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Microarrays, Volume 4, Issue 2 (June 2015), Pages 98-310

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Research

Jump to: Review

Open AccessArticle Immune-Signatures for Lung Cancer Diagnostics: Evaluation of Protein Microarray Data Normalization Strategies
Microarrays 2015, 4(2), 162-187; doi:10.3390/microarrays4020162
Received: 30 January 2015 / Revised: 23 March 2015 / Accepted: 25 March 2015 / Published: 2 April 2015
Cited by 1 | PDF Full-text (1369 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
New minimal invasive diagnostic methods for early detection of lung cancer are urgently needed. It is known that the immune system responds to tumors with production of tumor-autoantibodies. Protein microarrays are a suitable highly multiplexed platform for identification of autoantibody signatures against tumor-associated
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New minimal invasive diagnostic methods for early detection of lung cancer are urgently needed. It is known that the immune system responds to tumors with production of tumor-autoantibodies. Protein microarrays are a suitable highly multiplexed platform for identification of autoantibody signatures against tumor-associated antigens (TAA). These microarrays can be probed using 0.1 mg immunoglobulin G (IgG), purified from 10 µL of plasma. We used a microarray comprising recombinant proteins derived from 15,417 cDNA clones for the screening of 100 lung cancer samples, including 25 samples of each main histological entity of lung cancer, and 100 controls. Since this number of samples cannot be processed at once, the resulting data showed non-biological variances due to “batch effects”. Our aim was to evaluate quantile normalization, “distance-weighted discrimination” (DWD), and “ComBat” for their effectiveness in data pre-processing for elucidating diagnostic immune‑signatures. “ComBat” data adjustment outperformed the other methods and allowed us to identify classifiers for all lung cancer cases versus controls and small-cell, squamous cell, large-cell, and adenocarcinoma of the lung with an accuracy of 85%, 94%, 96%, 92%, and 83% (sensitivity of 0.85, 0.92, 0.96, 0.88, 0.83; specificity of 0.85, 0.96, 0.96, 0.96, 0.83), respectively. These promising data would be the basis for further validation using targeted autoantibody tests. Full article
(This article belongs to the Special Issue Advanced Methods in Microarrays for Cancer Research)
Open AccessArticle Tissue Microarray Technology for Molecular Applications: Investigation of Cross-Contamination between Tissue Samples Obtained from the Same Punching Device
Microarrays 2015, 4(2), 188-195; doi:10.3390/microarrays4020188
Received: 5 January 2015 / Revised: 23 March 2015 / Accepted: 26 March 2015 / Published: 2 April 2015
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Abstract
Background: Tissue microarray (TMA) technology allows rapid visualization of molecular markers by immunohistochemistry and in situ hybridization. In addition, TMA instrumentation has the potential to assist in other applications: punches taken from donor blocks can be placed directly into tubes and used for
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Background: Tissue microarray (TMA) technology allows rapid visualization of molecular markers by immunohistochemistry and in situ hybridization. In addition, TMA instrumentation has the potential to assist in other applications: punches taken from donor blocks can be placed directly into tubes and used for nucleic acid analysis by PCR approaches. However, the question of possible cross-contamination between samples punched with the same device has frequently been raised but never addressed. Methods: Two experiments were performed. (1) A block from mycobacterium tuberculosis (TB) positive tissue and a second from an uninfected patient were aligned side-by-side in an automated tissue microarrayer. Four 0.6 mm punches were cored from each sample and placed inside their corresponding tube. Between coring of each donor block, a mechanical cleaning step was performed by insertion of the puncher into a paraffin block. This sequence of coring and cleaning was repeated three times, alternating between positive and negative blocks. A fragment from the 6110 insertion sequence specific for mycobacterium tuberculosis was analyzed; (2) Four 0.6 mm punches were cored from three KRAS mutated colorectal cancer blocks, alternating with three different wild-type tissues using the same TMA instrument (sequence of coring: G12D, WT, G12V, WT, G13D and WT). Mechanical cleaning of the device between each donor block was made. Mutation analysis by pyrosequencing was carried out. This sequence of coring was repeated manually without any cleaning step between blocks. Results/Discussion: In both analyses, all alternating samples showed the expected result (samples 1, 3 and 5: positive or mutated, samples 2, 4 and 6: negative or wild-type). Similar results were obtained without cleaning step. These findings suggest that no cross-contamination of tissue samples occurs when donor blocks are punched using the same device, however a cleaning step is nonetheless recommended. Our result supports the use of TMA technology as an accessory to PCR applications. Full article
Open AccessArticle Re-Punching Tissue Microarrays Is Possible: Why Can This Be Useful and How to Do It
Microarrays 2015, 4(2), 245-254; doi:10.3390/microarrays4020245
Received: 15 February 2015 / Revised: 25 April 2015 / Accepted: 29 April 2015 / Published: 11 May 2015
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Abstract
Tissue microarray (TMA) methodology allows the concomitant analysis of hundreds of tissue specimens arrayed in the same manner on a recipient block. Subsequently, all samples can be processed under identical conditions, such as antigen retrieval procedure, reagent concentrations, incubation times with antibodies/probes, and
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Tissue microarray (TMA) methodology allows the concomitant analysis of hundreds of tissue specimens arrayed in the same manner on a recipient block. Subsequently, all samples can be processed under identical conditions, such as antigen retrieval procedure, reagent concentrations, incubation times with antibodies/probes, and escaping the inter-assays variability. Therefore, the use of TMA has revolutionized histopathology translational research projects and has become a tool very often used for putative biomarker investigations. TMAs are particularly relevant for large scale analysis of a defined disease entity. In the course of these exploratory studies, rare subpopulations can be discovered or identified. This can refer to subsets of patients with more particular phenotypic or genotypic disease with low incidence or to patients receiving a particular treatment. Such rare cohorts should be collected for more specific investigations at a later time, when, possibly, more samples of a rare identity will be available as well as more knowledge derived from concomitant, e.g., genetic, investigations will have been acquired. In this article we analyze for the first time the limits and opportunities to construct new TMA blocks using tissues from older available arrays and supplementary donor blocks. In summary, we describe the reasons and technical details for the construction of rare disease entities arrays. Full article
Open AccessArticle Data Integration for Microarrays: Enhanced Inference for Gene Regulatory Networks
Microarrays 2015, 4(2), 255-269; doi:10.3390/microarrays4020255
Received: 27 February 2015 / Accepted: 30 April 2015 / Published: 14 May 2015
Cited by 1 | PDF Full-text (129 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Microarray technologies have been the basis of numerous important findings regarding gene expression in the few last decades. Studies have generated large amounts of data describing various processes, which, due to the existence of public databases, are widely available for further analysis. Given
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Microarray technologies have been the basis of numerous important findings regarding gene expression in the few last decades. Studies have generated large amounts of data describing various processes, which, due to the existence of public databases, are widely available for further analysis. Given their lower cost and higher maturity compared to newer sequencing technologies, these data continue to be produced, even though data quality has been the subject of some debate. However, given the large volume of data generated, integration can help overcome some issues related, e.g., to noise or reduced time resolution, while providing additional insight on features not directly addressed by sequencing methods. Here, we present an integration test case based on public Drosophila melanogaster datasets (gene expression, binding site affinities, known interactions). Using an evolutionary computation framework, we show how integration can enhance the ability to recover transcriptional gene regulatory networks from these data, as well as indicating which data types are more important for quantitative and qualitative network inference. Our results show a clear improvement in performance when multiple datasets are integrated, indicating that microarray data will remain a valuable and viable resource for some time to come. Full article
(This article belongs to the Special Issue Computational Modeling and Analysis of Microarray Data: New Horizons)
Open AccessArticle “Upstream Analysis”: An Integrated Promoter-Pathway Analysis Approach to Causal Interpretation of Microarray Data
Microarrays 2015, 4(2), 270-286; doi:10.3390/microarrays4020270
Received: 17 March 2015 / Revised: 11 May 2015 / Accepted: 14 May 2015 / Published: 21 May 2015
Cited by 5 | PDF Full-text (993 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
A strategy is presented that allows a causal analysis of co-expressed genes, which may be subject to common regulatory influences. A state-of-the-art promoter analysis for potential transcription factor (TF) binding sites in combination with a knowledge-based analysis of the upstream pathway that control
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A strategy is presented that allows a causal analysis of co-expressed genes, which may be subject to common regulatory influences. A state-of-the-art promoter analysis for potential transcription factor (TF) binding sites in combination with a knowledge-based analysis of the upstream pathway that control the activity of these TFs is shown to lead to hypothetical master regulators. This strategy was implemented as a workflow in a comprehensive bioinformatic software platform. We applied this workflow to gene sets that were identified by a novel triclustering algorithm in naphthalene-induced gene expression signatures of murine liver and lung tissue. As a result, tissue-specific master regulators were identified that are known to be linked with tumorigenic and apoptotic processes. To our knowledge, this is the first time that genes of expression triclusters were used to identify upstream regulators. Full article
(This article belongs to the Special Issue Computational Modeling and Analysis of Microarray Data: New Horizons)
Open AccessArticle An Optimization-Driven Analysis Pipeline to Uncover Biomarkers and Signaling Paths: Cervix Cancer
Microarrays 2015, 4(2), 287-310; doi:10.3390/microarrays4020287
Received: 22 February 2015 / Revised: 27 April 2015 / Accepted: 13 May 2015 / Published: 28 May 2015
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Abstract
Establishing how a series of potentially important genes might relate to each other is relevant to understand the origin and evolution of illnesses, such as cancer. High‑throughput biological experiments have played a critical role in providing information in this regard. A special challenge,
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Establishing how a series of potentially important genes might relate to each other is relevant to understand the origin and evolution of illnesses, such as cancer. High‑throughput biological experiments have played a critical role in providing information in this regard. A special challenge, however, is that of trying to conciliate information from separate microarray experiments to build a potential genetic signaling path. This work proposes a two-step analysis pipeline, based on optimization, to approach meta-analysis aiming to build a proxy for a genetic signaling path. Full article
(This article belongs to the Special Issue Advanced Methods in Microarrays for Cancer Research)
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Review

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Open AccessReview Reverse Phase Protein Arrays—Quantitative Assessment of Multiple Biomarkers in Biopsies for Clinical Use
Microarrays 2015, 4(2), 98-114; doi:10.3390/microarrays4020098
Received: 15 January 2015 / Revised: 9 March 2015 / Accepted: 18 March 2015 / Published: 24 March 2015
Cited by 4 | PDF Full-text (862 KB) | HTML Full-text | XML Full-text
Abstract
Reverse Phase Protein Arrays (RPPA) represent a very promising sensitive and precise high-throughput technology for the quantitative measurement of hundreds of signaling proteins in biological and clinical samples. This array format allows quantification of one protein or phosphoprotein in multiple samples under the
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Reverse Phase Protein Arrays (RPPA) represent a very promising sensitive and precise high-throughput technology for the quantitative measurement of hundreds of signaling proteins in biological and clinical samples. This array format allows quantification of one protein or phosphoprotein in multiple samples under the same experimental conditions at the same time. Moreover, it is suited for signal transduction profiling of small numbers of cultured cells or cells isolated from human biopsies, including formalin fixed and paraffin embedded (FFPE) tissues. Owing to the much easier sample preparation, as compared to mass spectrometry based technologies, and the extraordinary sensitivity for the detection of low-abundance signaling proteins over a large linear range, RPPA have the potential for characterization of deregulated interconnecting protein pathways and networks in limited amounts of sample material in clinical routine settings. Current aspects of RPPA technology, including dilution curves, spotting, controls, signal detection, antibody validation, and calculation of protein levels are addressed. Full article
(This article belongs to the Special Issue New and Old Technologies for Generation of Microarrays)
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Open AccessReview Aptamer Microarrays—Current Status and Future Prospects
Microarrays 2015, 4(2), 115-132; doi:10.3390/microarrays4020115
Received: 30 January 2015 / Revised: 9 March 2015 / Accepted: 18 March 2015 / Published: 24 March 2015
Cited by 8 | PDF Full-text (544 KB) | HTML Full-text | XML Full-text
Abstract
Microarray technologies are state of the art in biological research, which requires fast genome, proteome and transcriptome analysis technologies. Often antibodies are applied in protein microarrays as proteomic tools. Since the generation of antibodies against toxic targets or small molecules including organic compounds
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Microarray technologies are state of the art in biological research, which requires fast genome, proteome and transcriptome analysis technologies. Often antibodies are applied in protein microarrays as proteomic tools. Since the generation of antibodies against toxic targets or small molecules including organic compounds remains challenging the use of antibodies may be limited in this context. In contrast to this, aptamer microarrays provide alternative techniques to circumvent these limitations. In this article we review the latest developments in aptamer microarray technology. We discuss similarities and differences between DNA and aptamer microarrays and shed light on the post synthesis immobilization of aptamers including corresponding effects on the microarray performance. Finally, we highlight current limitations and future prospects of aptamer microarray technology. Full article
(This article belongs to the Special Issue New and Old Technologies for Generation of Microarrays)
Open AccessReview 3D Cell Culture in Alginate Hydrogels
Microarrays 2015, 4(2), 133-161; doi:10.3390/microarrays4020133
Received: 31 January 2015 / Revised: 16 March 2015 / Accepted: 17 March 2015 / Published: 24 March 2015
Cited by 15 | PDF Full-text (1584 KB) | HTML Full-text | XML Full-text
Abstract
This review compiles information regarding the use of alginate, and in particular alginate hydrogels, in culturing cells in 3D. Knowledge of alginate chemical structure and functionality are shown to be important parameters in design of alginate-based matrices for cell culture. Gel elasticity as
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This review compiles information regarding the use of alginate, and in particular alginate hydrogels, in culturing cells in 3D. Knowledge of alginate chemical structure and functionality are shown to be important parameters in design of alginate-based matrices for cell culture. Gel elasticity as well as hydrogel stability can be impacted by the type of alginate used, its concentration, the choice of gelation technique (ionic or covalent), and divalent cation chosen as the gel inducing ion. The use of peptide-coupled alginate can control cell–matrix interactions. Gelation of alginate with concomitant immobilization of cells can take various forms. Droplets or beads have been utilized since the 1980s for immobilizing cells. Newer matrices such as macroporous scaffolds are now entering the 3D cell culture product market. Finally, delayed gelling, injectable, alginate systems show utility in the translation of in vitro cell culture to in vivo tissue engineering applications. Alginate has a history and a future in 3D cell culture. Historically, cells were encapsulated in alginate droplets cross-linked with calcium for the development of artificial organs. Now, several commercial products based on alginate are being used as 3D cell culture systems that also demonstrate the possibility of replacing or regenerating tissue. Full article
(This article belongs to the Special Issue Advantages of Three Dimensional (3D) Cell Cultures)
Open AccessReview Up-to-Date Applications of Microarrays and Their Way to Commercialization
Microarrays 2015, 4(2), 196-213; doi:10.3390/microarrays4020196
Received: 2 February 2015 / Revised: 1 April 2015 / Accepted: 14 April 2015 / Published: 23 April 2015
Cited by 3 | PDF Full-text (725 KB) | HTML Full-text | XML Full-text
Abstract
This review addresses up-to-date applications of Protein Microarrays. Protein Microarrays play a significant role in basic research as well as in clinical applications and are applicable in a lot of fields, e.g., DNA, proteins and small molecules. Additionally they are on the way
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This review addresses up-to-date applications of Protein Microarrays. Protein Microarrays play a significant role in basic research as well as in clinical applications and are applicable in a lot of fields, e.g., DNA, proteins and small molecules. Additionally they are on the way to enter clinics in routine diagnostics. Protein Microarrays can be powerful tools to improve healthcare. An overview of basic characteristics to mediate essential knowledge of this technique is given. To reach this goal, some challenges still have to be addressed. A few applications of Protein Microarrays in a medical context are shown. Finally, an outlook, where the potential of Protein Microarrays is depicted and speculations how the future of Protein Microarrays will look like are made. Full article
(This article belongs to the Special Issue New and Old Technologies for Generation of Microarrays)
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Open AccessReview NAPPA as a Real New Method for Protein Microarray Generation
Microarrays 2015, 4(2), 214-227; doi:10.3390/microarrays4020214
Received: 5 March 2015 / Revised: 30 March 2015 / Accepted: 14 April 2015 / Published: 24 April 2015
Cited by 1 | PDF Full-text (1061 KB) | HTML Full-text | XML Full-text
Abstract
Nucleic Acid Programmable Protein Arrays (NAPPA) have emerged as a powerful and innovative technology for the screening of biomarkers and the study of protein-protein interactions, among others possible applications. The principal advantages are the high specificity and sensitivity that this platform offers. Moreover,
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Nucleic Acid Programmable Protein Arrays (NAPPA) have emerged as a powerful and innovative technology for the screening of biomarkers and the study of protein-protein interactions, among others possible applications. The principal advantages are the high specificity and sensitivity that this platform offers. Moreover, compared to conventional protein microarrays, NAPPA technology avoids the necessity of protein purification, which is expensive and time-consuming, by substituting expression in situ with an in vitro transcription/translation kit. In summary, NAPPA arrays have been broadly employed in different studies improving knowledge about diseases and responses to treatments. Here, we review the principal advances and applications performed using this platform during the last years. Full article
(This article belongs to the Special Issue New and Old Technologies for Generation of Microarrays)
Open AccessReview Label and Label-Free Detection Techniques for Protein Microarrays
Microarrays 2015, 4(2), 228-244; doi:10.3390/microarrays4020228
Received: 28 February 2015 / Revised: 10 April 2015 / Accepted: 17 April 2015 / Published: 24 April 2015
Cited by 6 | PDF Full-text (752 KB) | HTML Full-text | XML Full-text
Abstract
Protein microarray technology has gone through numerous innovative developments in recent decades. In this review, we focus on the development of protein detection methods embedded in the technology. Early microarrays utilized useful chromophores and versatile biochemical techniques dominated by high-throughput illumination. Recently, the
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Protein microarray technology has gone through numerous innovative developments in recent decades. In this review, we focus on the development of protein detection methods embedded in the technology. Early microarrays utilized useful chromophores and versatile biochemical techniques dominated by high-throughput illumination. Recently, the realization of label-free techniques has been greatly advanced by the combination of knowledge in material sciences, computational design and nanofabrication. These rapidly advancing techniques aim to provide data without the intervention of label molecules. Here, we present a brief overview of this remarkable innovation from the perspectives of label and label-free techniques in transducing nano‑biological events. Full article
(This article belongs to the Special Issue New and Old Technologies for Generation of Microarrays)

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