Biology subjects

Dunn-Walters, D.

Publications and source records attributed to Dunn-Walters, D..

5 recordsLinked to original sources

bioRxiv2025

Multi-step antibody class switching in a primary human response is restricted after IGHG2 and dependent on B cell maturation stage.

Class switch recombination (CSR) allows the formation of functionally specialized antibodies. Understanding of CSR dynamics is key for better design and prediction of vaccines to protect mucosal surfaces. To investigate CSR in a primary human immune response under a controlled setting, we sampled healthy volunteers without COVID-19 history every other day during the first three weeks after SARS-CoV-2 vaccination, with additional time points up to six months. Leveraging bulk and single-cell B cell receptor repertoires, single-cell transcriptomics, and immunophenotyping, we uncover paradigm-shifting insights into CSR. Newly activated B cells produce sterile transcripts of all antibody isotype constant regions (IGHC) simultaneously up to IGHG2, challenging the view that sterile transcription occurs for only a single IGHC gene at a time. CSR follows a multistep progression along the IGHC locus; in this challenge vaccine-induced B cells switch from IGHM to IGHG3 and IGHG1, followed by a subsequent switching to IGHA1 and IGHG2 after secondary immunization. IGHA2 clones require pre-switching to IGHA1 clones. Notably, switching tendency, measured by IGHC sterile transcription, is memory B cell subtype dependent, particularly beyond IGHG2. Contrary to other vaccines, antigen-specific B cells are enriched in DN2, Cmem2 and DN4 subtypes after immunization. We also observe a temporal decoupling of CSR and somatic hypermutation (SHM), with the latter detectable only after six months post-immunization. Our data describes the dynamics between CSR, SHM, sterile transcription and B cell memory development during a human primary response, challenges textbook models of CSR and offers new insights to aid control of CSR direction. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=188 HEIGHT=200 SRC="FIGDIR/small/652638v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@785769org.highwire.dtl.DTLVardef@b2c54eorg.highwire.dtl.DTLVardef@b78c72org.highwire.dtl.DTLVardef@65b5aa_HPS_FORMAT_FIGEXP M_FIG C_FIG One Sentence SummaryClass switch recombination occurs independently of somatic hypermutation and in a multistep fashion up to IGHG2 during a primary response in humans.

immunology↗

bioRxiv2024

VCAb: A web-tool for structure-guided antibody engineering

Effective responses against different immune challenges require secretion of antibodies with various isotypes performing specific effector functions. Structural information on these isotypes is essential to engineer antibodies with desired physico-chemical features of their antigen-binding properties, and optimal stability and developability as potential therapeutic antibodies. In silico mutational scanning profiles on antibody structures would further pinpoint candidate mutations for enhancing antibody stability and function. Although a number of antibody structure databases exist, a public data resource which provides clear, consistent annotation of isotypes, species coverage of 3D antibody structures and their deep mutation profiles is currently lacking. The V and C region bearing antibody (VCAb) web tool is established with the purpose to clarify these annotations and provide an accessible and easily consultable resource to facilitate antibody engineering. VCAb currently provides data on 6,948 experimentally determined antibody structures including both V and C regions from different species. Additionally, VCAb provides annotations of species and isotypes with both V and C region numbering schemes applied, which can be interactively queried or downloaded in batch. Multiple in silico mutational scanning methods are applied on VCAb structures to provide an easily accessible interface for querying the impact of mutations on antibody stability. These features are implemented in a R shiny application to enable interactive data interrogation. VCAb is freely accessible at https://fraternalilab.cs.ucl.ac.uk/VCAb/. The source code to generate the VCAb database and the online R shiny application is available at https://github.com/Fraternalilab/VCAb, enabling users to set up local VCAb instances.

bioinformatics↗

bioRxiv2021

Pandemic, epidemic, endemic: B cell repertoire analysis reveals unique anti-viral responses to SARS-CoV-2, Ebola and Respiratory Syncytial Virus

Immunoglobulin gene heterogeneity reflects the diversity and focus of the humoral immune response towards different infections, enabling inference of B cell development processes. Detailed compositional and lineage analysis of long read IGH repertoire sequencing, combining examples of pandemic, epidemic and endemic viral infections with control and vaccination samples, demonstrates general responses including increased use of IGHV4-39 in both EBOV and COVID-19 infection cohorts. We also show unique characteristics absent in RSV infection or yellow fever vaccine samples: EBOV survivors show unprecedented high levels of class switching events while COVID-19 repertoires from acute disease appear underdeveloped. Despite the high levels of clonal expansion in COVID-19 IgG1 repertoires there is a striking lack of evidence of germinal centre mutation and selection. Given the differences in COVID-19 morbidity and mortality with age, it is also pertinent that we find significant differences in repertoire characteristics between young and old patients. Our data supports the hypothesis that a primary viral challenge can result in a strong but immature humoral response where failures in selection of the repertoire risks off-target effects.

immunology↗

bioRxiv2020

Single-cell transcriptomic analyses define distinct peripheral B cell subsets and discrete development pathways

Separation of B cells into different subsets has been useful to understand their different functions in various immune scenarios. In some instances, the subsets defined by phenotypic FACS separation are relatively homogeneous and so establishing the functions associated with them is straightforward. Other subsets, such as the "Double negative" (DN, CD19+CD27-IgD-) population, are more complex with reports of differing functionality which could indicate a heterogeneous population. Recent advances in single-cell techniques enable an alternative route to characterise cells based on their transcriptome. To maximise immunological insight, we need to match prior data from phenotype-based studies with the finer granularity of the single-cell transcriptomic signatures. We also need to be able to define meaningful B cell subsets from single cell analyses performed on PBMCs, where the relative paucity of a B cell signature means that defining B cell subsets within the whole is challenging. Here we provide a reference single-cell dataset based on phenotypically sorted B cells and an unbiased procedure to better classify functional B cell subsets in the peripheral blood, particularly useful in establishing a baseline cellular landscape and in extracting significant changes with respect to this baseline from single-cell datasets. We find 10 different clusters of B cells and applied a novel, geometry-inspired, method to RNA velocity estimates in order to evaluate the dynamical transitions between B cell clusters. This indicated the presence of two main developmental branches of memory B cells. One involves IgM memory cells and two DN subpopulations, culminating in a population thought to be associated with Age related B cells and the extrafollicular response. The other branch involves a third DN cluster which appears to be a precursor of classical memory cells. In addition, we identify a novel DN4 population, which is IgE rich and on its own developmental branch but with links to the classical memory branch.

immunology↗

bioRxiv2019

Natural IgE promotes epithelial hyperplasia and inflammation-driven tumour growth

IgE is the least abundant circulating antibody class but is constitutively present in healthy tissues bound to resident cells via its high-affinity receptor, Fc{varepsilon}RI. The physiological role of endogenous IgE is unclear but it is suggested to provide host protection against a variety of noxious environmental substances and parasitic infections at epithelial barrier surfaces. Here we show that skin inflammation enhances levels of IgE with natural specificities and with a similar repertoire, VDJ rearrangements and CDRH3 characteristics as in healthy tissue. IgE-bearing basophils are recruited to inflamed skin via CXCL12 and TSLP/IL-3-dependent upregulation of CXCR4. In the inflamed skin, IgE/Fc{varepsilon}RI-signalling in basophils promotes epithelial cell growth and differentiation, partly through histamine engagement of H1R and H4R. Furthermore, this natural IgE response strongly drives tumour outgrowth of epithelial cells harbouring oncogenic mutation. These findings indicate that natural IgE support skin barrier defences however during chronic tissue inflammation this may be subverted to promote tumour growth.

cancer biology↗