Multiplexed and microparticle-based analyses: quantitative tools for the large-scale analysis of biological systems

Toward predictive engineering of gene circuits

Many synthetic biology applications rely on programming living cells using gene circuits - the assembly and wiring of genetic elements to control cellular behaviors. Extensive progress has been made in constructing gene circuits with diverse functions and applications. For many circuit functions, however, it remains challenging to ensure that the circuits operate in a predictable manner. Although the notion of predictability may appear intuitive, close inspection suggests that it is not always clear what constitutes predictability. We dissect this concept and how it can be confounded by the complexity of a circuit, the complexity of the context, and the interplay between the two. We discuss circuit engineering strategies, in both computation and experiment, that have been used to improve the predictability of gene circuits.

Monoplex and multiplex immunoassays: approval, advancements, and alternatives

Immunoassays are a powerful diagnostic tool and are widely used for the quantification of proteins and biomolecules in medical diagnosis and research. Enzyme-linked immunosorbent assay (ELISA) is the most commonly used immunoassay format and allows the detection of biomarkers at a very low concentration. The diagnostic platforms such as enzyme immunoassay (EIA), chemiluminescence (CL) assay, polymerase chain reaction (PCR), flow cytometry (FC), and mass spectrometry (MS) have been used to identify molecular biomarkers. However, these diagnostic tools requiring expensive equipment, long testing time, and qualified personnel that is not always available in small local hospitals with limited resources. The lateral flow immunoassay (LFIA) platform was developed for rapidly obtaining laboratory results and to make urgent decisions in emergency medicine, as well as the recently introduced concept of testing at the site of care (point-of-care, POC). The simultaneous measurement of different substances from a single sample called multiplex assays have become increasingly significant for in vitro quantification of multiple analytes in a single sample, thereby minimising cost, time, and volume. In multiplex immunoassays, the ligands are immobilized either in planar format (flat surface) or on microspheres in suspension that binds to target analytes in sample. The multiplex technology has established itself in proteomic networks and pathways, validation of genomic discoveries, and in the development of clinical biomarkers. In the present review article, various types of monoplex/simplex and complex/multiplex immunoassays have been analysed that are increasingly being applied in laboratory medicine. Also, some advantages and disadvantages of these multiplex assays have also been included such as experimental animals, in vitro tests using cell lines and tissue samples, 3-dimensional modelling and bioprinting, in silico tests, organ-on-chip, and computer modelling.

Light-Regulated Natural Fluorescence of the PCC 6803@ZIF-8 Composite as an Encoded Microsphere for the Detection of Multiple Biomarkers

The use of color-encoded microspheres for a bead-based assay has attracted increasing attention for high-throughput multiplexed bioassays. A fluorescent PCC 6803@ZIF-8 composite was prepared as a bead-based assay platform by a self-assembled zeolitic imidazolate framework (ZIF-8) on the surface of inactivated PCC 6803 cells. The composite fluorescence owing to the presence of pigment proteins in PCC 6803 could be gradually bleached with the prolongation of the ultraviolet light irradiation time. The composites with different fluorescence intensities were therefore obtained as encoded microspheres for the multiplexed assay. ZIF-8 provides a stable, rigid shell and a large specific surface area for composites, which prevent the composites from breakage during use and storage, simplify the protein immobilization procedure, reduce non-specific adsorption, and enhance the detection sensitivity. The encoded composites were successfully used to detect multiple DNA insertion sequences of Mycobacterium tuberculosis. The presented strategy offers an innovative color-encoding method for high-throughput multiplexed bioassays without the need of using chemically synthesized fluorescent materials.

Multiplexed Affinity Characterization of Protein Binders Directly from a Crude Cell Lysate by Covalent Capture on Suspension Bead Arrays

The precise determination of affinity and specificity is a crucial step in the development of new protein reagents for therapy and diagnostics. Paradoxically, the selection of protein binders, e.g., antibody fragments, from large combinatorial repertoires is a rapid process compared to the subsequent characterization of selected clones. Here we demonstrate the use of suspension bead arrays (SBA) in combination with flow cytometry to facilitate the post-selection analysis of binder affinities. The array is designed to capture the proteins of interest (POIs) covalently on the surface of superparamagnetic color-coded microbeads directly from expression cell lysate, based on SpyTag-SpyCatcher coupling by isopeptide bond formation. This concept was validated by analyzing the affinities of a typical phage display output, i.e., clones consisting of single-chain variable fragment antibodies (scFvs), as SpyCatcher fusions in 12- and 24-plex SBA formats using a standard three-laser flow cytometer. We demonstrate that the equilibrium dissociation constants (K_d) obtained from multiplexed SBA assays correlate well with experiments performed on a larger scale, while the antigen consumption was reduced >100-fold compared to the conventional 96-well plate format. Protein screening and characterization by SBAs is a rapid and reagent-saving analytical format for combinatorial protein engineering to address specificity maturation and cross-reactivity profiling of antibodies.

Substitution Pattern-Controlled Fluorescence Lifetimes of Fluoranthene Dyes

The absorption and emission properties of organic dyes are generally tuned by altering the substitution pattern. However, tuning the fluorescence lifetimes over a range of several 10 ns while barely affecting the spectral features and maintaining a moderate fluorescence quantum yield is challenging. Such properties are required for lifetime multiplexing and barcoding applications. Here, we show how this can be achieved for the class of fluoranthene dyes, which have substitution-dependent lifetimes between 6 and 33 ns for single wavelength excitation and emission. We explore the substitution-dependent emissive properties in the crystalline solid state that would prevent applications. Furthermore, by analyzing dye mixtures and embedding the dyes in carboxy-functionalized 8 μm-sized polystyrene particles, the unprecedented potential of these dyes as labels and encoding fluorophores for time-resolved fluorescence detection techniques is demonstrated.

Polystyrene Microparticles with Convergently Grown Mesoporous Silica Shells as a Promising Tool for Multiplexed Bioanalytical Assays

Functional core/shell particles are highly sought after in analytical chemistry, especially in methods suitable for single-particle analysis such as flow cytometry because they allow for facile multiplexed detection of several analytes in a single run. Aiming to develop a powerful bead platform of which the core particle can be doped in a straightforward manner while the shell offers the highest possible sensitivity when functionalized with (bio)chemical binders, polystyrene particles were coated with different kinds of mesoporous silica shells in a convergent growth approach. Mesoporous shells allow us to obtain distinctly higher surface areas in comparison with conventional nonporous shells. While assessing the potential of narrow- as well as wide-pore silicas such as Mobil composition of matter no. 41 (MCM-41) and Santa Barbara amorphous material no. 15 (SBA-15), especially the synthesis of the latter shells that are much more suitable for biomolecule anchoring was optimized by altering the pH and both, the amount and type of the mediator salt. Our studies showed that the best performing material resulted from a synthesis using neutral conditions and MgSO₄ as an ionic mediator. The analytical potential of the particles was investigated in flow cytometric DNA assays after their respective functionalization for individual and multiplexed detection of short oligonucleotide strands. These experiments revealed that a two-step modification of the silica surface with amino silane and succinic anhydride prior to coupling of an amino-terminated capture DNA (c-DNA) strand is superior to coupling carboxylic acid-terminated c-DNA to aminated core/shell particles, yielding limits of detection (LOD) down to 5 pM for a hybridization assay, using labeled complementary single-stranded target DNA (t-DNA) 15mers. The potential of the use of the particles in multiplexed analysis was shown with the aid of dye-doped core particles carrying a respective SBA-15 shell. Characteristic genomic sequences of human papillomaviruses (HPV) were chosen as the t-DNA analytes here, since their high relevance as carcinogens and the high number of different pathogens is a relevant model case. The title particles showed a promising performance and allowed us to unequivocally detect the different high- and low-risk HPV types in a single experimental run.

Spectral-Time Multiplexing in FRET Complexes of AgInS2/ZnS Quantum Dot and Organic Dyes

Nowadays, multiplex analysis is very popular, since it allows to detect a large number of biomarkers simultaneously. Traditional multiplex analysis is usually based on changes of photoluminescence (PL) intensity and/or PL band spectral positions in the presence of analytes. Using PL lifetime as an additional parameter might increase the efficiency of multiplex methods. Quantum dots (QDs) can be used as luminescent markers for multiplex analysis. Ternary in-based QDs are a great alternative to the traditional Cd-based one. Ternary QDs possess all advantages of traditional QDs, including tunable photoluminescence in visible range. At the same time ternary QDs do not have Cd-toxicity, and moreover they possess long spectral dependent lifetimes. This allows the use of ternary QDs as a donor for time-resolved multiplex sensing based on Förster resonance energy transfer (FRET). In the present work, we implemented FRET from AgInS₂/ZnS ternary QDs to cyanine dyes absorbing in different spectral regions of QD luminescence with different lifetimes. As the result, FRET-induced luminescence of dyes differed not only in wavelengths but also in lifetimes of luminescence, which can be used for time-resolved multiplex analysis in biology and medicine.

Spatially isolated reactions in a complex array: using magnetic beads to purify and quantify nucleic acids with digital and quantitative real-time PCR in thousands of parallel microwells

Quantitative real-time PCR (qPCR) has been the standard for nucleic acid quantification as it has a large dynamic range and good sensitivity. Digital PCR is rapidly supplanting qPCR in many applications as it provides excellent quantitative precision. However, both techniques require extensive sample preparation, and highly multiplexed assays that quantify multiple targets can be difficult to design and optimize. Here we describe a new nucleic acid quantification method that we call Spatially Isolated Reactions in a Complex Array (SIRCA), a highly parallel nucleic acid preparation, amplification, and detection approach that uses superparamagnetic microbeads in an array of thousands of 100 fL microwells to simplify sample purification and reduce reagent dispensing steps. Primers, attached to superparamagnetic microbeads through a thermo-labile bond, capture and separate target sequences from the sample. The microbeads are then magnetically loaded into a microwell array such that wells predominately contain a single bead. Master mix, lacking primers, is added before sealing the reaction wells with hydrophobic oil. Thermocycling releases the primer pair from the beads during PCR amplification. At low target concentrations, most beads capture, on average, less than one target molecule, and precise, digital PCR quantification can be derived from the percentage of positive reactions. At higher concentrations, qPCR signal is used to determine the average number of target molecules per reaction, significantly extending the dynamic range beyond the digital saturation point. We demonstrate that SIRCA can quantify DNA and RNA targets using thousands of parallel reactions, achieving attomolar limits of detection and a linear dynamic range of 105. The work reported here is a first step towards multiplexed SIRCA assays.

Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition)

These guidelines are a consensus work of a considerable number of members of the immunology and flow cytometry community. They provide the theory and key practical aspects of flow cytometry enabling immunologists to avoid the common errors that often undermine immunological data. Notably, there are comprehensive sections of all major immune cell types with helpful Tables detailing phenotypes in murine and human cells. The latest flow cytometry techniques and applications are also described, featuring examples of the data that can be generated and, importantly, how the data can be analysed. Furthermore, there are sections detailing tips, tricks and pitfalls to avoid, all written and peer-reviewed by leading experts in the field, making this an essential research companion.

Ultrasimple Single-Cell Detection of Multiple Cytokines by a Nanowell Chip Integrated with Encoded Microarrays

Cytokine production is often regarded as the marker of immune cells' activation status. The spectrum and temporal secretion of cytokines are dramatically varied between cell phenotypes and even within the same phenotype. Multiparameter analysis of individual immune cell's cytokine secretion has always been a challenging and complicated process that needs special facilities in a laboratory setting. Herein, we present an ultrasimple method with high sensitivity and high robustness to quantify cytokine expression at the single-cell resolution. A microchip is developed based on poly(dimethylsiloxane) nanowells on sticky tape, while each nanowell is integrated with a DNA-antibody convertible microarray. Only pipetting is needed for the whole single-cell analysis process. The sensitivity of the assay is evaluated by measuring various concentrations of six recombinant cytokine proteins, which was found comparable to conventional methods. Once single cells are loaded to nanowells and incubated there, a Fluorinert FC-40 is used to isolate nanowells; so, cytokines from those cells are captured by separate microarrays. The rest of the sandwich enzyme-linked immunosorbent assay detection process is also executed simply by pipetting of various reagents. This method is validated by measuring cytokine production from hundreds of single cells. It has simplified a typically sophisticated multiplex single-cell assay into an instrument-free, point-of-detection technology, and thus it may find a broad utility in clinical diagnostics.

An open-source software analysis package for Microspheres with Ratiometric Barcode Lanthanide Encoding (MRBLEs)

Multiplexed bioassays, in which multiple analytes of interest are probed in parallel within a single small volume, have greatly accelerated the pace of biological discovery. Bead-based multiplexed bioassays have many technical advantages, including near solution-phase kinetics, small sample volume requirements, many within-assay replicates to reduce measurement error, and, for some bead materials, the ability to synthesize analytes directly on beads via solid-phase synthesis. To allow bead-based multiplexing, analytes can be synthesized on spectrally encoded beads with a 1:1 linkage between analyte identity and embedded codes. Bead-bound analyte libraries can then be pooled and incubated with a fluorescently-labeled macromolecule of interest, allowing downstream quantification of interactions between the macromolecule and all analytes simultaneously via imaging alone. Extracting quantitative binding data from these images poses several computational image processing challenges, requiring the ability to identify all beads in each image, quantify bound fluorescent material associated with each bead, and determine their embedded spectral code to reveal analyte identities. Here, we present a novel open-source Python software package (the mrbles analysis package) that provides the necessary tools to: (1) find encoded beads in a bright-field microscopy image; (2) quantify bound fluorescent material associated with bead perimeters; (3) identify embedded ratiometric spectral codes within beads; and (4) return data aggregated by embedded code and for each individual bead. We demonstrate the utility of this package by applying it towards analyzing data generated via multiplexed measurement of calcineurin protein binding to MRBLEs (Microspheres with Ratiometric Barcode Lanthanide Encoding) containing known and mutant binding peptide motifs. We anticipate that this flexible package should be applicable to a wide variety of assays, including simple bead or droplet finding analysis, quantification of binding to non-encoded beads, and analysis of multiplexed assays that use ratiometric, spectrally encoded beads.

Multifunctional Polystyrene Core/Silica Shell Microparticles with Antifouling Properties for Bead-Based Multiplexed and Quantitative Analysis

Commercial bead-based assays are commonly built upon polystyrene particles. The polymeric carrier can be encoded with organic dyes and has ideal material properties for cytometric applications such as low density and high refractive index. However, functional groups are conventionally integrated during polymerization and subsequent modification is limited to the reactivity of those groups. Additionally, polystyrene as the core material leads to many hydrophobic areas still being present on the beads' surfaces even after functionalization, rendering the particles prone to nonspecific adsorption during an application. The latter calls for several washing steps and the use of additives in (bio)analytical assays. In this contribution, we show how these limitations can be overcome by using monodisperse polystyrene (PS) core/silica (SiO₂) shell particles (SiO₂@PS). Two different hydrophobic BODIPY (boron-dipyrromethene) dyes were encapsulated inside a poly(vinylpyrrolidone) (PVP) -stabilized polystyrene core in different concentrations to create 5-plex arrays in two separate detection channels of a cytometer. A subsequent modification of the silica shell with an equimolar APTES/PEGS (aminopropyltriethoxysilane/polyethylene glycol silane) blend added multifunctional properties to the hybrid core/shell microparticles in a single step: APTES provides amino groups for the attachment of a caffeine derivative (as a hapten) to create antigen-coupled microspheres; the PEG moiety effectively suppresses nonspecific binding of antibodies, endowing the surface with antifouling properties. The particles were applied in a competitive fluorescence immunoassay in suspension, and a highly selective wash-free assay for the detection of caffeine in beverages was developed as a proof of concept.

Early diagnosis of disease using microbead array technology: A review

Early diagnosis of diseases (before they become advanced and incurable) is essential to reduce morbidity and mortality rates. With the advent of novel technologies in clinical laboratory diagnosis, microbead-based arrays have come to be recognized as an efficient approach, that demonstrates useful advantages over traditional assay methods for multiple disease-related biomarkers. Multiplexed microbead assays provide a robust, rapid, specific, and cost-effective approach for high-throughput and simultaneous screening of many different targets. Biomolecular binding interactions occur after applying a biological sample (such as blood plasma, saliva, cerebrospinal fluid etc.) containing the target analyte(s) to a set of microbeads with different ligand-specificities that have been coded in planar or suspension arrays. The ligand-receptor binding activity is tracked by optical signals generated by means of flow cytometry analysis in the case of suspension arrays, or by image processing devices in the case of planar arrays. In this review paper, we discuss diagnosis of cancer, neurological and infectious diseases by using optically-encoded microbead-based arrays (both multiplexed and single-analyte assays) as a reliable tool for detection and quantification of various analytes.

Rapid Differentiation of Host and Parasitic Exosome Vesicles Using Microfluidic Photonic Crystal Biosensor

Parasite extracellular vesicles (EVs) are potential biomarkers that could be exploited for the diagnosis of infectious disease. This paper reports a rapid bioassay to discriminate parasite and host EVs. The EV detection assay utilizes a label-free photonic crystal (PC) biosensor to detect the EVs using a host-specific transmembrane protein (CD63), which is present on EV secreted by host cells (modeled by murine macrophage cell line J774A.1) but is not expressed on EV secreted by parasitic nematodes such as the gastrointestinal nematode Ascaris suum. The surface of PC is functionalized to recognize CD63, and is sensitive to the changes in refractive index caused by the immobilization of EVs. The biosensor demonstrates a detection limit of 2.18 × 10⁹ EVs/mL and a capability to characterize the affinity constants of antibody-host EV bindings. The discrimination of murine host EVs from parasite EVs indicates the capability of the sensor to differentiate EVs from different origins. The label-free, rapid EV assay could be used to detection parasite infection and facilitate the exosome-based clinic diagnosis and exosome research.

Multiphoton-Polymerized 3D Protein Assay

Multiphoton polymerization (MPP) enables 3D fabrication of micro- and nanoscale devices with complex geometries. Using MPP, we create a 3D platform for protein assays. Elevating the protein-binding sites above the substrate surface allows an optically sectioned readout, minimizing the inevitable background signal from nonspecific protein adsorption at the substrate surface. Two fluorescence-linked immunosorbent assays are demonstrated, the first one relying on streptavidin-biotin recognition and the second one on antibody recognition of apolipoprotein A1, a major constituent of high-density lipoprotein particles. Signal-to-noise ratios exceeding 1000 were achieved. The platform has high potential for 3D multiplexed recognition assays with an increased binding surface for on-chip flow cells.

Cytokine-based Predictive Models to Estimate the Probability of Chronic Periodontitis: Development of Diagnostic Nomograms

Although a distinct cytokine profile has been described in the gingival crevicular fluid (GCF) of patients with chronic periodontitis, there is no evidence of GCF cytokine-based predictive models being used to diagnose the disease. Our objectives were: to obtain GCF cytokine-based predictive models; and develop nomograms derived from them. A sample of 150 participants was recruited: 75 periodontally healthy controls and 75 subjects affected by chronic periodontitis. Sixteen mediators were measured in GCF using the Luminex 100™ instrument: GMCSF, IFNgamma, IL1alpha, IL1beta, IL2, IL3, IL4, IL5, IL6, IL10, IL12p40, IL12p70, IL13, IL17A, IL17F and TNFalpha. Cytokine-based models were obtained using multivariate binary logistic regression. Models were selected for their ability to predict chronic periodontitis, considering the different role of the cytokines involved in the inflammatory process. The outstanding predictive accuracy of the resulting smoking-adjusted models showed that IL1alpha, IL1beta and IL17A in GCF are very good biomarkers for distinguishing patients with chronic periodontitis from periodontally healthy individuals. The predictive ability of these pro-inflammatory cytokines was increased by incorporating IFN gamma and IL10. The nomograms revealed the amount of periodontitis-associated imbalances between these cytokines with pro-inflammatory and anti-inflammatory effects in terms of a particular probability of having chronic periodontitis.

Fluorescence activated cell sorting via a focused traveling surface acoustic beam

Fluorescence activated cell sorting (FACS) has become an essential technique widely exploited in biological studies and clinical applications. However, current FACS systems are quite complex, expensive, bulky, and pose potential sample contamination and biosafety issues due to the generation of aerosols in an open environment. Microfluidic technology capable of precise cell manipulation has great potential to reinvent and miniaturize conventional FACS systems. In this work, we demonstrate a benchtop scale FACS system that makes use of a highly focused traveling surface acoustic wave beam to sort out micron-sized particles and biological cells upon fluorescence interrogation at ∼kHz rates. The highly focused acoustic wave beam has a width of ∼50 μm that enables highly accurate sorting of individual particles and cells. We have applied our acoustic FACS system to isolate fluorescently labeled MCF-7 breast cancer cells from diluted whole blood samples with the purity of sorted MCF-7 cells higher than 86%. The cell viability before and after acoustic sorting is higher than 95%, indicating excellent biocompatibility that should enable a variety of cell sorting applications in biomedical research.

A Microsphere-Supported Lipid Bilayer Platform for DNA Reactions on a Fluid Surface

We report a versatile microsphere-supported lipid bilayer system that can serve as a general-purpose platform for implementing DNA nanotechnologies on a fluid surface. To demonstrate our platform, we implemented both toehold-mediated strand displacement (TMSD) and DNAzyme reactions, which are typically performed in solution and which are the cornerstone of DNA-based molecular logic and dynamic DNA nanotechnology, on the surface. We functionalized microspheres bearing supported lipid bilayers (μSLBs) with membrane-bound nucleic acid components. Using functionalized μSLBs, we developed TMSD and DNAzyme reactions by optimizing reaction conditions to reduce nonspecific interactions between DNA and phospholipids and to enhance bilayer stability. Additionally, the physical and optical properties of the bilayer were tuned via lipid composition and addition of fluorescently tagged lipids to create stable and multiplexable μSLBs that are easily read out by flow cytometry. Multiplexed TMSD reactions on μSLBs enabled the successful operation of a Dengue serotyping assay that correctly identified all 16 patterns of target sequences to demonstrate detection of DNA strands derived from the sequences of all four Dengue serotypes. The limit of detection for this assay was 3 nM. Furthermore, we demonstrated DNAzyme reactions on a fluid lipid surface, which benefit from free diffusion on the surface. This work provides the basis for expansion of both TMSD and DNAzyme based molecular reactions on supported lipid bilayers for use in molecular logic and DNA nanotechnology. As our system is multiplexable and results in fluid surfaces, it may be of use in compartmentalization and improved kinetics of molecular logic reactions and as a useful building block in a variety of DNA nanotechnology systems.

Validation of two multiplex platforms to quantify circulating markers of inflammation and endothelial injury in severe infection

Biomarkers can prognosticate outcome and enable risk-stratification. In severe infection, focusing on multiple markers reflecting pathophysiological mechanisms of organ injury could enhance management and pathway-directed therapeutics. Limited data exist on the performance of multiplex biomarker platforms. Our goal was to compare endothelial and immune activation biomarkers in severe pediatric infections using two multiplex platforms. Frozen plasma from 410 children presenting to the Jinja Regional Hospital in Uganda with suspected infection was used to measure biomarkers of endothelial (Angiopoietin-2, sFlt-1, sVCAM-1, sICAM-1) and immune (IL-6, IP-10, sTNFR-1, CHI3L1) activation. Two multiplex platforms (Luminex®, Ella^TM) based on monoclonal antibody sandwich immunoassays using biotin-streptavidin conjugate chemistry were selected with reagents from R&D Systems. The two platforms differed in ease and time of completion, number of samples per assay, and dynamic concentration range. Intra-assay variability assessed using a coefficient of variation (CV%) was 2.2–3.4 for Luminex® and 1.2–2.9 for Ella^TM. Correlations for biomarker concentrations within dynamic range of both platforms were best for IL-6 (ρ = 0.96, p<0.0001), IP-10 (ρ = 0.94, p<0.0001) and sFlt-1 (ρ = 0.94, p<0.0001). Agreement between concentrations obtained by both methods assessed by the Bland-Altman test varied, with best agreement for CHI3L1. Our data suggest that biomarkers of endothelial and immune activation can be readily measured with multiplex platforms. Luminex® and Ella^TM produced reliable results with excellent CV% values. The Ella^TM platform was more automated and completed in 75 minutes, potentially compatible with near-patient use. Trends in concentrations obtained by these methods were highly correlated, although absolute values varied, suggesting caution is required when comparing data from different multiplex platforms.

Determination of Mycotoxin Production of Fusarium Species in Genetically Modified Maize Varieties by Quantitative Flow Immunocytometry

Levels of mycotoxins produced by Fusarium species in genetically modified (GM) and near-isogenic maize, were determined using multi-analyte, microbead-based flow immunocytometry with fluorescence detection, for the parallel quantitative determination of fumonisin B1, deoxynivalenol, zearalenone, T-2, ochratoxin A, and aflatoxin B1. Maize varieties included the genetic events MON 810 and DAS-59122-7, and their isogenic counterparts. Cobs were artificially infested by F. verticillioides and F. proliferatum conidia, and contained F. graminearum and F. sporotrichoides natural infestation. The production of fumonisin B1 and deoxynivalenol was substantially affected in GM maize lines: F. verticillioides, with the addition of F. graminearum and F. sporotrichoides, produced significantly lower levels of fumonisin B1 (~300 mg·kg-1) in DAS-59122-7 than in its isogenic line (~580 mg·kg-1), while F. proliferatum, in addition to F. graminearum and F. sporotrichoides, produced significantly higher levels of deoxynivalenol (~18 mg·kg-1) in MON 810 than in its isogenic line (~5 mg·kg-1). Fusarium verticillioides, with F. graminearum and F. sporotrichoides, produced lower amounts of deoxynivalenol and zearalenone than F. proliferatum, with F. graminearum and F. sporotrichoides. T-2 toxin production remained unchanged when considering the maize variety. The results demonstrate the utility of the Fungi-Plex™ quantitative flow immunocytometry method, applied for the high throughput parallel determination of the target mycotoxins.

Programmable Microfluidic Synthesis of Over One Thousand Uniquely Identifiable Spectral Codes

Encoded microparticles have become a powerful tool for a wide array of applications, including high-throughput sample tracking and massively parallel biological multiplexing. Spectral encoding, where particles are encoded with distinct luminescence spectra, provides a particularly appealing encoding strategy because of the ease of reading codes and assay flexibility. To date, spectral encoding has been limited in the number of codes that can be accurately resolved. Here, we demonstrate an automated 5-dimensional spectral encoding scheme using lanthanide nanophosphors that is capable of producing isotropic spherical microparticles with up to 1,100 unique codes, which we term MRBLEs (Microspheres with Ratiometric Barcode Lanthanide Encoding). We further develop a quantitative framework for evaluating global ability to distinguish codes and demonstrate that for six different sets of MRBLEs ranging from 106 to 1,101 codes in size, > 98% of MRBLEs can be assigned to a code with 99.99% confidence. These > 1,000 code sets represent the largest spectral code libraries built to date. We expect that these MRBLEs will enable a wide variety of novel multiplexed assays.

Transport of biomolecules to binding partners displayed on the surface of microbeads arrayed in traps in a microfluidic cell

Arrays of probe molecules integrated into a microfluidic cell are utilized as analytical tools to screen the binding interactions of the displayed probes against a target molecule. These assay platforms are useful in enzyme or antibody discovery, clinical diagnostics, and biosensing, as their ultraminiaturized design allows for high sensitivity and reduced consumption of reagents and target. We study here a platform in which the probes are first grafted to microbeads which are then arrayed in the microfluidic cell by capture in a trapping course. We examine a course which consists of V-shaped, half-open enclosures, and study theoretically and experimentally target mass transfer to the surface probes. Target binding is a two step process of diffusion across streamlines which convect the target over the microbead surface, and kinetic conjugation to the surface probes. Finite element simulations are obtained to calculate the target surface concentration as a function of time. For slow convection, large diffusive gradients build around the microbead and the trap, decreasing the overall binding rate. For rapid convection, thin diffusion boundary layers develop along the microbead surface and within the trap, increasing the binding rate to the idealized limit of untrapped microbeads in a channel. Experiments are undertaken using the binding of a target, fluorescently labeled NeutrAvidin, to its binding partner biotin, on the microbead surface. With the simulations as a guide, we identify convective flow rates which minimize diffusion barriers so that the transport rate is only kinetically determined and measure the rate constant.

Quantitative body fluid proteomics in medicine - A focus on minimal invasiveness

Identification of new biomarkers specific for various pathological conditions is an important field in medical sciences. Body fluids have emerging potential in biomarker studies especially those which are continuously available and can be collected by non-invasive means. Changes in the protein composition of body fluids such as tears, saliva, sweat, etc. may provide information on both local and systemic conditions of medical relevance. In this review, our aim is to discuss the quantitative proteomics techniques used in biomarker studies, and to present advances in quantitative body fluid proteomics of non-invasively collectable body fluids with relevance to biomarker identification. The advantages and limitations of the widely used quantitative proteomics techniques are also presented. Based on the reviewed literature, we suggest an ideal pipeline for body fluid analyses aiming at biomarkers discoveries: starting from identification of biomarker candidates by shotgun quantitative proteomics or protein arrays, through verification of potential biomarkers by targeted mass spectrometry, to the antibody-based validation of biomarkers. The importance of body fluids as a rich source of biomarkers is discussed.

SIGNIFICANCE

Quantitative proteomics is a challenging part of proteomics applications. The body fluids collected by non-invasive means have high relevance in medicine; they are good sources for biomarkers used in establishing the diagnosis, follow up of disease progression and predicting high risk groups. The review presents the most widely used quantitative proteomics techniques in body fluid analysis and lists the potential biomarkers identified in tears, saliva, sweat, nasal mucus and urine for local and systemic diseases.

High-resolution Antibody Array Analysis of Childhood Acute Leukemia Cells

Acute leukemia is a disease pathologically manifested at both genomic and proteomic levels. Molecular genetic technologies are currently widely used in clinical research. In contrast, sensitive and high-throughput proteomic techniques for performing protein analyses in patient samples are still lacking. Here, we used a technology based on size exclusion chromatography followed by immunoprecipitation of target proteins with an antibody bead array (Size Exclusion Chromatography-Microsphere-based Affinity Proteomics, SEC-MAP) to detect hundreds of proteins from a single sample. In addition, we developed semi-automatic bioinformatics tools to adapt this technology for high-content proteomic screening of pediatric acute leukemia patients.To confirm the utility of SEC-MAP in leukemia immunophenotyping, we tested 31 leukemia diagnostic markers in parallel by SEC-MAP and flow cytometry. We identified 28 antibodies suitable for both techniques. Eighteen of them provided excellent quantitative correlation between SEC-MAP and flow cytometry (p< 0.05). Next, SEC-MAP was applied to examine 57 diagnostic samples from patients with acute leukemia. In this assay, we used 632 different antibodies and detected 501 targets. Of those, 47 targets were differentially expressed between at least two of the three acute leukemia subgroups. The CD markers correlated with immunophenotypic categories as expected. From non-CD markers, we found DBN1, PAX5, or PTK2 overexpressed in B-cell precursor acute lymphoblastic leukemias, LAT, SH2D1A, or STAT5A overexpressed in T-cell acute lymphoblastic leukemias, and HCK, GLUD1, or SYK overexpressed in acute myeloid leukemias. In addition, OPAL1 overexpression corresponded to ETV6-RUNX1 chromosomal translocation.In summary, we demonstrated that SEC-MAP technology is a powerful tool for detecting hundreds of proteins in clinical samples obtained from pediatric acute leukemia patients. It provides information about protein size and reveals differences in protein expression between particular leukemia subgroups. Forty-seven of SEC-MAP identified targets were validated by other conventional method in this study.

Microfluidic Single-Cell Analysis with Affinity Beads

A micrometer-sized affinity bead (red) is (i) taken up into a cell by phagocytosis, (ii) photochemically released from phagosomes, (iii) optically trapped by the cell, and (iv) isolated by cell lysis for subsequent analysis of captured intracellular analyte (green).

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.

Reduction in aggregation and energy transfer of quantum dots incorporated in polystyrene beads by kinetic entrapment due to cross-linking during polymerization

We report the development of barcoded polystyrene microbeads, approximately 50 μm in diameter, which are encoded by incorporating multicolored semiconductor fluorescent nanocrystals (quantum dots or QDs) within the microbeads and using the emission spectrum of the embedded QDs as a spectral label. The polymer/nanocrystal bead composites are formed by polymerizing emulsified liquid droplets of styrene monomer and QDs suspended in an immiscible continuous phase (suspension polymerization). We focus specifically on the effect of divinylbenzene (DVB) added to cross-link the linearly growing styrene polymer chains and the effect of this cross-linking on the state of aggregation of the nanocrystals in the composite. Aggregated states of multicolor QDs give rise to nonradiative resonance energy transfer (RET) which distorts the emission label from a spectrum recorded in a reference solvent in which the nanocrystals are well dispersed and unaggregated. A simple barcode is chosen of a mixture of QDs emitting at 560 (yellow) and 620 nm (red). We find that for linear chain growth (no DVB), the QDs aggregate as is evident from the emission spectrum and the QD distribution as seen from confocal laser scanning microscopy (CLSM) and transmission electron microscopy (TEM) images. Increasing the extent of cross-linking by the addition of DVB is shown to significantly decrease the aggregation and provide a clear label. We suggest that in the absence of cross-linking, linearly growing polymer chains, through enthalpic and entropic effects, drive the nanocrystals into inclusions, while cross-linking kinetically entraps the particle and prevents their aggregation.

Novel calibration tools and validation concepts for microarray-based platforms used in molecular diagnostics and food safety control

Commercial platforms consisting of ready-to-use microarrays printed with target-specific DNA probes, a microarray scanner, and software for data analysis are available for different applications in medical diagnostics and food analysis, detecting, e.g., viral and bacteriological DNA sequences. The transfer of these tools from basic research to routine analysis, their broad acceptance in regulated areas, and their use in medical practice requires suitable calibration tools for regular control of instrument performance in addition to internal assay controls. Here, we present the development of a novel assay-adapted calibration slide for a commercialized DNA-based assay platform, consisting of precisely arranged fluorescent areas of various intensities obtained by incorporating different concentrations of a "green" dye and a "red" dye in a polymer matrix. These dyes present "Cy3" and "Cy5" analogues with improved photostability, chosen based upon their spectroscopic properties closely matching those of common labels for the green and red channel of microarray scanners. This simple tool allows to efficiently and regularly assess and control the performance of the microarray scanner provided with the biochip platform and to compare different scanners. It will be eventually used as fluorescence intensity scale for referencing of assays results and to enhance the overall comparability of diagnostic tests.

Mass transfer in the biomolecular binding of a target against probe molecules on the surface of microbeads sequestered in wells in a microfluidic cell

Diagnostic tools which screen the binding interactions of a protein target against a display of biomolecular probes to identify molecules which bind the target are central to cell proteomic studies, and to diagnostic assays. Here, we study a microfluidic design for screening interactions in which the probe molecules are hosted on microbeads sequestered in wells arranged at the bottom of a microfluidic flow channel. Assays are undertaken by streaming an analyte solution with a fluorescently labelled target through the cell, and identifying the fluorescing beads. Numerical simulations are first constructed for the analyte flow over the microbeads in the well array, and the increase in the target concentration on the microbead surface. The binding profile is expressed as a function of the ratio of the convective to the diffusive transport rates (Peclet number or Pe), and the ratio of the kinetic to the diffusive rates (Damkohler number, Da). For any Pe, as Da becomes small enough, the transport is determined by the intrinsic kinetic binding rate. As Pe increases, a thin concentration boundary layer develops over the top surface of the microbead because of the convective flow, and target binds more rapidly. However, the relatively stagnant layers of liquid in the well provide a diffusion barrier which slows the target transport, and for any Da and Pe the transport is slower than equivalent patches of probes arranged on the channel wall. Experiments are also undertaken at high Pe, using the binding of fluorescently labelled NeutrAvidin as a target to probes of its binding partner, biotin, on the microbead surface. The binding profile is compared to the simulations to measure the kinetic rate constant, and this comparison shows that the transport in the cell is not kinetically limited because of the diffusion barriers created by the stagnant liquid layer in the well. Simulations and experiments on microbeads which are only partially recessed in the well demonstrate an increase in the mass transfer rate as more of the microbead surface intersects the flow and the diffusion limitation due to the stagnant layer of liquid surrounding the bottom part of the microbead is minimized.

Biomineralized anisotropic gold microplate-macrophage interactions reveal frustrated phagocytosis-like phenomenon: a novel paclitaxel drug delivery vehicle

This study reports a facile biomineralization route for gold microplates (GMPs) synthesis using bovine serum albumin (BSA) as a reductant and stabilizing agent. Adding BSA to HAuCl4 solution yields spontaneous versatile anisotropic and partially hollow GMPs upon aging. We hypothesize that the instantaneous protein denaturation at low pH enabled access to serine and threonine hydroxyl, and sulfhydryl groups of BSA, which act as a reductant and stabilizer, respectively. This reaction could be hastened by increasing the temperature well beyond 65 °C. Transmission electron microscopy/X-ray diffraction studies revealed highly crystalline and anisotropic structures (triangle, pentagon, and rectangle). Atomic force microscopy/scanning electron microscopy analyses demonstrated unique morphology of microplates with a partially void core and BSA mineralized edge structure. RAW 264.7 mice peritoneal macrophage-microplate interaction studies using live cell confocal imaging reveal that cells are capable of selectively internalizing smaller GMPs. Large GMPs are preferentially picked with sharp vertices but cannot be internalized and exhibit frustrated phagocytosis-like phenomenon. We explored particle phagocytosis as an actin mediated process that recruits phagosome-like acidic organelles, shown by a lysosensor probe technique. The biocompatible GMPs exhibited ∼70% paclitaxel (PCL) loading and sustained release of PCL, showing antitumor activity with the MCF-7 cell line, and could be a novel drug carrier for breast cancer therapy.

Synthesis, characterization, and directional binding of anisotropic biohybrid microparticles for multiplexed biosensing

Anisotropic microarchitectures with different physicochemical properties have been developed as advanced materials for challenging industrial and biomedical applications including switchable displays, multiplexed biosensors and bioassays, spatially-controlled drug delivery systems, and tissue engineering scaffolds. In this study, anisotropic biohybrid microparticles (MPs) spatio-selectively conjugated with two different antibodies (Abs) are first developed for fluorescence-based, multiplexed sensing of biological molecules. Poly(acrylamide-co-acrylic acid) is chemically modified with maleimide- or acetylene groups to introduce different targeting biological moieties into each compartment of anisotropic MPs. Modified polymer solutions containing two different fluorescent dyes are separately used for electrohydrodynamic co-jetting with side-by-side needle geometry. The anisotropic MPs are chemically stabilized by thermal imidization, followed by bioconjugation of two different sets of polyclonal Abs with two individual compartments via maleimide-thiol coupling reaction and Huisgen 1,3-dipolar cycloaddition. Finally, two compartments of the anisotropic biohybrid MPs are spatio-selectively associated with the respective monoclonal Ab-immobilized substrate in the presence of the antigen by sandwich-type immunocomplex formation, resulting in their ordered orientation due to the spatio-specific molecular interaction, as confirmed by confocal laser scanning microscopy. In conclusion, anisotropic biohybrid MPs capable of directional binding have great potential as a new fluorescence-based multiplexing biosensing system.

NIR-emitting quantum dot-encoded microbeads through membrane emulsification for multiplexed immunoassays

NIR-emitting CdSeTe/CdS/ZnS core/shell/shell QD-encoded microbeads are combined with common flow cytometry with one laser for multiplexed detection of hepatitis B virus (HBV). A facile one-pot synthetic route is developed to prepare CdSeTe/CdS/ZnS core/shell/shell QDs with high photoluminescence quantum yield and excellent stability in liquid paraffin, and a Shirasu porous glass (SPG) membrane emulsification technique is applied to incorporate the QDs into polystyrene-maleic anhydride (PSMA) microbeads to obtain highly fluorescent QD-encoded microbeads. The relatively wide NIR photoluminescence full width half maximum of the CdSeTe/CdS/ZnS QDs is used to develop a 'single wavelength' encoding method to obtain different optical codes by changing the wavelengh and emission intensity of the QDs incorporated into the microbeads. Moreover, a detection platform combining NIR-emitting CdSeTe/CdS/ZnS QD-encoded microbeads and Beckman Coulter FC 500 flow cytometry with one laser of 488 nm is successfully used to conduct a 2-plex hybridization assay for hepatitis B surface antigen (HBsAg), hepatitis B e antigen (HBeAg), and a 3-plex hybridization assay for hepatitis B surface antibody (HBsAb), hepatitis B e antibody (HBeAb), and hepatitis B core antibody (HBcAb), which suggests the promising application of NIR QD-encoded microbeads for multiplex immunoassays.

Coupled solid phase extraction and microparticle-based stability and purity-indicating immunosensor for the determination of recombinant human myelin basic protein in transgenic milk

An optical immunosensor was developed and validated on the surface of microparticles for the determination of a biopharmaceutical protein. The recombinant human myelin basic protein (rhMBP) was produced in milk of transgenic cows as a His-tagged fusion protein. Previous work indicated exclusive association of rhMBP with milk casein micelles that hindered direct determination of the protein in milk. In this work, a solid phase extraction using a cation exchange matrix was developed in order to liberate rhMBP from casein micelles. A sandwich-type immunoassay was then used for in-process monitoring of the full-length protein in the presence of major milk proteins. The assay was successfully employed for detection of ultra-traces of rhMBP (LOD=6.04 ng mL(-1)≈0.3 n mol L(-1)) and for quantitative determination over a wide concentration range (10.00-10,000.00 ng mL(-1)). The assay was able also to detect the rhMBP in the presence of its human counterpart that lacks the His-tag. The high sensitivity along with the ability of the assay to determine the full length protein enabled monitoring of the stability of rhMBP. The testing protocol is particularly useful for intrinsically unstructured proteins that are extremely sensitive to proteolysis and lack a traceable enzymatic activity. This immunosensor provides a specific, ultrasensitive high throughput tool for in-process monitoring in biopharmaceutical industry.

Spectral flow cytometry

Interest in measuring the complete fluorescence spectra of individual cells in flow can be traced to the earliest days of flow cytometry. Recent advances in detectors, optics, and computation have made it possible to make full spectral measurements in the sub-millisecond time frame in which flow cytometry measurements typically occur. This opens up new possibilities for applying spectroscopy to the analysis of individual cells. This unit reviews historical and contemporary approaches to spectral flow cytometry, as well as instrument design, calibration, and data analysis for spectral flow cytometry applications.

Serum and plasma proteomics and its possible use as detector and predictor of radiation diseases

All tissues can be damaged by ionizing radiation. Early biomarkers of radiation injury are critical for triage, treatment and follow-up of large numbers of people exposed to ionizing radiation after terrorist attacks or radiological accident, and for prediction of normal tissue toxicity before, during and after a treatment by radiotherapy. The comparative proteomic approach is a promising and powerful tool for the discovery of new radiation biomarkers. In association with multivariate statistics, proteomics enables measurement of the level of hundreds or thousands of proteins at the same time and identifies set of proteins that can discriminate between different groups of individuals. Human serum and plasma are the preferred samples for the study of normal and disease-associated proteins. Extreme complexity, extensive dynamic range, genetic and physiological variations, protein modifications and incompleteness of sampling by two-dimensional electrophoresis and mass spectrometry represent key challenges to reproducible, high-resolution, and high-throughput analyses of serum and plasma proteomes. The future of radiation research will possibly lie in molecular networks that link genome, transcriptome, proteome and metabolome variations to radiation pathophysiology and serve as sensors of radiation disease. This chapter reviews recent advances in proteome analysis of serum and plasma as well as its applications to radiation biology and radiation biomarker discovery for both radiation exposure and radiation tissue toxicity.

Single cell analysis using surface enhanced Raman scattering (SERS) tags

Fluorescence is a mainstay of bioanalytical methods, offering sensitive and quantitative reporting, often in multiplexed or multiparameter assays. Perhaps the best example of the latter is flow cytometry, where instruments equipped with multiple lasers and detectors allow measurement of 15 or more different fluorophores simultaneously, but increases beyond this number are limited by the relatively broad emission spectra. Surface enhanced Raman scattering (SERS) from metal nanoparticles can produce signal intensities that rival fluorescence, but with narrower spectral features that allow a greater degree of multiplexing. We are developing nanoparticle SERS tags as well as Raman flow cytometers for multiparameter single cell analysis of suspension or adherent cells. SERS tags are based on plasmonically active nanoparticles (gold nanorods) whose plasmon resonance can be tuned to give optimal SERS signals at a desired excitation wavelength. Raman resonant compounds are adsorbed on the nanoparticles to confer a unique spectral fingerprint on each SERS tag, which are then encapsulated in a polymer coating for conjugation to antibodies or other targeting molecules. Raman flow cytometry employs a high resolution spectral flow cytometer capable of measuring the complete SERS spectra, as well as conventional flow cytometry measurements, from thousands of individual cells per minute. Automated spectral unmixing algorithms extract the contributions of each SERS tag from each cell to generate high content, multiparameter single cell population data. SERS-based cytometry is a powerful complement to conventional fluorescence-based cytometry. The narrow spectral features of the SERS signal enables more distinct probes to be measured in a smaller region of the optical spectrum with a single laser and detector, allowing for higher levels of multiplexing and multiparameter analysis.

Fluorescence-based multiplex protein detection using optically encoded microbeads

Potential utilization of proteins for early detection and diagnosis of various diseases has drawn considerable interest in the development of protein-based multiplex detection techniques. Among the various techniques for high-throughput protein screening, optically-encoded beads combined with fluorescence-based target monitoring have great advantages over the planar array-based multiplexing assays. This review discusses recent developments of analytical methods of screening protein molecules on microbead-based platforms. These include various strategies such as barcoded microbeads, molecular beacon-based techniques, and surface-enhanced Raman scattering-based techniques. Their applications for label-free protein detection are also addressed. Especially, the optically-encoded beads such as multilayer fluorescence beads and SERS-encoded beads are successful for generating a large number of coding.

A clinic-biological score for diagnosing early-onset neonatal infection in critically ill preterm infants

OBJECTIVE

To identify the best combination of serum cytokines and clinical parameters to diagnose rapidly early-onset neonatal infection (EONI) in critically ill preterm infants. At birth, most critically ill neonates are receiving broad-spectrum antibiotics pending bacterial culture results, because distinguishing infected from noninfected infants at birth is difficult.

DESIGN

Prospective study.

SETTING

Neonatal intensive care unit in a tertiary care hospital.

PATIENTS

Two hundred thirteen infants, born before 33 wks' gestation, admitted to the neonatal intensive care unit within 6 hrs of life with a presumptive diagnosis of EONI.

INTERVENTION

A presumptive diagnosis of EONI was associated with a 300-μL blood sample to measure six cytokine (interleukin [IL]-1β, IL-6, IL-8, IL-10, IL-12, tumor necrosis factor-α) concentrations, using the cytometric bead array technique.

MEASUREMENTS AND MAIN RESULTS

Of the 213 infants included, 31 had a definite or possible EONI and 182 were not infected. Concentrations of IL-6, IL-8, and IL-10 were significantly increased in infected neonates, in comparison with infants without EONI. In contrast, IL-1β, IL-12, and tumor necrosis factor-α concentrations were not. Logistic regression analyses were performed to construct multivariate predictive models that could distinguish infected from noninfected infants at birth. A clinical score was based on three parameters independently associated with EONI (i.e., interval of >12 hrs between the membranes rupture and delivery, prenatal maternal colonization and mechanical ventilation at birth). This score was compared with scores including clinical parameters and serum cytokines, alone or in combination. The best predictive model combined the three clinical parameters, IL-6 (positive threshold, 300 pg/mL) and IL-8 (positive threshold, 300 pg/mL) concentrations.

CONCLUSION

A predictive model combining serum IL-6 and IL-8 measurements and selected clinical variables could distinguish infected from noninfected preterm infants at birth and should help the clinician in reducing or shortening the unnecessary use of antibiotics.

Computational modeling of mammalian signaling networks

One of the most exciting developments in signal transduction research has been the proliferation of studies in which a biological discovery was initiated by computational modeling. In this study, we review the major efforts that enable such studies. First, we describe the experimental technologies that are generally used to identify the molecular components and interactions in, and dynamic behavior exhibited by, a network of interest. Next, we review the mathematical approaches that are used to model signaling network behavior. Finally, we focus on three specific instances of 'model-driven discovery': cases in which computational modeling of a signaling network has led to new insights that have been verified experimentally.

Accuracy and reproducibility of a multiplex immunoassay platform: a validation study

BACKGROUND

Multiplex immunoassays offer many advantages over singleplex assays for the analysis of multiple analytes in a single sample. We sought to validate a specific multiplex cytokine immunoassay (Human 9-plex cytokine array on the Searchlight® platform by Thermoscientific) prior to use in a large clinical study.

METHODS

We compared spike and recovery of recombinant proteins on the Searchlight® platform to singleplex immunoassays purchased from R&D Systems, measured identical patient samples on the two different platforms, and measured identical patient samples on different days to measure intra- and inter-assay variability.

RESULTS

Assays using the Searchlight® platform had inefficient recovery of spiked recombinant proteins compared to R&D Systems singleplex assays. Assaying identical patients samples on different days on the Searchlight platform had acceptable intra-assay variability (intra-assay coefficient of variation (CV%) range for all analytes of 9.1-13.7) but unacceptably high inter-assay variability (CV% range for all analytes 16.7-119.3) suggesting plate-to plate variability. Similar assays for individual cytokines on the R&D platform had an intra-assay CV% range of 1.6-6.4 and an inter-assay CV% range of 3.8-7.1. Some deficiencies in Searchlight® assay performance may be due to irregularities in spotting of capture antibodies during manufacturing.

CONCLUSIONS

We conclude that the Searchlight® multiplex immunoassay platform would require extensive additional assay optimization prior to widespread clinical research use.

Multiplexed protein analysis using encoded antibody-conjugated microbeads

We describe a method for multiplexed analysis of proteins using fluorescently encoded microbeads. The sensitivity of our method is comparable to the sensitivity obtained by enzyme-linked immunosorbent assay while only 5 µl sample volumes are needed. Streptavidin-coated, 1 µm beads are encoded with a combination of fluorophores at different intensity levels. As a proof of concept, we demonstrate that 27 microbead populations can be readily encoded by affinity conjugation using three intensity levels for each of three different biotinylated fluorescent dyes. Four populations of encoded microbeads are further conjugated with biotinylated capture antibodies and then combined and immobilized in a microfluidic flow cell for multiplexed protein analysis. Using four uniquely encoded microbead populations, we show that a cancer biomarker and three cytokine proteins can be analysed quantitatively in the picogram per millilitre range by fluorescence microscopy in a single assay. Our method will allow for the fabrication of high density, bead-based antibody arrays for multiplexed protein analysis using integrated microfluidic devices and automated sample processing.

Bead-based multiplexed analysis of analytes by flow cytometry

The Enzyme-Linked Immunosorbent Assay (ELISA) and Western Blot analysis have been workhorse techniques for the analysis of protein levels and state, such as phosphorylation. The ELISA is also useful for measuring the affinity of a molecule for its ligand. The disadvantage of these techniques is that only a single protein can be analyzed for ELISA and a few (up to three) proteins for Western Blotting. Exact quantification is difficult with Western Blotting and changes are often reported as fold differences. We present here protocols for using fluorescent microspheres coated with the selected capture molecule to perform in essence several hundred mini ELISAs with each microsphere representing an ELISA; this reduces the variability of the assay. In addition, it is possible to analyze up to 100 analytes simultaneously using microspheres because each fluorescent microsphere exhibits distinct fluorescence in the red and far red channels: the fluorescence intensity in the channels in the red and far red channels (up to ten different intensities for each channel leading to a 10 × 10 matrix of intensities) constitutes the address for each analyte.