Biology subjects

ten Brinke, A.

Publications and source records attributed to ten Brinke, A..

5 recordsLinked to original sources

bioRxiv2025

Enhanced human antigen-specific B cell responses using in vitro 3D tonsil cultures containing stromal cells

The structural complexity of secondary lymphoid organs (SLOs) and their role in shaping antigen-specific B cell responses, pose significant challenges in modeling human germinal center (GC) response in vitro. A human 3D lymphoid model incorporating lymphoid and stromal cell types recapitulates key immune and structural features, enabling the study of antigen-specific B and T cell interactions beyond current 2D culture limitations. In this study, human tonsil cells were cultured with and without tonsil-derived fibroblastic reticular cells (FRCs) either in 2D or within a 3D PEG-4MAL hydrogel culture. Antigen-specific B cell responses in co-cultures were studied by comparing unstimulated cultures to stimulation with antigen (SARS-CoV-2 spike (S) or Influenza hemagglutinin (HA), both with or without adjuvant R848), S-nanoparticles and influenza vaccines. Combination of FRCs with the 3D matrix significantly improved B and T cell survival and facilitated reaggregation into follicle-like structures. Antigen-specific responses were most pronounced in 3D FRC-supported co-cultures, with increasing S- or HA-specific B cell frequencies, antibody-secreting cell differentiation, and secretion of antigen-specific antibodies. Importantly, cell death and unspecific bystander activation was lowest in 3D FRC-supported cultures. Additionally, GC-associated chemokine receptors CXCR4 and CXCR5 showed distinct expression patterns on CD27CD38 B cells, reflecting GC-like dark and light zone organization typically observed in SLOs in vivo. Autologous and allogeneic FRC-supported cultures yielded comparable results, demonstrating the platforms potential for high-throughput applications. The 3D FRC-supported lymphoid cultures offer a physiologically relevant platform for studying human GC responses in vitro, supporting mechanistic research into adaptive immunity and enabling the screening of vaccine immunogens and adjuvants in a controlled setting.

immunology↗

bioRxiv2025

Identifying pyrogenic contaminants using transcriptomic profiling of monocyte activation test with machine learning

The monocyte activation test is an in vitro pyrogenicity assessment method that can utilise human peripheral blood mononuclear cells to detect pyrogens in injectable drugs, providing a binary outcome that indicates the presence or absence of a pyrogen. The added ability to distinguish between different types of pyrogens would greatly expand the applicability of the test, for example, by allowing to pinpoint the source of a contaminating pyrogen in pharmaceutical products. Pyrogens activate a unique set of pattern recognition receptors (PRRs), which contribute to inflammation, yielding distinct transcriptomic activation signatures. In this paper, we capture the unique expression signatures of activated monocytes through bulk RNA sequencing and introduce a data preprocessing pipeline that allows the training of a machine-learning model to classify pyrogenic contaminants. Using a dataset of 108 samples stimulated with five classes of PRR agonists, we could differentiate between these classes with more than 97% F1 on test data. We further demonstrate the models capacity to generalise on the previously unseen data using different ligands for the same PRRs as well as heat-killed Escherichia coli and Staphylococcus aureus.

bioinformatics↗

bioRxiv2024

Characterization of a heterogenous activated B cell compartment arising early after antigen exposure preceding long-lived memory B cell formation

Once formed, plasma cells and memory B cells (MBCs) are difficult to eradicate, posing a problem in the context of unwanted antibody responses. Characterizing early B cell differentiation stages after antigen encounter is thus crucial to target and prevent unwanted antibody formation. Here, we unravelled in-depth antigen-specific B cell responses longitudinally after SARS-CoV-2 mRNA vaccination in healthy individuals using multiparameter spectral flow cytometry. The early antigen-specific B cell response was dominated by spike-specific IgG+ CD27+ CD71+ activated B cells (ActBCs), previously assigned as germinal center-derived and DN2 extrafollicular B cells. Within the early IgG+ ActBC compartment, six distinct clusters were identified with specific contraction dynamics, whereby some of these clusters were more closely related to pre-ASCs and others more to long-lived MBCs. Some of the highly contracting ActBC clusters expressed CD11c, a marker previously used to define atypical B cells. The transient presence of different ActBC clusters could also be observed in total B cells when gated in an antigen- independent manner. Our results thus delineate the early stages of the antigen-specific B cell response, with a further dissection of the CD71+ ActBC compartment. Detection of ActBC clusters early after antigen encounter in total B cells opens avenues for future evaluation of their potential to serve as a proxy for antigen-reactive B cells in autoimmunity or other unwanted B cell responses.

immunology↗

bioRxiv2023

Deep profiling of antigen-specific B cells from different pathogens identifies novel compartments in the IgG memory B cell and antibody-secreting cell lineages

A better understanding of the bifurcation of human B cell differentiation into memory B cells (MBC) and antibody-secreting cells (ASC) and identification of MBC and ASC precursors is crucial to optimize vaccination strategies or block undesired antibody responses. To unravel the dynamics of antigen-induced B cell responses, we compared circulating B cells reactive to SARS-CoV-2 (Spike, RBD and Nucleocapsid) in COVID-19 convalescent individuals to B cells specific to Influenza-HA, RSV-F and TT, induced much longer ago. High-dimensional spectral flow cytometry indicated that the decision point between ASC- and MBC-formation lies in the CD43+CD71+IgG+ Activated B cell compartment, showing properties indicative of recent germinal center activity and recent antigen encounter. Within this Activated B cells compartment, CD86+ B cells exhibited close phenotypical similarity with ASC, while CD86- B cells were closely related to IgG+ MBCs. Additionally, different activation stages of the IgG+ MBC compartment could be further elucidated. The expression of CD73 and CD24, regulators of survival and cellular metabolic quiescence, discerned activated MBCs from resting MBCs. Activated MBCs (CD73-CD24lo) exhibited phenotypical similarities with CD86- IgG+ Activated B cells and were restricted to SARS-CoV-2 specificities, contrasting with the resting MBC compartment (CD73-/CD24hi) that exclusively encompassed antigen-specific B cells established long ago. Overall, these findings identify novel stages for IgG+ MBC and ASC formation and bring us closer in defining the decision point for MBC or ASC differentiation. ImportanceIn this study, researchers aimed to better understand human B cell differentiation and their role in establishing long-lived humoral immunity. Using high-dimensional flow cytometry, they studied B cells reactive to three SARS-CoV-2 antigens in individuals convalescent for COVID-19, and compared their phenotypes to B cells reactive to three distinct protein antigens derived from vaccines or viruses encountered months to decades before. Their findings showed that Activated B cells reflect recent germinal center graduates that may have diverse fates; with some feeding the pool of antibody-secreting cells and others fueling the resting memory B cell compartment. Activated B cells gradually differentiate into resting memory B cells through an activated MBC phase. Increased expression of the cellular metabolic regulators CD73 and CD24 in resting memory B cells distinguishes them from the activated memory B cells phase, and is likely involved in sustaining a durable memory of humoral immunity. These findings are crucial for the development of vaccines that provide lifelong protection and may show potential to define reactive B cells in diseases where the cognate-antigen is still unknown such as in autoimmunity, cancers, or novel viral outbreaks.

immunology↗

bioRxiv2022

Single-cell analysis reveals dynamics of human B cell differentiation and identifies novel B and antibody-secreting cell intermediates

Differentiation of B cells into antibody-secreting cells (ASCs) is a key process to generate protective humoral immunity. A detailed understanding of the cues controlling ASC differentiation is important to devise strategies to modulate antibody formation. Here, we dissected differentiation trajectories of human naive B cells into ASCs using single-cell RNA sequencing. By comparing transcriptomes of B cells at different stages of differentiation from an in vitro model with ex vivo B cells and ASCs, we uncovered a novel pre-ASC population present ex vivo in lymphoid tissues. For the first time, a germinal-center-like population is identified in vitro from human naive B cells and possibly progresses into a memory B cell population through an alternative route of differentiation, thus recapitulating in vivo human GC reactions. Our work allows further detailed characterization of human B cell differentiation into ASCs or memory B cells in both healthy and diseased conditions.

immunology↗