinical signs in animals, such as febrility, erythra, arthralgia and hemorrhagic fever, and cause significant economic losses and pose public health threat all over the world. The significant advantages of Luminex xMAP technology are high-throughput, high parallel and automation. This study aimed to establish a liquid bead array based on Luminex xMAP technology that was able to simultaneously detect multiple insect-borne pathogens.MethodsSpecific probes and primers to detect the nucleic acid of 10 insect-borne pathogens were designed. Probes were coupled with fluorescent carboxylated microspheres. The parameters of the system were optimized, including ratio of forward/reverse primers (1:2), hybridization temperature (50 °C) and duration (30 min) and quantity of PCR product (2 μl). The sensitivity and specificity of the system were also evaluated. Moreover mixed nucleic acid of 10 insect-borne pathogens, including Bluetongue virus, Epizootic hemorrhagic disease virus of deer, Coxiella burnetii, African swine fever virus, West Nile fever virus, Borrelia burgdorferi, vesicular stomatitis virus, Rift Valley fever virus, Ebola virus and Schmalenberg’s disease virus, and 3000 clinical samples were tested for practicability.ResultsThe optimized detection system showed high sensitivity, specificity and reproducibility. Each probe showed specific fluorescence signal intensity without any cross-hybridization for the other insect-borne pathogens tested, which included dengue virus, tick-borne encephalitis virus, Japanese encephalitis virus, Xinjiang hemorrhagic fever virus, spotted fever group rickettsiae, ehrlichiae and chikungunya virus. The limit of detection was 10 copies of target gene. Insect-borne pathogens were successfully detected among the 3000 clinical samples, and the results were consistent with those obtained using gold-standard assays or commercial nucleic acid detection kits.ConclusionsThis optimized liquid array detection system was high-throughput and highly specific and sensitive in screening of the insect-borne pathogens. It was promising in detection of these pathogens for molecular epidemiological studies.

A liquid bead array for the identification and characterization of fljB-positive and fljB-negative monophasic variants of Salmonella Typhimurium

Salmonella1,4,[5],12:i:- accounts currently for one of the most common serotypes observed worldwide. These isolates do not express the FljB flagellin and mostly derive from Salmonella Typhimurium. They are therefore termed Salmonella Typhimurium monophasic variants (STMV) and are considered of comparable public health risk. Since serological identification of the somatic and flagellar antigens of STMV is not sufficient to demonstrate relatedness with Salmonella Typhimurium, additional assays detecting genetic markers unique to Salmonella Typhimurium are required. In addition, identification of the mutations affecting expression of the flagellar gene fljB can be useful to support the monophasic character observed phenotypically. Finally, genetic subtyping of the various mono- and biphasic Salmonella Typhimurium clonal groups can facilitate their epidemiological follow-up. Here, we present a home-made liquid bead array able to fulfill these requirements. This array confirmed the monophasic character of 240 STMV isolates collected in Belgium during 2014–2015 and identified 10 genetic subtypes. Microevolution in and around the fljB locus linked to IS26 insertions is probably one of the driven force accounting for STMV population diversity. Thanks to its open design, other genetic signatures could later be merged to the assay to subtype additional STMV clonal groups and to detect rare mutations.

Genotyping of 19 red cell antigens, including RHD, using liquid bead arrays

BackgroundTraditionally, the determination of blood group has been performed using serological techniques. Due to the drawbacks of using antisera, molecular typing of blood groups has been introduced. However, the commonly used genotyping assays in blood banks have limitations because the panels for these were based on genetic variations in Caucasians. MethodsWe developed a multiplex human erythrocyte antigen genotyping assay using allele-specific primer extensions and hybridization with bead microarrays. Single nucleotide polymorphisms (SNP) were genotyped for the 18 red cell antigens and wild-type RHD, DEL, and complete deletion were examined for RHD. The cut-off of median fluorescence intensity (MFI) for each allele was optimized. In the evaluation stage, the results of 87 samples were compared with those from other genotyping methods, and 26 serologic results were also compared. ResultsThe cut-off values were determined using −1 and −2 standard deviation (SD) of the minimum adjusted MFI for SNP detection. Complete deletion was determined with raw MFI+2SD. In comparison with the other methods, the kappa values were 0.984 overall. Compared with serologic methods, our assay showed discrepancy in 2 S/s, 3 C/c, and 3 Dia/Dib antigens. ConclusionsOur method reliably predicts the presence or the absence of the 19 antigens.

Performance Assessment of Four Chimeric Trypanosoma cruzi Antigens Based on Antigen-Antibody Detection for Diagnosis of Chronic Chagas Disease.

The performance of serologic tests in chronic Chagas disease diagnosis largely depends on the type and quality of the antigen preparations that are used for detection of anti-Trypanosoma cruzi antibodies. Whole-cell T. cruzi extracts or recombinant proteins have shown variation in the performance and cross-reactivity. Synthetic chimeric proteins comprising fragments of repetitive amino acids of several different proteins have been shown to improve assay performances to detect Chagasic infections. Here, we describe the production of four chimeric T. cruzi proteins and the assessment of their performance for diagnostic purposes. Circular Dichroism spectra indicated the absence of well-defined secondary structures, while polydispersity evaluated by Dynamic Light Scattering revealed only minor aggregates in 50 mM carbonate-bicarbonate (pH 9.6), demonstrating that it is an appropriate buffering system for sensitizing microplates. Serum samples from T. cruzi-infected and non-infected individuals were used to assess the performance of these antigens for detecting antibodies against T. cruzi, using both enzyme-linked immunosorbent assay and a liquid bead array platform. Performance parameters (AUC, sensitivity, specificity, accuracy and J index) showed high diagnostic accuracy for all chimeric proteins for detection of specific anti-T. cruzi antibodies and differentiated seropositive individuals from those who were seronegative. Our data suggest that these four chimeric proteins are eligible for phase II studies.

Development and validation of a multiplex methylation specific PCR-coupled liquid bead array for liquid biopsy analysis

BackgroundLiquid biopsy is based on minimally invasive blood tests and has the potential to characterize the evolution of a solid tumor in real time, by extracting molecular information from circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA). Epigenetic silencing of tumor and metastasis suppressor genes plays a key role in survival and metastatic potential of cancer cells. Our group was the first to show the presence of epigenetic alterations in CTCs. MethodsWe present the development and analytical validation of a highly specific and sensitive Multiplex Methylation Specific PCR-coupled liquid bead array (MMSPA) for the simultaneous detection of the methylation status of three tumor and metastasis suppressor genes (CST6, SOX17 and BRMS1) in liquid biopsy material (CTCs, corresponding ctDNA) and paired primary breast tumors. ResultsIn the EpCAM-positive CTCs fraction we observed methylation of: a) CST6, in 11/30(37%) and 11/30(37%), b) BRMS1 in 8/30(27%) and 11/30(37%) c) SOX17 in 8/30(27%) and 13/30(43%) early breast cancer patients and patients with verified metastasis respectively. In ctDNA we observed methylation of: a) CST6, in 5/30(17%) and 10/31(32%), b) BRMS1 in 8/30 (27%) and 8/31 (26%) c) SOX17 in 5/30(17%) and 13/31(42%) early breast cancer patients and patients with verified metastasis respectively. ConclusionsOur results indicate a high cancerous load at the epigenetic level in EpCAM-positive CTCs fractions and corresponding ctDNA in breast cancer. The main principle of the developed methodology has the potential to be extended in a large number of gene-targets and be applied in many types of cancer.

Identification of serum miRNAs by nano-quantum dots microarray as diagnostic biomarkers for early detection of non-small cell lung cancer.

Circulating microRNAs (miRNAs) are potential noninvasive biomarkers for cancer detection. We used preoperative serum samples from non-small cell lung cancer (NSCLC) patients and healthy controls to investigate whether serum levels of candidate miRNAs could be used as diagnostic biomarkers in patients with resectable NSCLC and whether they were associated with clinicopathologic characteristics. We initially detected expression of 12 miRNAs using quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) in preoperative serum samples of 94 NSCLC patients and 58 healthy controls. We further validated our results using the fluorescence quantum dots liquid bead array for differentially expressed miRNAs in serum samples of 70 NSCLC patients and 54 healthy controls. Receiver operating characteristic (ROC) analysis was performed to select the best diagnostic miRNA cutoff value. A predictive model of miRNAs for NSCLC was derived by multivariate logistic regression. We found that five serum miRNAs (miR-16-5p, miR-17b-5p, miR-19-3p, miR-20a-5p, and miR-92-3p) were significantly downregulated in NSCLC, while miR-15b-5p was significantly upregulated (p < 0.05). Multivariate logistic regression analysis revealed that miR-15b-5p, miR-16-5p, and miR-20a-5p expression were independent diagnostic factors for the identification of patients with NSCLC after adjustment for patient's age and sex. In addition, the expression of serum miR-106-5p was higher in stage I than in stages IIa-IIIb, and no significant association was observed between expression of miRNAs and other variables including pathological type, tumor size, and lymph nodes status. Six serum miRNAs could potentially serve as noninvasive diagnostic biomarkers for resectable NSCLC. The predictive model combining miR-15b-5p, miR-16-5p, and miR-20a-5p was the best diagnostic approach.

A high-throughput liquid bead array-based screening technology for Bt presence in GMO manipulation.

The number of species and planting areas of genetically modified organisms (GMOs) has been rapidly developed during the past ten years. For the purpose of GMO inspection, quarantine and manipulation, we have now devised a high-throughput Bt-based GMOs screening method based on the liquid bead array. This novel method is based on the direct competitive recognition between biotinylated antibodies and beads-coupled antigens, searching for Bt presence in samples if it contains Bt Cry1 Aa, Bt Cry1 Ab, Bt Cry1 Ac, Bt Cry1 Ah, Bt Cry1 B, Bt Cry1 C, Bt Cry1 F, Bt Cry2 A, Bt Cry3 or Bt Cry9 C. Our method has a wide GMO species coverage so that more than 90% of the whole commercialized GMO species can be identified throughout the world. Under our optimization, specificity, sensitivity, repeatability and availability validation, the method shows a high specificity and 10-50 ng/mL sensitivity of quantification. We then assessed more than 1800 samples in the field and food market to prove capacity of our method in performing a high throughput screening work for GMO manipulation. Our method offers an applicant platform for further inspection and research on GMO plants.

Respiratory infectious phenotypes in acute exacerbation of COPD: an aid to length of stay and COPD Assessment Test.

PurposeTo investigate the respiratory infectious phenotypes and their impact on length of stay (LOS) and the COPD Assessment Test (CAT) Scale in acute exacerbation of COPD (AECOPD).Patients and methodsWe categorized 81 eligible patients into bacterial infection, viral infection, coinfection, and non-infectious groups. The respiratory virus examination was determined by a liquid bead array xTAG Respiratory Virus Panel in pharyngeal swabs, while bacterial infection was studied by conventional sputum culture. LOS and CAT as well as demographic information were recorded.ResultsViruses were detected in 38 subjects, bacteria in 17, and of these, seven had both. Influenza virus was the most frequently isolated virus, followed by enterovirus/rhinovirus, coronavirus, bocavirus, metapneumovirus, parainfluenza virus types 1, 2, 3, and 4, and respiratory syncytial virus. Bacteriologic analyses of sputum showed that Pseudomonas aeruginosa was the most common bacteria, followed by Acinetobacter baumannii, Klebsiella, Escherichia coli, and Streptococcus pneumoniae. The longest LOS and the highest CAT score were detected in coinfection group. CAT score was positively correlated with LOS.ConclusionRespiratory infection is a common causative agent of exacerbations in COPD. Respiratory coinfection is likely to be a determinant of more severe acute exacerbations with longer LOS. CAT score may be a predictor of longer LOS in AECOPD.

Optimizing multiplex SNP-based data analysis for genotyping of Mycobacterium tuberculosis isolates.

BackgroundMultiplex ligation-dependent probe amplification (MLPA) is a powerful tool to identify genomic polymorphisms. We have previously developed a single nucleotide polymorphism (SNP) and large sequence polymorphisms (LSP)-based MLPA assay using a read out on a liquid bead array to screen for 47 genetic markers in the Mycobacterium tuberculosis genome. In our assay we obtain information regarding the Mycobacterium tuberculosis lineage and drug resistance simultaneously. Previously we called the presence or absence of a genotypic marker based on a threshold signal level. Here we present a more elaborate data analysis method to standardize and streamline the interpretation of data generated by MLPA. The new data analysis method also identifies intermediate signals in addition to classification of signals as positive and negative. Intermediate calls can be informative with respect to identifying the simultaneous presence of sensitive and resistant alleles or infection with multiple different Mycobacterium tuberculosis strains.ResultsTo validate our analysis method 100 DNA isolates of Mycobacterium tuberculosis extracted from cultured patient material collected at the National TB Reference Laboratory of the National Center for Tuberculosis and Lung Diseases in Tbilisi, Republic of Georgia were tested by MLPA. The data generated were interpreted blindly and then compared to results obtained by reference methods. MLPA profiles containing intermediate calls are flagged for expert review whereas the majority of profiles, not containing intermediate calls, were called automatically. No intermediate signals were identified in 74/100 isolates and in the remaining 26 isolates at least one genetic marker produced an intermediate signal.ConclusionBased on excellent agreement with the reference methods we conclude that the new data analysis method performed well. The streamlined data processing and standardized data interpretation allows the comparison of the Mycobacterium tuberculosis MLPA results between different experiments. All together this will facilitate the implementation of the MLPA assay in different settings.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-572) contains supplementary material, which is available to authorized users.

A Multiplex Technology Platform for the Rapid Analysis of Clinically Actionable Genetic Alterations and Validation for BRAF p.V600E Detection in 1549 Cytologic and Histologic Specimens

Current clinicopathologic assessment of malignant neoplastic diseases entails the analysis of specific genetic alterations that provide diagnostic, prognostic, or therapy-determining information. To develop and validate a robust molecular method to detect clinically relevant mutations in various tissue types and anatomic pathology specimens. Genes of interest were amplified by multiplex polymerase chain reaction and sequence variants identified by liquid bead array cytometry. The BRAF assay was fully characterized by using plasmids and genomic DNA extracted from cell lines, metastatic colorectal cancer formalin-fixed, paraffin-embedded (FFPE) tissues, and thyroid nodule fine-needle aspirates. Qualitative multiplex assays for 22 different mutations in the BRAF, HRAS, KRAS, NRAS, or EGFR genes were established. The high signal-to-noise ratio of the technology enabled reproducible detection of BRAF c.1799T>A (p.V600E) at 0.5% mutant allele in 20 ng of genomic DNA. Precision studies with multiple operators and instruments showed very high repeatability and reproducibility with 100% (98.7%-100%) qualitative agreement among 292 individual measures in 38 runs. Evaluation of 1549 representative pathologic specimens in 2 laboratories relative to independent reference methods resulted in 99.0% (97.6%-99.6%) agreement for colorectal FFPE tissues (n = 416) and 98.9% (98.2%-99.4%) for thyroid fine-needle aspiration specimens (n = 1133) with an overall diagnostic odds ratio of 10 856 (2451-48 078). The multiplex assay system is a sensitive and reliable method to detect BRAF c.1799T>A mutation in colorectal and thyroid lesions. This optimized technology platform is suitable for the rapid analysis of clinically actionable genetic alterations in cytologic and histologic specimens.

Clinical evaluation of microRNA expression profiling in non small cell lung cancer

Deregulation of miRNAs expression levels has been detected in many human tumor types, and recent studies have demonstrated the critical roles of miRNAs in cancer pathogenesis. Numerous recent studies have shown that miRNAs are rapidly released from tissues into the circulation in many pathological conditions. The high relative stability of miRNAs in biofluids such as plasma and serum, and the ability of miRNA expression profiles to accurately classify discrete tissue types and disease states have positioned miRNAs as promising non-invasive new tumor biomarkers. In this study, we used liquid bead array technology (Luminex) to profile the expression of 320 mature miRNAs in a pilot testing group of 19 matched fresh frozen cancerous and non-cancerous tissues from NSCLC patients. We further validated our results by RT-qPCR for differentially expressed miRNAs in an independent group of 40 matched fresh frozen tissues, 37 plasma samples from NSCLC patients and 28 healthy donors.We found that eight miRNAs (miR-21, miR-30d, miR-451, miR-10a, miR-30e-5p and miR-126*, miR-126, miR-145) were differentially expressed by three different statistical analysis approaches. Two of them (miR-10a and miR-30e-5p) are reported here for the first time. Bead-array results were further verified in an independent group of 40 matched fresh frozen tissues by RT-qPCR. According to RT-qPCR miR-21 was significantly up-regulated (P=0.010), miR-126* (P=0.002), miR-30d (P=0.012), miR-30e-5p (P<0.001) and miR-451 (P<0.001) were down-regulated, while miR-10a was not differentiated (P=0.732) in NSCLC tissues. However, in NSCLC plasma samples, only three of these miRNAs (miR-21, miR-10a, and miR-30e-5p) displayed differential expression when compared to plasma of healthy donors. High expression of miR-21 was associated with DFI and OS both in NSCLC tissues (P=0.022 and P=0.037) and plasma (P=0.045 and P=0.065), respectively. Moreover, we report for the first time that low expression of miR-10a in NSCLC plasma samples was associated with worse DFI (P=0.050) and high expression of miR-30e-5p was found to be associated with shorter OS (P=0.048). In conclusion, circulating miR-21, miR-10a and miR-30e-5p in plasma should be further evaluated as potential non-invasive biomarkers in NSCLC.

Development and primary application of a fluorescent liquid bead array for the simultaneous identification of multiple genetically modified maize

An integration event-specific fluorescent liquid bead array was developed for the simultaneous identification of 10 genetically modified (GM) maize, including Bt176, Bt11, MON810, NK603, GA21, MON88017, MON89034, MIR604, T25 and MIR162, as well as one non-GM maize. The system comprised 11 specific oligonucleotide probes labeled with an amino group and coupled to fluorescence-encoded microspheres. To enable fluorescence detection, 11 pairs of primers labeled with biotin at the 5′ ends were used. The hybridization signal of biotinylated PCR product to the probe-coupled microspheres was then detected. The limit of detection of this assay was 0.1% for GM maize, which is lower than the current labeling threshold levels enforced in the EU (0.9%). The results of the positive and negative controls were consistent with their expected situation, which showed that the method was highly specific. We detected GM maize in 20 of the 1370 commercial food samples tested, which were labeled as containing maize. The overall sensitivity, specificity, rapidity and high throughput capacity of this liquid chip system suggest that it could provide a significant improvement over current methods, and potentially offer an improved platform for further research into the detection of other GM plants.

Abstract 1462: Development of a multiplexed RT-PCR-coupled liquid bead array assay for the molecular characterization of CTCs.

Abstract Introduction. The presence of circulating tumor cells (CTCs) in patients’ bloodstream is responsible for hematogenous metastases and as a “liquid biopsy” these cells should be considered as a useful tool for the detection and the characterization of micrometastasis. Molecular characterization of CTCs is really helpful for diagnostic and therapeutic purposes. We recently developed a liquid bead array hybridization assay for studying the expression of 6 genes in CTCs in breast cancer (Markou et al, Clin Chem 2011). The aim of the present study was to expand the potential of this assay by adding more genes of clinical interest in the genes panel. Materials and Methods. We designed and evaluated a multiplexed PCR-coupled liquid bead array for studying simultaneously the expression of 14 genes. We firstly designed in silico primers and capture probes for: a) breast cancer stem cell markers: ALDH1, CD24, CD44, b) EMT markers: SNAIL, TWIST-1 and VIM, c) breast cancer markers: ERBB2, mammaglobin A, MAGEA3, PTEN, d) epithelial markers: CK-19, e) housekeeping genes: PBGD, HPRT1, and PDCD4 as a gene related with apoptosis. The assay is based on the following steps: total RNA isolation, cDNA synthesis, multiplex PCR for 14 genes, biotinylation of multiplex PCR products, hybridization of the biotinylated multiplex PCR products to xMAP microspheres, addition of streptavidin-phycoerythrin and measurement in the Luminex® 100 analyzer. Every single step was optimized in terms of analytical specificity, repeatability and reproducibility using the breast cancer cell lines MCF-7, MDA-MB-231 and SK-BR-3. To evaluate the performance of this assay we used cancer cell lines originated from the following tissues: a. human colon (COLO-205), b. human cervix (HeLa) and c. human mammary gland (T-47D). Results. The total duration of the assay, including hands on work, is approximately 6h. The assay is highly specific for each gene in complex multiplexed formats. Intra-assay CVs (n=3) ranged from 0.2% to 15.3% and inter-assay CVs (n=3) ranged from 1.0% to 18.9%. The developed assay was successfully applied for studying gene expression in COLO-205, HeLa, MCF-7, MDA-MB-231, SK-BR-3 and T-47D cancer cell lines. Conclusions. The previously developed liquid bead array has been successfully expanded including 8 additional gene targets of clinical interest. The developed assay could be applied for the molecular characterization of CTCs, since the expression of 14 genes can be measured simultaneously and reliably, thereby saving precious sample and reducing the costs and time of analysis. The developed assay will be further extended to include additional gene targets. Citation Format: Cleo Parisi, Athina Markou, Areti Strati, Evi Lianidou. Development of a multiplexed RT-PCR-coupled liquid bead array assay for the molecular characterization of CTCs. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1462. doi:10.1158/1538-7445.AM2013-1462

Early Specific Host Response Associated with Starting Effective Tuberculosis Treatment in an Infection Controlled Placebo Controlled Mouse Study

Recently we proposed exploring the potential of treatment stimulated testing as diagnostic method for tuberculosis (TB). An infection controlled placebo controlled mouse study was performed to investigate whether serum cytokine levels changed measurably during the early phase of TB chemotherapy. Serum was collected prior to and during the first 3 weeks of isoniazid (INH) and rifampicin (RIF) chemotherapy, and levels of 23 selected cytokines/chemokines were measured using a liquid bead array. The serum levels of IFNγ, IP-10, MIG, MCP-1, IL-17 and IL-6 were elevated in the TB infected mice compared to non-infected mice at least at 1 time point measured. In infected mice, IFNγ, IP-10, MIG and MCP-1 levels decreased within 7 days of treatment with RIF+INH compared to placebo. Treatment of non-infected mice in the absence of tuberculosis infection had no effect on these cytokines. IL-17 and IL-6 had decreased to baseline in all infected mice prior to the initiation of treatment. This study demonstrates that systemic levels of some cytokines, more specifically IFNγ, IP-10, MIG and MCP-1, rapidly and specifically change upon starting TB chemotherapy only in the presence of infection in a mouse model. Thus, IFNγ, IP-10, MIG and MCP-1 are promising ‘Treat-to-Test’ targets for the diagnosis of TB and deserve further investigation in a study on human TB suspects.

An optimized technology platform for the rapid multiplex molecular analysis of genetic alterations associated with leukemia

Molecular methods play a critical role in the accurate diagnosis of leukemia by complementing morphologic, cytochemical, immunophenotypic, and cytogenetic analyses. We developed a multiplex reverse transcription-polymerase chain reaction (RT-PCR) method combined with liquid bead array cytometry for the rapid detection of genetic alterations associated with leukemia. Fusion transcripts corresponding to the most common recurrent chromosomal translocations were reproducibly detected in as low as 0.1-10 ng of total RNA with an analytical sensitivity of 0.01-1%. Multiday, multilot, multioperator, and multi-instrument precision studies, for a total of 678 independent measures in 46 runs, showed a very high reproducibility with 100% agreement among replicates. Using multiplex panels for four to 20 independent targets, we demonstrate the flexibility of the method to codetect rare splicing isoforms, discriminate among multiple variants generated by unique cytogenetic abnormalities, identify distinct chromosomal partners involved with 11q23 or 17q21 rearrangements, and assess cryptic abnormalities not detectable by standard cytogenetics such as the t(12;21), del(1p32), or NPM1 mutations. Overall, three different internal control transcripts and 34 variants resulting from 18 abnormal chromosomal sites were evaluated. These results underscore the value of the multiplex assay system as a sensitive and reliable technology platform for the characterization of relevant genetic alterations in leukemia.