Steric Hindrance Assay for Secreted Factors in Stem Cell Culture

An integrated perspective on measuring cytokines to inform CAR-T bioprocessing

Chimeric antigen receptor (CAR)-T cells are emerging as a generation-defining therapeutic however their manufacture remains a major barrier to meeting increased market demand. Monitoring critical quality attributes (CQAs) and critical process parameters (CPPs) during manufacture would vastly enrich acquired information related to the process and product, providing feedback to enable real-time decision making. Here we identify specific CAR-T cytokines as value-adding analytes and discuss their roles as plausible CPPs and CQAs. High sensitivity sensing technologies which can be easily integrated into manufacture workflows are essential to implement real-time monitoring of these cytokines. We therefore present biosensors as enabling technologies and evaluate recent advancements in cytokine detection in cell cultures, offering promising translatability to CAR-T biomanufacture. Finally, we outline emerging sensing technologies with future promise, and provide an overall outlook on existing gaps to implementation and the optimal sensing platform to enable cytokine monitoring in CAR-T biomanufacture.

Rationally Designed DNA-Based Scaffolds and Switching Probes for Protein Sensing

The detection of a protein analyte and use of this type of information for disease diagnosis and physiological monitoring requires methods with high sensitivity and specificity that have to be also easy to use, rapid and, ideally, single step. In the last 10 years, a number of DNA-based sensing methods and sensors have been developed in order to achieve quantitative readout of protein biomarkers. Inspired by the speed, specificity, and versatility of naturally occurring chemosensors based on structure-switching biomolecules, significant efforts have been done to reproduce these mechanisms into the fabrication of artificial biosensors for protein detection. As an alternative, in scaffold DNA biosensors, different recognition elements (e.g., peptides, proteins, small molecules, and antibodies) can be conjugated to the DNA scaffold with high accuracy and precision in order to specifically interact with the target protein with high affinity and specificity. They have several advantages and potential, especially because the transduction signal can be drastically enhanced. Our aim here is to provide an overview of the best examples of structure switching-based and scaffold DNA sensors, as well as to introduce the reader to the rational design of innovative sensing mechanisms and strategies based on programmable functional DNA systems for protein detection.

Ionic Strength and Hybridization Position near Gold Electrodes Can Significantly Improve Kinetics in DNA-Based Electrochemical Sensors

A variety of electrochemical (EC) biosensors play critical roles in disease diagnostics. More recently, DNA-based EC sensors have been established as promising for detecting a wide range of analyte classes. Since most of these sensors rely on the high specificity of DNA hybridization for analyte binding or structural control, it is crucial to understand the kinetics of hybridization at the electrode surface. In this work, we have used methylene blue-labeled DNA strands to monitor the kinetics of DNA hybridization at the electrode surface with square-wave voltammetry. By varying the position of the double-stranded DNA segment relative to the electrode surface as well as the bulk solution's ionic strength (0.125-1.00 M), we observed significant interferences with DNA hybridization closer to the surface, with more substantial interference at lower ionic strength. As a demonstration of the effect, toehold-mediated strand displacement reactions were slowed and diminished close to the surface, while strategic placement of the DNA binding site improved reaction rates and yields. This work manifests that both the salt concentration and DNA hybridization site relative to the electrode are important factors to consider when designing DNA-based EC sensors that measure hybridization directly at the electrode surface.

Biodetection Techniques for Quantification of Chemokines

Chemokines are a class of cytokine whose special properties, together with their involvement and relevant role in various diseases, make them a restricted group of biomarkers suitable for diagnosis and monitoring. Despite their importance, biodetection techniques dedicated to the selective determination of one or more chemokines are very scarce. For some years now, the critical diagnosis of inflammatory diseases by detecting both cytokine and chemokine biomarkers, has had a strong impact on the development of multiple detection platforms. However, it would be desirable to implement methodologies with a higher degree of selectivity for chemokines, in order to provide more precise information. In addition, better development of biosensor technology applied to this specific field would make it possible to address the main challenges of detection methods for several diseases with a high incidence in the population, avoiding high costs and low sensitivity. Taking this into account, this review aims to present the state of the art of chemokine biodetection techniques and emphasize the role of these systems in the prevention, monitoring and treatment of various diseases associated with chemokines as a starting point for future developments that are also analyzed throughout the article.

Extracellular Biomarkers of Inner Ear Disease and Their Potential for Point-of-Care Diagnostics

Rapid diagnostic testing has become a mainstay of patient care, using easily obtained samples such as blood or urine to facilitate sample analysis at the point-of-care. These tests rely on the detection of disease or organ-specific biomarkers that have been well characterized for a particular disorder. Currently, there is no rapid diagnostic test for hearing loss, which is one of the most prevalent sensory disorders in the world. In this review, potential biomarkers for inner ear-related disorders, their detection, and quantification in bodily fluids are described. The authors discuss lesion-specific changes in cell-free deoxyribonucleic acids (DNAs), micro-ribonucleic acids (microRNAs), proteins, and metabolites, in addition to recent biosensor advances that may facilitate rapid and precise detection of these molecules. Ultimately, these biomarkers may be used to provide accurate diagnostics regarding the site of damage in the inner ear, providing practical information for individualized therapy and assessment of treatment efficacy in the future.

DNA Nanosieve-Based Regenerative Electrochemical Biosensor Utilizing Nucleic Acid Flexibility for Accurate Allele Typing in Clinical Samples

Herein, an interface-based DNA nanosieve that has the ability to differentiate ssDNA from dsDNA has been demonstrated for the first time. The DNA nanosieve could be readily built through thiol-DNA's self-assembly on the gold electrode surface, and its cavity size was tunable by varying the concentration of thiol-DNAs. Electrochemical chronocoulometry using [Ru(NH₃)₆]³⁺ as redox revealed that the average probe-to-probe separation in the 1 μM thiol-DNA-modified gold electrode was 10.6 ± 0.3 nm so that the rigid dsDNA with a length of ∼17 nm could not permeate the nanosieve, whereas the randomly coiled ssDNA could enter it due to its high flexibility, which has been demonstrated by square wave voltammetry and methylene blue labels through an upside-down hybridization format. After combining the transiently binding characteristic of a short DNA duplex and introducing a regenerative probe (the counterpart of ssDNA), a highly reproducible nanosieve-based E-DNA model was obtained with a relative standard deviation (RSD) as low as 2.7% over seven cycles. Finally, we built a regenerative nanosieve-based E-DNA sensor using a ligation cycle reaction as an ssDNA amplification strategy and realized one-sensor-based continuous measurement to multiple clinical samples with excellent allele-typing performance. This work holds great potential in low-cost and high-throughput analysis between biosensors and biochips and also opens up a new avenue in nucleic acid flexibility-based DNA materials for future applications in DNA origami and molecular logic gates.

Immunoglobulin G-Based Steric Hindrance Assay for Protein Detection

With the imminent needs of rapid, accurate, simple point-of-care systems for global healthcare industry, electrochemical biosensors have been widely developed owing to their cost-effectiveness and simple instrumentation. However, typical electrochemical biosensors for direct analysis of proteins in the human biological sample still suffer from complex biosensor fabrication, lack of general method, limited sensitivity, and matrix-caused biofouling effect. To resolve these challenges, we developed a general electrochemical sensing strategy based on a designed steric hindrance effect on an antibody surface layer. This strategy utilizes the interaction pattern of protein-G and immunoglobulin G (Fc and Fab regions), providing a steric hindrance effect during the target capturing process. The provided steric hindrance effect minimizes the matrix effect-caused fouling surface and altered the path of electron transfer, delivering a low-fouling and high-sensitivity detection of protein in complex matrices. Also, an enzyme-based horseradish peroxidase/hydroquinone/H₂O₂ transduction system can also be applied to the system, demonstrating the versatility of this sensing strategy for general electrochemical sensing applications. We demonstrated this platform through the detection of Tau protein and programming death ligand 1 with a subpico molar detection limit within 10 min, satisfying the clinical point-of-care requirements for rapid turnaround time and ultrasensitivity.

A review on recent advancements in electrochemical biosensing using carbonaceous nanomaterials

This review, with 201 references, describes the recent advancement in the application of carbonaceous nanomaterials as highly conductive platforms in electrochemical biosensing. The electrochemical biosensing is described in introduction by classifying biosensors into catalytic-based and affinity-based biosensors and statistically demonstrates the most recent published works in each category. The introduction is followed by sections on electrochemical biosensors configurations and common carbonaceous nanomaterials applied in electrochemical biosensing, including graphene and its derivatives, carbon nanotubes, mesoporous carbon, carbon nanofibers and carbon nanospheres. In the following sections, carbonaceous catalytic-based and affinity-based biosensors are discussed in detail. In the category of catalytic-based biosensors, a comparison between enzymatic biosensors and non-enzymatic electrochemical sensors is carried out. Regarding the affinity-based biosensors, scholarly articles related to biological elements such as antibodies, deoxyribonucleic acids (DNAs) and aptamers are discussed in separate sections. The last section discusses recent advancements in carbonaceous screen-printed electrodes as a growing field in electrochemical biosensing. Tables are presented that give an overview on the diversity of analytes, type of materials and the sensors performance. Ultimately, general considerations, challenges and future perspectives in this field of science are discussed. Recent findings suggest that interests towards 2D nanostructured electrodes based on graphene and its derivatives are still growing in the field of electrochemical biosensing. That is because of their exceptional electrical conductivity, active surface area and more convenient production methods compared to carbon nanotubes. Graphical abstract Schematic representation of carbonaceous nanomaterials used in electrochemical biosensing. The content is classified into non-enzymatic sensors and affinity/ catalytic biosensors. Recent publications are tabulated and compared, considering materials, target, limit of detection and linear range of detection.

A Nucleic Acid Nanostructure Built through On-Electrode Ligation for Electrochemical Detection of a Broad Range of Analytes

For an assay to be most effective in point-of-care clinical analysis, it needs to be economical, simple, generalizable, and free from tedious workflows. While electrochemistry-based DNA sensors reduce instrumental costs and eliminate complicated procedures, there remains a need to address probe costs and generalizability, as numerous probes with multiple conjugations are needed to quantify a wide range of biomarkers. In this work, we have opened a route to circumvent complicated multiconjugation schemes using enzyme-catalyzed probe construction directly on the surface of the electrode. With this, we have created a versatile DNA nanostructure probe and validated its effectiveness by quantification of proteins (streptavidin, anti-digoxigenin, anti-tacrolimus) and small molecules (biotin, digoxigenin, tacrolimus) using the same platform. Tacrolimus, a widely prescribed immunosuppressant drug for organ transplant patients, was directly quantified with electrochemistry for the first time, with the assay range matching the therapeutic index range. Finally, the stability and sensitivity of the probe was confirmed in a background of minimally diluted human serum.

Peptide-Mediated Electrochemical Steric Hindrance Assay for One-Step Detection of HIV Antibodies

Diagnosis of infectious disease in patients, including human immunodeficiency virus (HIV) infection, can be achieved through the detection of specific antibodies produced by the immune system. We have previously shown that macromolecules such as antibodies can be efficiently detected in complex biological samples by sterically inhibiting the hybridization of conjugated complementary DNA strands to electrode-bound DNA strands. Here, we report a peptide-mediated electrochemical steric hindrance hybridization assay, PeSHHA, specially for the detection of antibodies against the gp41 protein of HIV-1. We show that the sensitivity of this PeSHHA can be significantly enhanced using nanostructured electrodes and demonstrate the rapid, one-step detection of HIV-1 antibodies directly in clinical samples.

A Hierarchical 3D Nanostructured Microfluidic Device for Sensitive Detection of Pathogenic Bacteria

Efficient capture and rapid detection of pathogenic bacteria from body fluids lead to early diagnostics of bacterial infections and significantly enhance the survival rate. We propose a universal nano/microfluidic device integrated with a 3D nanostructured detection platform for sensitive and quantifiable detection of pathogenic bacteria. Surface characterization of the nanostructured detection platform confirms a uniform distribution of hierarchical 3D nano-/microisland (NMI) structures with spatial orientation and nanorough protrusions. The hierarchical 3D NMI is the unique characteristic of the integrated device, which enables enhanced capture and quantifiable detection of bacteria via both a probe-free and immunoaffinity detection method. As a proof of principle, we demonstrate probe-free capture of pathogenic Escherichia coli (E. coli) and immunocapture of methicillin-resistant-Staphylococcus aureus (MRSA). Our device demonstrates a linear range between 50 and 10⁴ CFU mL^-1 , with average efficiency of 93% and 85% for probe-free detection of E. coli and immunoaffinity detection of MRSA, respectively. It is successfully demonstrated that the spatial orientation of 3D NMIs contributes in quantifiable detection of fluorescently labeled bacteria, while the nanorough protrusions contribute in probe-free capture of bacteria. The ease of fabrication, integration, and implementation can inspire future point-of-care devices based on nanomaterial interfaces for sensitive and high-throughput optical detection.