Biology subjects

Voss, L. F.

Publications and source records attributed to Voss, L. F..

7 recordsLinked to original sources

bioRxiv2026

A pro-inflammatory effector-memory T cell program links peripheral EBV priming to CNS autoimmunity

T and B cell-mediated immunosurveillance of the central nervous system (CNS) can become maladaptive in multiple sclerosis (MS). Epstein-Barr virus (EBV) is a likely driver of MS, yet how exactly EBV-specific T cells contribute remains unclear. We generated an antigen-resolved atlas of blood and cerebrospinal fluid (CSF) T cells from untreated MS patients and controls. T cell clones carrying a GZMK effector-memory program in blood were CSF-biased, particularly in MS, and associated with EBV reactivity. In CSF, EBV-reactive GZMK CD8 T cells engaged B lineage cells. Activated CD8 T cells promoted atypical B cell and plasmablast formation, whereas GZMK-enriched effector-memory cells induced IL-6 and IL-8 release from myeloid cells. Together, these findings identify an infection-imprinted, CNS-biased state and support a model in which EBV-specific CD8 T cells contribute to inflammation through a non-canonical mode of B cell and myeloid cell activation.

immunology↗

bioRxiv2026

Thymic Treg-derived T follicular regulatory cells prevent catastrophic humoral autoimmunity in response to TLR7-driven inflammation

T follicular regulatory cells (TFR) are a follicle-resident subset of regulatory T cells (TREG) that limit germinal center (GC) responses and enforce humoral tolerance. Although TFR are known to focus antibody responses to foreign antigens, how GC-specific regulation is maintained during inflammation remains unclear. Here, TLR7-driven inflammation unmasked a critical, non-redundant role for TFR in preserving immune tolerance. Selective loss of TFR caused severe autoimmunity and increased mortality, driven by inflammation-induced expansion of autoreactive B and T cell clones and epitope spreading. Autoreactivity resolved upon cessation of inflammation in TFR-sucicient mice but persisted in their absence. Mechanistically, TFR limited the establishment and expansion of spontaneous GCs in response to inflammation, and responding TFR displayed transcriptional, phenotypic, and clonal features of thymic TREG. This suggests that whereas TFH upregulate FoxP3 to shut down end-stage GCs, it is thymic TREG-derived TFR that safeguard GC integrity under inflammatory stress to prevent lethal autoimmunity.

immunology↗

bioRxiv2025

ITRAP2, a flexible and robust strategy to assign antigen recognition of T-cells in a coupled single-cell TCR-pMHC assay

Determining T-cell specificity forms a crucial step toward understanding T-cell involvement in health and disease. Single-cell sequencing technologies allow for co-capture of TCR alpha and beta chains, and their antigen specificity can be determined through peptide-MHC (pMHC) multimer binding and capture of a co-attached barcode oligo. However, SC sequencing often includes a high level of dropouts and risk of cross-contamination. Similarly, barcoded pMHC readouts often suffer from significant background noise. These issues complicate the automatic assignment of pMHC recognition to TCR clonotypes. To overcome these challenges, we developed a method for data denoising - Improved T-cell Receptor Antigen Paring 2 (ITRAP2). This approach significantly reduces noise in single-cell pMHC readouts and allows for accurate identification of TCR specificity. ITRAP2 incorporates statistical tests and confidence metrics for each TCR-pMHC pairing, offering user flexibility in pairing rigor, and allows multiple pMHC assignments to the same T-cell clone in the event of cross-binding within the pMHC multimer library. We tested this method on an in-house generated dataset of 8141 single cells, screened for CD8 T-cell binding using a panel of 100 different barcode-labelled pMHC multimers holding virus-derived peptides, and on a larger public dataset from 10x Genomics with 208,589 T-cells evaluated for recognition using a panel of 50 different pMHCs. In both datasets, ITRAP2 was able to recover TCR-pMHC hits that were missed either when investigating the raw data or analyzing the data using alternative tools. Importantly, we demonstrate that the size of the pMHC multimer library is crucial for accurate pMHC-TCR pairing and that a minimum of 25 pMHC multimer should be included to optimally determine background characteristic, and assigning true positive events.

bioinformatics↗

bioRxiv2025

Antigen-scaffolds drive preferential expansion of functional genetically engineered CAR and TCR T cells

The engineering of autologous T cells to express chimeric antigen receptors (CARs) can induce profound clinical responses in haematological malignancies, while T cell receptor-engineered T (TCR T) cells have led to durable responses in clinical trials for solid tumours. However, clinical manufacturing of engineered T cells is resource-intensive and often yields highly differentiated, exhausted effector T cells. To circumvent this, we have developed an antigen-scaffold (Ag-scaffold) technology to preferentially expand genetically engineered T cells. Such Ag-scaffolds present cognate antigen together with stimulatory factors such as cytokines. By providing a specific and receptor-engaging stimulation to CAR/TCR T cells, the expanded product is highly enriched for engineered T cells with a favourable proliferative and efficacious phenotype. We expanded TCR T cells with Ag-scaffolds presenting peptide MHC (pMHC), and anti-CD19 CAR T cells with Ag-scaffolds presenting CD19 antigen. By applying cognate pMHC Ag-scaffolds, we achieved >80% antigen-specific T cells (83.62%{+/-}9.2%) after 14 days of culture with a distinct cytotoxic, proliferative phenotypical profile. Ag-scaffold expansion enhanced initial TCR and CAR cytotoxicity; sustained control was observed after repeated rechallenges of CAR T cells. In vivo, Ag-scaffold-expanded CRISPR/Cas9-engineered anti-CD19 CAR T also showed complete tumour eradication in a B-cell lymphoma xenograft model with a low dose of CAR T cells, which was not achieved using IL2/7/15 expansion.

immunology↗

bioRxiv2025

Mapping of CD8 T-cell recognition to latent EBV infection and neuroantigens reveals HLA-specific depletion of T-cell responses in multiple sclerosis

Multiple sclerosis (MS) is a complex autoimmune disease with an unclear contribution from antigen-specific CD8 T cells. To enumerate adaptive immune responses associated with MS and to identify MS-related epitopes recognized by CD8 T cells, we evaluated T-cell recognition of 1,158 predicted major histocompatibility complex (MHC)-binding peptides derived from latent EBV antigens (laEBVs) and selected neuroantigens (NAgs) using DNA barcode-labelled pMHC multimers. HLA-B*07:02+ individuals living with relapsing-remitting MS (RRMS) and progressive MS (PMS) were characterized by a relative reduction in EBNA6-specific and MAG-specific CD8 T cells compared to healthy donors. Furthermore, both RRMS and PMS patients exhibited a delayed expansion of CMV- and laEBV-specific CD8 T cells compared to healthy donors indicating an age-specific interaction with disease. Female RRMS patients were moreover characterized by a specific reduction of laEBV-specific CD8 T cells compared to male RRMS patients. NAg-specific CD8 T cells recognized heterogeneous peptides, were of low cellular frequency in peripheral blood, and exhibited a circulating, naive-like, anergic phenotype. In contrast, virus-specific CD8 T cells were characterized by high-frequency cellular responses with an effector-like, tissue-homing phenotype. These immunophenotypes were largely shared between MS and healthy donors. Collectively, our data provide novel insights into CD8 T-cell recognition of both NAg and laEBV antigens in MS and constitute a key reference map of epitopes for further immunomonitoring of EBV- and self-specific CD8 T cells in health and disease.

immunology↗

bioRxiv2023

Simultaneous analysis of pMHC binding and reactivity unveils virus-specific CD8 T cell immunity to a concise epitope set

Knowledge of widely recognized T-cell epitopes against common virus infections are vital for immune monitoring and characterization of relevant antigen-specific CD8 T cells and their antigen receptors. We therefore aimed to establish a concise and validated epitope panel for monitoring human virus-specific immunity complete with data on both prevalence of recognition and reactivity in humans. To achieve this, we first establish TCR downregulation, and loss of peptide major histocompatibility (pMHC) multimer-binding, as an early and sensitive marker of T cell reactivity after peptide stimulation. We next applied TCR downregulation in a high-throughput assay by monitoring binding, and loss of binding (i.e. reactivity), to libraries of DNA-barcode labelled pMHC multimers in paired unstimulated/stimulated samples. This novel method allowed us to access T-cell responses in 48 donors towards 929 epitopes recorded in the Immune Epitope Database (IEDB) encompassing 29 virus common infections and 25 different HLA alleles. This yielded a concise panel of 137 virus epitopes, many of which were underrepresented in the public domain, recognized by T cells in peripheral blood. 84% of these epitopes exhibited prevalent reactivity to peptide stimulation, which was associated with effector and long-term memory phenotypes. Conversely, non-reactive responses correlated with naive and immunosenescence phenotypes. This study represents the largest effort to unbiasedly assess T-cell recognition and reactivity to common virus infections in healthy individuals providing a minimal epitope panel for monitoring adaptive immune responses in humans. Significance StatementCD8 T-cell epitopes are widely available in public databases yet many are not recognized in the general population. Here we undertook an exhaustive screening process using "state-of-the-art" methods to assess both T-cell recognition and reactivity against common virus infections, which holds significant implications for shaping T-cell immunity and disease protection. We identify 137 commonly recognized epitopes from common virus infections to which T cell responses are expected to occur in human donors. Importantly, several of the verified epitopes were underreported in public databases compared to their observed prevalence of recognition and high cellular frequency making this an important reference dataset and resource for immunologists studying antigen-specific T cells across different immunopathologies and contexts including autoimmunity, infectious disease and cancer immunotherapy.

immunology↗

bioRxiv2022

Germinal center block exacerbates extrafollicular responses and accelerates autoimmune disease progression in a murine lupus model

Many autoimmune diseases are characterized by germinal center (GC) derived affinity-matured, class-switched autoantibodies. Strategies to block GC formation and progression are currently being explored clinically, however, extrafollicular responses may also contribute to early events in autoimmunity. To investigate the relative contribution of these two pathways in autoimmune disease development, we leveraged a transgenic strategy to genetically block the GC pathway. Surprisingly, this accelerated extrafollicular responses and failed to curb autoimmune progression in two lupus models. In vitro, loss of the GC transcription factor Bcl-6 prevented cellular expansion and accelerated plasma cell differentiation, suggesting the in vivo phenotype was caused by rewiring of B cell intrinsic transcriptional programming. In a competitive scenario in vivo, B cells harboring the genetic GC block contributed disproportionately to the plasma cell output. Taken together, this emphasizes the extrafollicular pathway as a key contributor to autoimmune progression, and suggests that strategies aimed at blocking GCs should simultaneously target this pathway to avoid rerouting the pathogenic response. Highlights- A genetic GC block fails to prevent autoimmune progression in two lupus models - An intrinsic GC block drives B cell differentiation into terminally differentiated plasma cells in vitro - B cells harboring a GC block competitively contribute to the plasma cell compartment in an autoreactive setting in vivo - Lupus mice with a GC block display immune complex deposition in kidney glomeruli that is indistinguishable from their wild-type counterparts SummaryAffinity-matured autoantibodies generated in germinal centers are a hallmark of autoimmune diseases. Voss et al. block germinal centers in two autoimmune models, but surprisingly find that disease progresses unimpeded. They identify the extrafollicular pathway as a backdoor to autoimmunity.

immunology↗