Enhanced Protein Profiling Arrays with ELISA-Based Amplification for High-Throughput Molecular Changes of Tumor Patients’ Plasma

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.

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.

Biosensors in Health Care: The Milestones Achieved in Their Development towards Lab-on-Chip-Analysis

Immense potentiality of biosensors in medical diagnostics has driven scientists in evolution of biosensor technologies and innovating newer tools in time. The cornerstone of the popularity of biosensors in sensing wide range of biomolecules in medical diagnostics is due to their simplicity in operation, higher sensitivity, ability to perform multiplex analysis, and capability to be integrated with different function by the same chip. There remains a huge challenge to meet the demands of performance and yield to its simplicity and affordability. Ultimate goal stands for providing point-of-care testing facility to the remote areas worldwide, particularly the developing countries. It entails continuous development in technology towards multiplexing ability, fabrication, and miniaturization of biosensor devices so that they can provide lab-on-chip-analysis systems to the community.

The anti-diabetic drug metformin inhibits vascular endothelial growth factor expression via the mammalian target of rapamycin complex 1/hypoxia-inducible factor-1α signaling pathway in ELT-3 cells

The aim of this study was to elucidate whether metformin can regulate the expression of vascular endothelial growth factor (VEGF) in rat-derived uterine leiomyoma cells (ELT-3 cells). In vitro studies were conducted using ELT-3 cells. Under normoxic conditions, metformin suppressed VEGF protein levels in the supernatant and cells in a dose-dependent manner. In hypoxia-mimicking conditions, VEGF and hypoxia-inducible factor-1α (HIF-1α) proteins were both highly expressed and were suppressed by the metformin treatment. Metformin did not affect HIF-1α mRNA levels, which indicated that its effects occurred at the post-translational level. Metformin inhibited mammalian target of rapamycin complex 1 (mTORC1) activity by phosphorylating the mTORC1 component raptor. This study revealed the anti-angiogenic activity of metformin in ELT-3 cells by suppressing the expression of VEGF via the mTORC1/HIF-1α pathway. These results indicate that metformin may represent an effective alternative in the future treatment of uterine leiomyomas.

An array of possibilities in cancer research using cytokine antibody arrays

Protein arrays have shown potential applications in cancer research. After several decades of research, it has become evident that many cytokines are central to the development of cancer and its treatment. Cytokine antibody arrays that have been designed to simultaneously detect multiple cytokines are not only available, but show a diversity of applications in the study of many diseases in addition to cancer. This review will focus on the implementation of cytokine antibody arrays in many aspects of cancer research, such as biomarker discovery, molecular mechanisms of cancer development, preclinical studies and the effects of cancer compounds.

The application of monoclonal antibodies in cancer diagnosis

Cancer becomes the second leading cause of death in the world. An effective strategy for early diagnosis of the disease is key to reduce the mortality and morbidity. Development of effective monoclonal antibody (mAb)-based assays or diagnostic imaging techniques for detection of antigens and small molecules that are released from cancerous cells will enhance modern diagnostic medicine of cancer significantly. Although mAb technology is still under development, recent advances in preparation of recombinant antigen and antibody engineering techniques have dramatically enhanced the applications of this technology in cancer diagnosis. Compared with other methods, mAb-based assays may provide spatial, temporal, accurate and quantitative measurement for diagnosis of the disease. This review summarizes the progress of the mAb-based assays in the field of molecular diagnosis of cancer.

Discovery of cancer biomarkers using antibody arrays

BACKGROUND

The cancer biomarkers field is being enriched by molecular profiling obtained by high-throughput approaches. In the context of other proteomic technologies, targeted antibody arrays are contributing strongly to the identification of protein cancer biomarker candidates.

OBJECTIVE

To describe innovative strategies multiplexing protein measurements of protein extracts of cultured cells, tissue and body fluids using antibody arrays that, combined with appropriate validation approaches, are enabling the discovery of cancer-associated biomarkers.

METHOD

The strategies and cancer biomarker candidates identified using antibody arrays reported so far that may assist in the diagnosis, surveillance and prognosis, and potentially for predictive and therapeutic purposes for patients affected with solid and hematological neoplasias.

RESULTS/CONCLUSION

Owing to their versatility, novel technological and experimental design implementations are broadening the applications of antibody arrays also for biomarker discovery. However, the cancer biomarker candidates delivered so far using this technology are still at an early developmental phase, requiring validation with many specimens focusing on specific clinical end points.

Antibody microarrays as tools for biomarker discovery

The cancer biomarkers field is being enriched by molecular profiling obtained by high-throughput approaches. Targeted antibody arrays are strongly contributing to the identification of protein cancer -biomarker candidates and functional proteomic analyses. Due to their versatility, novel technological and experimental design implementations are broadening the applications of antibody arrays. However, the cancer biomarker candidates delivered to date using this technology are still in their early developmental phase, requiring validation with high number of specimens focusing on specific clinical endpoints. Innovative strategies multiplexing protein measurements of protein extracts of cultured cells, tissue and body fluids using antibody arrays combined with appropriate validation approaches are enabling the -discovery of cancer-associated biomarkers. This review describes these strategies and cancer biomarker candidates reported to date that may assist in the diagnosis, surveillance, prognosis, and potentially for predictive and therapeutic purposes for patients affected with solid and hematological neoplasias.

Up-regulated proteins in the fluid bathing the tumour cell microenvironment as potential serological markers for early detection of cancer of the breast

Breast cancer is by far the most common diagnosed form of cancer and the leading cause of cancer death in women today. Clinically useful biomarkers for early detection of breast cancer could lead to a significant reduction in mortality. Here we describe a detailed analysis using gel-based proteomics in combination with mass spectrometry and immunohistochemistry (IHC) of the tumour interstitial fluids (TIF) and normal interstitial fluids (NIF) collected from 69 prospective breast cancer patients. The goal of this study was to identify abundant cancer up-regulated proteins that are externalised by cells in the tumour microenvironment of most if not all these lesions. To this end, we applied a phased biomarker discovery research strategy to the analysis of these samples rather than comparing all samples among each other, with inherent inter and intra-sample variability problems. To this end, we chose to use samples derived from a single tumour/benign tissue pair (patient 46, triple negative tumour), for which we had well-matched samples in terms of epithelial cell numbers, to generate the initial dataset. In this first phase we found 110 proteins that were up-regulated by a factor of 2 or more in the TIF, some of which were confirmed by IHC. In the second phase, we carried out a systematic computer assisted analysis of the 2D gels of the remaining 68 TIF samples in order to identify TIF 46 up-regulated proteins that were deregulated in 90% or more of all the available TIFs, thus representing common breast cancer markers. This second phase singled out a set of 26 breast cancer markers, most of which were also identified by a complementary analysis using LC-MS/MS. The expression of calreticulin, cellular retinoic acid-binding protein II, chloride intracellular channel protein 1, EF-1-beta, galectin 1, peroxiredoxin-2, platelet-derived endothelial cell growth factor, protein disulfide isomerase and ubiquitin carboxyl-terminal hydrolase 5 were further validated using a tissue microarray containing 70 malignant breast carcinomas of various grades of atypia. A significant number of these proteins have already been detected in the blood/plasma/secretome by others. The next steps, which include biomarker prioritization based on the hierarchal evaluation of these markers, antibody and antigen development, assay development, analytical validation, and preliminary testing in the blood of healthy and breast cancer patients, are discussed.

Elevated level of plasma vascular endothelial growth factor after gonadotropin-releasing hormone agonist treatment for leiomyomata

OBJECTIVE

Uterine leiomyomata are the most common gynecological benign tumor and greatly affect reproductive health and well-being. The pathophysiology and epidemiology of fibroids are poorly understood. Gonadotropin-releasing hormone agonist (GnRH-a) pretreatment is one of the unfavourable factors for leiomyomata treatment with uterine artery embolisation (UAE). In this study, we investigated the plasma level of vascular endothelial growth factor (VEGF) in uterine leiomyoma patients with or without GnRH-a pretreatment.

STUDY DESIGN

Thirty-two women who underwent UAE for symptomatic uterine leiomyoma were analysed. The plasma level of VEGF was studied before UAE.

RESULTS

The level of plasma VEGF was significantly higher in the GnRH-a pretreated group compared with the non-treated group.

CONCLUSION

A compensative reaction for vasculature after GnRH-a treatment is speculated. Higher level of VEGF in GnRH-a pretreatment group could be one of the unfavourable factors for the treatment of uterine leiomyomata by UAE.

Biosensor technology: technology push versus market pull

Biosensor technology is based on a specific biological recognition element in combination with a transducer for signal processing. Since its inception, biosensors have been expected to play a significant analytical role in medicine, agriculture, food safety, homeland security, environmental and industrial monitoring. However, the commercialization of biosensor technology has significantly lagged behind the research output as reflected by a plethora of publications and patenting activities. The rationale behind the slow and limited technology transfer could be attributed to cost considerations and some key technical barriers. Analytical chemistry has changed considerably, driven by automation, miniaturization, and system integration with high throughput for multiple tasks. Such requirements pose a great challenge in biosensor technology which is often designed to detect one single or a few target analytes. Successful biosensors must be versatile to support interchangeable biorecognition elements, and in addition miniaturization must be feasible to allow automation for parallel sensing with ease of operation at a competitive cost. A significant upfront investment in research and development is a prerequisite in the commercialization of biosensors. The progress in such endeavors is incremental with limited success, thus, the market entry for a new venture is very difficult unless a niche product can be developed with a considerable market volume.

Dissecting cancer serum protein profiles using antibody arrays

Antibody arrays represent one of the high-throughput techniques enabling detection of multiple proteins simultaneously. One of the main advantages of the technology over other proteomic approaches resides on that the identities of the measured proteins are known at front of the experimental design or can be readily characterized, facilitating a biological interpretation of the obtained results. This chapter overviews the technical issues of the main antibody array formats as well as various applications using serum specimens in the context of neoplastic diseases. Clinical applications of antibody arrays vary from biomarker discovery for diagnosis, prognosis, and drug response to characterization of s protein pathways and modification changes associated with disease development and progression. As a high-throughput tool addressing protein levels and post-translational modifications, it improves the functional characterization of molecular bases for cancer. Furthermore, the identification and validation of protein expression patterns characteristic of cancer progression and tumor subtypes may enable tailored therapeutic intervention and improvement in the clinical management of cancer patients. Technical requirements such as lower sample volume, antibody concentration, format versatility, and high reproducibility support their increasing impact in cancer research.

Mass spectrometry-based "omics" technologies in cancer diagnostics

Many "omics" techniques have been developed for one goal: biomarker discovery and early diagnosis of human cancers. A comprehensive review of mass spectrometry-based "omics" approaches performed on various biological samples for molecular diagnosis of human cancers is presented in this article. Furthermore, the existing and potential problems/solutions (both de facto experimental and bioinformatic challenges), and future prospects have been extensively discussed. Although the use of present omic methods as diagnostic tools are still in their infant stage and consequently not ready for immediate clinical use, it can be envisaged that the "omics"-based cancer diagnostics will gradually enter into the clinic in next 10 years as an important supplement to current clinical diagnostics.

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.

Antibody Arrays: Technical Considerations and Clinical Applications in Cancer

Antibody arrays represent one of the high-throughput techniques that are able to detect multiple proteins simultaneously. One of the main advantages of this technology over other proteomic approaches is that the identities of the measured proteins are known or can be readily characterized, allowing a biological interpretation of the results. Features such as lower sample volume and antibody concentration requirements, higher format versatility, and reproducibility support the increasing use of antibody arrays in cancer research. Clinical applications include disease marker discovery for diagnosis, prognosis, and drug response, characterization of signaling and protein pathways, and modifications associated with disease development and progression. This report presents an overview of technical issues of the main antibody array formats and various applications in cancer research. Antibody arrays are high-throughput tools that improve the functional characterization of molecular bases for disease. Furthermore, identification and validation of protein expression patterns, characteristic of cancer progression, and tumor subtypes may intervene and improve tailored therapies in the clinical management of cancer patients.

Angiogenin: a review of the pathophysiology and potential clinical applications

Angiogenin is a member of the ribonuclease (RNase) superfamily: enzymes of innate substrate specificity, but divergent functional capacities. Angiogenin is a normal constituent of the circulation and contained in a vasculature that rarely undergoes proliferation, but in some physiological and pathological conditions its levels increase in blood, promoting neovascularization. Hence, angiogenesis is a common pathophysiological attribute of angiogenin. In malignant disease, the most studied pathological state in regard to angionenin, abnormally high levels are seen, which may be of prognostic significance. Angiogenin has also been studied in other non-malignant pathological states. The aim of this review article is to provide an overview of the biochemistry and physiology of angiogenin, specifically in relation to the human pathological states where angiogenin has been implicated and finally, its potential clinical applications.

Rarity gives a charm: evaluation of trace proteins in plasma and serum

Since plasma potentially contacts every cell as it circulates through the body, it may carry clues both to diagnosis and treatment of disease. It is commonly expected that the growing ability to detect and characterize trace proteins will result in discovery of novel therapeutics and biomarkers; however, the familiar, super-abundant plasma proteins remain a fundamental stumbling block. Furthermore, robust validation of proteomic data is a sometimes overlooked but always necessary component for the eventual development of clinical reagents. This review surveys some of the uses of typical and atypical low-abundance proteins, current analytical methods, existing impediments to discovery, and some innovations that are overcoming the challenges to evaluation of trace proteins in plasma and serum.

Multiplexed protein measurement: technologies and applications of protein and antibody arrays

The ability to measure the abundance of many proteins precisely and simultaneously in experimental samples is an important, recent advance for static and dynamic, as well as descriptive and predictive, biological research. The value of multiplexed protein measurement is being established in applications such as comprehensive proteomic surveys, studies of protein networks and pathways, validation of genomic discoveries and clinical biomarker development. As standards do not yet exist that bridge all of these applications, the current recommended best practice for validation of results is to approach study design in an iterative process and to integrate data from several measurement technologies. This review describes current and emerging multiplexed protein measurement technologies and their applications, and discusses the remaining challenges in this field.

Changes of plasma vascular endothelial growth factor level after uterine artery embolisation for leiomyomata

Uterine artery embolisation (UAE) has become an alternative treatment for symptomatic uterine leiomyomata. Most reports suggest that it is well tolerated and effective, although there have been no reports of studies of biological parameters after UAE. In this study, we analysed the plasma level of vascular endothelial growth factor (VEGF) and the pulsatility index (PI) of uterine arteries before and after UAE. The level of plasma VEGF increased significantly after UAE (on day 1 and day 3) and decreased on day 7, and then increased again on day 30. The level of VEGF reached a peak value within three days after UAE. A significant inverse correlation was found between uterine artery PI and the level of VEGF on day 30, suggesting that VEGF may have negative effect on the efficacy of treatment of uterine leiomyomata by UAE.

Antibody Microarray Profiling Reveals Individual and Combined Serum Proteins Associated with Pancreatic Cancer

We used antibody microarrays to probe the associations of multiple serum proteins with pancreatic cancer and to explore the use of combined measurements for sample classification. Serum samples from pancreatic cancer patients (n = 61), patients with benign pancreatic disease (n = 31), and healthy control subjects (n = 50) were probed in replicate experiment sets by two-color, rolling circle amplification on microarrays containing 92 antibodies and control proteins. The antibodies that had reproducibly different binding levels between the patient classes revealed different types of alterations, reflecting inflammation (high C-reactive protein, alpha-1-antitrypsin, and serum amyloid A), immune response (high IgA), leakage of cell breakdown products (low plasma gelsolin), and possibly altered vitamin K usage or glucose regulation (high protein-induced vitamin K antagonist-II). The accuracy of the most significant antibody microarray measurements was confirmed through immunoblot and antigen dilution experiments. A logistic-regression algorithm distinguished the cancer samples from the healthy control samples with a 90% and 93% sensitivity and a 90% and 94% specificity in duplicate experiment sets. The cancer samples were distinguished from the benign disease samples with a 95% and 92% sensitivity and an 88% and 74% specificity in duplicate experiment sets. The classification accuracies were significantly improved over those achieved using individual antibodies. This study furthered the development of antibody microarrays for molecular profiling, provided insights into the nature of serum-protein alterations in pancreatic cancer patients, and showed the potential of combined measurements to improve sample classification accuracy.

Antibody arrays in cancer research

Antibody arrays have valuable applications in cancer research. Many different antibody array technologies have been developed, each with particular advantages, disadvantages, and optimal applications. The methods have been demonstrated on various sample types, such as serum, plasma, and other bodily fluids; cell culture supernatants; tissue culture lysates; and resected tumor specimens. The applications to cancer research have included profiling proteins to identify candidate biomarkers, characterizing signaling pathways, and the measurement of changes in modification or expression level of cancer-related proteins. Further innovations in the methods and experimental strategies are broadening the scope of the applications and the type of information that can be gathered. These alternate formats and uses of antibody arrays include arrays to measure whole cells, arrays to measure enzyme activities, reverse phase arrays, and bead-based arrays. This article reviews the various types of antibody array methods and their applications to cancer research.