Development of a Quenchbody for the Detection and Imaging of the Cancer-Related Tight-Junction-Associated Membrane Protein Claudin

Quenchbodies That Enable One-Pot Detection of Antigens: A Structural Perspective

Quenchbody (Q-body) is a unique, reagentless, fluorescent antibody whose fluorescent intensity increases in an antigen-concentration-dependent manner. Q-body-based homogeneous immunoassay is superior to conventional immunoassays as it does not require multiple immobilization, reaction, and washing steps. In fact, simply mixing the Q-body and the sample containing the antigen enables the detection of the target antigen. To date, various Q-bodies have been developed to detect biomarkers of interest, including haptens, peptides, proteins, and cells. This review sought to describe the principle of Q-body-based immunoassay and the use of Q-body for various immunoassays. In particular, the Q-bodies were classified from a structural perspective to provide useful information for designing Q-bodies with an appropriate objective.

The Dawn of a New Era: Targeting the "Undruggables" with Antibody-Based Therapeutics

The high selectivity and affinity of antibodies toward their antigens have made them a highly valuable tool in disease therapy, diagnosis, and basic research. A plethora of chemical and genetic approaches have been devised to make antibodies accessible to more "undruggable" targets and equipped with new functions of illustrating or regulating biological processes more precisely. In this Review, in addition to introducing how naked antibodies and various antibody conjugates (such as antibody-drug conjugates, antibody-oligonucleotide conjugates, antibody-enzyme conjugates, etc.) work in therapeutic applications, special attention has been paid to how chemistry tools have helped to optimize the therapeutic outcome (i.e., with enhanced efficacy and reduced side effects) or facilitate the multifunctionalization of antibodies, with a focus on emerging fields such as targeted protein degradation, real-time live-cell imaging, catalytic labeling or decaging with spatiotemporal control as well as the engagement of antibodies inside cells. With advances in modern chemistry and biotechnology, well-designed antibodies and their derivatives via size miniaturization or multifunctionalization together with efficient delivery systems have emerged, which have gradually improved our understanding of important biological processes and paved the way to pursue novel targets for potential treatments of various diseases.

Ultrasensitive Multiplex Imaging of Cell Surface Proteins via Core-Shell Surface-Enhanced Raman Scattering Nanoprobes

Cell surface proteins, as important components of biological membranes, cover a wide range of important markers of diseases and even cancers. In this regard, precise detection of their expression levels is of crucial importance for both cancer diagnosis and the development of responsive therapeutic strategies. Herein, a size-controlled core-shell Au@ Copper(II) benzene-1,3,5-tricarboxylate (Au@Cu-BTC) nanomaterial was synthesized for specific and simultaneous imaging of multiple protein expression levels on cell membranes. The porous shell of Cu-BTC constructed on Au nanoparticles enabled effective loading of Raman reporter molecules, followed by further modification of the targeting moieties, which equipped the nanoprobe with good specificity and stability. Additionally, given the flexibility of the types of Raman reporter molecules available for loading, the nanoprobes were also demonstrated with good multichannel imaging capabilities. Ultimately, the present strategy of electromagnetic and chemical dual Raman scattering enhancement was successfully applied for the simultaneous detection of varied proteins on cell surfaces with high sensitivity and accuracy. The proposed nanomaterial holds promising applications in biosensing and therapeutic fields, which could not only provide a general strategy for the synthesis of metal-organic framework-based core-shell surface-enhanced Raman scattering nanoprobes but also enable further utilization in multitarget and multichannel cell imaging.

Immunosensor for realtime monitoring of the expression of recombinant proteins during bioprocess

Recombinant protein expression and purification are crucial in modern life sciences research. A fluorescent immunosensor termed Quenchbody (Q-body) was developed for real-time monitoring of FLAG-fused protein expression. Detection results showed that the limit of detection of the 3 × FLAG peptide detected by the TAMRA-labeled anti-FLAG Q-body was as low as 3.1 nM, with a half-maximal effective concentration of 21.4 nM. Furthermore, the anti-FLAG Q-body was used for detecting different proteins fused with a FLAG-tag at the N- or C-terminal. Subsequently, the constructed Q-body was used to monitor the real-time fermentation process of single-strand DNA-binding protein in Escherichia coli. Unlike previously reported Q-bodies that widely used Fab or scFv, the present study used a full-length anti-FLAG IgG for the first time. Owing to its excellent detection speed and sensitivity, the FLAG Q-body immunosensor has the potential to quantify and monitor target recombinant proteins in multiple biological processes in real-time.

VH-Based Mini Q-Body: A Novel Quench-Based Immunosensor

Quenchbodies (Q-bodies), a type of biosensor, are antibodies labeled with a fluorescent dye near the antigen recognition site. In the absence of an antigen, the dye is quenched by tryptophans in the antibody sequence; however, in its presence, the dye is displaced and therefore de-quenched. Although scFv and Fab are mainly used to create Q-bodies, this is the first report where a single-domain heavy chain V_H from a semi-synthetic human antibody library formed the basis. To create a proof of concept "mini Q-body", a human anti-lysozyme single-domain V_H antibody C3 was used. Mini Q-bodies were successfully developed using seven dyes. Different responses were observed depending on the dye and linker length; it was concluded that the optimal linker length for the TAMRA dye was C5, and rhodamine 6G was identified as the dye with the largest de-quenching response. Three single-domain antibodies with sequences similar to that of the C3 antibody were chosen, and the results confirmed the applicability of this method in developing mini Q-bodies. In summary, mini Q-bodies are an easy-to-use and time-saving method for detecting proteins.

Isolation of a human SARS-CoV-2 neutralizing antibody from a synthetic phage library and its conversion to fluorescent biosensors

Since late 2019, the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the resultant spread of COVID-19 have given rise to a worldwide health crisis that is posing great challenges to public health and clinical treatment, in addition to serving as a formidable threat to the global economy. To obtain an effective tool to prevent and diagnose viral infections, we attempted to obtain human antibody fragments that can effectively neutralize viral infection and be utilized for rapid virus detection. To this end, several human monoclonal antibodies were isolated by bio-panning a phage-displayed human antibody library, Tomlinson I. The selected clones were demonstrated to bind to the S1 domain of the spike glycoprotein of SARS-CoV-2. Moreover, clone A7 in Fab and IgG formats were found to effectively neutralize the binding of S protein to angiotensin-converting enzyme 2 in the low nM range. In addition, this clone was successfully converted to quench-based fluorescent immunosensors (Quenchbodies) that allowed antigen detection within a few minutes, with the help of a handy fluorometer.

Creation of a quick and sensitive fluorescent immunosensor for detecting the mineralocorticoid steroid hormone aldosterone

Aldosterone (ALD) is a steroid hormone secreted by the zona glomerulosa of the adrenal cortex that mainly acts on the kidney to regulate sodium ion and water reabsorption. Detection of ALD plays an important role in the diagnosis of primary aldosteronism in patients with hypertension. For the first time, the gene encoding the anti-ALD antibody, A2E11, was successfully cloned and analyzed using phage display technology. The antibody had an affinity of 2.5 nM against ALD, and after binding to ALD, it reached saturation within 5 s. Using this antibody, a Quenchbody (Q-body) was constructed by labeling the N-termini of heavy and light chains of the antigen-binding fragment of A2E11 with the fluorescent dye ATTO520 to detect ALD based on the principle of photoinduced electron transfer. The sensor detected ALD in 2 min, and the limit of detection was 24.1 pg/mL with a wide detection range from 24.1 pg/mL to 10 µg/mL and a half-maximal effective concentration of 42.3 ng/mL. At the highest concentration of ALD in the assay, the fluorescence intensity increased by 5.0-fold compared to the original fluorescence intensity of the Q-body solution. The Q-body could be applied to analyze 50% of human serum without a significant influence of the matrix. The recoveries of ALD in spiked serum samples with the Q-body assay were confirmed to range from 90.3% to 98.2%, suggesting their potential applications in the diagnosis of diseases, such as essential hypertension.

Intra Q-body: an antibody-based fluorogenic probe for intracellular proteins that allows live cell imaging and sorting

Although intracellular biomarkers can be imaged with fluorescent dye(s)-labeled antibodies, the use of such probes for precise imaging of intracellular biomarkers in living cells remains challenging due to background noise from unbound probes. Herein, we describe the development of a conditionally active Fab-type Quenchbody (Q-body) probe derived from a monoclonal antibody (DO-1) with the ability to both target and spatiotemporally visualize intracellular p53 in living cells with low background signal. p53 is a key tumor suppressor and validated biomarker for cancer diagnostics and therapeutics. The Q-body displayed up to 27-fold p53 level-dependent fluorescence enhancement in vitro with a limit of detection of 0.72 nM. In fixed and live cells, 8.3- and 8.4-fold enhancement was respectively observed. Furthermore, we demonstrate live-cell sorting based on p53 expression. This study provides the first evidence of the feasibility and applicability of Q-body probes for the live-cell imaging of intrinsically intracellular proteins and opens a novel avenue for research and diagnostic applications on intracellular target-based live-cell sorting.

A fluorescent immunosensor that lights up tumor biomarker p53 in living cells was developed based on the Q-body technology. The technology was further applied to the live cell monitoring of p53 levels, and live cell sorting based on p53 expression.

Quench-Release-Based Fluorescent Immunosensor for the Rapid Detection of Tumor Necrosis Factor α

Tumor necrosis factor α (TNF-α) is used as a biomarker for the diagnosis of various inflammatory and autoimmune diseases. In recent years, numerous approaches have been used for the qualitative and quantitative analyses of TNF-α. However, these methods have several drawbacks, such as a tedious and time-consuming process, high pH and temperature sensitivity, and increased chances of denaturation in vitro. Quenchbody (Q-body) is a fluorescence immunoprobe that functions based on the principle of photoinduced electron transfer and has been successful in detecting various substances. In this study, we constructed two Q-bodies based on a therapeutic antibody, adalimumab, to rapidly detect human TNF-α. Both sensors could detect TNF-α within 5 min. The results showed that the limit of detection (LOD) of TNF-α was as low as 0.123 ng/mL with a half-maximal effective concentration (EC₅₀) of 25.0 ng/mL using the TAMRA-labeled Q-body, whereas the ATTO520-labeled Q-body had a LOD of 0.419 ng/mL with an EC₅₀ of 65.6 ng/mL, suggesting that the Q-bodies could rapidly detect TNF-α with reasonable sensitivity over a wide detection range. These biosensors will be useful tools for the detection and monitoring of inflammatory biomarkers.

Real-time imaging of cell-surface proteins with antibody-based fluorogenic probes

Cell-surface proteins, working as key agents in various diseases, are the targets for around 66% of approved human drugs. A general strategy to selectively detect these proteins in a real-time manner is expected to facilitate the development of new drugs and medical diagnoses. Although brilliant successes were attained using small-molecule probes, they could cover a narrow range of targets due to the lack of suitable ligands and some of them suffer from selectivity issues. We report herein an antibody-based fluorogenic probe prepared via a two-step chemical modification under physiological conditions, to fulfill the selective recognition and wash-free imaging of membrane proteins, establishing a modular strategy with broad implications for biochemical research and for therapeutics.

Recent Advances in Quenchbody, a Fluorescent Immunosensor

The detection of viruses, disease biomarkers, physiologically active substances, drugs, and chemicals is of great significance in many areas of our lives. Immunodetection technology is based on the specificity and affinity of antigen–antibody reactions. Compared with other analytical methods such as liquid chromatography coupled with mass spectrometry, which requires a large and expensive instrument, immunodetection has the advantages of simplicity and good selectivity and is thus widely used in disease diagnosis and food/environmental monitoring. Quenchbody (Q-body), a new type of fluorescent immunosensor, is an antibody fragment labeled with fluorescent dyes. When the Q-body binds to its antigen, the fluorescence intensity increases. The detection of antigens by changes in fluorescence intensity is simple, easy to operate, and highly sensitive. This review comprehensively discusses the principle, construction, application, and current progress related to Q-bodies.

Development of a fluorescent probe for the detection of hPD-L1

Interaction of human programmed death factor-1 (hPD-1) of T cells and one of its ligands hPD-L1 which is expressed on cancer cells suppresses effector T cell functions. Studies showed that the hPD-1/hPD-L1 pathway is associated with killing mechanisms of tumor cells evading the immune system. Immunotherapy based on the checkpoint inhibitor on hPD-1 has been an important approach to treat cancer; however, not all cancer cells over-express hPD-L1. Detection of hPD-L1 over-expression in cancer cells may be a key factor for deciding on whether immunotherapy should be conducted. In the present study, we produced recombinant hPD-1 using Escherichia coli, and created a fluorescent probe termed quenched hPD-1 (QPD-1) for the detection of hPD-L1. We found that hPD-1 can quench fluorescence of carboxytetramethylrhodamine labeled on its N-terminal and QPD-1 is a convenient tool to rapidly detect hPD-L1 with a limit of detection of 10 nM and detectable range of 10 nM-1000 nM. QPD-1 may also function as a probe to screen for hPD-L1 over-expressing tumor cells and promote appropriate medical procedure through tumor immunotherapy.

Synthesis of Quenchbodies for One-Pot Detection of Stimulant Drug Methamphetamine

The problem of illicit drug use and addiction is an escalating issue worldwide. As such, fast and precise detection methods are needed to help combat the problem. Herein, the synthesis method for an anti-methamphetamine Quenchbody (Q-body), a promising sensor for use in simple and convenient assays, has been described. The fluorescence intensity of the Q-body generated by two-site labeling of Escherichia coli produced anti-methamphetamine antigen-binding fragment (Fab) with TAMRA-C2-maleimide dyes increased 5.1-fold over background in the presence of a hydroxyl methamphetamine derivative, 3-[(2S)-2-(methylamino)propyl]phenol. This derivative has the closest structure to methamphetamine of the chemicals available for use in a laboratory. Our results indicate the potential use of this Q-body as a novel sensor for the on-site detection of methamphetamine, in such occasions as drug screening at workplace, suspicious substance identification, and monitoring patients during drug rehabilitation.

Detection and destruction of HER2-positive cancer cells by Ultra Quenchbody-siRNA complex

Ultra Quenchbody (UQ-body) is a biosensor that utilizes the quenching behavior of the fluorescent dye linked to the antibody V region. When the corresponding antigen is bound to the UQ-body, the fluorescence is restored and allows the detection of target molecules easily and sensitively. In this paper, we constructed UQ-bodies to sensitively detect the human epidermal growth factor receptor 2 (HER2) cancer marker in solution or on cancer cells, which was further used to kill the cancer cells. A synthetic Fab fragment of anti-HER2 antibody Fab37 with many Trp residues at hypervariable region was prepared and labeled with fluorescent dyes to obtain the UQ-bodies. The UQ-body could detect HER2 in solution at concentrations as low as 20 pM with an EC₅₀ of 0.3 nM with a fourfold response. Fluorescence imaging of HER2-positive cells was successfully performed without any washing steps. To deliver small interfering RNA (siRNA) to cancer cells, a modified UQ-body with C-terminal 9R sequence was also prepared. HER2-positive cancer cells were effectively killed by polo-like kinase 1 siRNA intracellularly delivered by the UQ-body-9R. The novel approach employing siRNA-empowered UQ-body could detect and image the HER2 antigen easily and sensitively, and effectively kill the HER2-positive cancer cells.

Single-Step Detection of the Influenza Virus Hemagglutinin Using Bacterially-Produced Quenchbodies

We have successfully generated a Quenchbody that enables the detection of the influenza virus hemagglutinin (HA), in a simple and convenient manner. By two-site labeling of the bacterially-produced anti-HA Fab with ATTO520, its fluorescence intensity was increased to 4.4-fold, in the presence of a nanomolar concentration of H1N1 HA. Our results indicate the potential use of this Quenchbody, as a sensor for the simple in situ detection of influenza A virus.

Construction of Quenchbodies to detect and image amyloid β oligomers

A quenchbody (Q-body) is an antibody-based biosensor that employs fluorescence quenching of the dye(s) attached to the antibody fragment, which are de-quenched upon antigen binding. In this study, we aimed to develop Fab type Q-bodies (UQ-bodies) to aid the diagnosis of Alzheimer's disease (AD). Characteristic senile plaques in AD consist of amyloid-β peptide (Aβ) generated from the amyloid precursor protein. Aβ42, one of the major peptide forms, aggregates fast and manifests higher neurotoxicity. Recent studies showed that Aβ oligomers, such as Aβ-derived diffusible ligand (ADDL), are more toxic than fibrils. Thus, detection of Aβ and its oligomers in body fluid might help detect deterioration caused by the disease. To this end, the Fab fragment of the anti-Aβ antibody h12A11, which binds preferentially to ADDL, was expressed in Escherichia coli, and labeled with a fluorescent dye at the N terminus of either the heavy chain, or the heavy and light chains, via Cys-containing tag(s) to prepare UQ-bodies. As a result, the double-labeled UQ-bodies detected ADDL with higher sensitivity than that for the Aβ peptide. In addition, the UQ-body could be used to image aggregated Aβ with a low background, which suggested the potential of UQ-bodies as a fast bioimaging tool.