Multiplexed Detection of Epigenetic Markers Using Quantum Dot (QD)-Encoded Hydrogel Microparticles

A fluorescence-based immunochromatographic assay using quantum dot-encapsulated nanoparticles for the rapid and sensitive detection of fetuin-B

Coronary artery disease (CAD) is the leading cause of death worldwide. Earlier detection of CAD improves treatment outcomes and secondary prevention. The circulating fetuin-B protein is considered to be a promising biomarker for the early detection of CAD. However, a facile and reliable clinical test for fetuin-B is still lacking. Herein, we describe a reliable fluorescent biosensor for detecting fetuin-B in plasma that combines quantum dots-doped polystyrene nanoparticles with an immunochromatographic assay strip (QNPs-ICAS). The QNPs served as detection signals in the QNPs-ICAS sensor system, which was based on a double-antibody sandwich structure. Under optimum experimental conditions, the biosensor exhibited a broad linear range of 1-200 ng mL-1 and a low detection limit of 0.299 ng mL-1. Furthermore, the proposed immunosensor demonstrated high sensitivity, satisfactory selectivity, good reproducibility, and excellent recovery. Finally, the performance and applicability of our QNPs-based ICAS system were validated in clinical samples using a commercial ELISA kit with excellent correlations (r = 0.98451, n = 116). To conclude, the proposed sensor served as a rapid, sensitive, and accurate method for detecting fetuin-B in actual clinical samples, thereby demonstrating its potential for preliminary CAD screening and diagnosis.

Spatially Defined Cell-Secreted Protein Detection Using Granular Hydrogels: μGeLISA

Intercellular communication through secreted proteins is necessary in essential processes such as embryo and limb development, disease progression, and immune responses. There exist many techniques to study bulk solution protein concentrations, but there is a limited set of tools to study the concentrations of cell-secreted proteins in situ within diverse cell platforms while retaining spatial information. In this study, we have developed a microgel system that is able to quantitatively measure the cell-secreted protein concentration within defined three-dimensional culture configurations with single-cell spatial resolution, called μGeLISA (microgel-linked immunosorbent assay). This system, which is based on the surface modification of polyethylene glycol microgels, was able to detect interleukin 6 (IL-6) concentrations of 2.21-21.86 ng/mL. Microgels were also able to detect cell spheroid-secreted IL-6 and distinguish between low- and high-secreting single cells. The system was also adapted to measure the concentration of cell-secreted matrix metalloproteinase-2 (MMP-2). μGeLISA represents a highly versatile system with a straightforward fabrication process that can be adapted toward the detection of secreted proteins within a diverse range of cell culture configurations.

Single-Color Barcoding for Multiplexed Hydrogel Bead-Based Immunoassays

Current developments in precision medicine require the simultaneous detection of an increasing number of biomarkers in heterogeneous, complex solutions, such as blood samples. To meet this need, immunoassays on barcoded hydrogel beads have been proposed, although the encoding and decoding of these barcodes is usually complex and/or resource-intensive. Herein, an efficient method for the fabrication of barcoded, functionalized hydrogel beads is presented. The hydrogel beads are generated using droplet-based microfluidics in combination with photochemically induced C-H insertion reactions, allowing photo-crosslinking, (bio-) functionalization, and barcode integration to be performed in a single step. The generated functionalized beads carry single-color barcodes consisting of green-fluorescent particles of different sizes and concentrations, allowing simple and simultaneous readout with a standard plate reader. As a test example, the performance of barcoded hydrogel beads (3 × 3 matrix) functionalized with capture molecules of interest (e.g., antigens) is investigated for the detection of Lyme-disease-specific antibodies in patient sera. The described barcoding strategy for hydrogel beads does not interfere with the bioanalytical process and captivates by its simplicity and versatility, making it an attractive candidate for multiplex bioanalytical processes.

Multiplex SNP Genotyping Using SWITCH: Sequence-Specific Nanoparticle with Interpretative Toehold-Mediated Sequence Decoding in Hydrogel

Single nucleotide polymorphisms (SNPs) that can alter phenotypes of individuals play a pivotal role in disease development and, more importantly, responses to therapy. However, SNP genotyping has been challenging due to the similarity of SNP alleles and their low concentration in biological samples. Sequence-specific nanoparticle with interpretative toehold-mediated sequence decoding in hydrogel (SWITCH) for multiplex SNP genotyping is presented. The encoding with gold nanoparticle probes transduces each SNP target to ≈1000 invaders with prominently different sequences between wild and mutant types, featuring polymerase chain reaction (PCR)-free amplification. Subsequently, the toehold-mediated DNA replacement in hydrogel microparticles decodes the invaders via SNP-specific fluorescence signals. The 4-plex detection of the warfarin-associated SNP targets spiked in commercially validated human serum (S1-100ML, Merck) is successfully demonstrated with excellent specificity. This work is the first technology development presenting PCR-free, multiplex SNP genotyping with a single reporting fluorophore, to the best of knowledge.

Hydrogel-based hybridization chain reaction (HCR) for detection of urinary exosomal miRNAs as a diagnostic tool of prostate cancer

Although urinary exosomal microRNAs (miRNAs) have recently emerged as potential biomarkers, clinical applications are still limited due to their low concentration in small volumes of clinical samples. Therefore, the development of a non-invasive, specific diagnostic tool, along with profiling exosomal miRNA markers from urine, remains a significant challenge. Here, we present hydrogel-based hybridization chain reaction (HCR) for multiplex signal amplification to detect urinary exosomal miRNAs from human clinical samples. We succeeded in identifying small amounts (~amol) of exosomal miRNAs from 600 μL of urine with up to ~35-fold amplification and enhanced detection limits by over an order of magnitude for two miRNA biomarker candidates, hsa-miR-6090 and hsa-miR-3665. Furthermore, we proposed ratiometric analysis without requiring normalization to a reference miRNA and validated the clinical diagnostic potential toward differentiating prostate cancer patients from healthy controls. Our hydrogel-based HCR could serve as a new diagnostic platform for a non-invasive liquid biopsy before burdensome tissue biopsy of various diseases, including prostate cancer screening, complementing the PSA test.

Microfluidic platform for selective microparticle parking and paired particle isolation in droplet arrays

Immobilizing microscale objects (e.g., cells, spheroids, and microparticles) in arrays for direct observation and analysis is a critical step of many biological and chemical assays; however, existing techniques are often limited in their ability to precisely capture, arrange, isolate, and recollect objects of interest. In this work, we present a microfluidic platform that selectively parks microparticles in hydrodynamic traps based on particle physical characteristics (size, stiffness, and internal structure). We present an accompanying scaling analysis for the particle parking process to enable rational design of microfluidic traps and selection of operating conditions for successful parking of desired particles with specific size and elastic modulus. Our platform also enables parking of encoded particle pairs in defined spatial arrangements and subsequent isolation of these pairs in aqueous droplets, creating distinct microenvironments with no cross-contamination. In addition, we demonstrate the ability to recollect objects of interest (i.e., one particle from each pair) after observation within the channel. This integrated device is ideal for multiplexed assays or microenvironment fabrication for controlled biological studies.

Microparticle parking and isolation for highly sensitive microRNA detection

Isolating small objects, such as particles, cells, and molecules, in individual aqueous droplets is useful for chemical and biological assays. We have developed a simple microfluidic platform to immobilize (park) microparticles at defined locations, and isolate particles in monodisperse droplets surrounded by immiscible oil. While conventional methods can only achieve stochastic encapsulation of objects within larger droplets, our in situ method ensures that a single particle is entrapped in a similar-sized droplet, with ∼95% yield for parking and isolation. This enables time-lapse studies of reactions in confined volumes and can be used to perform enzymatic amplification of a desired signal to improve the sensitivity of diagnostic assays. To demonstrate the utility of our technique, we perform highly sensitive, multiplexed microRNA detection by isolating encoded, functional hydrogel microparticles in small aqueous droplets. Non-fouling hydrogel microparticles are attractive for microRNA detection due to favorable capture kinetics. By encapsulating these particles in droplets and employing a generalizable enzyme amplification scheme, we demonstrate an order of magnitude improvement in detection sensitivity compared to a non-amplified assay.

Bioengineering Microgels and Hydrogel Microparticles for Sensing Biomolecular Targets

Hydrogels, and in particular microgels, are playing an increasingly important role in a diverse range of applications due to their hydrophilic, biocompatible, and highly flexible chemical characteristics. On this basis, solution-like environment, non-fouling nature, easy probe accessibility and target diffusion, effective inclusion of reporting moieties can be achieved, making them ideal substrates for bio-sensing applications. In fact, hydrogels are already successfully used in immunoassays as well as sensitive nucleic acid assays, also enabling hydrogel-based suspension arrays. In this review, we discuss key parameters of hydrogels in the form of micron-sized particles to be used in sensing applications, paying attention to the protein and oligonucleotides (i.e., miRNAs) targets as most representative kind of biomarkers.

Flow lithography in ultraviolet-curable polydimethylsiloxane microfluidic chips

Flow Lithography (FL) is the technique used for the synthesis of hydrogel microparticles with various complex shapes and distinct chemical compositions by combining microfluidics with photolithography. Although polydimethylsiloxane (PDMS) has been used most widely as almost the sole material for FL, PDMS microfluidic chips have limitations: (1) undesired shrinkage due to the thermal expansion of masters used for replica molding and (2) interfacial delamination between two thermally cured PDMS layers. Here, we propose the utilization of ultraviolet (UV)-curable PDMS (X-34-4184) for FL as an excellent alternative material of the conventional PDMS. Our proposed utilization of the UV-curable PDMS offers three key advantages, observed in our study: (1) UV-curable PDMS exhibited almost the same oxygen permeability as the conventional PDMS. (2) The almost complete absence of shrinkage facilitated the fabrication of more precise reverse duplication of microstructures. (3) UV-cured PDMS microfluidic chips were capable of much stronger interfacial bonding so that the burst pressure increased to ∼0.9 MPa. Owing to these benefits, we demonstrated a substantial improvement of productivity in synthesizing polyethylene glycol diacrylate microparticles via stop flow lithography, by applying a flow time (40 ms) an order of magnitude shorter. Our results suggest that UV-cured PDMS chips can be used as a general platform for various types of flow lithography and also be employed readily in other applications where very precise replication of structures on micro- or sub-micrometer scales and/or strong interfacial bonding are desirable.

Versatile design and synthesis of nano-barcodes

This review provides a critical discussion on the versatile designing and usage of nano-barcodes for various existing and emerging applications.

A novel strategy towards designing a CdSe quantum dot-metallohydrogel composite material

We have described here an efficient method to disperse hydrophobic CdSe quantum dots (QDs) in an aqueous phase using cetyltrimethylammonium bromide (CTAB) micelles without any surface ligand exchange. The water soluble QDs were then embedded in 3D self assembled fibrillar networks (SAFINs) of a hydrogel showing homogeneous dispersibility as evidenced from optical and electron microscopic techniques. The photophysical studies of the hydrogel-QD composite are reported for the first time. These composite materials may have potential applications in biology, optoelectronics, sensors, non-linear optics and materials science.