Recent advances in microarray technologies for proteomics

Synthetic Approaches of Epoxysuccinate Chemical Probes

Synthetic chemical probes are powerful tools for investigating biological processes. They are particularly useful for proteomic studies such as activity-based protein profiling (ABPP). These chemical methods initially used mimics of natural substrates. As the techniques gained prominence, more and more elaborate chemical probes with increased specificity towards given enzyme/protein families and amenability to various reaction conditions were used. Among the chemical probes, peptidyl-epoxysuccinates represent one of the first types of compounds used to investigate the activity of the cysteine protease papain-like family of enzymes. Structurally derived from the natural substrate, a wide body of inhibitors and activity- or affinity-based probes bearing the electrophilic oxirane unit for covalent labeling of active enzymes now exists. Herein, we review the literature regarding the synthetic approaches to epoxysuccinate-based chemical probes together with their reported applications, from biological chemistry and inhibition studies to supramolecular chemistry and the formation of protein arrays.

Multiplex Identification of Post-Translational Modifications at Point-of-Care by Deep Learning-Assisted Hydrogel Sensors

Multiplex detection of protein post-translational modifications (PTMs), especially at point-of-care, is of great significance in cancer diagnosis. Herein, we report a machine learning-assisted photonic crystal hydrogel (PCH) sensor for multiplex detection of PTMs. With closely-related PCH sensors microfabricated on a single chip, our design achieved not only rapid screening of PTMs at specific protein sites by using only naked eyes/cellphone, but also the feasibility of real-time monitoring of phosphorylation reactions. By taking advantage of multiplex sensor chips and a neural network algorithm, accurate prediction of PTMs by both their types and concentrations was enabled. This approach was ultimately used to detect and differentiate up/down regulation of different phosphorylation sites within the same protein in live mammalian cells. Our developed method thus holds potential for POC identification of various PTMs in early-stage diagnosis of protein-related diseases.

Highly-Sensitive, Label-Free Detection of Microorganisms and Viruses via Interferometric Reflectance Imaging Sensor

Pathogenic microorganisms and viruses can easily transfer from one host to another and cause disease in humans. The determination of these pathogens in a time- and cost-effective way is an extreme challenge for researchers. Rapid and label-free detection of pathogenic microorganisms and viruses is critical in ensuring rapid and appropriate treatment. Sensor technologies have shown considerable advancements in viral diagnostics, demonstrating their great potential for being fast and sensitive detection platforms. In this review, we present a summary of the use of an interferometric reflectance imaging sensor (IRIS) for the detection of microorganisms. We highlight low magnification modality of IRIS as an ensemble biomolecular mass measurement technique and high magnification modality for the digital detection of individual nanoparticles and viruses. We discuss the two different modalities of IRIS and their applications in the sensitive detection of microorganisms and viruses.

Research progress in protein microarrays: Focussing on cancer research

Although several effective treatment modalities have been developed for cancers, the morbidity and mortality associated with cancer continues to increase every year. As one of the most exciting emerging technologies, protein microarrays represent a powerful tool in the field of cancer research because of their advantages such as high throughput, small sample usage, more flexibility, high sensitivity and direct readout of results. In this review, we focus on the research progress in four types of protein microarrays (proteome microarray, antibody microarray, lectin microarray and reversed protein array) with emphasis on their application in cancer research. Finally, we discuss the current challenges faced by protein microarrays and directions for future developments. We firmly believe that this novel systems biology research tool holds immense potential in cancer research and will become an irreplaceable tool in this field.

Aptamer-Based Gold Nanoparticles-PDMS Composite Stamps as a Platform for Micro-Contact Printing

In the present study, a functional template made up of in situ synthesised gold nanoparticles (AuNPs) is prepared on polydimethylsiloxane (PDMS) for patterning of target protein onto the desired solid substrates. Unlike previous studies in which bioreceptor probes are randomly attached to the PDMS stamp through electrostatic interactions, herein, we propose an AuNPs-PDMS stamp, which provides a surface for the attachment of thiol-modified biorecognition probes to link to the stamp surface through a dative bond with a single anchoring point based on thiol chemistry. By using this platform, we have developed the ability for microcontact printing (µCP) to selectively capture and transfer target protein onto solid surfaces for detection purposes. After µCP, we also investigated whether liquid crystals (LCs) could be used as a label-free approach for identifying transfer protein. Our reported approach provides promise for biosensing of various analytes.

Drop Impact on a Superhydrophilic Spot Surrounded by a Superhydrophobic Surface

The spatial variation in the wettability of a surface can have a significant effect on the spreading and retraction behavior of an impacting droplet and hence the overall impact dynamics. Although composite surfaces have proven applications, there is a lack of understanding of droplet impact on surfaces with a sudden jump in wettability. Here, we study the behavior of a liquid drop impacting a composite surface having a superhydrophilic (SHL) spot surrounded by a superhydrophobic (SHB) region. We find that the droplet exhibits different regimes: no-splitting, jetting, and splashing, depending upon the spot size (β_s) and the Weber number (We). At a smaller β_s, the behavior shifts from the stable to jetting regime and then to the splashing regime, with increasing We. We find that by increasing the value of β_s, one can avoid the undesirable splashing and jetting regimes and attain a stable regime even at a higher We. Our study reveals that β_s has a significant influence on the maximum spreading diameter β_max at a smaller We but a negligible effect at a higher We. We show that the dominance of capillary energy at a smaller We and viscous energy at a higher We underpins the phenomena. We employ an energy conservation approach to develop an analytical model to predict β_max on a composite SHL-SHB surface by considering the total energy of the system before the impact and at the maximum spread position. We find K = (Re^1/2/We) emerges as a key parameter in the model that accurately predicts the experimentally measured β_max. Our study reveals the existence of an inertia-viscous dominated regime at a smaller K and an inertia-capillary dominated regime at a larger K. The outcome of our study may find applications in stable and precise positioning of impacting droplets.

Biopatterning: The Art of Patterning Biomolecules on Surfaces

Patterning biomolecules on surfaces provides numerous opportunities for miniaturizing biological assays; biosensing; studying proteins, cells, and tissue sections; and engineering surfaces that include biological components. In this Feature Article, we summarize the themes presented in our recent Langmuir Lecture on patterning biomolecules on surfaces, miniaturizing surface assays, and interacting with biointerfaces using three key technologies: microcontact printing, microfluidic networks, and microfluidic probes.

Three-Dimensional Interfacing of Cells with Hierarchical Silicon Nano/Microstructures for Midinfrared Interrogation of In Situ Captured Proteins

Label-free optical detection of biomolecules is currently limited by a lack of specificity rather than sensitivity. To exploit the much more characteristic refractive index dispersion in the mid-infrared (IR) regime, we have engineered three-dimensional IR-resonant silicon micropillar arrays (Si-MPAs) for protein sensing. By exploiting the unique hierarchical nano- and microstructured design of these Si-MPAs attained by CMOS-compatible silicon-based microfabrication processes, we achieved an optimized interrogation of surface protein binding. Based on spatially resolved surface functionalization, we demonstrate controlled three-dimensional interfacing of mammalian cells with Si-MPAs. Spatially controlled surface functionalization for site-specific protein immobilization enabled efficient targeting of soluble and membrane proteins into sensing hotspots directly from cells cultured on Si-MPAs. Protein binding to Si-MPA hotspots at submonolayer level was unambiguously detected by conventional Fourier transform IR spectroscopy. The compatibility with cost-effective CMOS-based microfabrication techniques readily allows integration of this novel IR transducer into fully fledged bioanalytical microdevices for selective and sensitive protein sensing.

Microarrays Incorporating Gold Grid Patterns for Protein Quantification

Protein microarrays are miniaturized two-dimensional arrays, incorporating thousands of immobilized proteins, typically printed in minute amounts on functionalized solid substrates, which can be analyzed in a high-throughput fashion. Irreproducibility of the printing techniques adopted, resulting in inconsistently and nonuniformly deposited microscopic spots, nonuniform signal intensities from the printed microspots, and significantly high background noise are some of the critical issues that affect protein analysis using traditional protein microarrays. To overcome such issues, in this study, we introduced a novel gold grid pattern-based protein microarray. The grid patterns incorporated in our microarray are equivalent to the spots used for protein analysis in conventional protein microarrays. We utilized the signal intensities from the grid patterns acting as spots for quantifying the protein concentration levels. To demonstrate the utility of our novel design concept, we quantified as low as 66.7 ng/mL of bovine serum albumin using our gold grid pattern-based protein microarray. Our grid pattern-based design concept for protein quantification overcame the signal nonuniformity issues and ensured that the dominance of any distorted signal from a single spot did not affect the overall protein quantification results as encountered in conventional protein microarrays.

A magnetic SERS immunosensor for highly sensitive and selective detection of human carboxylesterase 1 in human serum samples

Hepatocellular carcinoma (HCC) is a common and lethal cancer. New serum markers for detecting HCC are urgently needed. Human carboxylesterase 1 (hCE1) is an important member of the serine hydrolase superfamily and is closely related to the occurrence of HCC. It can be used as a good serum marker for early diagnosis of HCC. Here, we developed a surface enhanced Raman scattering (SERS)- based magnetic immunosensor that specifically recognizes and detects trace amounts of hCE1 in human serum via a sandwich structure consisting of a SERS tags, magnetic supporting substrates, and target antigen (hCE1). The SERS tags are 4-mercaptobenzoic acid (4-MBA)-labeled AgNPs, and the SERS supporting substrates are composed of a raspberry-like morphology of Fe₃O₄@SiO₂@AgNPs magnetic nanocomposites surface-functionalized with a hCE1 antibody. The prepared SERS magnetic immunosensor exhibits excellent selectivity and extremely high sensitivity for hCE1 detection. The SERS signal and logarithm of hCE1 concentration presented a wide linear response range of 0.1 ng mL^-1 to 1.0 mg mL^-1, and the detection limit of hCE1 was 0.1 ng mL^-1. The results indicate that the immunosensor can be used for the rapid determination of hCE1 in human serum without a complicated sample pre-treatment. Furthermore, the immunosensor has good reproducibility and stability, and has a promising prospect for the quantitative detection of other tumor markers in early clinical diagnosis.

The Surface Science of Microarray Generation-A Critical Inventory

Microarrays are powerful tools in biomedical research and have become indispensable for high-throughput multiplex analysis, especially for DNA and protein analysis. The basis for all microarray processing and fabrication is surface modification of a chip substrate and many different strategies to couple probe molecules to such substrates have been developed. We present here a critical assessment of typical biochip generation processes from a surface science point of view. While great progress has been made from a molecular biology point of view on the development of qualitative assays and impressive results have been obtained on the detection of rather low concentrations of DNA or proteins, quantitative chip-based assays are still comparably rare. We argue that lack of stable and reliable deposition chemistries has led in many cases to suboptimal quantitative reproducibility, impeded further progress in microarray development and prevented a more significant penetration of microarray technology into the diagnostic market. We suggest that surface-attached hydrogel networks might be a promising strategy to achieve highly sensitive and quantitatively reproducible microarrays.

Dl-3-n-Butylphthalide Reduces Cognitive Impairment Induced by Chronic Cerebral Hypoperfusion Through GDNF/GFRα1/Ret Signaling Preventing Hippocampal Neuron Apoptosis

Hippocampal neuron death is a key factor in vascular dementia (VD) induced by chronic cerebral hypoperfusion (CCH). Dl-3-n-butylphthalide (NBP) is a multiple-effects drug. Therefore, the potential molecular mechanisms underlying CCH and its feasible treatment should be investigated. This study had two main purposes: first, to identify a potential biomarker in a rat model of CCH induced VD using antibody microarrays; and second, to explore the neuroprotective role of NBP at targeting the potential biomarker. Glial cell line-derived neurotrophic factor (GDNF)/GDNF family receptor alpha-1 (GFRα1)/receptor tyrosine kinase (Ret) signaling is altered in the hippocampus of CCH rats; however, NBP treatment improved cognitive function, protected against hippocampal neuron apoptosis via regulation of GDNF/GFRα1/Ret, and activated the phosphorylation AKT (p-AKT) and ERK1/2 (p-ERK1/2) signaling. We also found that 1 h oxygen-glucose deprivation (OGD) followed by 48 h reperfusion (R) in cultured hippocampal neurons led to downregulation of GDNF/GFRα1/Ret. NBP upregulated the signaling and increased neuronal survival. Ret inhibitor (NVP-AST487) inhibits Ret and downstream effectors, including p-AKT and p-ERK1/2. Additionally, both GDNF and GFRα1 expression are markedly inhibited in hippocampal neurons by coincubation with NVP-AST487, particularly under conditions of OGD/R. GDNF/GFRα1/Ret signaling and neuronal viability can be maintained by NBP, which activates p-AKT and p-ERK1/2, increases expression of Bcl-2, and decreases expression of Bax and cleaved caspase-3. The current study showed that GDNF/GFRα1/Ret signaling plays an essential role in the CCH induced VD. NBP was protective against hippocampal neuron apoptosis, and this was associated with regulation of GDNF/GFRα1/Ret and AKT/ERK1/2 signaling pathways, thus reducing cognitive impairment.

Structural Features of Transcription Factors Associating with Nucleosome Binding

Fate-changing transcription factors (TFs) scan chromatin to initiate new genetic programs during cell differentiation and reprogramming. Yet the protein structure domains that allow TFs to target nucleosomal DNA remain unexplored. We screened diverse TFs for binding to nucleosomes containing motif-enriched sequences targeted by pioneer factors in vivo. FOXA1, OCT4, ASCL1/E12α, PU1, CEBPα, and ZELDA display a range of nucleosome binding affinities that correlate with their cell reprogramming potential. We further screened 593 full-length human TFs on protein microarrays against different nucleosome sequences, followed by confirmation in solution, to distinguish among factors that bound nucleosomes, such as the neuronal AP-2α/β/γ, versus factors that only bound free DNA. Structural comparisons of DNA binding domains revealed that efficient nucleosome binders use short anchoring α helices to bind DNA, whereas weak nucleosome binders use unstructured regions and/or β sheets. Thus, specific modes of DNA interaction allow nucleosome scanning that confers pioneer activity to transcription factors.

Autoimmune Epilepsy

The field of autoimmune epilepsy has evolved substantially in the last few decades with discovery of several neural autoantibodies and improved mechanistic understanding of these immune-mediated syndromes. A considerable proportion of patients with epilepsy of unknown etiology have been demonstrated to have an autoimmune cause. The majority of the patients with autoimmune epilepsy usually present with new-onset refractory seizures along with subacute progressive cognitive decline and behavioral or psychiatric dysfunction. Neural specific antibodies commonly associated with autoimmune epilepsy include leucine-rich glioma-inactivated protein 1 (LGI1), N-methyl-D-aspartate receptor (NMDA-R), and glutamic acid decarboxylase 65 (GAD65) IgG. Diagnosis of these cases depends on the identification of the clinical syndrome and ancillary studies including autoantibody evaluation. Predictive models (Antibody Prevalence in Epilepsy and Encephalopathy [APE2] and Response to Immunotherapy in Epilepsy and Encephalopathy [RITE2] scores) based on clinical features and initial neurological assessment may be utilized for selection of cases for autoimmune epilepsy evaluation and management. In this article, we will review the recent advances in autoimmune epilepsy and provide diagnostic and therapeutic algorithms for epilepsies with suspected autoimmune etiology.

Origins and clinical relevance of proteoforms in pediatric malignancies

INTRODUCTION

Cancer changes the proteome in complex ways that reach well beyond simple changes in protein abundance. Genomic and transcriptional variations and post-translational protein modification create functional variants of a protein, known as proteoforms. Childhood cancers have fewer genomic alterations but show equally dramatic phenotypic changes as malignant cells in adults. Therefore, unraveling the complexities of the proteome is even more important in pediatric malignancies. Areas covered: In this review, the biological origins of proteoforms and technological advancements in the study of proteoforms are discussed. Particular emphasis is given to their implication in childhood malignancies and the critical role of cancer-specific proteoforms for the next generation of cancer therapies and diagnostics. Expert opinion: Recent advancements in technology have led to a better understanding of the underlying mechanisms of tumorigenesis. This has been critical for the development of more effective and less harmful treatments that are based on direct targeting of altered proteins and deregulated pathways. As proteome coverage and the ability to detect complex proteoforms increase, the most need for change is in data compilation and database availability to mediate high-level data analysis and allow for better functional annotation of proteoforms.

A self-assembling peptide hydrogel for ultrarapid 3D bioassays

Biosensing analytical platforms rely on the intimate structure-function relationship of immobilized probes. In this context, hydrogels are appealing semi-wet systems to locally confine biomolecules while preserving their structural integrity and function. Yet, limitations imposed by biomolecule diffusion rates or fabrication difficulties still hamper their broad application. Here, using a self-assembling peptide, a printable and self-adhesive hydrogel was obtained and applied to fabricate arrays of localized bio-functional 3D microenvironments on analytical interfaces. This soft matrix represents a robust and versatile material, allowing fast and selective tuning of analyte diffusion, which is exploited here to run in-gel immunoassays under solution-like conditions in an unprecedented (<10 min) time frame. The developed material overcomes major limitations associated with hydrogels for bioassays, widening the prospects for easy fabrication of multifunctional bio-interfaces for high-throughput, molecular recognition assays.

The role of systems biology approaches in determining molecular signatures for the development of more effective vaccines

INTRODUCTION

Emerging infectious diseases are a major threat to public health, and while vaccines have proven to be one of the most effective preventive measures for infectious diseases, we still do not have safe and effective vaccines against many human pathogens, and emerging diseases continually pose new threats. The purpose of this review is to discuss how the creation of vaccines for these new threats has been hindered by limitations in the current approach to vaccine development. Recent advances in high-throughput technologies have enabled scientists to apply systems biology approaches to collect and integrate increasingly large datasets that capture comprehensive biological changes induced by vaccines, and then decipher the complex immune response to those vaccines.

AREAS COVERED

This review covers advances in these technologies and recent publications that describe systems biology approaches to understanding vaccine immune responses and to understanding the rational design of new vaccine candidates.

EXPERT OPINION

Systems biology approaches to vaccine development provide novel information regarding both the immune response and the underlying mechanisms and can inform vaccine development.

MSN-on-a-Chip: Cell-Based Screenings Made Possible on a Small-Molecule Microarray of Native Natural Products

Standard small-molecule microarrays (SMMs) are not well-suited for cell-based screening assays. Of the few attempts made thus far to render SMMs cell-compatible, all encountered major limitations. Here we report the first mesoporous silica nanoparticle (MSN)-on-a-chip platform capable of allowing high-throughput cell-based screening to be conducted on SMMs. By making use of a glass surface on which hundreds of MSNs, each encapsulated with a different native natural product, were immobilized in spatially defined manner, followed by on-chip mammalian cell growth and on-demand compound release, high-content screening was successfully carried out with readily available phenotypic detection methods. By combining this new MSN-on-a-chip system with small interfering RNA technology for the first time, we discovered that (+)-usniacin possesses synergistic inhibitory properties similar to those of olaparib (an FDA-approved drug) in BRCA1-knockdown cancer cells.

A printable hydrogel microarray for drug screening avoids false positives associated with promiscuous aggregating inhibitors

A significant problem in high-throughput drug screening is the disproportionate number of false hits associated with drug candidates that form colloidal aggregates. Such molecules, referred to as promiscuous inhibitors, nonspecifically inhibit multiple enzymes and are thus not useful as potential drugs. Here, we report a printable hydrogel-based drug-screening platform capable of non-ambiguously differentiating true enzyme inhibitors from promiscuous aggregating inhibitors, critical for accelerating the drug discovery process. The printed hydrogels can both immobilize as well as support the activity of entrapped enzymes against drying or treatment with a protease or chemical denaturant. Furthermore, the printed hydrogel can be applied in a high-throughput microarray-based screening platform (consistent with current practice) to rapidly ( <25 min) and inexpensively identify only clinically promising lead compounds with true inhibitory potential as well as to accurately quantify the dose–response relationships of those inhibitors, all while using 95% less sample than required for a solution assay.

False positive results significantly slow down the drug discovery process. Here, the authors developed a gel serving as a screening platform in which enzymes can be stored, stabilized, and protected from most of the compounds that typically cause these misleading results.

Plug-and-actuate on demand: multimodal individual addressability of microarray plates using modular hybrid acoustic wave technology

The microarray titre plate remains a fundamental workhorse in genomic, proteomic and cellomic analyses that underpin the drug discovery process. Nevertheless, liquid handling technologies for sample dispensing, processing and transfer have not progressed significantly beyond conventional robotic micropipetting techniques, which are not only at their fundamental sample size limit, but are also prone to mechanical failure and contamination. This is because alternative technologies to date suffer from a number of constraints, mainly their limitation to carry out only a single liquid operation such as dispensing or mixing at a given time, and their inability to address individual wells, particularly at high throughput. Here, we demonstrate the possibility for true sequential or simultaneous single- and multi-well addressability in a 96-well plate using a reconfigurable modular platform from which MHz-order hybrid surface and bulk acoustic waves can be coupled to drive a variety of microfluidic modes including mixing, sample preconcentration and droplet jetting/ejection in individual or multiple wells on demand, thus constituting a highly versatile yet simple setup capable of improving the functionality of existing laboratory protocols and processes.

DNA-Directed Antibody Immobilization for Robust Protein Microarrays: Application to Single Particle Detection 'DNA-Directed Antibody Immobilization

Protein microarrays are emerging tools which have become very powerful in multiplexed detection technologies. A variety of proteins can be immobilized on a sensor chip allowing for multiplexed diagnostics. Therefore, various types of analyte in a small volume of sample can be detected simultaneously. Protein immobilization is a crucial step for creating a robust and sensitive protein microarray-based detection system. In order to achieve a successful protein immobilization and preserve the activity of the proteins after immobilization, DNA-directed immobilization is a promising technique. Here, we present the design and the use of DNA-directed immobilized (DDI) antibodies in fabrication of robust protein microarrays. We focus on application of protein microarrays for capturing and detecting nanoparticles such as intact viruses. Experimental results on Single-particle interferometric reflectance imaging sensor (SP-IRIS) are used to validate the advantages of the DDI method.

Enzyme Activity Assays for Protein Kinases: Strategies to Identify Active Substrates

Protein kinases are an important class of enzymes and drug targets. New opportunities to discover medicines for neglected diseases can be leveraged by the extensive kinase tools and knowledge created in targeting human kinases. A valuable tool for kinase drug discovery is an enzyme assay that measures catalytic function. The functional assay can be used to identify inhibitors, estimate affinity, characterize molecular mechanisms of action (MMOAs) and evaluate selectivity. However, establishing an enzyme assay for a new kinases requires identification of a suitable substrate. Identification of a new kinase's endogenous physiologic substrate and function can be extremely costly and time consuming. Fortunately, most kinases are promiscuous and will catalyze the phosphotransfer from ATP to alternative substrates with differing degrees of catalytic efficiency. In this manuscript we review strategies and successes in the identification of alternative substrates for kinases from organisms responsible for many of the neglected tropical diseases (NTDs) towards the goal of informing strategies to identify substrates for new kinases. Approaches for establishing a functional kinase assay include measuring auto-activation and use of generic substrates and peptides. The most commonly used generic substrates are casein, myelin basic protein, and histone. Sequence homology modeling can provide insights into the potential substrates and the requirement for activation. Empirical approaches that can identify substrates include screening of lysates (which may also help identify native substrates) and use of peptide arrays. All of these approaches have been used with a varying degree of success to identify alternative substrates.

Monitoring few molecular binding events in scalable confined aqueous compartments by raster image correlation spectroscopy (CADRICS)

The assembly of scalable liquid compartments for binding assays in array formats constitutes a topic of fundamental importance in life sciences. This challenge can be addressed by mimicking the structure of cellular compartments with biological native conditions. Here, inkjet printing is employed to develop up to hundreds of picoliter aqueous droplet arrays stabilized by oil-confinement with mild surfactants (Tween-20). The aqueous environments constitute specialized compartments in which biomolecules may exploit their function and a wide range of molecular interactions can be quantitatively investigated. Raster Image Correlation Spectroscopy (RICS) is employed to monitor in each compartment a restricted range of dynamic intermolecular events demonstrated through protein-binding assays involving the biotin/streptavidin model system.

Screening Mammalian Cells on a Hydrogel: Functionalized Small Molecule Microarray

Mammalian cell-based microarray technology has gained wide attention, for its plethora of promising applications. The platform is able to provide simultaneous information on multiple parameters for a given target, or even multiple target proteins, in a complex biological system. Here we describe the preparation of mammalian cell-based microarrays using selectively captured of human prostate cancer cells (PC-3). This platform was then used in controlled drug release and measuring the associated drug effects on these cancer cells.

Cancer microarray data feature selection using multi-objective binary particle swarm optimization algorithm

Cancer investigations in microarray data play a major role in cancer analysis and the treatment. Cancer microarray data consists of complex gene expressed patterns of cancer. In this article, a Multi-Objective Binary Particle Swarm Optimization (MOBPSO) algorithm is proposed for analyzing cancer gene expression data. Due to its high dimensionality, a fast heuristic based pre-processing technique is employed to reduce some of the crude domain features from the initial feature set. Since these pre-processed and reduced features are still high dimensional, the proposed MOBPSO algorithm is used for finding further feature subsets. The objective functions are suitably modeled by optimizing two conflicting objectives i.e., cardinality of feature subsets and distinctive capability of those selected subsets. As these two objective functions are conflicting in nature, they are more suitable for multi-objective modeling. The experiments are carried out on benchmark gene expression datasets, i.e., Colon, Lymphoma and Leukaemia available in literature. The performance of the selected feature subsets with their classification accuracy and validated using 10 fold cross validation techniques. A detailed comparative study is also made to show the betterment or competitiveness of the proposed algorithm.

Two-Photon Small Molecule Enzymatic Probes

Enzymes are essential for life, especially in the development of disease and on drug effects, but as we cannot yet directly observe the inside interactions and only partially observe biochemical outcomes, tools "translating" these processes into readable information are essential for better understanding of enzymes as well as for developing effective tools to fight against diseases. Therefore, sensitive small molecule probes suitable for direct in vivo monitoring of enzyme activities are ultimately desirable. For fulfilling this desire, two-photon small molecule enzymatic probes (TSMEPs) producing amplified fluorescent signals based on enzymatic conversion with better photophysical properties and deeper penetration in intact tissues and whole animals have been developed and demonstrated to be powerful in addressing the issues described above. Nonetheless, currently available TSMEPs only cover a small portion of enzymes despite the distinct advantages of two-photon fluorescence microscopy. In this Account, we would like to share design principles for TSMEPs as potential indicators of certain pathology-related biomarkers together with their applications in disease models to inspire more elegant work to be done in this area. Highlights will be addressed on how to equip two-photon fluorescent probes with features amenable for direct assessment of enzyme activities in complex pathological environments. We give three recent examples from our laboratory and collaborations in which TSMEPs are applied to visualize the distribution and activity of enzymes at cellular and organism levels. The first example shows that we could distinguish endogenous phosphatase activity in different organelles; the second illustrates that TSMEP is suitable for specific and sensitive detection of a potential Parkinson's disease marker (monoamine oxidase B) in a variety of biological systems from cells to patient samples, and the third identifies that TSMEPs can be applied to other enzyme families (proteases). Indeed, TSMEPs have helped to uncover new biological roles and functions of a series of enzymes; therefore, we hope to encourage more TSMEPs to be developed for diverse enzymes. Meanwhile, improvements in the TSMEP properties (such as new two-photon fluorophores with longer excitation and emission wavelengths and strategies allowing high specificity) are also indispensable for producing high-fidelity information inside biological systems. We are enthusiastic however that, with these efforts and wider applications of TSMEPs in both research studies and further clinical diagnoses, comprehensive knowledge of enzyme contributions to various physiologies will be obtained.

Developing an Efficient and General Strategy for Immobilization of Small Molecules onto Microarrays Using Isocyanate Chemistry

Small-molecule microarray (SMM) is an effective platform for identifying lead compounds from large collections of small molecules in drug discovery, and efficient immobilization of molecular compounds is a pre-requisite for the success of such a platform. On an isocyanate functionalized surface, we studied the dependence of immobilization efficiency on chemical residues on molecular compounds, terminal residues on isocyanate functionalized surface, lengths of spacer molecules, and post-printing treatment conditions, and we identified a set of optimized conditions that enable us to immobilize small molecules with significantly improved efficiencies, particularly for those molecules with carboxylic acid residues that are known to have low isocyanate reactivity. We fabricated microarrays of 3375 bioactive compounds on isocyanate functionalized glass slides under these optimized conditions and confirmed that immobilization percentage is over 73%.

Development and application of an antibody-based protein microarray to assess physiological stress in grizzly bears (Ursus arctos)

A novel antibody-based protein microarray was developed that simultaneously determines expression of 31 stress-associated proteins in skin samples collected from free-ranging grizzly bears (Ursus arctos) in Alberta, Canada. The microarray determines proteins belonging to four broad functional categories associated with stress physiology: hypothalamic-pituitary-adrenal axis proteins, apoptosis/cell cycle proteins, cellular stress/proteotoxicity proteins and oxidative stress/inflammation proteins. Small skin samples (50-100 mg) were collected from captured bears using biopsy punches. Proteins were isolated and labelled with fluorescent dyes, with labelled protein homogenates loaded onto microarrays to hybridize with antibodies. Relative protein expression was determined by comparison with a pooled standard skin sample. The assay was sensitive, requiring 80 µg of protein per sample to be run in triplicate on the microarray. Intra-array and inter-array coefficients of variation for individual proteins were generally <10 and <15%, respectively. With one exception, there were no significant differences in protein expression among skin samples collected from the neck, forelimb, hindlimb and ear in a subsample of n = 4 bears. This suggests that remotely delivered biopsy darts could be used in future sampling. Using generalized linear mixed models, certain proteins within each functional category demonstrated altered expression with respect to differences in year, season, geographical sampling location within Alberta and bear biological parameters, suggesting that these general variables may influence expression of specific proteins in the microarray. Our goal is to apply the protein microarray as a conservation physiology tool that can detect, evaluate and monitor physiological stress in grizzly bears and other species at risk over time in response to environmental change.

PMD: A Resource for Archiving and Analyzing Protein Microarray data

Protein microarray is a powerful technology for both basic research and clinical study. However, because there is no database specifically tailored for protein microarray, the majority of the valuable original protein microarray data is still not publically accessible. To address this issue, we constructed Protein Microarray Database (PMD), which is specifically designed for archiving and analyzing protein microarray data. In PMD, users can easily browse and search the entire database by experimental name, protein microarray type, and sample information. Additionally, PMD integrates several data analysis tools and provides an automated data analysis pipeline for users. With just one click, users can obtain a comprehensive analysis report for their protein microarray data. The report includes preliminary data analysis, such as data normalization, candidate identification, and an in-depth bioinformatics analysis of the candidates, which include functional annotation, pathway analysis, and protein-protein interaction network analysis. PMD is now freely available at www.proteinmicroarray.cn.

Flow-pattern Guided Fabrication of High-density Barcode Antibody Microarray

Antibody microarray as a well-developed technology is currently challenged by a few other established or emerging high-throughput technologies. In this report, we renovate the antibody microarray technology by using a novel approach for manufacturing and by introducing new features. The fabrication of our high-density antibody microarray is accomplished through perpendicularly oriented flow-patterning of single stranded DNAs and subsequent conversion mediated by DNA-antibody conjugates. This protocol outlines the critical steps in flow-patterning DNA, producing and purifying DNA-antibody conjugates, and assessing the quality of the fabricated microarray. The uniformity and sensitivity are comparable with conventional microarrays, while our microarray fabrication does not require the assistance of an array printer and can be performed in most research laboratories. The other major advantage is that the size of our microarray units is 10 times smaller than that of printed arrays, offering the unique capability of analyzing functional proteins from single cells when interfacing with generic microchip designs. This barcode technology can be widely employed in biomarker detection, cell signaling studies, tissue engineering, and a variety of clinical applications.

Dual improvement of DNA-directed antibody immobilization utilizing magnetic fishing and a polyamine coated surface

The magnetic improvement of DNA-directed antibody immobilization in terms of a highly efficient sensing platform for anti-prostate-specific membrane antigen immobilization has been reported.

Accelerated cellular on- and off-target screening of bioactive compounds using microarrays

In situ target screening of bioactive compounds using microarrays.

Fast assembling microarrays of superparamagnetic Fe3O4@Au nanoparticle clusters as reproducible substrates for surface-enhanced Raman scattering

It is currently a very active research area to develop new types of substrates which integrate various nanomaterials for surface-enhanced Raman scattering (SERS) techniques. Here we report a unique approach to prepare SERS substrates with reproducible performance. It features silicon mold-assisted magnetic assembling of superparamagnetic Fe3O4@Au nanoparticle clusters (NCs) into arrayed microstructures on a wafer scale. This approach enables the fabrication of both silicon-based and hydrogel-based substrates in a sequential manner. We have demonstrated that strong SERS signals can be harvested from these substrates due to an efficient coupling effect between Fe3O4@Au NCs, with enhancement factors >10(6). These substrates have been confirmed to provide reproducible SERS signals, with low variations in different locations or batches of samples. We investigate the spatial distributions of electromagnetic field enhancement around Fe3O4@Au NCs assemblies using finite-difference-time-domain (FDTD) simulations. The procedure to prepare the substrates is straightforward and fast. The silicon mold can be easily cleaned out and refilled with Fe3O4@Au NCs assisted by a magnet, therefore being re-useable for many cycles. Our approach has integrated microarray technologies and provided a platform for thousands of independently addressable SERS detection, in order to meet the requirements of a rapid, robust, and high throughput performance.

Controlled proliferation and screening of mammalian cells on a hydrogel-functionalized small molecule microarray

A hydrogel-functionalized small molecule microarray has been developed, on which PC-3 cancer cells were selectively grown. Subsequent controlled release of immobilized bioactive compounds enabled cell-based screening to be directly carried out on this platform.

A SERS-Assisted 3D Barcode Chip for High-Throughput Biosensing

A surface enhanced Raman scattering (SERS)-assisted 3D barcode chip has been developed for high-throughput biosensing. The 3D barcode is realized through joint 2D spatial encoding with the Raman spectroscopic encoding, which stores the SERS fingerprint information in the format of a 2D array. Here, the concept of SERS-assisted 3D barcode is demonstrated through multiplex immunoassay, where simultaneous detection of multiple targets in different samples has been achieved using a microfluidic platform. First, multiple proteins in different samples are spatially separated using a microfluidic patterned antibody barcode substrate, forming a 2D hybridization array. Then the SERS probes are used to identify and quantify the proteins. As different SERS probes are labeled with different Raman reporters, they could be employed as "SERS tags" to incorporate spectroscopic information into the 3D barcode. In this 3D barcode, the 2D spatial information helps to differentiate the samples and targets while the SERS information allows quantitative multiplex detection. It is found that the SERS-assisted 3D barcode chip can not only accomplish one-step multiplex detection within 30 min but also achieve an ultrasensitivity down to 10 fg mL(-1) (≈70 aM), which is expected to provide a promising tool for high-throughput biomedical applications.

Antibody microarrays utilizing site-specific antibody-oligonucleotide conjugates

Protein arrays are typically made by random absorption of proteins to the array surface, potentially limiting the amount of properly oriented and functional molecules. We report the development of a DNA encoded antibody microarray utilizing site-specific antibody-oligonucleotide conjugates that can be used for cell immobilization as well as the detection of genes and proteins. This technology allows for the facile generation of antibody microarrays while circumventing many of the drawbacks of conventionally produced antibody arrays. We demonstrate that this method can be used to capture and detect SK-BR-3 cells (Her2+ breast cancer cells) at concentrations as low as 10(2) cells/mL (which is equivalent to 10 cells per 100 μL array) without the use of microfluidics, which is 100- to 10(5)-fold more sensitive than comparable techniques. Additionally, the method was shown to be able to detect cells in a complex mixture, effectively immobilizing and specifically detecting Her2+ cells at a concentration of 10(2) SK-BR-3 cells/mL in 4 × 10(6) white blood cells/mL. Patients with a variety of cancers can have circulating tumor cell counts of between 1 and 10(3) cells/mL in whole blood, well within the range of this technology.

A critical comparison of protein microarray fabrication technologies

Of the diverse analytical tools used in proteomics, protein microarrays possess the greatest potential for providing fundamental information on protein, ligand, analyte, receptor, and antibody affinity-based interactions, binding partners and high-throughput analysis. Microarrays have been used to develop tools for drug screening, disease diagnosis, biochemical pathway mapping, protein-protein interaction analysis, vaccine development, enzyme-substrate profiling, and immuno-profiling. While the promise of the technology is intriguing, it is yet to be realized. Many challenges remain to be addressed to allow these methods to meet technical and research expectations, provide reliable assay answers, and to reliably diversify their capabilities. Critical issues include: (1) inconsistent printed microspot morphologies and uniformities, (2) low signal-to-noise ratios due to factors such as complex surface capture protocols, contamination, and static or no-flow mass transport conditions, (3) inconsistent quantification of captured signal due to spot uniformity issues, (4) non-optimal protocol conditions such as pH, temperature, drying that promote variability in assay kinetics, and lastly (5) poor protein (e.g., antibody) printing, storage, or shelf-life compatibility with common microarray assay fabrication methods, directly related to microarray protocols. Conventional printing approaches, including contact (e.g., quill and solid pin), non-contact (e.g., piezo and inkjet), microfluidics-based, microstamping, lithography, and cell-free protein expression microarrays, have all been used with varying degrees of success with figures of merit often defined arbitrarily without comparisons to standards, or analytical or fiduciary controls. Many microarray performance reports use bench top analyte preparations lacking real-world relevance, akin to "fishing in a barrel", for proof of concept and determinations of figures of merit. This review critiques current protein-based microarray preparation techniques commonly used for analytical and function-based proteomics and their effects on array-based assay performance.

Ag@SiO2-entrapped hydrogel microarray: a new platform for a metal-enhanced fluorescence-based protein assay

We developed a novel silver-based metal-enhanced fluorescence (MEF) biosensing platform that consisted of poly(ethylene glycol)(PEG) hydrogel microstructures entrapping silica-coated silver nanoparticles (Ag@SiO₂).

The role of protein and peptide separation before mass spectrometry analysis in clinical proteomics

The purpose of clinical proteomics is to characterise protein profiles of a plethora of diseases with the aim of finding specific biomarkers. These are particularly valuable for early diagnosis, and represent key molecules suitable to elucidate pathogenic mechanisms. Samples deriving from patients (i.e. blood, urine, cerebrospinal fluid, biopsies) are the sources for clinical proteomics. Due to the complexity of the extracted samples their direct analysis is unachievable. Any analytical clinical proteomics study should start with the choice of the optimal combination of strategies with respect to both sample preparations and MS approaches. Protein or peptide fractionation (off-line or on-line) is essential to reduce complexity of biological samples and to achieve the most complete and reproducible analysis. The aim of this review is to introduce the readers to a functional range of strategies to help scientists in their proteomics set up. In particular, the separation approaches of proteins or peptides (both gel-based and gel-free) are reviewed with special attention paid to their advantages and limitations, and to the different liquid chromatography techniques used to peptide fractionation after protein enzymatic digestion and before their detection. Finally, the role of mass spectrometry (MS) for protein identification and quantification is discussed including emerging MS data acquisition strategies.

Immobilization techniques for microarray: challenges and applications

The highly programmable positioning of molecules (biomolecules, nanoparticles, nanobeads, nanocomposites materials) on surfaces has potential applications in the fields of biosensors, biomolecular electronics, and nanodevices. However, the conventional techniques including self-assembled monolayers fail to position the molecules on the nanometer scale to produce highly organized monolayers on the surface. The present article elaborates different techniques for the immobilization of the biomolecules on the surface to produce microarrays and their diagnostic applications. The advantages and the drawbacks of various methods are compared. This article also sheds light on the applications of the different technologies for the detection and discrimination of viral/bacterial genotypes and the detection of the biomarkers. A brief survey with 115 references covering the last 10 years on the biological applications of microarrays in various fields is also provided.

Array-based proteomic approaches to study signal transduction pathways: prospects, merits and challenges

Very often dysfunctional aspects of various signalling networks are found to be associated with human diseases and disorders. The major characteristics of signal transduction pathways are specificity, amplification of the signal, desensitisation and integration, which is accomplished not solely, but majorly by proteins. Array-based profiling of protein-protein and other biomolecular interactions is a versatile approach, which holds immense potential for multiplex interactome mapping and provides an inclusive representation of the signal transduction pathways and networks. Protein microarrays such as analytical protein microarrays (antigen-antibody interactions, autoantibody screening), RP microarrays (interaction of a particular ligand with all the possible targets in cell), functional protein microarrays (protein-protein or protein-ligand interactions) are implemented for various applications, including analysis of protein interactions and their significance in signalling cascades. Additionally, successful amalgamation of the array-based approaches with different label-free detection techniques allows real-time analysis of interaction kinetics of multiple interaction events simultaneously. This review discusses the prospects, merits and limitations of different variants of array-based techniques and their promising applications for studying the modifications and interactions of biomolecules, and highlights the studies associated with signal transduction pathways and their impact on disease pathobiology.

Global analysis of human nonreceptor tyrosine kinase specificity using high-density peptide microarrays

Protein kinases phosphorylate substrates in the context of specific phosphorylation site sequence motifs. The knowledge of the specific sequences that are recognized by kinases is useful for mapping sites of phosphorylation in protein substrates and facilitates the generation of model substrates to monitor kinase activity. Here, we have adapted a positional scanning peptide library method to a microarray format that is suitable for the rapid determination of phosphorylation site motifs for tyrosine kinases. Peptide mixtures were immobilized on glass slides through a layer of a tyrosine-free Y33F mutant avidin to facilitate the analysis of phosphorylation by radiolabel assay. A microarray analysis provided qualitatively similar results in comparison with the solution phase peptide library “macroarray” method. However, much smaller quantities of kinases were required to phosphorylate peptides on the microarrays, which thus enabled a proteome scale analysis of kinase specificity. We illustrated this capability by microarray profiling more than 80% of the human nonreceptor tyrosine kinases (NRTKs). Microarray results were used to generate a universal NRTK substrate set of 11 consensus peptides for in vitro kinase assays. Several substrates were highly specific for their cognate kinases, which should facilitate their incorporation into kinase-selective biosensors.