Antibodies in diagnostics - from immunoassays to protein chips

Sensing the Future-Frontiers in Biosensors: Exploring Classifications, Principles, and Recent Advances

Biosensors are transforming healthcare by delivering swift, precise, and economical diagnostic solutions. These analytical instruments combine biological indicators with physical transducers to identify and quantify biomarkers, thereby improving illness detection, management, and patient surveillance. Biosensors are widely utilized in healthcare for the diagnosis of chronic and infectious diseases, tailored treatment, and real-time health monitoring. This thorough overview examines several categories of biosensors and their uses in the detection of numerous biomarkers, including glucose, proteins, nucleic acids, and infections. Biosensors are commonly classified based on the type of transducer employed or the specific biorecognition element utilized. This review introduces a novel classification based on substrate morphology, offering a comprehensive perspective on biosensor categorization. Considerable emphasis is placed on the advancement of point-of-care biosensors, facilitating decentralized diagnostics and alleviating the strain on centralized healthcare systems. Recent advancements in nanotechnology have significantly improved the sensitivity, selectivity, and downsizing of biosensors, rendering them more efficient and accessible. The study examines problems such as stability, reproducibility, and regulatory approval that must be addressed to enable the widespread implementation of biosensors in clinical environments. The study examines the amalgamation of biosensors with wearable devices and smartphones, emphasizing the prospects for ongoing health surveillance and individualized medical care. This viewpoint clarifies the distinct types of biosensors and their particular roles, together with recent developments in the "smart biosensor" sector, facilitated by artificial intelligence and the Internet of Medical Things (IoMT). This novel approach seeks to deliver a comprehensive evaluation of the present condition of biosensor technology in healthcare, recent developments, and prospective paths, emphasizing their significance in influencing the future of medical diagnostics and patient care.

Human monoclonal antibody cloning and expression with overlap extension PCR and short DNA fragments

Monoclonal antibodies are powerful therapeutic, diagnostic, and research tools. Methods utilized to generate monoclonal antibodies are evolving rapidly. We created a transfectable linear antibody expression cassette from a 2-h high-fidelity overlapping PCR reaction from synthesized DNA fragments. We coupled heavy and light chains into a single linear sequence with a promoter, self-cleaving peptide, and poly(A) signal to increase the flexibility of swapping variable regions from any sequence available in silico. Transfection of the linear cassette tended to generate similar levels to the two-plasmid system and generated an average of 47 μg (14-98 μg) after 5 days in 2 ml cultures with 15 unique antibody sequences. The levels of antibodies produced were sufficient for most downstream applications in less than a week. The method presented here reduces the time, cost, and complexity of cloning steps.

Surface-functionalized PAN fiber membranes for the sensitive detection of airborne specific markers

PAN fibers are characterized by having a large surface-to-volume ratio and small pores, which are beneficial for applications in filtration and specific molecular detection systems. Naturally, larger items are filtered, and a lower ratio between specific and nonspecific binding is expected since small pores do not allow larger elements to penetrate through membranes; thus, nonspecific binding is enhanced. We prepared and tested fiber membranes (diameter cca 700 nm) functionalized with a specific antibody to prove that even microscopic systems such as bacteria could be specifically identified. In addition, we established a methodology that enabled the effective binding of bacteria in not only an aqueous environment but also air. Our data clearly prove that even large systems such as bacteria could be specifically identified by fiber membranes surface-functionalized with a specific antibody. This research opens the door to the construction of biosensors for the fast, inexpensive, and sensitive identification of airborne bacterial contaminants and other airborne pollutants.

Modular binder technology by NGS-aided, high-resolution selection in yeast of designed armadillo modules

Establishing modular binders as diagnostic detection agents represents a cost- and time-efficient alternative to the commonly used binders that are generated one molecule at a time. In contrast to these conventional approaches, a modular binder can be designed in silico from individual modules to, in principle, recognize any desired linear epitope without going through a selection and hit-validation process, given a set of preexisting, amino acid-specific modules. Designed armadillo repeat proteins (dArmRP) have been developed as modular binder scaffolds, and we report here the generation of highly specific dArmRP modules by yeast surface display selection, performed on a rationally designed dArmRP library. A selection strategy was developed to distinguish the binding difference resulting from a single amino acid mutation in the target peptide. Our reverse-competitor strategy introduced here employs the designated target as a competitor to increase the sensitivity when separating specific from cross-reactive binders that show similar affinities for the target peptide. With this switch in selection focus from affinity to specificity, we found that the enrichment during this specificity sort is indicative of the desired phenotype, regardless of the binder abundance. Hence, deep sequencing of the selection pools allows retrieval of phenotypic hits with only 0.1% abundance in the selectivity sort pool from the next-generation sequencing data alone. In a proof-of-principle study, a binder was created by replacing all corresponding wild-type modules with a newly selected module, yielding a binder with very high affinity for the designated target that has been successfully validated as a detection agent in western blot analysis.

Recombinant monoclonal antibody production in yeasts: Challenges and considerations

Monoclonal antibodies (mAbs) are laboratory-based engineered protein molecules with a monovalent affinity or multivalent avidity towards a specific target or antigen, which can mimic natural antibodies that are produced in the human immune systems to fight against detrimental pathogens. The recombinant mAb is one of the most effective classes of biopharmaceuticals produced in vitro by cloning and expressing synthetic antibody genes in a suitable host. Yeast is one of the potential hosts among others for the successful production of recombinant mAbs. However, there are very few yeast-derived mAbs that got the approval of the regulatory agencies for direct use for treatment purposes. Certain challenges encountered by yeasts for recombinant antibody productions need to be overcome and a few considerations related to antibody structure, host engineering, and culturing strategies should be followed for the improved production of mAbs in yeasts. In this review, the drawbacks related to the metabolic burden of the host, culturing conditions including induction mechanism and secretion efficiency, solubility and stability, downstream processing, and the pharmacokinetic behavior of the antibody are discussed, which will help in developing the yeast hosts for the efficient production of recombinant mAbs.

Subtractive Immunization as a Method to Develop Respiratory Syncytial Virus (RSV)-Specific Monoclonal Antibodies

Respiratory Syncytial Virus (RSV) is a significant cause of lower respiratory tract infections in the young, the elderly, and in immunodeficient patients. As such, the virus represents an important cause of morbidity and mortality worldwide. Development of monoclonal antibodies against RSV has resulted in a commercial prophylaxis, palivizumab (Synagis®), and different antibodies that have improved our understanding of the structure of the viral proteins. In this study, a different immunization technique, subtractive immunization, was evaluated for its applicability to develop RSV-specific antibodies. One hybridoma which produced antibodies with the strongest staining of RSV infected cells, ATAC-0025, was selected for further characterization. This antibody belongs to the IgG1 class, has neutralizing capacity and recognizes the envelope F-protein. The antibody has a broad reactivity against a range of RSV reference strains and clinical isolates.

Multiplex Assays of MicroRNAs by Using Single Particle Electrochemical Collision in a Single Run

It is important to quantify multiple biomarkers in a single run due to the advantages of precious samples and diagnostic accuracy. Based on the distinguishability of two types of current signals from single particle electrochemical collision (SPEC), step-type current transients produced by Pt nanoparticles (PtNPs) catalyzed hydrazine oxidation and peak-type current transients produced by Ag nanoparticles (AgNPs) oxidation, a kind of multiplex immunoassay of target microRNAs (miRNA-21 and Let-7a) have been established during SPEC in a single run. When the single-stranded DNA (ssDNA1) that was perfectly complementary to miRNA-21 was coupled to the surface of PtNPs, the SPEC of PtNPs electrocatalysis was inhibited and the step-type current transients disappeared, while the single-stranded DNA (ssDNA2) that was perfectly complementary to Let-7a was coupled to the surface of AgNPs, the SPEC of AgNPs oxidation was inhibited, and the peak-type current transients disappeared, thus the signals were in the "off" state at this time. After that, miRNA-21 and Let-7a were added into solution, complementary base pairing disrupted the weak DNA-NP interaction and restored the electrocatalysis of PtNPs and the electrooxidation of AgNPs, and the step-type current signals and peak-type current signals were in the "on" state. Moreover, the frequencies from two different recovered signals (PtNPs catalysis and AgNPs oxidation) corresponded to the amount of added miRNA-21 and Let-7a, thus a multiplex immunoassay method for dual quantification of miRNA-21 and Let-7a in a single run was established.

Design of Tetra-Peptide Ligands of Antibody Fc Regions Using In Silico Combinatorial Library Screening

Peptides, or short chains of amino-acid residues, are becoming increasingly important as active ingredients of drugs and as crucial probes and/or tools in medical, biotechnological, and pharmaceutical research. Situated at the interface between small molecules and larger macromolecular systems, they pose a difficult challenge for computational methods. We report an in silico peptide library generation and prioritization workflow using CmDock for identifying tetrapeptide ligands that bind to Fc regions of antibodies that is analogous to known in vitro recombinant peptide libraries' display and expression systems. The results of our in silico study are in accordance with existing scientific literature on in vitro peptides that bind to antibody Fc regions. In addition, we postulate an evolving in silico library design workflow that will help circumvent the combinatorial problem of in vitro comprehensive peptide libraries by focusing on peptide subunits that exhibit favorable interaction profiles in initial in silico peptide generation and testing.

Production and Characterization of Monoclonal Antibodies Against Structural Proteins of Hirame Novirhabdovirus

Hirame novirhabdovirus (HIRRV) is a significant viral pathogen of Japanese flounder (Paralichthys olivaceus). In this study, seven monoclonal antibodies (mAbs) against HIRRV (isolate CA-9703) were produced and characterized. Three mAbs (1B3, 5G6, and 36D3) were able to recognize nucleoprotein (N) (42 kDa) and four mAbs (11-2D9, 15-1G9, 17F11, and 24-1C6) recognized matrix (M) protein (24 kDa) of HIRRV. Western blot, Enzyme-linked immunosorbent assay, and indirect fluorescent antibody technique (IFAT) results indicated that the developed mAbs were specific to HIRRV without any cross-reactivity against other different fish viruses and epithelioma papulosum cyprini cells. All the mAbs comprised IgG1 heavy chain and κ light chain except 5G6, which has a heavy chain of IgG2a class. These mAbs can be very useful in development of immunodiagnosis of HIRRV infection.

Rapid and sensitive immunoassay for alpha-fetoprotein in serum by fabricating primary antibody-enzyme complexes using protein self-assembly

Primary antibody-enzyme complexes (PAECs) are ideal immunosensing elements that simplify the immunoassay process and improve the uniformity of results due to their ability to both recognize antigens and catalyze substrates. However, the conventional fabrication methods of PAECs, such as direct gene fusion expression, chemical conjugation, enzymatic conjugation, etc., have low efficiency, poor reliability, and other defects, which limit the widespread application of PAECs. Therefore, we developed a convenient method for the fabrication of homogeneous multivalent PAECs using protein self-assembly and validated it using anti-alpha-fetoprotein nanobody (A1) and alkaline phosphatase (ALP) as models. Heptavalent PAECs showed a 4-fold enhancement in enzymatic catalytic activity compared to monovalent PAECs. Further, to verify the application of developed heptavalent PAECs in immunoassay, heptavalent PAECs were used as bifunctional probes to construct a double-antibody sandwich ELISA to detect AFP. The detection limit of the developed heptavalent PAEC-based ELISA is 0.69 ng mL^-1, which is about 3 times higher than that of monovalent PAECs, and the whole detection process can be completed within 3 hours. In short, the proposed protein self-assembling method is a promising technology for developing high-performance heptavalent PACEs, which can simplify the detection process and improve detection sensitivity in various immunoassays.

Biomarker Detection in Early Diagnosis of Cancer: Recent Achievements in Point-of-Care Devices Based on Paper Microfluidics

Microfluidics is very crucial in lab-on-a-chip systems for carrying out operations in a large-scale laboratory environment on a single chip. Microfluidic systems are miniaturized devices in which the fluid behavior and control can be manipulated on a small platform, with surface forces on the platform being greater than volumetric forces depending on the test method used. In recent years, paper-based microfluidic analytical devices (μPADs) have been developed to be used in point-of-care (POC) technologies. μPADs have numerous advantages, including ease of use, low cost, capillary action liquid transfer without the need for power, the ability to store reagents in active form in the fiber network, and the capability to perform multiple tests using various measurement techniques. These benefits are critical in the advancement of paper-based microfluidics in the fields of disease diagnosis, drug application, and environment and food safety. Cancer is one of the most critical diseases for early detection all around the world. Detecting cancer-specific biomarkers provides significant data for both early diagnosis and controlling the disease progression. μPADs for cancer biomarker detection hold great promise for improving cure rates, quality of life, and minimizing treatment costs. Although various types of bioanalytical platforms are available for the detection of cancer biomarkers, there are limited studies and critical reviews on paper-based microfluidic platforms in the literature. Hence, this article aims to draw attention to these gaps in the literature as well as the features that future platforms should have.

Proteolytic Biosensors with Functional Nanomaterials: Current Approaches and Future Challenges

Proteolytic enzymes are one of the important biomarkers that enable the early diagnosis of several diseases, such as cancers. A specific proteolytic enzyme selectively degrades a certain sequence of a polypeptide. Therefore, a particular proteolytic enzyme can be selectively quantified by changing detectable signals causing degradation of the peptide chain. In addition, by combining polypeptides with various functional nanomaterials, proteolytic enzymes can be measured more sensitively and rapidly. In this paper, proteolytic enzymes that can be measured using a polypeptide degradation method are reviewed and recently studied functional nanomaterials-based proteolytic biosensors are discussed. We anticipate that the proteolytic nanobiosensors addressed in this review will provide valuable information on physiological changes from a cellular level for individual and early diagnosis.

Biofunctionalization of Multiplexed Silicon Photonic Biosensors

Silicon photonic (SiP) sensors offer a promising platform for robust and low-cost decentralized diagnostics due to their high scalability, low limit of detection, and ability to integrate multiple sensors for multiplexed analyte detection. Their CMOS-compatible fabrication enables chip-scale miniaturization, high scalability, and low-cost mass production. Sensitive, specific detection with silicon photonic sensors is afforded through biofunctionalization of the sensor surface; consequently, this functionalization chemistry is inextricably linked to sensor performance. In this review, we first highlight the biofunctionalization needs for SiP biosensors, including sensitivity, specificity, cost, shelf-stability, and replicability and establish a set of performance criteria. We then benchmark biofunctionalization strategies for SiP biosensors against these criteria, organizing the review around three key aspects: bioreceptor selection, immobilization strategies, and patterning techniques. First, we evaluate bioreceptors, including antibodies, aptamers, nucleic acid probes, molecularly imprinted polymers, peptides, glycans, and lectins. We then compare adsorption, bioaffinity, and covalent chemistries for immobilizing bioreceptors on SiP surfaces. Finally, we compare biopatterning techniques for spatially controlling and multiplexing the biofunctionalization of SiP sensors, including microcontact printing, pin- and pipette-based spotting, microfluidic patterning in channels, inkjet printing, and microfluidic probes.

Electrochemiluminescence Systems for the Detection of Biomarkers: Strategical and Technological Advances

Electrochemiluminescence (ECL)-based sensing systems rely on light emissions from luminophores, which are generated by high-energy electron transfer reactions between electrogenerated species on an electrode. ECL systems have been widely used in the detection and monitoring of diverse, disease-related biomarkers due to their high selectivity and fast response times, as well as their spatial and temporal control of luminance, high controllability, and a wide detection range. This review focuses on the recent strategic and technological advances in ECL-based biomarker detection systems. We introduce several sensing systems for medical applications that are classified according to the reactions that drive ECL signal emissions. We also provide recent examples of sensing strategies and technologies based on factors that enhance sensitivity and multiplexing abilities as well as simplify sensing procedures. This review also discusses the potential strategies and technologies for the development of ECL systems with an enhanced detection ability.

Protposer: the web server that readily proposes protein stabilizing mutations with high PPV

Protein stability is a requisite for most biotechnological and medical applications of proteins. As natural proteins tend to suffer from a low conformational stability ex vivo, great efforts have been devoted toward increasing their stability through rational design and engineering of appropriate mutations. Unfortunately, even the best currently used predictors fail to compute the stability of protein variants with sufficient accuracy and their usefulness as tools to guide the rational stabilisation of proteins is limited. We present here Protposer, a protein stabilising tool based on a different approach. Instead of quantifying changes in stability, Protposer uses structure- and sequence-based screening modules to nominate candidate mutations for subsequent evaluation by a logistic regression model, carefully trained to avoid overfitting. Thus, Protposer analyses PDB files in search for stabilization opportunities and provides a ranked list of promising mutations with their estimated success rates (eSR), their probabilities of being stabilising by at least 0.5 kcal/mol. The agreement between eSRs and actual positive predictive values (PPV) on external datasets of mutations is excellent. When Protposer is used with its Optimal kappa selection threshold, its PPV is above 0.7. Even with less stringent thresholds, Protposer largely outperforms FoldX, Rosetta and PoPMusiC. Indicating the PDB file of the protein suffices to obtain a ranked list of mutations, their eSRs and hints on the likely source of the stabilization expected. Protposer is a distinct, straightforward and highly successful tool to design protein stabilising mutations, and it is freely available for academic use at http://webapps.bifi.es/the-protposer.

Oxytocin-Selective Nanogel Antibody Mimics

Oxytocin imprinted polymer nanoparticles were synthesized by glass bead supported solid phase synthesis, with NMR and molecular dynamics studies used to investigate monomer-template interactions. The nanoparticles were characterized by dynamic light scattering, scanning- and transmission electron microscopy and X-ray photoelectron spectroscopy. Investigation of nanoparticle-template recognition using quartz crystal microbalance-based studies revealed sub-nanomolar affinity, kd ≈ 0.3 ± 0.02 nM (standard error of the mean), comparable to that of commercial polyclonal antibodies, kd ≈ 0.02-0.2 nM.

Recombinant antibodies and their use for food immunoanalysis

Antibodies are widely employed as biorecognition elements for the detection of a plethora of compounds including food and environmental contaminants, biomarkers, or illicit drugs. They are also applied in therapeutics for the treatment of several disorders. Recent recommendations from the EU on animal protection and the replacement of animal-derived antibodies by non-animal-derived ones have raised a great controversy in the scientific community. The application of recombinant antibodies is expected to achieve a high growth rate in the years to come thanks to their versatility and beneficial characteristics in comparison to monoclonal and polyclonal antibodies, such as stability in harsh conditions, small size, relatively low production costs, and batch-to-batch reproducibility. This review describes the characteristics, advantages, and disadvantages of recombinant antibodies including antigen-binding fragments (Fab), single-chain fragment variable (scFv), and single-domain antibodies (VHH) and their application in food analysis with especial emphasis on the analysis of biotoxins, antibiotics, pesticides, and foodborne pathogens. Although the wide application of recombinant antibodies has been hampered by a number of challenges, this review demonstrates their potential for the sensitive, selective, and rapid detection of food contaminants.

EASINESS: E. coli Assisted Speedy affINity-maturation Evolution SyStem

Antibodies are one of the most important groups of biomolecules for both clinical and basic research and have been developed as potential therapeutics. Affinity is the key feature for biological activity and clinical efficacy of an antibody, especially of therapeutic antibodies, and thus antibody affinity improvement is indispensable and still remains challenging. To address this issue, we developed the E. coli Assisted Speed affINity-maturation Evolution SyStem (EASINESS) for continuous directed evolution of Ag-Ab interactions. Two key components of EASINESS include a mutation system modified from error-prone DNA polymerase I (Pol I) that selectively mutates ColE1 plasmids in E. coli and a protein-protein interaction selection system from mDHFR split fragments. We designed a GCN4 variant which barely forms a homodimer, and during a single round of evolution, we reversed the homodimer formation activity from the GCN4 variant to verify the feasibility of EASINESS. We then selected a potential therapeutic antibody 18A4Hu and improved the affinity of the antibody (18A4Hu) to its target (ARG2) 12-fold in 7 days while requiring very limited hands-on time. Remarkably, these variants of 18A4Hu revealed a significant improved ability to inhibit melanoma pulmonary metastasis in a mouse model. These results indicate EASINESS could be as an attractive choice for antibody affinity maturation.

Peptide-Based Capture of Chikungunya Virus E2 Protein Using Porous Silicon Biosensor

The detection of pathogens presents specific challenges in ensuring that biosensors remain operable despite exposure to elevated temperatures or other extreme conditions. The most vulnerable component of a biosensor is typically the bioreceptor. Accordingly, the robustness of peptides as bioreceptors offers improved stability and reliability toward harsh environments compared to monoclonal antibodies that may lose their ability to bind target molecules after such exposures. Here, we demonstrate peptide-based capture of the Chikungunya virus E2 protein in a porous silicon microcavity biosensor at room temperature and after exposure of the peptide-functionalized biosensor to high temperature. Contact angle measurements, attenuated total reflectance-Fourier transform infrared spectra, and optical reflectance measurements confirm peptide functionalization and selective E2 protein capture. This work opens the door for other pathogenic biomarker detection using peptide-based capture agents on porous silicon and other surface-based sensor platforms.

Shelf-Life Extension of Fc-Fused Single Chain Fragment Variable Antibodies by Lyophilization

Generation of sequence defined antibodies from universal libraries by phage display has been established over the past three decades as a robust method to cope with the increasing market demand in therapy, diagnostics and research. For applications requiring the bivalent antigen binding and an Fc part for detection, phage display generated single chain Fv (scFv) antibody fragments can rapidly be genetically fused to the Fc moiety of an IgG for the production in eukaryotic cells of antibodies with IgG-like properties. In contrast to conversion of scFv into IgG format, the conversion to scFv-Fc requires only a single cloning step, and provides significantly higher yields in transient cell culture production than IgG. ScFv-Fcs can be effective as neutralizing antibodies in vivo against a panel of pathogens and toxins. However, different scFv fragments are more heterologous in respect of stability than Fab fragments. While some scFv fragments can be made extremely stable, this may change due to few mutations, and is not predictable from the sequence of a newly selected antibody. To mitigate the necessity to assess the stability for every scFv-Fc antibody, we developed a generic lyophilization protocol to improve their shelf life. We compared long-term stability and binding activity of phage display-derived antibodies in the scFv-Fc and IgG format, either stored in liquid or lyophilized state. Conversion of scFv-Fcs into the full IgG format reduced protein degradation and aggregation, but in some cases compromised binding activity. Comparably to IgG conversion, lyophilization of scFv-Fc resulted in the preservation of the antibodies' initial properties after storage, without any drop in affinity for any of the tested antibody clones.

Generation of Nanoyeast Single-Chain Variable Fragments as High-Avidity Biomaterials for Dengue Virus Detection

Bioengineered yeast bio-nanomaterials termed nanoyeasts displaying antibody single-chain variable fragments (scFvs) against diagnostic targets are a promising alternative to monoclonal antibodies (mAbs). A potential limitation for translating nanoyeasts into diagnostic tools is batch-to-batch variability. Herein, we demonstrate a systematic approach for cost-efficient production of highly specific nanoyeasts that enabled accurate dengue virus (DENV) detection by immunoassay (2.5% CV). Yeasts bioengineered to surface express DENV-specific scFvs (up to 66% of the total cell population) were fragmented into nanoyeast fractions trialing sonication, bead beating, and high-pressure disruption methods. Nanoyeast fractions from sonication had optimal target binding, uniform particle size (±89 nm), were stable, and retained diagnostic activity for 7 days at 37 °C compared to traditional mAbs that lost activity after 1 day at 37 °C. We engineered a panel of nanoyeast scFvs targeting DENV nonstructural protein 1 (NS1): (i) specific for serotyping DENV 1-4 and (ii) cross-reactive anti-DENV scFvs that are suitable for "yes/no" diagnostic applications. We demonstrate highly specific nanoyeast scFvs for serotyping DENV. We show that nanoyeast scFvs specifically detect NS1 in simulated patient plasma with a limit of detection of 250 ng/mL, the concentration found in infected patients.

Direct-MS analysis of antibody-antigen complexes

In recent decades, antibodies (Abs) have attracted the attention of academia and the biopharmaceutical industry due to their therapeutic properties and versatility in binding a vast spectrum of antigens. Different engineering strategies have been developed for optimizing Ab specificity, efficacy, affinity, stability and production, enabling systematic screening and analysis procedures for selecting lead candidates. This quality assessment is critical but usually demands time-consuming and labor-intensive purification procedures. Here, we harnessed the direct-mass spectrometry (direct-MS) approach, in which the analysis is carried out directly from the crude growth media, for the rapid, structural characterization of designed Abs. We demonstrate that properties such as stability, specificity and interactions with antigens can be defined, without the need for prior purification.

Surface enhanced Raman scattering for the multiplexed detection of pathogenic microorganisms: towards point-of-use applications

Surface enhanced Raman scattering (SERS) is a technique that demonstrates a number of advantages for the rapid, specific and sensitive detection of pathogenic microorganisms. In this review, an overview of label-free and label-based SERS approaches, including microfluidics, nucleic acid detection and immunoassays, for the multiplexed detection of pathogenic bacteria and viruses from the last decade will be discussed, as well as their transition into promising point-of-use detection technologies in industrial and medical settings.

Multiplexed DNA-Directed Patterning of Antibodies for Applications in Cell Subpopulation Analysis

Antibodies provide the functional biospecificity that has enabled the development of sensors, diagnostic tools, and assays in both laboratory and clinical settings. However, as multimarker screening becomes increasingly necessary due to the heterogeneity and complexity of human pathology, new methods must be developed that are capable of coordinating the precise assembly of multiple, distinct antibodies. To address this technological challenge, we engineered a bottom-up, high-throughput method in which DNA patterns, comprising unique 20-base pair oligonucleotides, are patterned onto a substrate using photolithography. These microfabricated surface patterns are programmed to hybridize with, and instruct the multiplexed assembly of, antibodies conjugated with the complementary DNA strands. We demonstrate that this simple, yet robust, approach preserves the antibody-binding functionality in two common applications: antibody-based cell capture and label-free surface marker screening. Using a simple proof-of-concept capture device, we achieved high purity separation of a breast cancer cell line, MCF-7, from a blood cell line, Jurkat, with capture purities of 77.4% and 96.6% when using antibodies specific for the respective cell types. We also show that antigen-antibody interactions slow cell trajectories in flow in the next-generation microfluidic node-pore sensing (NPS) device, enabling the differentiation of MCF-7 and Jurkat cells based on EpCAM surface-marker expression. Finally, we use a next-generation NPS device patterned with antibodies against E-cadherin, N-cadherin, and β-integrin-three markers that are associated with epithelial-mesenchymal transitions-to perform label-free surface marker screening of MCF10A, MCF-7, and Hs 578T breast epithelial cells. Our high-throughput, highly versatile technique enables rapid development of customized, antibody-based assays across a host of diverse diseases and research thrusts.

Progress and challenges in mass spectrometry-based analysis of antibody repertoires

Humoral immunity is divided into the cellular B cell and protein-level antibody responses. High-throughput sequencing has advanced our understanding of both these fundamental aspects of B cell immunology as well as aspects pertaining to vaccine and therapeutics biotechnology. Although the protein-level serum and mucosal antibody repertoire make major contributions to humoral protection, the sequence composition and dynamics of antibody repertoires remain underexplored. This limits insight into important immunological and biotechnological parameters such as the number of antigen-specific antibodies, which are for example, relevant for pathogen neutralization, microbiota regulation, severity of autoimmunity, and therapeutic efficacy. High-resolution mass spectrometry (MS) has allowed initial insights into the antibody repertoire. We outline current challenges in MS-based sequence analysis of antibody repertoires and propose strategies for their resolution.

Multivalent Nanosheet Antibody Mimics for Selective Microbial Recognition and Inactivation

Antibodies are widely used as recognition elements in sensing and therapy, but they suffer from poor stability, long discovery time, and high cost. Herein, a facile approach to create antibody mimics with flexible recognition phases and luminescent rigid scaffolds for the selective recognition, detection, and inactivation of pathogenic bacteria is reported. Tripeptides with a nitriloacetate-Cu group are spontaneously assembled on transition metal dichalcogenide (TMD) nanosheets via coordination bonding, providing a diversity of TMD-tripeptide assembly (TPA) antibody mimics. TMD-TPA antibody mimics can selectively recognize various pathogenic bacteria with nanomolar affinities. The bacterial binding sites for TMD-TPA are identified by experiments and molecular dynamics simulations, revealing that the dynamic and multivalent interactions of artificial antibodies play a crucial role for their recognition selectivity and affinity. The artificial antibodies allow the rapid and selective detection of pathogenic bacteria at single copy in human serum and urine, and their effective inactivation for therapy of infected mice. This work demonstrates the potential of TMD-TPA antibody mimics as an alternative to natural antibodies for sensing and therapy.

Design of synthetic polymer nanoparticles that inhibit glucose absorption from the intestine

Synthetic polymers prepared using several functional monomers have attracted attention as cost-effective protein affinity reagents and alternative to antibodies. We previously reported the synthesis of poly NIPAm-based nanoparticles (NPs) using several functional monomers that can capture target molecules. In this study, we designed NPs for capturing glucose and inhibiting intestinal absorption in living mice. For capturing glucose, we focused on the Maillard reaction between primary amines and aldehyde residues. We hypothesized that the primary amine-containing NPs can capture the open-chain structure of glucose via the Maillard reaction and inhibit intestinal absorption. NPs were prepared by the precipitation polymerization of NIPAm, N-tert-butylacrylamide (TBAm), trifluoroacetate-protected N-(3-aminopropyl)methacrylamide (T-APM), and N,N'-methylenebisacrylamide. Then, T-APM in NPs was deprotected by NH₃ (aq). The amount of glucose captured by NPs depended on the percentage of TBAm and APM in vitro. After 24 h, only 2% of orally administered NPs remained in the body after administration, suggesting that many NPs were excreted without being absorbed. The prepared NPs significantly inhibited an increase in blood glucose concentration after the oral administration of glucose and NPs, indicating that NPs capture glucose and inhibit intestinal absorption. These results show the potential of using synthetic polymer nanoparticles for inhibiting postprandial hyperglycemia.

Periplasmic expression of SpyTagged antibody fragments enables rapid modular antibody assembly

Antibodies are essential tools in research and diagnostics. Although antibody fragments typically obtained from in vitro selection can be rapidly produced in bacteria, the generation of full-length antibodies or the modification of antibodies with probes is time and labor intensive. Protein ligation such as SpyTag technology could covalently attach domains and labels to antibody fragments equipped with a SpyTag. However, we found that the established periplasmic expression of antibody fragments in E. coli led to quantitative cleavage of the SpyTag by the proteases Tsp and OmpT. Here we report successful periplasmic expression of SpyTagged Fab fragments and demonstrate the coupling to separately prepared SpyCatcher modules. We used this modular toolbox of SpyCatcher proteins to generate reagents for a variety of immunoassays and measured their performance in comparison with traditional reagents. Furthermore, we demonstrate surface immobilization, high-throughput screening of antibody libraries, and rapid prototyping of antibodies based on modular antibody assembly.

Immunoassay Biosensing of Foodborne Pathogens with Surface Plasmon Resonance Imaging: A Review

Surface plasmon resonance imaging (SPRi) has been increasingly used in the label-free detections of various biospecies, such as organic toxins, proteins, and bacteria. In combination with the well-developed microarray immunoassay, SPRi has the advantages of rapid detection in tens of minutes and multiplex detection of different targets with the same biochip. Both prism-based and prism-free configurations of SPRi have been developed for highly integrated portable immunosensors, which have shown great potential on pathogen detection and living cell imaging. This review summarizes the recent advances in immunoassay biosensing with SPRi, with special emphasis on the multiplex detections of foodborne pathogens. Additionally, various spotting techniques, surface modification protocols, and signal amplification methods have been developed to improve the specificity and sensitivity of the SPRi biochip. The challenges in multiplex detections of foodborne pathogens in real-world samples are addressed, and future perspectives of miniaturizing SPRi immunosensors with nanotechnologies are discussed.

A general strategy to control antibody specificity against targets showing molecular and biological similarity: Salmonella case study

The control of antibody specificity plays pivotal roles in key technological fields such as diagnostics and therapeutics. During the development of immunoassays (IAs) for the biosensing of pathogens in food matrices, we have found a way to rationalize and control the specificity of polyclonal antibodies (sera) for a complex analytical target (the Salmonella genus), in terms of number of analytes (Salmonella species) and potential cross-reactivity with similar analytes (other bacteria strains). Indeed, the biosensing of Salmonella required the development of sera and serum mixtures displaying homogeneous specificity for a large set of strains showing broad biochemical variety (54 Salmonella serovars tested in this study), which partially overlaps with the molecular features of other class of bacteria (like specific serogroups of E. coli). To achieve a trade-off between specificity harmonisation and maximization, we have developed a strategy based on the conversion of the specificity profiles of individual sera in to numerical descriptors, which allow predicting the capacity of serum mixtures to detect multiple bacteria strains. This approach does not imply laborious purification steps and results advantageous for process scaling-up, and may help in the customization of the specificity profiles of antibodies needed for diagnostic and therapeutic applications such as multi-analyte detection and recombinant antibody engineering, respectively.

Structure-based design and discovery of novel anti-tissue factor antibodies with cooperative double-point mutations, using interaction analysis

The generation of a wide range of candidate antibodies is important for the successful development of drugs that simultaneously satisfy multiple requirements. To find cooperative mutations and increase the diversity of mutants, an in silico double-point mutation approach, in which 3D models of all possible double-point mutant/antigen complexes are constructed and evaluated using interaction analysis, was developed. Starting from an antibody with very high affinity, four double-point mutants were designed in silico. Two of the double-point mutants exhibited improved affinity or affinity comparable to that of the starting antibody. The successful identification of two active double-point mutants showed that a cooperative mutation could be found by utilizing information regarding the interactions. The individual single-point mutants of the two active double-point mutants showed decreased affinity or no expression. These results suggested that the two active double-point mutants cannot be obtained through the usual approach i.e. a combination of improved single-point mutants. In addition, a triple-point mutant, which combines the distantly located active double-point mutation and an active single-point mutation collaterally obtained in the process of the double-point mutation strategy, was designed. The triple-point mutant showed improved affinity. This finding suggested that the effects of distantly located mutations are independent and additive. The double-point mutation approach using the interaction analysis of 3D structures expands the design repertoire for mutants, and hopefully paves a way for the identification of cooperative multiple-point mutations.

Antibody Conjugate Assembly on Ultrasound-Confined Microcarrier Particles

Bioconjugates are important next-generation drugs and imaging agents. Assembly of these increasingly complex constructs requires precise control over processing conditions, which is a challenge for conventional manual synthesis. This inadequacy has motivated the pursuit of new approaches for efficient, controlled modification of high-molecular-weight biologics such as proteins, carbohydrates, and nucleic acids. We report a novel, hands-free, semiautomated platform for synthetic manipulation of biomolecules using acoustically responsive microparticles as three-dimensional reaction substrates. The microfluidic reactor incorporates a longitudinal acoustic trap that controls the chemical reactions within a localized acoustic field. Forces generated by this field immobilize the microscale substrates against the continuous flow of participating chemical reagents. Thus, the motion of substrates and reactants is decoupled, enabling exquisite control over multistep reaction conditions and providing high-yield, high-purity products with minimal user input. We demonstrate these capabilities by conjugating clinically relevant antibodies with a small molecule. The on-bead synthesis comprises capture of the antibody, coupling of a fluorescent tag, product purification, and product release. Successful capture and modification of a fluorescently labeled antibody are confirmed via fold increases of 49 and 11 in the green (antibody)- and red (small-molecule dye)-channel median intensities determined using flow cytometry. Antibody conjugates assembled on acoustically responsive, ultrasound-confined microparticles exhibit similar quality and quantity to those prepared manually by a skilled technician.

Production of a polyclonal antibody against inosine-uridine preferring nucleoside hydrolase of Acanthamoeba castellanii and its access to diagnosis of Acanthamoeba keratitis

Acanthamoeba keratitis (AK) is a rare disease but its prevalence throughout the globe continues to grow, primarily due to increased contact lens usage. Since early-stage symptoms associated with AK closely resemble those from other corneal infections, accurate diagnosis is difficult and this often results in delayed treatment and exacerbation of the disease, which can lead to permanent visual impairment. Accordingly, developing a rapid Acanthamoeba–specific diagnostic method is highly desired. In the present study, a rapid and differential method for AK diagnosis was developed using the secretory proteins derived from the pathogenic Acanthamoeba. Among the vast quantities of proteins secreted by the pathogenic Acanthamoeba, an open reading frame of the inosine-uridine preferring nucleoside hydrolase (IPNH) gene was obtained. After expressing and purifying the IPNH protein using the pGEX 4T-3 vector system, mice were immunized with the purified proteins for polyclonal antibody generation. Western blot was performed using protein lysates of the human corneal cell, non-pathogenic amoeba, pathogenic amoeba, and clinical amoeba isolate along with lysates from other causes of keratitis such as Staphylococcus aureus, Pseudomonas aeruginosa, and Fusarium solani to confirm Acanthamoeba-specificity. Western blot using the polyclonal IPNH antibody revealed that IPNH was Acanthamoeba-specific since these proteins were only observed in lysates of Acanthamoeba origin or its culture media. Our findings indicate that the IPNH antibody of Acanthamoeba may serve as a potential agent for rapid and differential AK diagnosis.

Probing the Kinetic and Thermodynamic Fingerprints of Anti-EGF Nanobodies by Surface Plasmon Resonance

Despite the widespread use of antibodies in clinical applications, the precise molecular mechanisms underlying antibody-antigen (Ab-Ag) interactions are often poorly understood. In this study, we exploit the technical features of a typical surface plasmon resonance (SPR) biosensor to dissect the kinetic and thermodynamic components that govern the binding of single-domain Ab or nanobodies to their target antigen, epidermal growth factor (EGF), a key oncogenic protein that is involved in tumour progression. By carefully tuning the experimental conditions and transforming the kinetic data into equilibrium constants, we reveal the complete picture of binding thermodynamics, including the energetics of the complex-formation transition state. This approach, performed using an experimentally simple and high-throughput setup, is expected to facilitate mechanistic studies of Ab-based therapies and, importantly, promote the rational development of new biological drugs with suitable properties.

Positive Selection of Specific Antibodies Produced against Fusion Proteins

A method for the positive selection of specific antibodies for target proteins expressed as fusion proteins for the production of antiserum is presented. As proof of concept, the fusion protein FLAG::His::GFP::His::FLAG was expressed in Escherichia coli, purified, and used for the immunization of rabbits. The obtained serum was precleared via protein A affinity. A CusF::FLAG fusion protein was expressed in the periplasm of E. coli and purified. GFP without tags was also expressed in E. coli and purified via organic extraction. These proteins were then coupled to NHS-activated sepharose and used for the positive selection of Anti-GFP and Anti-FLAG antibodies. The obtained sera were tested for their specificity against different protein samples and fusion proteins in Western blots. A high specificity of the antibodies could be achieved by a single affinity chromatography step. In general, we advise to express the target protein with different tags and in different E. coli compartments for antibody production and affinity chromatography.

Electrochemical aptasensors based on the gold nanostructures

Electrochemical aptasensors as novel diagnostic tools have attracted sufficient research interest in biomedical sciences. In this review, recent leading trends about gold (Au) nanostructures based electrochemical aptasensors have been collected, reviewed, and compared. Here, the considered electrochemical aptasensors were categorized based on the analytes and diagnostic techniques. Pharmaceutical analytes and biomolecules were reviewed in a separate section consisting of a variety of antibiotics, analgesics, and other biomolecules. Various aptasensors have also measured toxins, ions, and hazardous chemicals, and the findings of them have also been reviewed. Many aptasensors have been designed to detect different disease biomarkers that will play an essential role in the future of early diagnosis of diseases. Pathogen microorganisms have been considered as the analyte in several designed electrochemical aptasensors in recent researches, and their results have been reviewed and discussed as another section. Important aspects considered in the review of the mentioned aptasensors were the type of analyte, features of the aptamer as the biorecognition element, type of Au nanostructures, diagnostic technique, diagnostic mechanism, detection range and the limit of detection (LOD). In the last section, an in-depth analysis has been provided based on the crucial features of all included aptasensors.

Programmable Bivalent Peptide-DNA Locks for pH-Based Control of Antibody Activity

The ability to control antibody activity by pH has important applications in diagnostics, therapeutic antibody targeting, and antibody-guided imaging. Here, we report the rational design of bivalent peptide-DNA ligands that allow pH-dependent control of antibody activity. Our strategy uses a pH-responsive DNA triple helix to control switching from a tight-binding bivalent peptide-DNA lock into a weaker-binding monovalent ligand. Different designs are introduced that allow antibody activation at both basic and acidic pHs, either autonomously or in the presence of an additional oligonucleotide trigger. The pH of antibody activation could be precisely tuned by changing the DNA triple helix sequence. The peptide-DNA locks allowed pH-dependent antibody targeting of tumor cells both in bulk and for single cells confined in water-in-oil microdroplets. The latter approach enables high-throughput antibody-mediated detection of single tumor cells based on their distinctive metabolic activity.

Inhibition of Pore-Forming Proteins

Perforation of cellular membranes by pore-forming proteins can affect cell physiology, tissue integrity, or immune response. Since many pore-forming proteins are toxins or highly potent virulence factors, they represent an attractive target for the development of molecules that neutralize their actions with high efficacy. There has been an assortment of inhibitors developed to specifically obstruct the activity of pore-forming proteins, in addition to vaccination and antibiotics that serve as a plausible treatment for the majority of diseases caused by bacterial infections. Here we review a wide range of potential inhibitors that can specifically and effectively block the activity of pore-forming proteins, from small molecules to more specific macromolecular systems, such as synthetic nanoparticles, antibodies, antibody mimetics, polyvalent inhibitors, and dominant negative mutants. We discuss their mechanism of inhibition, as well as advantages and disadvantages.

Tethered imidazole mediated duplex stabilization and its potential for aptamer stabilization

Previous investigations of the impact of an imidazole-tethered thymidine in synthetic DNA duplexes, monitored using UV and NMR spectroscopy, revealed a base context dependent increase in thermal stability of these duplexes and a striking correlation with the imidazolium pK_a. Unrestrained molecular dynamics (MD) simulations demonstrated the existence of a hydrogen bond between the imidazolium and the Hoogsteen side of a nearby guanosine which, together with electrostatic interactions, form the basis of the so-called pK_a-motif responsible for these duplex-stabilizing and pK_a-modulating properties. Here, the robustness and utility of this pK_a-motif was explored by introducing multiple imidazole-tethered thymidines at different positions on the same dsDNA duplex. For all constructs, sequence based expectations as to pK_a-motif formation were supported by MD simulations and experimentally validated using NOESY. Based on the analysis of the pK_a values and melting temperatures, guidelines are formulated to assist in the rational design of oligonucleotides modified with imidazolium-tethered thymidines for increased thermal stability that should be generally applicable, as demonstrated through a triply modified construct. In addition, a proof-of-principle study demonstrating enhanced stability of the l-argininamide binding aptamer modified with an imidazole-tethered thymidine in the presence and absence of ligand, demonstrates its potential for the design of more stable aptamers.

Nonspecific Binding in Immunoassays for Autoantibodies

Immunoassays are invaluable for detection and quantification of numerous analytes, including autoantibodies. However, human sera often yield high nonspecific binding in such assays, and this may result in false positive or sometimes false negative results. The causes of nonspecific binding are numerous and it correlates with inflammatory parameters. Since the results of autoantibody testing are used for diagnosis and treatment of autoimmune diseases, it is mandatory to be aware of all possible causes of nonspecific binding for each individual assay and to correct for it whenever possible. General guidelines for this are described in this chapter.

Novel Surface-Enhanced Raman Spectroscopy Techniques for DNA, Protein and Drug Detection

Surface-enhanced Raman spectroscopy (SERS) is a vibrational spectroscopic technique in which the Raman scattering signal strength of molecules, absorbed by rough metals or the surface of nanoparticles, experiences an exponential growth (10³-10⁶ times and even 10¹⁴-10¹⁵ times) because of electromagnetic or chemical enhancements. Nowadays, SERS has attracted tremendous attention in the field of analytical chemistry due to its specific advantages, including high selectivity, rich informative spectral properties, nondestructive testing, and the prominent multiplexing capabilities of Raman spectroscopy. In this review, we present the applications of state-of-the-art SERS for the detection of DNA, proteins and drugs. Moreover, we focus on highlighting the merits and mechanisms of achieving enhanced SERS signals for food safety and clinical treatment. The machine learning techniques, combined with SERS detection, are also indicated herein. This review concludes with recommendations for future studies on the development of SERS.

Direct Diagnostic Tests for Lyme Disease

Borrelia burgdorferi was discovered to be the cause of Lyme disease in 1983, leading to seroassays. The 1994 serodiagnostic testing guidelines predated a full understanding of key B. burgdorferi antigens and have a number of shortcomings. These serologic tests cannot distinguish active infection, past infection, or reinfection. Reliable direct-detection methods for active B. burgdorferi infection have been lacking in the past but are needed and appear achievable. New approaches have effectively been applied to other emerging infections and show promise in direct detection of B. burgdorferi infections.

Whole-Cell Biosensor with Tunable Limit of Detection Enables Low-Cost Agglutination Assays for Medical Diagnostic Applications

Whole-cell biosensors can form the basis of affordable, easy-to-use diagnostic tests that can be readily deployed for point-of-care (POC) testing, but to date the detection of analytes such as proteins that cannot easily diffuse across the cell membrane has been challenging. Here we developed a novel biosensing platform based on cell agglutination using an E. coli whole-cell biosensor surface-displaying nanobodies which bind selectively to a target protein analyte. As a proof-of-concept, we show the feasibility of this design to detect a model analyte at nanomolar concentrations. Moreover, we show that the design architecture is flexible by building assays optimized to detect a range of model analyte concentrations using straightforward design rules and a mathematical model. Finally, we re-engineer our whole-cell biosensor for the detection of a medically relevant biomarker by the display of two different nanobodies against human fibrinogen and demonstrate a detection limit as low as 10 pM in diluted human plasma. Overall, we demonstrate that our agglutination technology fulfills the requirement of POC testing by combining low-cost nanobody production, customizable detection range and low detection limits. This technology has the potential to produce affordable diagnostics for field-testing in the developing world, emergency or disaster relief sites, as well as routine medical testing and personalized medicine.

Gold Nanoparticle Probe-Assisted Antigen-Counting Chip Using SEM

Currently, it remains challenging to count protein-biomarker molecules present in a small droplet of biological samples. Herein, we propose a gold nanoparticle (GNP) probe-assisted sandwich-counting strategy that relies on a GNP probe, an antibody-functionalized chip to "count" antigen molecules using a scanning electron microscope. Both standard carcinoembryonic antigen (CEA) and two real CEA-related tumor samples (tumor tissues and serum) were assayed to demonstrate the proof-of-concept of the counting strategy. Results show that our method is excellently correlative with enzyme-linked immuno-sorbent assay (ELISA) that is widely used in clinics for antigen or antibody detection and the limit of detection of our enumeration strategy reaches down to 0.045 ng/mL, which is ∼40 times more sensitive than the conventional ELISA. Therefore, our GNP probe-assisted sandwich-counting strategy has the potential to be used for quantification of protein biomarkers at ultralow concentrations in early tumor specimens and detection of target proteins in much diluted concentrations.

Recognition of proximally phosphorylated tyrosine residues and continuous analysis of phosphatase activity using a stable europium complex

The recognition of proteins and their post-translational modifications using synthetic molecules is an active area of research. A common post-translational modification is the phosphorylation of serine, threonine or tyrosine residues. The phosphorylation of proximal tyrosine residues occurs in over 1000 proteins in the human proteome, including in disease-related proteins, so the recognition of this motif is of particular interest. We have developed a luminescent europium(III) complex, [Eu.1]+ , capable of the discrimination of proximally phosphorylated tyrosine residues, from analogous mono- and non-phosphorylated tyrosine residues, more distantly-related phosphotyrosine residues and over proximally phosphorylated serine and threonine residues. [Eu.1]+ was used to continuously monitor the phosphatase catalysed dephosphorylation of a peptide containing proximally phosphorylated tyrosine residues.

Protein sensing and discrimination using highly functionalised ruthenium(ii) tris(bipyridyl) protein surface mimetics in an array format

Ruthenium(ii) tris(bipyridyl) protein surface mimetics are used in an array format to sense and discriminate proteins including therapeutically relevant targets, hDM2 and MCL-1, using linear discriminant analysis (LDA).