Affinity Selection in Germinal Centers: Cautionary Tales and New Opportunities

Antigen density and applied force control enrichment of nanobody-expressing yeast cells in microfluidics

In vitro display technologies such as yeast display have been instrumental in developing the selection of new antibodies, antibody fragments or nanobodies that bind to a specific target, with affinity towards the target being the main factor that influences selection outcome. However, the roles of mechanical forces are being increasingly recognized as a crucial factor in the regulation and activation of effector cell function. It would thus be of interest to isolate binders behaving optimally under the influence of mechanical forces. We developed a microfluidic assay allowing the selection of yeast displaying nanobodies through antigen-specific immobilization on a surface under controlled hydrodynamic flow. This approach enabled enrichment of model yeast mixtures using tunable antigen density and applied force. This new force-based selection method opens the possibility of selecting binders by relying on both their affinity and force resistance, with implications for the design of more efficient immunotherapeutics.

B cell receptors and free antibodies have different antigen-binding kinetics

Since the pioneering works of Berg and Purcell, discriminating between diffusion followed by binding has played a central role in understanding cell signaling. B cell receptors (BCR) and antibodies (Ab) challenge that simplified view as binding to the antigen follows after a chain of diffusion and rotations, including whole molecule rotation and independent tilts and twists of their Fab arms due to their Y-shaped structure and flexibility. In this paper, we combine analytical calculations with Brownian simulations to derive the first-passage times due to these three rotations positioning the Fab paratopes at a proper distance and orientation required for antigen binding. Our results indicate that when measuring Ab-Ag effective kinetic binding rates, using experimental methods in which the analyte is in solution only gives values proportional to the intrinsic binding rates, [Formula: see text], and [Formula: see text], for values of [Formula: see text] up to [Formula: see text]. Beyond that, a plateau of the effective 3D on rate between [Formula: see text] and [Formula: see text] is attained. Additionally, for BCR-Ag interactions, the effective 2D on and off binding rates can only be inferred from the corresponding effective 3D on and off rates for values of effective 3D on rates lower than [Formula: see text]. This is highly relevant when trying to relate BCR-antigen-binding strength and B cell response, especially during germinal center reactions. Therefore, there is a pressing need to reexamine our current understanding of the BCR-antigen kinetic rates in germinal centers using the latest experimental assays for BCR-Ag interactions.

A Mechanical Assay for the Quantification of Anti-RBD IgG Levels in Finger-Prick Whole Blood

A large portion of the global population has been vaccinated with various vaccines or infected with SARS-CoV-2, the virus that causes COVID-19. The resulting IgG antibodies that target the receptor binding domain (RBD) of SARS-CoV-2 play a vital role in reducing infection rates and severe disease outcomes. Different immune histories result in the production of anti-RBD IgG antibodies with different binding affinities to RBDs of different variants, and the levels of these antibodies decrease over time. Therefore, it is important to have a low-cost, rapid method for quantifying the levels of anti-RBD IgG in decentralized testing for large populations. In this study, we describe a 30 min assay that allows for the quantification of anti-RBD IgG levels in a single drop of finger-prick whole blood. This assay uses force-dependent dissociation of nonspecifically absorbed RBD-coated superparamagnetic microbeads to determine the density of specifically linked microbeads to a protein A-coated transparent surface through anti-RBD IgGs, which can be measured using a simple light microscope and a low-magnification lens. The titer of serially diluted anti-RBD IgGs can be determined without any additional sample processing steps. The limit of detection for this assay is 0.7 ± 0.1 ng/mL referenced to the CR3022 anti-RBD IgG. The limits of the technology and its potential to be further developed to meet the need for point-of-care monitoring of immune protection status are discussed.

Fluid nanoporous microinterface enables multiscale-enhanced affinity interaction for tumor-derived extracellular vesicle detection

Tumor-derived extracellular vesicles (T-EVs) represent valuable markers for tumor diagnosis and treatment guidance. However, nanoscale sizes and the low abundance of marker proteins of T-EVs restrict interfacial affinity reaction, leading to low isolation efficiency and detection sensitivity. Here, we engineer a fluid nanoporous microinterface (FluidporeFace) in a microfluidic chip by decorating supported lipid bilayers (SLBs) on nanoporous herringbone microstructures with a multiscale-enhanced affinity reaction for efficient isolation of T-EVs. At the microscale level, the herringbone micropattern promotes the mass transfer of T-EVs to the surface. At the nanoscale level, nanoporousity can overcome boundary effects for close contact between T-EVs and the interface. At the molecular level, fluid SLBs afford clustering of recognition molecules at the binding site, enabling multivalent binding with an ∼83-fold increase of affinity compared with the nonfluid interface. With the synergetic enhanced mass transfer, interface contact, and binding affinity, FluidporeFace affords ultrasensitive detection of T-EVs with a limit of detection of 10 T-EVs μL −1 , whose PD-L1 expression levels successfully distinguish cancer patients from healthy donors. We expect this multiscale enhanced interfacial reaction strategy will inspire the biosensor design and expand liquid biopsy applications, especially for low-abundant targets in clinical samples.

From affinity selection to kinetic selection in Germinal Centre modelling

Affinity maturation is an evolutionary process by which the affinity of antibodies (Abs) against specific antigens (Ags) increases through rounds of B-cell proliferation, somatic hypermutation, and positive selection in germinal centres (GC). The positive selection of B cells depends on affinity, but the underlying mechanisms of affinity discrimination and affinity-based selection are not well understood. It has been suggested that selection in GC depends on both rapid binding of B-cell receptors (BcRs) to Ags which is kinetically favourable and tight binding of BcRs to Ags, which is thermodynamically favourable; however, it has not been shown whether a selection bias for kinetic properties is present in the GC. To investigate the GC selection bias towards rapid and tight binding, we developed an agent-based model of GC and compared the evolution of founder B cells with initially identical low affinities but with different association/dissociation rates for Ag presented by follicular dendritic cells in three Ag collection mechanisms. We compared an Ag collection mechanism based on association/dissociation rates of B-cell interaction with presented Ag, which includes a probabilistic rupture of bonds between the B-cell and Ag (Scenario-1) with a reference scenario based on an affinity-based Ag collection mechanism (Scenario-0). Simulations showed that the mechanism of Ag collection affects the GC dynamics and the GC outputs concerning fast/slow (un)binding of B cells to FDC-presented Ags. In particular, clones with lower dissociation rates outcompete clones with higher association rates in Scenario-1, while remaining B cells from clones with higher association rates reach higher affinities. Accordingly, plasma cell and memory B cell populations were biased towards B-cell clones with lower dissociation rates. Without such probabilistic ruptures during the Ag extraction process (Scenario-2), the selective advantage for clones with very low dissociation rates diminished, and the affinity maturation level of all clones decreased to the reference level.

Adaptive immunity is one of the vital defence mechanisms of the human body to fight virtually unlimited types of pathogens by producing antigen-specific high-affinity antibodies that bind to pathogens and neutralise them or mark them for further elimination. Affinity is a quantity used to measure and report the strength of interaction between antibodies and antigens that depends both on how fast antibodies bind to antigens (association rate) and how long the bond lasts (dissociation rate). The affinity of produced antibodies for a specific antigen increases in germinal centres through a process called affinity maturation, during which B cells with higher affinities have a competitive advantage and get positively selected to differentiate to antibody-producing plasma cells. Our research shows that the mechanism by which B cells capture Ag affects GC dynamics and GC output with respect to B-cell receptor kinetics. Notably, in a mechanism where rupture of CC-FDC bonds is possible during Ag extraction, B-cell clones with low dissociation rates outcompete clones with high association rates over time. Understanding how B cells get selected in germinal centres could help to develop an optimised and effective immune response against a disease through vaccination for a fast-operating and long-lasting immune response.