Diagnostic challenges for multiplexed protein microarrays

Modular probe integrating with quantum dots based versatile platform for sensitive and label-free biomarker detection

Multiplexed analysis of biomarkers in a single sample tube is essential for accurate diagnosis and therapy of diseases. However, the existing detection platforms suffer from many drawbacks, such as low specificity, limited applicable sceneries, and complicated operation. Hence, it is highly important to develop a versatile biomarker detection platform that can be used for disease diagnosis and pathophysiological research. In this study, we provide a versatile method for detecting biomarkers using dual-loop probes and quantum dots (QDs). This approach utilizes a dual-loop probe that consists of a recognition module for identifying specific targets, a template recognition module for initiating subsequent chain replacement cycles, and a signal module for facilitating the fixation of QDs on the 96-well plate. The lower limit of detection for miRNA-21 is determined to be at the aM level. Furthermore, this design may be easily expanded to simultaneously detect several targets, such as miRNA and C-reactive protein. The experimental results demonstrated the successful construction of the versatile biomarkers detection platform, and indicated that the sensitive and versatile platform has significant potential in the areas of bio-sensing, clinical diagnostics, and environmental sample analysis.

Review of the Use of Liquid Chromatography-Tandem Mass Spectrometry in Clinical Laboratories: Part II-Operations

Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is increasingly utilized in clinical laboratories because it has advantages in terms of specificity and sensitivity over other analytical technologies. These advantages come with additional responsibilities and challenges given that many assays and platforms are not provided to laboratories as a single kit or device. The skills, staff, and assays used in LC-MS/MS are internally developed by the laboratory, with relatively few exceptions. Hence, a laboratory that deploys LC-MS/MS assays must be conscientious of the practices and procedures adopted to overcome the challenges associated with the technology. This review discusses the post-development landscape of LC-MS/MS assays, including validation, quality assurance, operations, and troubleshooting. The content knowledge of LC-MS/MS users is quite broad and deep and spans multiple scientific fields, including biology, clinical chemistry, chromatography, engineering, and MS. However, there are no formal academic programs or specific literature to train laboratory staff on the fundamentals of LC-MS/MS beyond the reports on method development. Therefore, depending on their experience level, some readers may be familiar with aspects of the laboratory practices described herein, while others may be not. This review endeavors to assemble aspects of LC-MS/MS operations in the clinical laboratory to provide a framework for the thoughtful development and execution of LC-MS/MS applications.

Towards precision medicine: the role and potential of protein and peptide microarrays

Techniques to comprehensively analyze protein signatures are pivotal to unravel disease mechanisms, develop novel biomarkers and targeted therapies. In this frame, protein and peptide microarrays can play a major role in fuelling precision medicine.

Reproducibility and Crossplatform Validation of Reverse-Phase Protein Array Data

Reverse-phase protein array (RPPA) technology is a high-throughput antibody- and microarray-based approach for the rapid profiling of levels of proteins and protein posttranslational modifications in biological specimens. The technology consumes small amounts of samples, can sensitively detect low-abundance proteins and posttranslational modifications, enables measurements of multiple signaling pathways in parallel, has the capacity to analyze large sample numbers, and offers robust interexperimental reproducibility. These features of RPPA experiments have motivated and enabled the use of RPPA technology in various biomedical, translational, and clinical applications, including the delineation of molecular mechanisms of disease, profiling of druggable signaling pathway activation, and search for new prognostic markers. Owing to the complexity of many of these applications, such as developing multiplex protein assays for diagnostic laboratories or integrating posttranslational modification-level data using large-scale proteogenomic approaches, robust and well-validated data are essential. There are many distinct components of an RPPA workflow, and numerous possible technical setups and analysis parameter options exist. The differences between RPPA platform setups around the world offer opportunities to assess and minimize interplatform variation. Crossplatform validation may also aid in the evaluation of robust, platform-independent protein markers of disease and response to therapy.

Nanoparticle Enhancement Cascade for Sensitive Multiplex Measurements of Biomarkers in Complex Fluids with Surface Plasmon Resonance Imaging

There is a large unmet need for reliable biomarker measurement systems for clinical application. Such systems should meet challenging requirements for large scale use, including a large dynamic detection range, multiplexing capacity, and both high specificity and sensitivity. More importantly, these requirements need to apply to complex biological samples, which require extensive quality control. In this paper, we present the development of an enhancement detection cascade for surface plasmon resonance imaging (SPRi). The cascade applies an antibody sandwich assay, followed by neutravidin and a gold nanoparticle enhancement for quantitative biomarker measurements in small volumes of complex fluids. We present a feasibility study both in simple buffers and in spiked equine synovial fluid with four cytokines, IL-1β, IL-6, IFN-γ, and TNF-α. Our enhancement cascade leads to an antibody dependent improvement in sensitivity up to 40 000 times, resulting in a limit of detection as low as 50 fg/mL and a dynamic detection range of more than 7 logs. Additionally, measurements at these low concentrations are highly reliable with intra- and interassay CVs between 2% and 20%. We subsequently showed this assay is suitable for multiplex measurements with good specificity and limited cross-reactivity. Moreover, we demonstrated robust detection of IL-6 and IL-1β in spiked undiluted equine synovial fluid with small variation compared to buffer controls. In addition, the availability of real time measurements provides extensive quality control opportunities, essential for clinical applications. Therefore, we consider this method is suitable for broad application in SPRi for multiplex biomarker detection in both research and clinical settings.

Quality assurance for multiplexed assays - how can it be achieved?

Multiplexed assays are now a common form of analysis in routine clinical and research laboratories. Assuring the quality of this type of complex, massively-parallel testing poses challenges not encountered in the traditional single-plex assay. A range of quality assurance measures is implemented at different stages in a multiplex assay, beginning in the manufacturing process, and the ensuing analytical and data interpretation stages. This article explores quality issues and the quality assurance measures that have been devised for multiplex assays ranging from simple two-plex assays to the types of assays that involve simultaneous testing on millions of test sites on a single analytical device.

ELISA in the multiplex era: potentials and pitfalls

Multiplex immunoassays confer several advantages over widely adopted singleplex immunoassays including increased efficiency at a reduced expense, greater output per sample volume ratios and higher throughput predicating more resolute, detailed diagnostics and facilitating personalised medicine. Nonetheless, to date, relatively few protein multiplex immunoassays have been validated for in vitro diagnostics in clinical/point-of-care settings. This review article will outline the challenges, which must be ameliorated prior to the widespread integration of multiplex immunoassays in clinical settings: (i) biomarker validation; (ii) standardisation of immunoassay design and quality control (calibration and quantification); (iii) availability, stability, specificity and cross-reactivity of reagents; (iv) assay automation and the use of validated algorithms for transformation of raw data into diagnostic results. A compendium of multiplex immunoassays applicable to in vitro diagnostics and a summary of the diagnostic products currently available commercially are included, along with an analysis of the relative states of development for each format (namely planar slide based, suspension and planar/microtitre plate based) with respect to the aforementioned issues.

Bioanalytical chemistry of cytokines--a review

Cytokines are bioactive proteins produced by many different cells of the immune system. Due to their role in different inflammatory disease states and maintaining homeostasis, there is enormous clinical interest in the quantitation of cytokines. The typical standard methods for quantitation of cytokines are immunoassay-based techniques including enzyme-linked immusorbent assays (ELISA) and bead-based immunoassays read by either standard or modified flow cytometers. A review of recent developments in analytical methods for measurements of cytokine proteins is provided. This review briefly covers cytokine biology and the analysis challenges associated with measurement of these biomarker proteins for understanding both health and disease. New techniques applied to immunoassay-based assays are presented along with the uses of aptamers, electrochemistry, mass spectrometry, optical resonator-based methods. Methods used for elucidating the release of cytokines from single cells as well as in vivo collection methods are described.

Aqueous two-phase system patterning of detection antibody solutions for cross-reaction-free multiplex ELISA

Accurate disease diagnosis, patient stratification and biomarker validation require the analysis of multiple biomarkers. This paper describes cross-reactivity-free multiplexing of enzyme-linked immunosorbent assays (ELISAs) using aqueous two-phase systems (ATPSs) to confine detection antibodies at specific locations in fully aqueous environments. Antibody cross-reactions are eliminated because the detection antibody solutions are co-localized only to corresponding surface-immobilized capture antibody spots. This multiplexing technique is validated using plasma samples from allogeneic bone marrow recipients. Patients with acute graft versus host disease (GVHD), a common and serious condition associated with allogeneic bone marrow transplantation, display higher mean concentrations for four multiplexed biomarkers (HGF, elafin, ST2 and TNFR1) relative to healthy donors and transplant patients without GVHD. The antibody co-localization capability of this technology is particularly useful when using inherently cross-reactive reagents such as polyclonal antibodies, although monoclonal antibody cross-reactivity can also be reduced. Because ATPS-ELISA adapts readily available antibody reagents, plate materials and detection instruments, it should be easily transferable into other research and clinical settings.

Quality control, analysis and secure sharing of Luminex® immunoassay data using the open source LabKey Server platform

BACKGROUND

Immunoassays that employ multiplexed bead arrays produce high information content per sample. Such assays are now frequently used to evaluate humoral responses in clinical trials. Integrated software is needed for the analysis, quality control, and secure sharing of the high volume of data produced by such multiplexed assays. Software that facilitates data exchange and provides flexibility to perform customized analyses (including multiple curve fits and visualizations of assay performance over time) could increase scientists' capacity to use these immunoassays to evaluate human clinical trials.

RESULTS

The HIV Vaccine Trials Network and the Statistical Center for HIV/AIDS Research and Prevention collaborated with LabKey Software to enhance the open source LabKey Server platform to facilitate workflows for multiplexed bead assays. This system now supports the management, analysis, quality control, and secure sharing of data from multiplexed immunoassays that leverage Luminex xMAP® technology. These assays may be custom or kit-based. Newly added features enable labs to: (i) import run data from spreadsheets output by Bio-Plex Manager™ software; (ii) customize data processing, curve fits, and algorithms through scripts written in common languages, such as R; (iii) select script-defined calculation options through a graphical user interface; (iv) collect custom metadata for each titration, analyte, run and batch of runs; (v) calculate dose-response curves for titrations; (vi) interpolate unknown concentrations from curves for titrated standards; (vii) flag run data for exclusion from analysis; (viii) track quality control metrics across runs using Levey-Jennings plots; and (ix) automatically flag outliers based on expected values. Existing system features allow researchers to analyze, integrate, visualize, export and securely share their data, as well as to construct custom user interfaces and workflows.

CONCLUSIONS

Unlike other tools tailored for Luminex immunoassays, LabKey Server allows labs to customize their Luminex analyses using scripting while still presenting users with a single, graphical interface for processing and analyzing data. The LabKey Server system also stands out among Luminex tools for enabling smooth, secure transfer of data, quality control information, and analyses between collaborators. LabKey Server and its Luminex features are freely available as open source software at http://www.labkey.com under the Apache 2.0 license.

Plasma cytokine profiling in sibling pairs discordant for autism spectrum disorder

OBJECTIVE

Converging lines of evidence point to the existence of immune dysfunction in autism spectrum disorder (ASD), which could directly affect several key neurodevelopmental processes. Previous studies have shown higher cytokine levels in patients with autism compared with matched controls or subjects with other developmental disorders. In the current study, we used plasma-cytokine profiling for 25 discordant sibling pairs to evaluate whether these alterations occur within families with ASD.

METHODS

Plasma-cytokine profiling was conducted using an array-based multiplex sandwich ELISA for simultaneous quantitative measurement of 40 unique targets. We also analyzed the correlations between cytokine levels and clinically relevant quantitative traits (Vineland Adaptive Behavior Scale in Autism (VABS) composite score, Social Responsiveness Scale (SRS) total T score, head circumference, and full intelligence quotient (IQ)). In addition, because of the high phenotypic heterogeneity of ASD, we defined four subgroups of subjects (those who were non-verbal, those with gastrointestinal issues, those with regressive autism, and those with a history of allergies), which encompass common and/or recurrent endophenotypes in ASD, and tested the cytokine levels in each group.

RESULTS

None of the measured parameters showed significant differences between children with ASD and their related typically developing siblings. However, specific target levels did correlate with quantitative clinical traits, and these were significantly different when the ASD subgroups were analyzed. It is notable that these differences seem to be attributable to a predisposing immunogenetic background, as no other significant differences were noticed between discordant sibling pairs. Interleukin-1β appears to be the cytokine most involved in quantitative traits and clinical subgroups of ASD.

CONCLUSIONS

In the present study, we found a lack of significant differences in plasma-cytokine levels between children with ASD and in their related non-autistic siblings. Thus, our results support the evidence that the immune profiles of children with autism do not differ from their typically developing siblings. However, the significant association of cytokine levels with the quantitative traits and the clinical subgroups analyzed suggests that altered immune responses may affect core feature of ASD.

Surface Adjustment of Reverse Phase Protein Arrays using Positive Control Spots

Reverse phase protein arrays (RPPA) measure the relative expression levels of a protein in many samples simultaneously. Observed signal from these arrays is a combination of true signal, additive background, and multiplicative spatial effects. Background subtraction alone is not sufficient to remove all nonbiological trends from the data. We developed a surface adjustment that uses information from positive control spots to correct for spatial trends on the array beyond additive background. This method uses a generalized additive model to estimate a smoothed surface from positive controls. When positive controls are printed in a dilution series, a nested surface adjustment performs an intensity-based correction. When applicable, surface adjustment is able to remove spatial trends and increase within slide replicate agreement better than background subtraction alone as demonstrated on two sets of arrays. This work demonstrates the importance of including positive control spots on the array.

Cytokines as potential biomarkers for Parkinson's disease: a multiplex approach

Cytokines, which are immunological messengers facilitating both intra- and inter-system communication, are considered central players in the neuroinflammatory cascades associated with the neurodegenerative process in Parkinson's disease (PD) and other neurological disorders. They have also been implicated in depression and other cognitive (e.g., memory impairment, dementia) and affective disturbances (e.g., anxiety) that show high co-morbidity with neurodegenerative diseases. As such, cytokines may hold great promise as serological biomarkers in PD, with potential applications ranging from early diagnosis and disease staging, to prognosis, drug discovery, and tracking the response to treatment. Subclassification or risk stratification in PD could be based (among other things) on reliably determined cytokine panel profiles or "signatures" of particular co-morbid disease states or at-risk groups (e.g., PD alone, PD with depression and/or dementia). Researchers and clinicians seeking to describe cytokine variations in health vs. disease will benefit greatly from technologies that allow a high degree of multiplexing and thus permit the simultaneous determination of a large roster of cytokines in single small-volume samples. The need for such highly paralleled assays is underscored by the fact that cytokines do not act in isolation but rather against a backdrop of complementary and antagonistic cytokine effects; ascribing valence to the actions of any one cytokine thus requires specific knowledge about the larger cytokine milieu. This chapter provides a technological overview of the major cytokine multiplex assay platforms before discussing the implications of such tools for biomarker discovery and related applications in PD and its depressive and cognitive co-morbidities.

Protein microarrays for personalized medicine

BACKGROUND

Over the last 10 years, DNA microarrays have achieved a robust analytical performance, enabling their use for analyzing the whole transcriptome or for screening thousands of single-nucleotide polymorphisms in a single experiment. DNA microarrays allow scientists to correlate gene expression signatures with disease progression, to screen for disease-specific mutations, and to treat patients according to their individual genetic profiles; however, the real key is proteins and their manifold functions. It is necessary to achieve a greater understanding of not only protein function and abundance but also their role in the development of diseases. Protein concentrations have been shown to reflect the physiological and pathologic state of an organ, tissue, or cells far more directly than DNA, and proteins can be profiled effectively with protein microarrays, which require only a small amount of sample material.

CONTENT

Protein microarrays have become well-established tools in basic and applied research, and the first products have already entered the in vitro diagnostics market. This review focuses on protein microarray applications for biomarker discovery and validation, disease diagnosis, and use within the area of personalized medicine.

SUMMARY

Protein microarrays have proved to be reliable research tools in screening for a multitude of parameters with only a minimal quantity of sample and have enormous potential in applications for diagnostic and personalized medicine.

Antibody-based protein multiplex platforms: technical and operational challenges

BACKGROUND

The measurement of multiple protein biomarkers may refine risk stratification in clinical settings. This concept has stimulated development of multiplexed immunoassay platforms that provide multiple, parallel protein measurements on the same specimen.

CONTENT

We provide an overview of antibody-based multiplexed immunoassay platforms and discuss technical and operational challenges. Multiplexed immunoassays use traditional immunoassay principles in which high-affinity capture ligands are immobilized in parallel arrays in either planar format or on microspheres in suspension. Development of multiplexed immunoassays requires rigorous validation of assay configuration and analytical performance to minimize assay imprecision and inaccuracy. Challenges associated with multiplex configuration include selection and immobilization of capture ligands, calibration, interference between antibodies and proteins and assay diluents, and compatibility of assay limits of quantification. We discuss potential solutions to these challenges. Criteria for assessing analytical multiplex assay performance include the range of linearity, analytical specificity, recovery, and comparison to a quality reference method. Quality control materials are not well developed for multiplexed protein immunoassays, and algorithms for interpreting multiplex quality control data are needed.

SUMMARY

Technical and operational challenges have hindered implementation of multiplexed assays in clinical settings. Formal procedures that guide multiplex assay configuration, analytical validation, and quality control are needed before broad application of multiplexed arrays can occur in the in vitro diagnostic market.

Long-Term Quality Control of the Cytokine & Growth Factors and Cell Adhesion Molecule Arrays at the Randox Evidence Investigator

Multi component assays are a promising development in laboratory medicine. Reproducibility and standardization of the used technology is crucial for the quality of the results. In our laboratory several studies were carried out in a period of more than two years using the Randox Evidence Investigator. We applied the Cytokine & Growth Factors and Cell Adhesion Molecule Array from which reference values could be obtained. Cytokines are not useful in low grade inflammation or in normal persons as the levels are too low to detect. However growth factors and cell adhesion molecules could be determined in those studies. Outcomes with the arrays were compared with conventional assays such as ELISA. The correlations of IL-6 and IL-10 were very good and that of s-ICAM acceptable. Inter-assay coefficients of variation could be calculated by using the same control level material during those years. The system turned out to be easy to handle and very stable over a long period of time with CV's of about 8-12%. The results obtained are not dependent of the lot number of the arrays or apparatus as two different apparatus gave same outcomes.

Variable slope normalization of reverse phase protein arrays

MOTIVATION

Reverse phase protein arrays (RPPA) measure the relative expression levels of a protein in many samples simultaneously. A set of identically spotted arrays can be used to measure the levels of more than one protein. Protein expression within each sample on an array is estimated by borrowing strength across all the samples, but using only within array information. When comparing across slides, it is essential to account for sample loading, the total amount of protein printed per sample. Currently, total protein is estimated using either a housekeeping protein or the sample median across all slides. When the variability in sample loading is large, these methods are suboptimal because they do not account for the fact that the protein expression for each slide is estimated separately.

RESULTS

We propose a new normalization method for RPPA data, called variable slope (VS) normalization, that takes into account that quantification of RPPA slides is performed separately. This method is better able to remove loading bias and recover true correlation structures between proteins.

AVAILABILITY

Code to implement the method in the statistical package R and anonymized data are available at (http://bioinformatics.mdanderson.org/supplements.html).

Protein microarrays: effective tools for the study of inflammatory diseases

Inflammation is a defense reaction of an organism against harmful stimuli such as tissue injury or infectious agents. The relationship between the infecting microorganism and the immune, inflammatory, and coagulation responses of the host is intricately intertwined. Due to its complex nature, the molecular mechanisms of inflammation are not yet understood in detail and additional diagnostic tools are required to clarify further aspects. In recent years, protein microarray-based research has moved from being technology-based to application-oriented. Protein microarrays are perfect tools for studying inflammatory diseases. High-density protein arrays enable new classes of autoantibodies, which cause autoimmune diseases, to be discovered. Protein arrays consisting of miniaturized multiplexed sandwich immunoassays allow the simultaneous expression analysis of dozens of signaling molecules such as the cytokines and chemokines involved in the regulation of the immune system. The data enable statements to be made on the status of the disease and its progression as well as support for the clinicians in choosing patient-specific treatment. This chapter reviews the technology and the applications of protein microarrays in diagnosing and monitoring inflammatory diseases.

Clinical application of antibody microarray in chronic kidney disease: How far to go?

Chronic kidney disease (CKD) that affects about 10% of the adult population has been shown as a worldwide public health problem in recent years. Both basic and clinical investigations have identified complex disease-associated protein networks involved in the pathophysiologic processes of CKD. The traditional single-assay approach and proteomic analysis of those related proteins have given birth to a steadily increasing panel of molecules that may have the potential to serve as biomarkers for CKD. However, both approaches suffered from some shortcomings from a technological point of view. Antibody microarray (AbM) is characterized by high sensitivity, specificity, and quantitative ability for a particular set of known proteins. However, its application in CKD has been very limited so far. The objective of this review, therefore, is to address the potential applications of AbM in studying of CKD. We will briefly discuss the proteins involved in the development of CKD, future directions in which AbM approaches would probably display its potential and also some key issues that need to be considered in application of this novel technique.

[Protein arrays and perspectives of medical applications]

Protein microarrays make it possible to detect molecular interactions with various partners (proteins, peptides, nucleic acids, sugars, etc.). Their advantages are crucial for high-throughput analysis of proteomes of different organisms. Moreover, the recent data reveal the performance of microarrays over current immunological methods. Therefore, the antigen and antibody microarrays become indispensable for medical applications, in particular, for diagnosis and prognosis of microbial infections, autoimmune and allergic diseases. The further technological progress might provide the extension of the miniaturized assays for multiparametric monitoring of human pathologies in practical medicine.

High-throughput antibody microarrays for quantitative proteomic analysis

The antibody microarray is an intrinsically robust and quantitative system that delivers high-throughput and parallel measurements on particular sets of known proteins. It has become an important proteomics research tool, complementary to the conventional unbiased separation-based and mass spectrometry-based approaches. This review summarizes the technical aspects of production and the application for quantitative proteomic analysis with an emphasis on disease proteomics, especially the identification of biomarkers. Quality control, data analysis methods and the challenges for quantitative assays are also discussed.