Global Detection of Proteins by Label-Based Antibody Array.

Because of narrow availability of antibody pairs and potential cross-reactivity between antibodies, the development of sandwich-based antibody arrays which need a pair of antibodies for each target has been restricted to higher density resulting in limited proteomic breadth of detection. Label-based array is one way to overcome this obstacle by directly labeling all targets in samples with fluorescent dyes such as Cy3 and Cy5. The labeled samples are then applied on the antibody array chip composed of capture antibodies. In this chapter, we will introduce this technology including array production and sample detection assay.

Enhanced Protein Profiling Arrays for High-Throughput Quantitative Measurement of Cytokine Expression.

The antibody array has become a powerful technology in recent years and is widely used to detect the expression levels of various proteins such as cytokines, growth factors, chemokines, and angiogenic factors, some of which are involved in cancer progression. In this chapter, we describe a protein array technology called enhanced protein profiling array, which can simultaneously and quantitatively measure the expression levels of a few proteins in hundreds or thousands of samples, and an example of its use is presented.

Methods for Membranes and Other Absorbent Surfaces.

Membrane arrays are a unique array platform option for the detection of multiple analytes or materials simultaneously. Their naturally absorptive properties and near universal use in various laboratory methods make it an excellent source with which to probe multiple factors simultaneously. Any liquid sample type can be probed, from bacterial strains, tissue lysates, secreted proteins, to DNA aptamers. Below, we will describe some considerations in how to print a membrane array and then a specific usage of the membrane arrays as it relates to a sandwich-based antibody array technique for simultaneously detection of secreted proteins in a liquid sample.

Quantitative screening of serum protein biomarkers by reverse phase protein arrays.

Screening biomarkers in serum samples for different diseases has always been of great interest because it presents an early, reliable, and, most importantly, noninvasive means of diagnosis and prognosis. Reverse phase protein arrays (RPPAs) are a high-throughput platform that can measure single or limited sets of proteins from thousands of patients' samples in parallel. They have been widely used for detection of signaling molecules involved in diseases, especially cancers, and related regulation pathways in cell lysates. However, this approach has been difficult to adapt to serum samples. Previously, we developed a sensitive method called the enhanced protein array to quantitatively measure serum protein levels from large numbers of patient samples. Here, we further refine the technology on several fronts: 1. simplifying the experimental procedure; 2. optimizing multiple parameters to make the assay more robust, including the support matrix, signal reporting method, background control, and antibody validation; and 3. establishing a method for more accurate quantification. Using this technology, we quantitatively measured the expression levels of 10 proteins: alpha-fetoprotein (AFP), beta 2 microglobulin (B2M), Carcinoma Antigen 15-3(CA15-3), Carcinoembryonic antigen (CEA), golgi protein 73 (GP73), Growth differentiation factor 15 (GDF15), Human Epididymis Protein 4 (HE4), Insulin Like Growth Factor Binding Protein 2 (IGFBP2), osteopontin (OPN) and Beta-type platelet-derived growth factor receptor (PDGFRB) from serum samples of 132 hepatocellular carcinoma (HCC) patients and 78 healthy volunteers. We found that 6 protein expression levels are significantly increased in HCC patients. Statistical and bioinformatical analysis has revealed decent accuracy rates of individual proteins, ranging from 0.617 (B2M) to 0.908 (AFP) as diagnostic biomarkers to distinguish HCC from healthy controls. The combination of these 6 proteins as a specific HCC signature yielded a higher accuracy of 0.923 using linear discriminant analysis (LDA), logistic regression (LR), random forest (RF) and support vector machine (SVM) predictive model analyses. Our work reveals promise for using reverse phase protein arrays for biomarker discovery and validation in serum samples.

Network-driven plasma proteomics expose molecular changes in the Alzheimer's brain.

BACKGROUND: Biological pathways that significantly contribute to sporadic Alzheimer's disease are largely unknown and cannot be observed directly. Cognitive symptoms appear only decades after the molecular disease onset, further complicating analyses. As a consequence, molecular research is often restricted to late-stage post-mortem studies of brain tissue. However, the disease process is expected to trigger numerous cellular signaling pathways and modulate the local and systemic environment, and resulting changes in secreted signaling molecules carry information about otherwise inaccessible pathological processes. RESULTS: To access this information we probed relative levels of close to 600 secreted signaling proteins from patients' blood samples using antibody microarrays and mapped disease-specific molecular networks. Using these networks as seeds we then employed independent genome and transcriptome data sets to corroborate potential pathogenic pathways. CONCLUSIONS: We identified Growth-Differentiation Factor (GDF) signaling as a novel Alzheimer's disease-relevant pathway supported by in vivo and in vitro follow-up experiments, demonstrating the existence of a highly informative link between cellular pathology and changes in circulatory signaling proteins.

Protein expression profiling by antibody array analysis with use of dried blood spot samples on filter paper.

Dried blood spot samples (DBSS) on filter paper offer several advantages compared to conventional serum/plasma samples: they do not require any phlebotomy or separation of blood by centrifugation; they are less invasive; they allow sample stability and shipment at room temperature; and they pose a negligible risk of infection with blood-borne viruses, such as HIV, HBV and HCV, to those who handle them. Therefore dried blood spot samples (DBSS) on filter paper can be a quick, convenient and inexpensive means of obtaining blood samples for biomarker discovery, disease screening, diagnosis and treatment monitoring in non-hospitalized, public health settings. In this study, we investigated for the first time the potential application of dried blood spot samples (DBSS) in protein expression profiling using antibody array technology. First, optimal conditions for array assay performance using dried blood spot samples (DBSS) was established, including sample elution buffer, elution time, elution temperature and assay blocking buffer. Second, we analyzed dried blood spot samples (DBSS) using three distinct antibody array platforms, including sandwich-based antibody arrays, quantitative antibody arrays and biotin-label-based antibody arrays. In comparison with paired serum samples, detection of circulating proteins in dried blood spot samples (DBSS) correlated well for both low- and high-abundance proteins on all three antibody array platforms. In conclusion, our study strongly indicates the novel application of multiplex antibody array platforms to analyze dried blood spot samples (DBSS) on filter paper represents a viable, cost-effective method for protein profiling, biomarker discovery and disease screening in a large, population-based survey.

Identification of five serum protein markers for detection of ovarian cancer by antibody arrays.

BACKGROUND: Protein and antibody arrays have emerged as a promising technology to study protein expression and protein function in a high-throughput manner. These arrays also represent a new opportunity to profile protein expression levels in cancer patients' samples and to identify useful biosignatures for clinical diagnosis, disease classification, prediction, drug development and patient care. We applied antibody arrays to discover a panel of proteins which may serve as biomarkers to distinguish between patients with ovarian cancer and normal controls. METHODOLOGY/PRINCIPAL FINDINGS: Using a case-control study design of 34 ovarian cancer patients and 53 age-matched healthy controls, we profiled the expression levels of 174 proteins using antibody array technology and determined the CA125 level using ELISA. The expression levels of those proteins were analyzed using 3 discriminant methods, including artificial neural network, classification tree and split-point score analysis. A panel of 5 serum protein markers (MSP-alpha, TIMP-4, PDGF-R alpha, and OPG and CA125) was identified, which could effectively detect ovarian cancer with high specificity (95%) and high sensitivity (100%), with AUC =0.98, while CA125 alone had an AUC of 0.87. CONCLUSIONS/SIGNIFICANCE: Our pilot study has shown the promising set of 5 serum markers for ovarian cancer detection.

Enhanced chemosensitization in multidrug-resistant human breast cancer cells by inhibition of IL-6 and IL-8 production.

Drug resistance remains a major hurdle to successful cancer treatment. Many mechanisms such as overexpression of multidrug-resistance related proteins, increased drug metabolism, decreased apoptosis, and impairment of signal transduction pathway can contribute multidrug resistance (MDR). Recent studies strongly suggest a close link between cytokines and drug resistance. To identify new targets involved in drug resistance, we established a multidrug-resistant human breast cancer cell line MCF-7/R and examined the cytokine profile using cytokine antibody array technology. Among 120 cytokines/chemokines screened, IL-6, IL-8, and 13 other proteins were found to be markedly increased in drug-resistant MCF-7/R cell line as compared to sensitive MCF-7/S cell line, while 7 proteins were specifically reduced in drug-resistant MCF-7/R cells. Neutralizing antibodies against IL-6 and IL-8 partially reversed the drug resistance of MCF-7/R to paclitaxel and doxorubicin, while a neutralizing antibody against MCP-1 had no significant effect. Inhibition of endogenous IL-6 or IL-8 by siRNA technology significantly enhanced drug sensitivity of MCF-7/R cells. Furthermore, overexpression of IL-6 or IL-8 expression by transfection increased the ADM resistance in MCF-7/S cells. Our data suggest that increased expression levels of IL-6 and IL-8 may contribute to MDR in human breast cancer cells.

A biotin label-based antibody array for high-content profiling of protein expression.

BACKGROUND/AIM: Profiling protein expression on a global scale will have significant impact on biomedical research, particularly in the discovery and development of drugs and biomarkers. Through the years, several antibody array systems have been invented and developed for multiple protein detection. However, a reliable and high-content system for protein profiling from many biological samples has yet been developed. This study aimed to develop a reliable, easy to use and cost effective method to profile protein expression levels in high-content manner with sufficient sensitivity and specificity. MATERIALS AND METHODS: To address this problem, a high density antibody array was developed and used this technology to uncover the potential biomarkers of ovarian cancer. In this system, biological samples are labeled with biotin. The biotinylated proteins are then incubated with antibody chips. The presence of proteins captured by the antibody chip is detected using streptavidin-conjugated fluorescent dye (Cy3 equivalent) as a reporter. The signals, which are visualized by laser scanning, are normalized using positive, negative, and internal controls. RESULTS: Using this biotin label-based antibody array technology, the expression levels of 507 human, 308 mouse and 90 rat target proteins can be simultaneously detected, including of cytokines, chemokines, adipokines, growth factors, angiogenic factors, proteases, soluble receptors, soluble adhesion molecules, and other proteins in a variety of samples. Most proteins can be detected at pg/ml and ng/ml levels, with a coefficient of variation of less than 20%. Using human biotin-based antibody arrays, we screened the serum expression profiles of 507 proteins in ovarian cancer patients and healthy individuals. A panel of protein expression showed significant difference between normal and cancer samples (p<0.05). By classification analysis and split-point score analysis of these two groups, a small group of proteins were found to be useful in distinguishing ovarian cancer patients from normal subjects. CONCLUSION: Our results suggest the biotin label-based antibody arrays that we have developed have great potential in applications for biomarker discovery.

Concurrent down-regulation of Egr-1 and gelsolin in the majority of human breast cancer cells.

UNLABELLED: A growing body of evidence suggests that early growth response-1 (Egr-1), a transcription factor, may function as a tumor suppressor. The aim of this study was to gain more evidence to support the role of Egr-1 in the suppression of cancer cell growth and to examine the potential correlation between Egr-1 and gelsolin. MATERIALS AND METHODS: Histochemical staining coupled with breast cancer tissue arrays were used to examine the expression levels of Egr-1 and gelsolin. Reporter assays and gel shift were used to study the transcriptional activity of Egr-1 on the regulation of gelsolin. RESULTS: Our data showed that most normal mammary tissues expressed high levels of Egr-1, while the majority of breast cancer tissues expressed very small amounts of Egr-1. The expression pattern of Egr-1 in human breast cancer tissues was highly correlated with gelsolin expression. Induction of Egr-1 by serum stimulation accompanied the increase of gelsolin expression. In cells lacking the induction of Egr-1 in response to serum stimulation, gelsolin expression remained unchanged. Furthermore, gelsolin promoter activity was profoundly reduced in Egr-1 null mouse embryonic fibroblasts compared to Egr-1 wild-type mouse embryonic fibroblasts. Gel shift experiments indicated that Egr-1 can directly bind to the gelsolin promoter. CONCLUSION: Our results suggest that Egr-1 may be an important breast cancer marker and that an as yet uncharacterized pathway involved in Egr-1 and gelsolin expression exists which leads to breast cancer cell development.

Early Growth Response-1 Suppresses Human Fibrosarcoma Cell Invasion and Angiogenesis.

The development of malignant tumors is the result of sequential genetic and epigenetic lesions that lead to alterations in a number of gene expressions, which are primarily controlled by transcription factors. A growing body of evidence suggests that early growth response-1 (Egr-1), a transcription factor, may function as a tumor suppressor. Here, the possible role of Egr-1 in the suppression of tumor cell invasion, angiogenesis and metastasis was investigated. Expression of Egr-1 significantly reduced the invasion of human fibrosarcoma cells through matrigel. Mouse embryonic fibroblasts, from Egr-1 knockout mice, also showed increased invasion through matrigel compared with MEFs from wild-type mice. Conditioned medium from Egr-1-transfected cells compared with control transfected cells also reduced proliferation, invasion through matrigel and tube formation of human umbilical cord vein endothelial cells and human microvascular endothelial cells. In addition, Egr-1-transfected cells inhibited vessel formation in mouse skin plug assays. To study the possible molecular mechanisms responsible for this function, the expression of multiple cytokines, chemokines, growth factors and angiogenic factors were examined by using human cytokine antibody array technology it was observed that tissue inhibitor of metalloproteinase-2 (TIMP-2) expression was up-regulated in Egr-1-transfected cells. Addition of Egr-1-transfected cell conditioned medium and TIMP-2 recombinant protein suppressed fibrosarcoma cell invasion. In summary, it was shown that Egr-1 may have novel functions in the suppression of tumor cell invasion and angiogenesis, while TIMP-2 may be involved in the suppression of tumor cell invasion and angiogenesis in Egr-1-transfected cells.

Enhanced protein profiling arrays for quantitative measurement of protein expression in multiple samples.

Simultaneous measurement of molecules from many samples is particularly useful for screening of certain molecules from different samples, for targeting verification of results obtained from protein and cDNA arrays, and for molecular epidemiology-based investigations. Described herein is a sensitive and quantitative approach, referred to as enhanced protein profiling arrays, that measures molecular expression levels from numerous samples. Enhanced protein profiling arrays can easily be constructed from tissue lysates, cell lysates, conditioned media, and body fluids, along with standard proteins and appropriate controls onto antibody-coated surfaces of solid supports. Coupled with many common detection techniques, the expression levels of certain molecules can be determined quantitatively. An account of the successful development and application of this enhanced protein profiling array technology is presented.

The promise of cytokine antibody arrays in the drug discovery process.

The introduction of cytokine antibody arrays has added a new approach for investigators to simultaneously measure multiple cytokine levels in biological samples. Several different platforms have been developed. The ability to measure hundreds of cytokine levels with high specificity and sensitivity within a very limited amount of samples is a powerful tool. Many investigators worldwide have applied this novel technology in their biomedical research, particularly in drug discovery. Undoubtedly, the technology will continue to be improved and the application increased in the next several years.

Identification of interleukin-8 as estrogen receptor-regulated factor involved in breast cancer invasion and angiogenesis by protein arrays.

With the goal of identifying key factors involved in human breast cancer progression, we applied human cytokine antibody arrays we have developed to screen cytokine expression levels in human breast cancer cell lines and identified interleukin (IL)-8 as a key factor involved in breast cancer invasion and angiogenesis. Elevated expression of IL-8 in breast cancer cells was associated with breast cancer invasiveness and angiogenesis. Neutralization of antibody against IL-8 specifically blocked IL-8-mediated tumor cell invasion and angiogenesis. Furthermore, IL-8 levels in human breast cancer cells were closely related to estrogen receptor (ER) status. ER positive cells expressed low levels of IL-8 whereas ER negative cells expressed high levels of IL-8. Expression of exogenous ERalpha substantially inhibited IL-8 expression. Our findings raise intriguing questions regarding the role of IL-8 in the development and progression of human breast cancer in association with ER status.

Enhanced protein profiling arrays with ELISA-based amplification for high-throughput molecular changes of tumor patients' plasma.

PURPOSE: The purpose of this study is to develop a high-throughput approach to detect protein expression from hundreds and thousands of samples and to apply this technology to profile circulating angiogenic factor protein levels in patients with gynecological tumors. EXPERIMENTAL DESIGN: Analytes containing a mixture of protein are immobilized onto antibody-coated surface of support in array format. The presence of protein in analytes is detected with biotin-labeled antibody coupled with an enhanced chemiluminescence or fluorescence detection system. The exact amount of protein can be quantitatively measured. The expression levels of five angiogenic factors (angiogenin, interleukin 8, vascular endothelial growth factor, platelet-derived growth factor, and epidermal growth factor) from 157 samples were quantitatively measured using this novel protein array technology and were statistically analyzed. The expression patterns of angiogenic factors were analyzed using two-way hierarchical cluster analysis approach. RESULTS: A novel protein array technology, which can simultaneously and quantitatively measure few protein levels from hundreds and thousands of samples was developed. Only minute amounts of sample are required for the assay. This approach also features high sensitivity and specificity. Using this novel protein array approach, we analyzed the plasma expression levels of five angiogenic factors in 137 patients diagnosed with a tumor and 20 controls. Statistical analysis reveals different expression levels of angiogenic factors between patients and controls. Cluster analysis suggests a possible classification of normal subjects from patients. CONCLUSIONS: Enhanced protein profiling arrays provide a high-throughput and sensitive system to detect one or few protein from hundreds and thousands of samples. Such an approach should have broad application in biomedical discovery.

Molecular Profiling of Circulating Cytokine Levels in Human Ovarian Cancer Patients.

BACKGROUND: Growing evidence suggests that cytokines not only are associated with ovarian cancer development, drug resistance and metastasis, but also may provide valuable markers for ovarian cancer diagnosis and prognosis. Here, we determined the expression profiles of 43 plasma cytokines in ovarian cancer patients using this high throughput protein array technology developed in our laboratory. MATERIALS AND METHODS: The expression of 43 cytokines from 13 ovarian cancer patients and 12 normal women was determined simultaneously using human cytokine antibody microarray technology. The differential expression of cytokines was analyzed using the Student's t-test and two-way hierarchical cluster analysis approach. RESULTS: Our data showed that 22 cytokines were significantly increased in the plasma of ovarian cancer patients compared to normal women (t-test, two-tailed, p<0.05). The results from cytokine antibody array assays were in agreement with the published data, but also revealed a new group of cytokines whose expression levels were altered in ovarian cancer. Cluster analysis suggested an interesting link between cytokine profile and ovarian cancer. CONCLUSION: Human cytokine antibody arrays are a valuable tool to profile cytokine expression from patients' specimen. The cytokine profile may prove to be of diagnostic and prognostic significance in ovarian cancer.

Profiling of cytokine expression by biotin-labeled-based protein arrays.

Global analysis of protein expression holds great promise in basic research and patient care. Previously we demonstrated that multiple cytokines could be detected simultaneously using an enzyme-linked immunosorbent assay protein array system with high sensitivity and specificity. In this paper, we described a biotin-labeled-based protein array system to detect multiple cytokines simultaneously from biological samples. In this new approach, proteins from a variety of biological sources are labeled with biotin. The biotin-labeled proteins are then incubated with antibody chips. Targeted proteins are captured by the array antibodies spotted on the antibody chips. The presence of targeted proteins is detected using Cy3- or Cy5-conjugated streptavidin and signals are imaged by laser scanner. The system also can be easily adapted to a two-color binding assay, allowing measurement of the levels of proteins in a test sample with respect to a reference sample at the same chip. To demonstrate its potential applications, we applied this technology to profile human cytokines, chemokines, growth factors, angiogenic factors and proteases in estrogen receptor (ER)+ and ER- cells. These results suggest that biotin-labeled-based antibody chip technology can provide a practical and powerful means of profiling hundreds or thousands of proteins for research and clinical purposes.

Detection of multiple cytokines by protein arrays from cell lysate and tissue lysate.

Previously we demonstrated that multiple cytokines could be simultaneously detected using an antibody-based protein array system with high sensitivity and specificity from conditioned medium and serum. Here, we created a higher density array system to simultaneously detect 35 cytokines from cell lysates and tissue lysates. This assay combines the advantages of the specificity of enzyme-linked immunosorbent assays (ELISA), sensitivity of enhanced chemiluminescence (ECL), and high-throughput of microspot. In this system, capture antibodies dissolved in methanol were spotted onto polyvinylidene difluoride (PVDF) membranes. The membranes were then incubated with tissue lysates or cell lysates. After removing unbound proteins by extensive washing, the membranes were exposed to horseradish peroxidase (HRP)-conjugated antibody(ies). The signals were visualized with an ECL system. High specificity, sensitivity, and accuracy of this approach were demonstrated. This approach can be used in any general laboratory setting without any sophisticated equipment. It should be feasible to extend this concept to develop a high-throughput protein array system. Combining nitrocellulose membrane-based and PVDF membrane-based approaches, the human cytokine array system can be applied to detect multiple cytokine expression from cell lysate, tissue lysate, serum, plasma, and conditioned medium. Future applications of this new approach include direct protein expression profiling, immunological disease diagnostics, and discovery of new biomarkers.

Profiling of human cytokines in healthy individuals with vitamin E supplementation by antibody array.

Previously, we demonstrated that vitamin E supplementation decreases autoantibodies to oxidized lipid-protein complexes (J. Med. Food 1 (2000) 247). Utilizing an in vitro modeling system, we also demonstrated that vitamin E blocks the tumor promotion process in liver epithelial cells (Carcinogenesis 20 (1999) 485 and Mol. Carcinog. 30 (2001) 209). To investigate the molecular mechanisms of vitamin E function, we developed a human cytokine array system that is capable of detecting the expression of 35 cytokines simultaneously. Using this new technology, we analyzed the potential vitamin E-regulated cytokines in vitamin E supplementation individuals. The cytokine arrays showed that expression of several cytokines, particularly monocyte chemoattractant protein-1 (MCP-1), was profoundly reduced in vitamin E supplementation individuals. Moreover, addition of vitamin E to several cultured cells significantly down-regulated the expression of MCP-1. Our results suggested that MCP-1 may be one of the most important targets of antioxidant vitamin E. To the best of our knowledge, this is the first report describing the down-regulation of MCP-1 in vitamin E supplementation in vivo.