Biology subjects

Freund, N.

Publications and source records attributed to Freund, N..

8 recordsLinked to original sources

bioRxiv2026

DiverScan: attention-guided exploratory analysis of animal behaviour across diverse comparative experiments

High-throughput tracking yields rich time-series data of animal behaviour, yet extracting biological insight remains a bottleneck, even for simple control--treatment comparisons. Existing analyses struggle to pinpoint the multiple, nonlinearly intertwined differences hidden in the data and fail to generalise across diverse recording set-ups. Here we present DiverScan, a deep-learning framework for attention-guided exploratory analysis of behavioural time series. DiverScan disentangles condition-dependent behavioural differences by pairing a loss function tailored to data exploration with an attention-branch architecture, and highlights condition-specific behavioural features visually and with explanatory text generated by a large language model. DiverScan is validated on a synthetic benchmark and on datasets from seven laboratories spanning multiple species and both single- and multi-animal behaviour. Beyond recovering known phenotypes, we demonstrate that DiverScan helps researchers generate new hypotheses across these diverse datasets. Available as Jupyter notebooks with a graphical user interface and flexible input formats, DiverScan can integrate into existing behavioural-analysis pipelines.

animal behavior and cognition↗

bioRxiv2026

CTCF-mediated cis-regulatory chromatin insulation enforces a central B-cell tolerance checkpoint

The generation of a diverse and self-tolerant B cell repertoire is essential for adaptive immunity and is achieved through V(D)J recombination. In mice, Ig{kappa} is the dominant light chain, whereas Ig{lambda} rearrangement typically occurs in response to nonproductive or autoreactive Ig{kappa} recombination, a process termed receptor editing. Recombination at the RS element deletes the Ig{kappa} constant exon, silencing the locus and enabling Ig{lambda} expression. However, the epigenetic regulatory framework that orchestrates and governs receptor editing remains poorly defined. Here, we identify a CTCF-binding insulator element (CBE) within the 3' Ig{kappa} super-enhancer (3'-SE{kappa}) that regulates receptor editing and directs the {kappa}-to-{lambda} switch required for Ig{lambda} B-cell development. Mechanistically, loss of this CBE activates an insulated enhancer within the 3'-SE{kappa}, causing aberrant V{kappa} rearrangements and altered chromatin interactions through disrupted loop extrusion dynamics. Notably, loss of this CBE in mice leads to increased autoantibody production by ten weeks of age, demonstrating that CBE-mediated chromatin architecture shapes B cell fate by constraining autoreactive potential. Collectively, our findings define a novel CTCF-dependent cis-regulatory insulation checkpoint that connects chromatin loop extrusion to antigen-driven receptor editing, thereby enforcing B-cell tolerance.

immunology↗

bioRxiv2025

Decoy Antibodies Block Extracellular HSP70, Prevent Self Signaling and Inhibit Melanoma Cell Survival

Melanoma cells actively secrete melanosomes-large, extracellular vesicles (EVs) enriched with oncogenic factors that reprogram the tumor microenvironment, enhance self-signaling, and promote tumor growth. Despite their abundance and immunogenic potential, humoral responses to melanoma-derived melanosomes remain unexplored. Here, we identify a novel immune surveillance mechanism in which melanosome-elicited decoy antibodies target melanoma-derived melanosomes by binding to the extracellular form of heat shock protein 70 (HSP70), a chaperone broadly implicated in cancer cell survival and stress adaptation. Anti-HSP70 decoy antibodies potently and effector-independently inhibit growth and survival of both murine and human melanoma cells and suppress key transcriptional programs involved in proliferation, cytoskeletal dynamics, and metabolism. In a preclinical B16 melanoma model, prophylactic administration of decoy monoclonal antibodies Mel322-34 and Mel321-35 conferred significant survival benefits of 27% and 48%, respectively. Strikingly, anti-HSP70 antibodies were enriched in the sera of melanoma patients achieving complete responses to immune checkpoint blockade, in contrast to non-responders with progressive disease. Collectively, our findings uncover a novel EV-antibody axis as a promising avenue to block cancer-promoting signaling pathways. Decoy autoantibodies targeting the extracellular form of HSP70 advance the understanding of tumor-intrinsic vulnerability and promote biomarker-driven immunotherapy in melanoma.

immunology↗

bioRxiv2025

Monoclonal Antibodies from COVID-19 Convalescent Patients Target Cryptic Epitopes for Universal SARS-CoV-2 Neutralization

The COVID-19 pandemic, which has resulted in over seven million global fatalities, poses a substantial threat to public health and precipitated a global economic crisis. Emerging variants of concern (VOCs) with enhanced transmissibility and improved immune evasion may compromise the efficacy of current antiviral and immunotherapies, necessitating comprehensive investigations into the immune response to SARS-CoV-2. The conformational dynamics of the receptor binding domain (RBD) in SARS-CoV-2 spike and the presentation of neutralizing antibody epitopes influence viral transmission and infection rates. In this study, we have identified highly conserved non-RBM epitopes for two potent monoclonal antibodies (mAbs), TAU-1109 and TAU-2310, isolated from convalescent human patients, which contribute to the broad neutralizing activity of these mAbs against all the circulating VOCs, including the recently emerged Omicron subvariants. We employed high- resolution structural data in conjunction with systematic biochemical investigation to elucidate the neutralization mechanism of TAU-1109 and TAU-2310. The mechanism involves antibody-mediated destabilization of the spike trimer, resulting in the premature shedding of the S1 subunit and rendering the spike incapable of mediating host cell entry. The identification of conserved cryptic epitopes in our study advances the mechanistic understanding of immune response against SARS-CoV-2, providing novel avenues for the development of universal therapeutic antibodies and vaccines to combat COVID-19.

biochemistry↗

bioRxiv2025

Early Antibody-Mediated Immunity to Tuberculosis in Mice Requires NLRP3

While antibodies have emerged as potential mediators of protective immunity against Mycobacterium tuberculosis (Mtb), their mechanisms of action remain incompletely understood. Here, we demonstrate that immune complexes of Mtb and monoclonal antibodies targeting the Mtb phosphate transporter subunit PstS1 robustly activate the NLRP3 inflammasome in human and murine macrophages, leading to enhanced interleukin-1{beta} secretion. Surprisingly, antibody-mediated inflammasome activation occurred independently of cell-surface Fc{gamma} receptors, as confirmed using Fc-domain glycosylation mutant mAbs and macrophages from Fc{gamma} receptor-deficient mice. Crucially, NLRP3 is indispensable for early antibody-mediated protection in vivo, as both pharmacological inhibition, and genetic deletion of NLRP3 completely abolished protective effects of PstS1-specific antibodies in Mtb-infected mice. This mechanism extends beyond monoclonal antibodies, as polyclonal sera from intravenously BCG-immunized rhesus macaques also required NLRP3 for protective efficacy. Our findings reveal a previously unrecognized mechanism by which Mtb-specific antibodies enhance host defense through inflammasome activation, potentially informing novel approaches for tuberculosis vaccine development.

immunology↗

bioRxiv2025

Potent Neutralization by Antibodies Targeting the Mpox A28 Protein

Mpox is the most pathogenic Poxvirus in circulation. While several antigens have been identified as targets for neutralizing antibodies, many proteins remain unexplored. We isolated and characterized four monoclonal antibodies (mAbs) targeting the Mpox A28 (OPG153), a virulence factor present on mature Mpox virions. The antibodies were isolated from convalescent individuals, alongside 14 additional mAbs targeting the A35 and H3 proteins. Anti-A28 mAbs potently neutralized Mpox and Vaccinia virus (VACV) through complement-dependent mechanisms involving C1q and C3 deposition. High resolution crystal structures of Anti-A28 mAbs 10M2146 and 8M2110 in complex with VACV A26 revealed two proximal epitopes within the N-terminal domain. Passive transfer of 8M2110 attenuated disease in infected mice. Moreover, immunization with A28 elicited antigen-specific B cells and robust neutralizing antibody responses and provided complete protection against lethal VACV challenge. These findings support Mpox A28 as a promising target for the induction of neutralizing antibodies and antiviral interventions.

immunology↗

bioRxiv2023

Evaluation of the Ability of AlphaFold to Predict the Three-Dimensional Structures of Antibodies and Epitopes

Being able to accurately predict the three-dimensional structure of an antibody can facilitate fast and precise antibody characterization and epitope prediction, with important diagnostic and clinical implications. In the current study, we evaluate the ability of AlphaFold to predict the structures of 222 recently published, non-redundant, high resolution Fab heavy and light chain structures of antibodies from different species (human, Macaca mulatta, mouse, rabbit, rat) directed against different antigens. Our analysis reveals that while the overall prediction quality of antibody chains is in line with the results available in CASP14, other antibody regions like the complementarity-determining regions (CDRs) of the heavy chain, which are prone to higher genetic variation, generate a less accurate prediction. Moreover, we discovered that AlphaFold often mis-predicts the bending angles between the variable and constant domains within a Fab. To evaluate the ability of AlphaFold to model antibody:antigen interactions based only on sequence, we used AlphaFold-multimer in combination with ZDOCK docking to predict the structures of 26 known antibody:antigen complexes. ZDOCK succeeded in predicting 11, and AlphaFold only two, out of 26 models with medium or high accuracy, with significant deviations in the docking contacts predicted in the rest of the molecules. In summary, our study provides important information about the abilities and limitations of using AlphaFold to predict antibody:antigen interactions and suggests areas for possible improvement. Key PointsO_LIAlphaFold was used to predict 222 new 3D hi-res atomic structures of Ab chains. C_LIO_LILow accuracy was observed in the prediction of HC-CDR3 and the elbow angles. C_LIO_LIPredicting Ab-Ag complexes and epitope mapping using AlphaFold-Multimer was limited. C_LI

immunology↗

bioRxiv2020

Multi-Clonal Live SARS-CoV-2 In Vitro Neutralization by Antibodies Isolated from Severe COVID-19 Convalescent Donors

The interactions between antibodies, SARS-CoV-2 and immune cells contribute to the pathogenesis of COVID-19 and protective immunity. To understand the differences between antibody responses in mild versus severe cases of COVID-19, we analyzed the B cell responses in patients 1.5 months post SARS-CoV-2 infection. Severe and not mild infection correlated with high titers of IgG against Spike receptor binding domain (RBD) that were capable of viral inhibition. B cell receptor (BCR) sequencing revealed two VH genes, VH3-38 and VH3-53, that were enriched during severe infection. Of the 22 antibodies cloned from two severe donors, six exhibited potent neutralization against live SARS-CoV-2, and inhibited syncytia formation. Using peptide libraries, competition ELISA and RBD mutagenesis, we mapped the epitopes of the neutralizing antibodies (nAbs) to three different sites on the Spike. Finally, we used combinations of nAbs targeting different immune-sites to efficiently block SARS-CoV-2 infection. Analysis of 49 healthy BCR repertoires revealed that the nAbs germline VHJH precursors comprise up to 2.7% of all VHJHs. We demonstrate that severe COVID-19 is associated with unique BCR signatures and multi-clonal neutralizing responses that are relatively frequent in the population. Moreover, our data support the use of combination antibody therapy to prevent and treat COVID-19.

immunology↗