Magnetic particles in ultrasensitive biomarker protein measurements for cancer detection and monitoring

Label-free designed nanomaterials enrichment and separation techniques for phosphoproteomics based on mass spectrometry

The surface chemical characteristics of nanomaterials have a substantial impact on the affinity probe used to enrich proteins and peptides for MALDI-MS analysis of a real human sample. Detecting phosphoproteins involved in signalling is always difficult, even with recent developments in mass spectrometry, because protein phosphorylation is often temporary from complicated mixtures. This review summarizes current research on the successful enrichment of various intriguing glycoproteins and glycol peptides using surface affinity materials with distinctive qualities such as low cost, excellent structural stability, diversity, and multifunction. As a consequence, this review will provide a quick overview of the scholars from various backgrounds who are working in this intriguing interdisciplinary field. Label-free cancer biomarkers and other diseases will benefit from future challenges.

Imaging, Identification and Inhibition of Microorganisms Using AIEgens

Microorganisms, including bacteria, viruses and fungi, are ubiquitous in nature. Some are extremely beneficial to life on Earth, whereas some cause diseases and disrupt normal human physiology. Pathogenic microorganisms can also undergo mutations and develop resistance to antimicrobial agents, which complicates diagnostic and therapeutic regimens. This calls for continuing efforts to develop new strategies and tools that can provide fast, sensitive and accurate diagnosis, as well as effective treatment of ever-evolving infectious diseases. Aggregation-induced emission luminogens (AIEgens) have shown promise in imaging, identification and inhibition of various microbial species. Compared to conventional organic fluorophores, AIEgens can offer improved photostability, and have found utilities in imaging microorganisms. AIEgens have been shown to detect microbial viability and differentiate among different microbial strains. Theranostic AIEgens that integrate imaging and killing of microbes have also been developed. This review highlights examples in the literature where AIEgens have been employed as molecular probes in the imaging, discrimination and killing of bacteria, viruses and fungi.

Oligonucleotide sensor based on magnetic capture and photoligation of upconverting nanoparticles in solid surfaces

In this work, we present a luminescence platform that can be used as point of care system for determining the presence and concentration of specific oligonucleotide sequences. This sensor exhibited a limit of detection as low as 50 fM by means of: (i) the use of single-stranded DNA (ssDNA) functionalized magnetic microparticles that captured and concentrated ssDNA-upconverting nanoparticles (ssDNA-UCNPs) on a solid support, when the target sequence (miR-21-5p DNA-analogue) was in the sample, and (ii) a photoligation reaction that covalently linked the ssDNA-UCNPs and the ssDNA magnetic microparticles, allowing stringent washes. The presented sensor showed a similar limit of detection when the assays were conducted in samples containing total miRNA extracted from human serum, demonstrating its suitability for detecting small specific oligonucleotide sequences under real-like conditions. The strategy of combining UCNPs, magnetic microparticles, and a photoligation reaction provides new insight into low-cost, rapid, and ultra-sensitive detection of oligonucleotide sequences.

Nanoparticle enhanced optical biosensing technologies for Prostate Specific Antigen biomarker detection

Prostate Cancer (PCa) is one of the deadliest forms of Cancer among men. Early screening process for PCa is primarily conducted with the help of a FDA approved biomarker known as Prostate Specific Antigen (PSA). The PSA-based screening is challenged with the inability to differentiate between the cancerous PSA and Benign Prostatic Hyperplasia (BPH), resulting in high rates of false-positives. Optical techniques such as optical absorbance, scattering, surface plasmon resonance (SPR), and fluorescence have been extensively employed for Cancer diagnostic applications. One of the most important diagnostic applications involves utilization of nanoparticles (NPs) for highly specific, sensitive, rapid, multiplexed, and high performance Cancer detection and quantification. The incorporation of NPs with these optical biosensing techniques allow realization of low cost, point-of-care, highly sensitive, and specific early cancer detection technologies, especially for PCa. In this work, the current state-of-the-art, challenges, and efforts made by the researchers for realization of low cost, point-of-care (POC), highly sensitive, and specific NP enhanced optical biosensing technologies for PCa detection using PSA biomarker are discussed and analyzed.

Recent Progress of Biomarker Detection Sensors

Early cancer diagnosis and treatment are crucial research fields of human health. One method that has proven efficient is biomarker detection which can provide real-time and accurate biological information for early diagnosis. This review presents several biomarker sensors based on electrochemistry, surface plasmon resonance (SPR), nanowires, other nanostructures, and, most recently, metamaterials which have also shown their mechanisms and prospects in application in recent years. Compared with previous reviews, electrochemistry-based biomarker sensors have been classified into three strategies according to their optimizing methods in this review. This makes it more convenient for researchers to find a specific fabrication method to improve the performance of their sensors. Besides that, as microfabrication technologies have improved and novel materials are explored, some novel biomarker sensors-such as nanowire-based and metamaterial-based biomarker sensors-have also been investigated and summarized in this review, which can exhibit ultrahigh resolution, sensitivity, and limit of detection (LoD) in a more complex detection environment. The purpose of this review is to understand the present by reviewing the past. Researchers can break through bottlenecks of existing biomarker sensors by reviewing previous works and finally meet the various complex detection needs for the early diagnosis of human cancer.

A critical insight into the development pipeline of microfluidic immunoassay devices for the sensitive quantitation of protein biomarkers at the point of care

The latest clinical procedures for the timely and cost-effective diagnosis of chronic and acute clinical conditions, such as cardiovascular diseases, cancer, chronic respiratory diseases, diabetes or sepsis (i.e. the biggest causes of death worldwide), involve the quantitation of specific protein biomarkers released into the blood stream or other physiological fluids (e.g. urine or saliva). The clinical thresholds are usually in the femtomolar to picolomar range, and consequently the measurement of these protein biomarkers heavily relies on highly sophisticated, bulky and automated equipment in centralised pathology laboratories. The first microfluidic devices capable of measuring protein biomarkers in miniaturised immunoassays were presented nearly two decades ago and promised to revolutionise point-of-care (POC) testing by offering unmatched sensitivity and automation in a compact POC format; however, the development and adoption of microfluidic protein biomarker tests has fallen behind expectations. This review presents a detailed critical overview into the pipeline of microfluidic devices developed in the period 2005-2016 capable of measuring protein biomarkers from the pM to fM range in formats compatible with POC testing, with a particular focus on the use of affordable microfluidic materials and compact low-cost signal interrogation. The integration of these two important features (essential unique selling points for the successful microfluidic diagnostic products) has been missed in previous review articles and explain the poor adoption of microfluidic technologies in this field. Most current miniaturised devices compromise either on the affordability, compactness and/or performance of the test, making current tests unsuitable for the POC measurement of protein biomarkers. Seven core technical areas, including (i) the selected strategy for antibody immobilisation, (ii) the surface area and surface-area-to-volume ratio, (iii) surface passivation, (iv) the biological matrix interference, (v) fluid control, (vi) the signal detection modes and (vii) the affordability of the manufacturing process and detection system, were identified as the key to the effective development of a sensitive and affordable microfluidic protein biomarker POC test.

New trends in plasmonic (bio)sensing

The strong enhancement and localization of electromagnetic field in plasmonic systems have found applications in many areas, which include sensing and biosensing. In this paper, an overview will be provided of the use of plasmonic phenomena in sensors and biosensors with emphasis on two main topics. The first is related to possible ways to enhance the performance of sensors and biosensors based on surface plasmon resonance (SPR), where examples are given of functionalized magnetic nanoparticles, magnetoplasmonic effects and use of metamaterials for SPR sensing. The other topic is focused on surface-enhanced Raman scattering (SERS) for sensing, for which uniform, flexible, and reproducible SERS substrates have been produced. With such recent developments, there is the prospect of improving sensitivity and lowering the limit of detection in order to overcome the limitations inherent in ultrasensitive detection of chemical and biological analytes, especially at single molecule levels.

Quantification of cardiac troponin I in human plasma by immunoaffinity enrichment and targeted mass spectrometry

Quantification of cardiac troponin I (cTnI), a protein biomarker used for diagnosing myocardial infarction, has been achieved in native patient plasma based on an immunoaffinity enrichment strategy and isotope dilution (ID) liquid chromatography-tandem mass spectrometry (LC-MS/MS) method. The key steps in the workflow involved isolating cTnI from plasma using anti-cTnI antibody coupled to magnetic nanoparticles, followed by an enzymatic digestion with trypsin. Three tryptic peptides from cTnI were monitored and used for quantification by ID-LC-MS/MS via multiple reaction monitoring (MRM). Measurements were performed using a matrix-matched calibration system. NIST SRM 2921 Human Cardiac Troponin Complex acted as the calibrant and a full-length isotopically labeled protein analog of cTnI was used as an internal standard. The method was successfully demonstrated on five patient plasma samples, with cTnI concentrations measuring between 4.86 μg/L and 11.3 μg/L (signifying moderate myocardial infarctions). LC-MS/MS measurement precision was validated by three unique peptides from cTnI and two MRM transitions per peptide. Relative standard deviation (CV) from the five plasma samples was determined to be ≤14.3%. This study has demonstrated that quantification of cTnI in native plasma from myocardial infarction patients can be achieved based on an ID-LC-MS/MS method. The development of an ID-LC-MS/MS method for cTnI in plasma is a first step for future certification of matrix-based reference materials, which may be used to help harmonize discordant cTnI clinical assays. Graphical abstract A schematic of the workflow for measuring cardiac troponin I (cTnI), a low-abundant protein biomarker used for diagnosing myocardial infarction, in human plasma by isotope-dilution LC-MS/MS analysis.

Sensitive detection of the IS6110 sequence of Mycobacterium tuberculosis complex based on PCR-magnetic bead ELISA

Tuberculosis (TB) is ranked as the top killer among infectious diseases worldwide. Early and accurate diagnosis of the disease is crucial to end the global TB epidemic. The current commercially available molecular tests are still unaffordable by most TB affected communities. Herein, we developed a novel rapid and sensitive diagnostic method to detect the IS6110 sequence of Mycobacterium tuberculosis (M. tuberculosis) complex using PCR-magnetic bead ELISA. PCR amplification ofa 123 bp repetitive sequence of the IS6110 gene was performed by using digoxigenin (DIG) and biotin-labelled primers. Streptavidin-conjugated magnetic beads were used to collect the dual-labelled amplicons and subsequently, colourimetric detection was done by using horseradish peroxidase (HRP)-conjugated anti-DIG antibody. This method is able to detect M. tuberculosis DNA down to 0.5 fg per reaction within 3 hours. The sensitivity of IS6110 PCR detection by magnetic bead ELISA is 100 times higher than that of conventional agarose gel electrophoresis. The assay specificity was determined using a panel of DNA extracted from 10 common bacteria causing lower respiratory tract infections. No cross-reactivity was detected from those bacteria by IS6110 PCR-magnetic bead ELISA. Thus, the novel highly sensitive and specific, reduced assay time and simplicity of this PCR-magnetic bead ELISA for the detection of the specific gene of M. tuberculosis complex makes it an attractive diagnostic tool for large-scale screening of tuberculosis in standard clinical laboratories.

Tuberculosis (TB) is ranked as the top killer among infectious diseases worldwide.

Sensors and bioassays powered by upconverting materials

In recent years, considerable efforts have been done to better understand the peculiar emission properties of upconverting materials due to their widespread applications in different and important technological fields such as upconversion-based photoactivated cancer therapies, photoactivated drug-delivery, magnetic resonance imaging contrast agents, bioimaging. However, one of the most promising applications of upconverting materials concerns the field of sensing, due to their unique emission properties. In fact, the minimal autofluorescence, blinking, photo-bleaching, and high photostability makes them an excellent alternative to organic dyes or quantum dots. This article reviews the state-of-the-art, design, and sensing strategies of upconversion-based sensing platforms, with special attention to upconverting nanoparticles, as well as how the incorporation of these materials into pre-existing diagnostic tests and bioassays have improved their capabilities for the detection of different kinds of analytes.

Microchip-based ultrafast serodiagnostic assay for tuberculosis

Access to point-of-care (POC), rapid, inexpensive, sensitive, and instrument-free tests for the diagnosis of tuberculosis (TB) remains a major challenge. Here, we report a simple and low-cost microchip-based TB ELISA (MTBE) platform for the detection of anti-mycobacterial IgG in plasma samples in less than 15 minutes. The MTBE employs a flow-less, magnet-actuated, bead-based ELISA for simultaneous detection of IgG responses against multiple mycobacterial antigens. Anti-trehalose 6,6′-dimycolate (TDM) IgG responses were the strongest predictor for differentiating active tuberculosis (ATB) from healthy controls (HC) and latent tuberculosis infections (LTBI). The TDM-based MTBE demonstrated superior sensitivity compared to sputum microscopy (72% vs. 56%) with 80% and 63% positivity among smear-positive and smear-negative confirmed ATB samples, respectively. Receiver operating characteristic analysis indicated good accuracy for differentiating ATB from HC (AUC = 0.77). Thus, TDM-based MTBE can be potentially used as a screening device for rapid diagnosis of active TB at the POC.

Quantification of antibody coupled to magnetic particles by targeted mass spectrometry

Quantifying the amount of antibody on magnetic particles is a fundamental, but often overlooked step in the development of magnetic separation-based immunoaffinity enrichment procedures. In this work, a targeted mass spectrometry (MS)-based method was developed to directly measure the amount of antibody covalently bound to magnetic particles. Isotope-dilution liquid chromatography-tandem MS (ID-LC-MS/MS) has been extensively employed as a gold-standard method for protein quantification. Here, we demonstrate the utility of this methodology for evaluating different antibody coupling processes to magnetic particles of different dimensions. Synthesized magnetic nanoparticles and pre-functionalized microparticles activated with glutaraldehyde or epoxy surface groups were used as solid supports for antibody conjugation. The key steps in this quantitative approach involved an antibody-magnetic particle coupling process, a wash step to remove unreacted antibody, followed by an enzymatic digestion step (in situ with the magnetic particles) to release tryptic antibody peptides. Our results demonstrate that nanoparticles more efficiently bind antibody when compared to microparticles, which was expected due to the larger surface area per unit mass of the nanoparticles compared to the same mass of microparticles. This quantitative method is shown to be capable of accurately and directly measuring antibody bound to magnetic particles and is independent of the conjugation method or type of magnetic particle. Graphical Abstract Schematic illustration of the isotope-dilution mass spectrometry-based workflow to directly measure antibody bound to magnetic particles (MP).

Evaluation of different strategies for magnetic particle functionalization with DNA aptamers

The optimal bio-functionalization of magnetic particles is essential for developing magnetic particle-based bioassays. Whereas functionalization with antibodies is generally well established, immobilization of DNA probes, such as aptamers, is not yet fully explored. In this work, four different types of commercially available magnetic particles, coated with streptavidin, maleimide or carboxyl groups, were evaluated for their surface coverage with aptamer bioreceptors, efficiency in capturing target protein and non-specific protein adsorption on their surface. A recently developed aptamer against the peanut allergen, Ara h 1 protein, was used as a model system. Conjugation of biotinylated Ara h 1 aptamer to the streptavidin particles led to the highest surface coverage, whereas the coverage of maleimide particles was 25% lower. Carboxylated particles appeared to be inadequate for DNA functionalization. Streptavidin particles also showed the greatest target capturing efficiency, comparable to the one of particles functionalized with anti-Ara h 1 antibody. The performance of streptavidin particles was additionally tested in a sandwich assay with the aptamer as a capture receptor on the particle surface. While the limit of detection obtained was comparable to the same assay system with antibody as capture receptor, it was superior to previously reported values using the same aptamer in similar assay schemes with different detection platforms. These results point to the promising application of the Ara h 1 aptamer-functionalized particles in bioassay development.

Electrochemistry-based approaches to low cost, high sensitivity, automated, multiplexed protein immunoassays for cancer diagnostics

Early detection and reliable diagnostics are keys to effectively design cancer therapies with better prognoses. The simultaneous detection of panels of biomarker proteins holds great promise as a general tool for reliable cancer diagnostics. A major challenge in designing such a panel is to decide upon a coherent group of biomarkers which have higher specificity for a given type of cancer. The second big challenge is to develop test devices to measure these biomarkers quantitatively with high sensitivity and specificity, such that there are no interferences from the complex serum or tissue matrices. Lastly, integrating all these tests into a technology that does not require exclusive training to operate, and can be used at point-of-care (POC) is another potential bottleneck in futuristic cancer diagnostics. In this article, we review electrochemistry-based tools and technologies developed and/or used in our laboratories to construct low-cost microfluidic protein arrays for the highly sensitive detection of a panel of cancer-specific biomarkers with high specificity which at the same time has the potential to be translated into POC applications.

Towards the electrochemical diagnosis of cancer: nanomaterial-based immunosensors and cytosensors

In this review, nanomaterial based electrochemical biosensors including electrochemical immunosensors and cytosensors towards cancer detection are covered.

Enzymatic conversion of magnetic nanoparticles to a non-magnetic precipitate: a new approach to magnetic sensing

Magnetic sensing utilizes loss of signal via enzymatic transformation of magnetic nanoparticles (MNPs).

Enzymatic synthesis of magnetic nanoparticles

We report the first in vitro enzymatic synthesis of paramagnetic and antiferromagnetic nanoparticles toward magnetic ELISA reporting. With our procedure, alkaline phosphatase catalyzes the dephosphorylation of l-ascorbic-2-phosphate, which then serves as a reducing agent for salts of iron, gadolinium, and holmium, forming magnetic precipitates of Fe_45±14Gd_5±2O_50±15 and Fe_42±4Ho_6±4O_52±5. The nanoparticles were found to be paramagnetic at 300 K and antiferromagnetic under 25 K. Although weakly magnetic at 300 K, the room-temperature magnetization of the nanoparticles found here is considerably greater than that of analogous chemically-synthesized Ln_xFe_yO_z (Ln = Gd, Ho) samples reported previously. At 5 K, the nanoparticles showed a significantly higher saturation magnetization of 45 and 30 emu/g for Fe_45±14Gd_5±2O_50±15 and Fe_42±4Ho_6±4O_52±5, respectively. Our approach of enzymatically synthesizing magnetic labels reduces the cost and avoids diffusional mass-transfer limitations associated with pre-synthesized magnetic reporter particles, while retaining the advantages of magnetic sensing.

Pre-clinical validation study of a miniaturized electrochemical immunoassay based on square wave voltammetry for early detection of carcinoembryonic antigen in human serum

BACKGROUND

The ELISA format for measuring carcinoembryonic antigen (CEA) serves as a reference standard against which other assays are compared. Because the World Health Organization (WHO) increasingly recommends the use of serum CEA as a diagnostic tool for cancer, it is relevant to explore the reliability of the new decentralized CEA point-of-care-testing (POCT) technologies that are available to physicians and patients, in compliance with mandates of the clinical laboratories' regulatory agencies.

METHODS

Electrochemical immunoassay (ECIA) based on trace lead (Pb) analysis by anodic stripping techniques using sandwich-type immunocomplex conjugates: (MB)Ab/AgCEA/Ab(PbS), and a commercial ELISA test system with optical transmission.

RESULTS

The ECIA provides better analytical performance than does the ELISA. The within assay precision coefficient of variance (%CVw) of the ECIA is lower than the value recommended by the Hong Kong Association of Medical Laboratories (HKAML), and the recoveries of CEA at 1.0, 5.0, 10.0, 25.0 and 50.0 ng/ml are in the range of 99-110% for control serum samples. The ECIA showed a minimal positive bias of 0.0267 ± 0.3270 ng/ml (P=0.9389).

CONCLUSIONS

The proposed CEA screening technology can be practically employed for decentralized clinical analysis of CEA in human serum. Therefore, it can be viewed as a control method for personalized therapy.

Current trends in magnetic particle enrichment for mass spectrometry-based analysis of cardiovascular protein biomarkers

Magnetic particles have traditionally been utilized to isolate and enrich various cardiovascular protein biomarkers for mass spectrometry-based proteomic analysis. The application of functionalized magnetic particles for immunocapture is attractive due to their easy manipulation, large surface area-to-volume ratios for maximal antibody binding, good recovery and high magnetic saturation. Magnetic particle enrichment coupled with mass spectrometry can act as a complementary tool for clinical sandwich-immunoassay development since it can provide improved target specificity and true metrological traceability. The purpose of this review is to summarize current separation methods and technologies that use magnetic particles to enrich protein biomarkers from complex matrices, specifically focusing on cardiovascular disease-related proteins and the advantages of magnetic particles over existing techniques.

Ultrasensitive immuno-detection using viral nanoparticles with modular assembly using genetically-directed biotinylation

We report a novel, modular approach to immuno-detection based on antibody recognition and PCR read-out that employs antibody-conjugated bacteriophage and easily-manipulated non-pathogenic viruses as affinity agents. Our platform employs phage genetically tagged for in vivo biotinylation during phage maturation that can easily be linked, through avidin, to any biotinylated affinity agent, including full-length antibodies, peptides, lectins or aptamers. The presence of analyte is reported with high sensitivity through real-time PCR. This approach avoids the need to clone antibody-encoding DNA fragments, allows the use of full-length, high affinity antibodies and, by having DNA reporters naturally encapsulated inside the bacteriophage, greatly reduces nonspecific binding of DNA. We validate the efficacy of this new approach through the detection of Vascular Endothelial Growth Factor, a known angiogenic cancer biomarker protein, at attomolar concentrations in bronchoalveolar lavage fluid.

Ultrasensitive immuno-detection using viral nanoparticles with modular assembly using genetically-directed biotinylation

We report a novel, modular approach to immuno-detection based on antibody recognition and PCR read-out that employs antibody-conjugated bacteriophage and easily-manipulated non-pathogenic viruses as affinity agents. Our platform employs phage genetically tagged for in vivo biotinylation during phage maturation that can easily be linked, through avidin, to any biotinylated affinity agent, including full-length antibodies, peptides, lectins or aptamers. The presence of analyte is reported with high sensitivity through real-time PCR. This approach avoids the need to clone antibody-encoding DNA fragments, allows the use of full-length, high affinity antibodies and, by having DNA reporters naturally encapsulated inside the bacteriophage, greatly reduces nonspecific binding of DNA. We validate the efficacy of this new approach through the detection of Vascular Endothelial Growth Factor, a known angiogenic cancer biomarker protein, at attomolar concentrations in bronchoalveolar lavage fluid.

Nanomaterials and biomaterials in electrochemical arrays for protein detection

Nanomaterials and biomaterials are important components of new electrochemical arrays designed for sensitive detection of proteins in biological fluids. Such multiplexed protein arrays are predicted to have an important future in personalized medical diagnostics, especially for cancer and heart disease. Sandwich immunoassays for proteins benefit greatly in sensitivity from the use of nanostructured sensor surfaces and multilabeled detection strategies involving nano- or microparticles. In these assays, capture agents such as antibodies or aptamers are attached to sensor surfaces in the array. Target proteins with large binding constants for the affinity agents are captured from liquid samples with high efficiency, either on the sensors or on magnetic bioconjugate particles decorated with many copies of labels and antibodies. After target proteins are captured on the sensor surfaces, the labels are detected by electrochemical techniques. This feature article begins with an overview of the recent history of nanoparticles in electrochemical protein sensors, then moves on to specific examples from our own laboratories. We discuss fabrication of nanostructured sensors and arrays with the aim of multiplexed detection as well as reusability. Following this, we describe systems that integrate particle-based protein sensing with microfluidics for multiplexed protein detection. We end with predictions on the diagnostic future of protein detection.

On-line protein capture on magnetic beads for ultrasensitive microfluidic immunoassays of cancer biomarkers

Accurate, sensitive, multiplexed detection of biomarker proteins holds significant promise for personalized cancer diagnostics. Here we describe the incorporation of a novel on-line chamber to capture cancer biomarker proteins on magnetic beads derivatized with 300,000 enzyme labels and 40,000 antibodies into a modular microfluidic immunoarray. Capture and detection chambers are produced from PDMS on machined molds and do not require lithography. Protein analytes are captured from serum or other biological samples in the stirred capture chamber on the beads held in place magnetically. The beads are subsequently washed free of sample components, and wash solutions sent to waste. Removal of the magnet and valve switching sends the magnetic bead-protein bioconjugates into a detection chamber where they are captured on 8 antibody-decorated gold nanoparticle-film sensors and detected amperometrically. Most steps in the immunoassay including protein capture, washing and measurement are incorporated into the device. In simultaneous assays, the microfluidic system gave ultralow detection limits of 5 fg mL(-1) for interleukin-6 (IL-6) and 7 fg mL(-1) for IL-8 in serum. Accuracy was demonstrated by measuring IL-6 and IL-8 in conditioned media from oral cancer cell lines and showing good correlations with standard ELISAs. The on-line capture chamber facilitates rapid, sensitive, repetitive protein separation and measurement in 30 min in a semi-automated system adaptable to multiplexed protein detection.

Mutation scanning using MUT-MAP, a high-throughput, microfluidic chip-based, multi-analyte panel

Targeted anticancer therapies rely on the identification of patient subgroups most likely to respond to treatment. Predictive biomarkers play a key role in patient selection, while diagnostic and prognostic biomarkers expand our understanding of tumor biology, suggest treatment combinations, and facilitate discovery of novel drug targets. We have developed a high-throughput microfluidics method for mutation detection (MUT-MAP, mutation multi-analyte panel) based on TaqMan or allele-specific PCR (AS-PCR) assays. We analyzed a set of 71 mutations across six genes of therapeutic interest. The six-gene mutation panel was designed to detect the most common mutations in the EGFR, KRAS, PIK3CA, NRAS, BRAF, and AKT1 oncogenes. The DNA was preamplified using custom-designed primer sets before the TaqMan/AS-PCR assays were carried out using the Biomark microfluidics system (Fluidigm; South San Francisco, CA). A cross-reactivity analysis enabled the generation of a robust automated mutation-calling algorithm which was then validated in a series of 51 cell lines and 33 FFPE clinical samples. All detected mutations were confirmed by other means. Sample input titrations confirmed the assay sensitivity with as little as 2 ng gDNA, and demonstrated excellent inter- and intra-chip reproducibility. Parallel analysis of 92 clinical trial samples was carried out using 2-100 ng genomic DNA (gDNA), allowing the simultaneous detection of multiple mutations. DNA prepared from both fresh frozen and formalin-fixed, paraffin-embedded (FFPE) samples were used, and the analysis was routinely completed in 2-3 days: traditional assays require 0.5-1 µg high-quality DNA, and take significantly longer to analyze. This assay can detect a wide range of mutations in therapeutically relevant genes from very small amounts of sample DNA. As such, the mutation assay developed is a valuable tool for high-throughput biomarker discovery and validation in personalized medicine and cancer drug development.

Highly efficient binding of paramagnetic beads bioconjugated with 100,000 or more antibodies to protein-coated surfaces

We report here the first kinetic characterization of 1 μm diameter superparamagnetic particles (MP) decorated with over 100,000 antibodies binding to protein antigens attached to flat surfaces. Surface plasmon resonance (SPR) was used to show that these antibody-derivatized MPs (MP-Ab(2)) exhibit irreversible binding with 100-fold increased association rates compared to free antibodies. The estimated upper limit for the dissociation constant of MP-Ab(2) from the SPR sensor surface is 5 fM, compared to 3-8 nM for the free antibodies. These results are explained by up to 2000 interactions of MP-Ab(2) with protein-decorated surfaces. Findings are consistent with highly efficient capture of protein antigens in solution by the MP-Ab(2) and explain in part the utility of these beads for ultrasensitive protein detection into the fM and aM range. Aggregation of these particles on the SPR chip, probably due to residual magnetic microdomains in the particles, also contributes to ultrasensitive detection and may also help drive the irreversible binding.

Aptamer-capture based assays for human neutrophil elastase

Human neutrophil elastase (HNE) is a multifunctional serine protease, involved in infection defense, inflammatory process regulation, and physiopathological processes of several diseases. We developed aptamer-capture based assays for human neutrophil elastase with different substrates and solid supports to meet different demands, such as simplicity, sensitivity, and high throughput. Aptamers against HNE were immobilized on magnetic beads or microplates as affinity ligands to capture HNE, and then the enriched HNE catalyzed the conversion of chromogenic substrates or fluorogenic substrates to products. The measurement of the generated enzymatic products enabled the final detection of HNE. In the assay using chromogenic substrates and aptamer modified magnetic beads, 0.4 pM HNE could be successfully detected. The sensitivity of the assay was further improved by using fluorogenic substrates, and a detection limit of HNE at 20 fM was achieved. The use of aptamer-coated microplates instead of aptamer modified magnetic beads in the assays also allowed the sensitive detection of HNE, offering advantages in fast sample handling and measurement. The established assays for HNE displayed good specificity, and proteins including serum albumin, transferrin, immunoglobulin G, thrombin, porcine pancreatic elastase, trypsin, proteinase K, chymotrypsin, lysozyme, cathepsin G, and proteinase 3 did not cause interference in the detection of HNE.

Electrochemical immunosensors for detection of cancer protein biomarkers

Bioanalytical methods have experienced unprecedented growth in recent years, driven in large part by the need for faster, more sensitive, more portable ("point of care") systems to detect protein biomarkers for clinical diagnosis. Electrochemical detection strategies, used in conjunction with immunosensors, offer advantages because they are fast, simple, and low cost. Recent developments in electrochemical immunosensors have significantly improved the sensitivity needed to detect low concentrations of biomarkers present in early stages of cancer. Moreover, the coupling of electrochemical devices with nanomaterials, such as gold nanoparticles, carbon nanotubes, magnetic particles, and quantum dots, offers multiplexing capability for simultaneous measurements of multiple cancer biomarkers. This review will discuss recent advances in the development of electrochemical immunosensors for the next generation of cancer diagnostics, with an emphasis on opportunities for further improvement in cancer diagnostics and treatment monitoring. Details will be given for strategies to increase sensitivity through multilabel amplification, coupled with high densities of capture molecules on sensor surfaces. Such sensors are capable of detecting a wide range of protein quantities, from nanogram to femtogram (depending on the protein biomarkers of interest), in a single sample.

Nanomaterials-based electrochemical immunosensors for proteins

For this special issue on 90 years of polarography, the following personal account describes how my early research in electrochemistry and polarography in the laboratory of Prof. Petr Zuman led to a major research effort in the determination of proteins for cancer detection and monitoring. It reviews the very recent history of nanoparticle labels and multiplexed detection in protein immunosensors. It then describes our journey of discovery that has led to ultrasensitive protein immunosensors achieved by combining nanostructured electrodes with particles labeled with up to ½ million enzymes that can detect down to as little as 1 fg mL(-1) protein in diluted serum. Our most mature multiple protein detection system is a microfluidic device with eight sensors coated with 5-nm gold nanoparticles that uses off-line protein detection with heavily labeled magnetic particles. This approach has led to reliable sub pg mL(-1) detection limits for multiple proteins, provides excellent correlation with referee ELISA methods, and is currently being used for validation of panels of biomarkers for oral and prostate cancer. The article ends with a section on future perspectives.