Direct single-molecule imaging for diagnostic and blood screening assays

Rapid Assessment of Biomarkers on Single Extracellular Vesicles Using 'Catch and Display' on Ultrathin Nanoporous Silicon Nitride Membranes

Extracellular vesicles (EVs) are particles secreted by all cells that carry bioactive cargo and facilitate intercellular communication with roles in normal physiology and disease pathogenesis. EVs have tremendous diagnostic and therapeutic potential and accordingly, the EV field has grown exponentially in recent years. Bulk assays lack the sensitivity to detect rare EV subsets relevant to disease, and while single EV analysis techniques remedy this, they are undermined by complicated detection schemes often coupled with prohibitive instrumentation. To address these issues, we propose a microfluidic technique for EV characterization called 'catch and display for liquid biopsy (CAD-LB)'. CAD-LB rapidly captures fluorescently labeled EVs in the similarly-sized pores of an ultrathin silicon nitride membrane. Minimally processed sample is introduced via pipette injection into a simple microfluidic device which is directly imaged using fluorescence microscopy for a rapid assessment of EV number and biomarker colocalization. In this work, nanoparticles were first used to define the accuracy and dynamic range for counting and colocalization by CAD-LB. Following this, the same assessments were made for purified EVs and for unpurified EVs in plasma. Biomarker detection was validated using CD9 in which Western blot analysis confirmed that CAD-LB faithfully recapitulated differing expression levels among samples. We further verified that CAD-LB captured the known increase in EV-associated ICAM-1 following the cytokine stimulation of endothelial cells. Finally, to demonstrate CAD-LB's clinical potential, we show that EV biomarkers indicative of immunotherapy responsiveness are successfully detected in the plasma of bladder cancer patients undergoing immune checkpoint blockade.

A Facile Strategy for Multiplex Protein Detection by a Fluorescent Microsphere-Based Digital Immunoassay

The digital immunoassay is a highly sensitive detection technique based on single-molecule counting and is widely used in the ultrasensitive detection of biomarkers. Herein, we developed a fluorescent microsphere-based digital immunoassay (FMDIA) by employing fluorescent microspheres as both the carriers for immunoreaction and fluorescent reports for imaging. In this approach, the target protein in the sample was captured by fluorescent microspheres to form a biotin-labeled sandwich immunocomplex, and then, the fluorescent microspheres containing the target protein molecules were captured by adding streptavidin-coated magnetic beads (SA-MBs). By counting the proportion of fluorescence-positive magnetic beads, the concentration of the target protein can be precisely quantified. As a proof of concept, α fetoprotein (AFP) and human interleukin-6 (IL-6) were used to assess the analytical performance of the proposed FMDIA, and limit of detection (LOD) values of 21 pg/mL (0.30 pM) and 0.19 pg/mL (7.3 fM) were achieved, respectively. The results of AFP detection in serum samples of patients and healthy people were consistent with the reference values given by the hospital. Furthermore, by adding fluorescent microspheres of various colors for encoding, the proposed FMDIA can easily realize the simultaneous detection of multiple proteins without the need to introduce multiple modified magnetic beads. This multiplex protein detection strategy, in which the reactions are first carried out on the fluorescent microspheres and then magnetic beads are used to capture the fluorescent reporters containing the target molecules, provides a new idea for digital assays.

A method for parallel microscale protein labeling and precise control over the average degree of labeling (aDoL)

A widely used approach for protein conjugation is through the lysine residues reacting with NHS- or other active esters. However, it is a challenge to precisely control the degree of labeling (DoL) due to the instability of active ester and variability of reaction efficiencies. Here, we provide a protocol for better control of aDoL using existing Copper-free Click Chemistry reagents. It is a two-step reaction with one purification in between. Briefly, proteins of interest were first activated with azide-NHS. After removing unreacted azide-NHS, the protein-N₃ is then reacted with a limited amount of complementary click tag. Our studies have shown the click tag will fully react with the protein-N₃ after 24 h' incubation, and therefore does not require additional purification steps. As such, the aDoL is equal to the input molar ratio of the click tag and the protein. Furthermore, this approach offers a much simpler and more economical way to perform parallel microscale labeling. Once a protein is pre-activated with N₃-NHS, any fluorophore or molecule with the complementary click tag can be attached to the protein by mixing the two ingredients. Quantities of the protein used in the click reaction can be at any desired amount. In one example, we labeled an antibody in parallel with 9 different fluorophores using a total of 0.5 mg of antibody. In another example, we labeled Ab with targeted aDoL value from 2 to 8. In a stability comparison study, we have found the conjugated fluorophore using the suggested click protocol stayed attached to the protein longer than with standard NHS-fluorophore labeling.

First-passage time analysis of diffusion-controlled reactions in single-molecule detection

Single-molecule detection (SMD) aims to achieve the ultimate limit-of-detection (LOD) in biosensing. This method detects a countable number of targeted analyte molecules in solution, where the dynamics of molecule diffusion, capturing, identification and delivery greatly impact the SMD's efficiency and accuracy. In this study, we adopt the first-passage time method to investigate the diffusion-controlled reaction process in SMD. We analyze the influence of detection conditions on incubation time and the expected coefficient of variation (CV) under three SMD molecule capturing strategies, including solid-phase capturing (one-dimensional solid-liquid interface fixation), liquid-phase magnetic bead (MB) capturing, and liquid-phase direct fluorescence pair labeling. We find that inside a finite-sized reaction chamber, a finite average reaction time exists in all three capturing strategies, while the liquid-phase strategies are in general more efficient than the solid-phase approaches. CV can be estimated by averaging first-passage time solely in all three strategies, and the CV reduction is achievable given an extended reaction time. To further enable zeptomolar detection, extra treatments, such as adopting liquid-phase fluorescence pairs with high diffusion rates to label the molecule, or designing specific sensing devices with large effective sensing areas would be required. This framework provides solid theoretical support to guide the design of SMD sensing strategies and sensor structures to achieve desired measurement time and CV.

Epifluorescent single-molecule counting with Streptavidin-Phycoerythrin conjugates

Single-molecule methods, specifically single-molecule counting, convey high sensitivity in research applications. However, single-molecule counting experiments require specialized equipment or consumables to perform. We demonstrate the utility of using bright Streptavidin-Phycoerythrin (SA-PE) conjugates and an epifluorescence microscope, for single-molecule counting applications. In this work, we show that we can visualize single-molecules on glass surfaces, perform single-molecule diagnostic assays on magnetic microparticles, and image individual foci on cell surfaces. This approach is simple and effective for researchers interested in single-molecule counting.

Affinity of anti-spike antibodies to three major SARS-CoV-2 variants in recipients of three major vaccines

Background

Measuring anti-viral antibody affinity in blood plasma or serum is a rational quantitative approach to assess humoral immune response and acquired protection. Three common vaccines against SARS-CoV-2—Comirnaty developed by Pfizer/BioNTech, Spikevax developed by Moderna/NIAID, and Jcovden (previously Janssen COVID-19 Vaccine) developed by Johnson & Johnson/Janssen (J&J)—induce antibodies to a variety of immunogenic epitopes including the epitopes located in the ACE2 receptor-binding domain (RBD) of the spike protein. Blocking RBD with antibodies interferes with the binding of the virus to ACE2 thus protecting against infection.

Methods

We perform measurements in the serum of the recipients of Pfizer, Moderna, and J&J vaccines, and we compare the apparent affinities of vaccine-induced antibodies against the RBD of the ancestral SARS-CoV-2 virus and the Delta and Omicron variants. We use our recently published method to determine the apparent affinity of anti-spike protein antibodies directly in human serum. This involves probing antibody-antigen equilibria with a small number of antigen-coated magnetic microparticles and imaging them on a fluorescence microscope.

Results

Recipients of two-dose Pfizer and Moderna vaccines, as well as recipients of the single-dose J&J vaccine, develop high-affinity antibodies toward RBD derived from ancestral SARS-CoV-2. Affinities of these antibodies to Delta-RBD are approximately 10 times weaker, and even more drastically reduced (∼1000-fold) toward Omicron-RBD.

Conclusions

Vaccine-induced antibodies against ancestral SARS-CoV-2 RBD demonstrate ~10-fold and ~1000-fold weaker affinities toward Delta- and Omicron-RBD, respectively. Our approach offers a direct means for evaluating vaccine-induced adaptive immunity and can be helpful in designing or updating vaccines.

Vaccination results in the production of proteins called antibodies that can bind viruses. The strength (affinity) of the binding between an antibody and a virus gives an indication of how well vaccination can prevent infection by the virus. Here, we compare the affinity of antibodies towards different types (variants) of SARS-CoV-2 viral protein in the serum of individuals who have been vaccinated with vaccines produced by Pfizer (Comirnaty), Moderna (Spikevax), and Johnson & Johnson (Jcovden). We discovered that all three vaccines generated antibodies that strongly bind the original SARS-CoV-2 virus, but the binding of the Delta variant was ten-times weaker. Moreover, the binding of the antibodies to the Omicron variant was more than a thousand-times weaker. Our findings explain why current vaccines are less efficient at preventing infection by the Delta and Omicron SARS-CoV-2 variants.

Macdonald, Schaub et al. measure apparent antibody affinities to the ACE-2 receptor binding domain of the SARS-CoV-2 spike protein in recipients of the Pfizer, Moderna and J&J vaccines. All vaccinated individuals develop high-affinity antibodies, however the affinities are weaker to Delta and Omicron variants compared to ancestral virus.

Affinity of anti-spike antibodies in SARS-CoV-2 patient plasma and its effect on COVID-19 antibody assays

Background

Measuring anti-spike protein antibodies in human plasma or serum is commonly used to determine prior exposure to SARS-CoV-2 infection and to assess the anti-viral protection capacity. According to the mass-action law, a lesser concentration of tightly binding antibody can produce the same quantity of antibody-antigen complexes as higher concentrations of lower affinity antibody. Thus, measurements of antibody levels reflect both affinity and concentration. These two fundamental parameters cannot be disentangled in clinical immunoassays, and so produce a bias which depends on the assay format.

Methods

To determine the apparent affinity of anti-spike protein antibodies, a small number of antigen-coated magnetic microparticles were imaged by fluorescence microscopy after probing antigen-antibody equilibria directly in patient plasma. Direct and indirect anti-SARS-CoV-2 immunoassays were used to measure antibody levels in the blood of infected and immunised individuals.

Findings

We observed affinity maturation of antibodies in convalescent and vaccinated individuals, showing that higher affinities are achieved much faster by vaccination. We demonstrate that direct and indirect immunoassays for measuring anti-spike protein antibodies depend differently on antibody affinity which, in turn, affects accurate interpretation of the results.

Interpretation

Direct immunoassays show substantial antibody affinity dependence. This makes them useful for identifying past SARS-CoV-2 exposure. Indirect immunoassays provide more accurate quantifications of anti-viral antibody levels.

Funding

The authors are all full-time employees of Abbott Laboratories. Abbott Laboratories provided all operating funds. No external funding sources were used in this study.