Biology subjects

Braun, A.

Publications and source records attributed to Braun, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Supplementation via DAF-16 and pnk-1 driven pantothenate-coenzyme A flux improves disease related stress resistance in C. elegans

Metabolic pathways are increasingly recognized as tractable targets in aging and disease. Building on prior work demonstrating that supplementation with low-molecular weight metabolites (amino acids, vitamins, and their intermediates) can extend lifespan in Caenorhabditis elegans, we focused on pantothenate (vitamin B5), which is dysregulated in sarcopenic muscle and in several neurodegenerative and metabolic disorders. Pantothenate is the obligate precursor of coenzyme A through a short, highly conserved biosynthetic pathway in which loss-of-function mutations can cause neurodegeneration with brain iron accumulation. In C. elegans, the longevity curtailing transcription factor DAF-16/FOXO has a conserved binding element in the promoter region of pnk-1, encoding the first enzyme (PNK-1) in the coenzyme A pathway, and pnk-1 is markedly upregulated in long-lived daf-2 (insulin/-like receptor) mutants, implicating coenzyme A metabolism in longevity. Here, we demonstrate that CoA levels naturally increase during early life and decrease towards older age in C. elegans. Dietary pantothenate supplementation increases coenzyme A levels with minimal effects on lifespan but systemic effects on lipid metabolism, mitochondrial dynamics, and muscle structure under basal conditions. Under DAF-16-associated stress conditions, including heat and oxidative stress, pnk-1 expression is upregulated and pantothenate supplementation robustly extends lifespan and improves mobility. Finally, we demonstrate dysregulation of daf-16 and pnk-1 expression in amyotrophic lateral sclerosis (ALS) models, in which pantothenate supplementation confers both lifespan extension and cholinergic neuroprotection.

neuroscience↗

bioRxiv2026

Leishmaniamajor co-opts IL-7 feedback in monocytes to suppress CD4⁺ T-cell immunity

During immune responses, pro-and anti-inflammatory mechanisms must be balanced to ensure pathogen clearance while limiting tissue damage. Monocyte-derived cells contribute to both processes, yet the underlying regulatory circuits remain incompletely defined. Here, we show that a subset of PDPN+IL-7R+ monocyte-derived cells that impair effector CD4 T cell-mediated control of intracellular pathogens, and thus perpetuate the infection. Fibroblast-derived IL-7 drives this immunosuppressive program, which is up-regulated in response to IFN{gamma}. We thus uncover a cytokine-dependent feedback circuit in which elevated IFN{gamma} induces IL-7 production by fibroblasts, licensing immunosuppressive monocyte-derived cells that restrain CD4 T cell responses. This mechanism links excessive inflammation to immune suppression at the expense of pathogen control. Targeting this feedback loop may enable therapeutic strategies that enhance antimicrobial immunity while preserving tissue integrity.

immunology↗

bioRxiv2026

Co-expression-based models improve eQTL predictions and highlightnovel transcriptome-wide genes associated with schizophrenia

Non-coding genetic variants statistically associated with complex heritability phenotypes are thought to act primarily through transcriptome regulatory mechanisms. Predictions of gene expression in tissue like the human brain traditionally rely primarily on cis-eQTLs. Here, we introduce INGENE and MODULE, trans-eQTLs models designed to enhance the prediction of gene expression by capturing the collective impact of candidate trans-eQTLs acting within co-expression networks. Exploiting RNA-seq data in six post-mortem brain regions (amygdala, caudate nucleus, dorsal/subgenual anterior cingulate cortex, dorsolateral prefrontal cortex, and hippocampus), we validate our models on two testing datasets, demonstrating increased gene predictability compared to both an original cis-based model and to EpiXcan, the leading benchmark in cis-model performance. Integration of cis- and trans-predictions significantly improves gene-level expression imputation (MLE = 0.05) for 18,744 genes across the six brain regions considered. Applying cis and trans models to PGC wave 3 genotypes identifies 766 SCZ-associated genes across brain regions (pFDR < .01), emphasizing the complementary nature of cis and trans predictions in trait association discovery. Of these genes, 641 represent novel transcriptome-wide associations with schizophrenia, highlighting the role of trans-heritability and genetic interactions underlying risk for this disorder, in addition to further supporting 125 previous candidates.

genomics↗

bioRxiv2026

Immunopeptidomics reveals peptide antigens preferentially presented in psoriasis lesional skin of HLA-C*06:02 carriers

BackgroundHuman leukocyte antigen (HLA)-C*06:02 is a major genetic risk factor for psoriasis and understanding the HLA-C*06:02-presented peptide antigen repertoire (immunopeptidome) in the skin of patients is crucial for identifying autoantigens. Yet, no skin immunopeptidome data from patients stratified by their HLA-C*06:02 status exists. ObjectiveWe analysed biopsies from lesional and non-lesional skin of patients with psoriasis vulgaris (n=12), guttate psoriasis (n=8), or from skin of healthy controls (n=16). MethodsHLA class I and class II peptide complexes were isolated by serial immunoprecipitation and HLA-bound peptides identified by liquid chromatography-tandem mass spectrometry. HLA-C*06:02 genotyping was performed by polymerase chain reaction. ResultsOver 99,000 non-redundant peptide ligands were identified across all samples. Substantially more HLA class I and class II peptides were detected in lesional psoriatic skin compared to matched non-lesional and healthy skin. Three peptides predicted to bind HLA-C*06:02, including MRASSFLIV from the known psoriasis marker peptidase inhibitor 3 (PI3), were identified in all lesions of HLA-C*06:02-positive patients but were rarely detected or absent in HLA-C*06:02-negative patient lesional skin and not detected at all in unaffected skin. Keratinocyte differentiation-associated protein (KRTDAP) was a notable source of lesion-specific HLA class II ligands contributing three out of six peptides detected in more than half of the lesional samples. ConclusionActive psoriatic lesions display an altered and expanded immunopeptidome compared to unaffected skin. We have identified numerous unreported, lesion-specific HLA-bound peptides and their source proteins. These findings offer insights into the pathobiology of psoriasis and provide a resource for future functional studies. CAPSULE SUMMARYA selection of immunopeptides is presented exclusively in lesional skin of HLA-C*06:02+ patients with psoriasis that may represent antigenic drivers of disease.

immunology↗

bioRxiv2026

History-dependent Biases in Perceptual Decisions Depend on NMDA Receptors

Perceptual decisions are governed not only by current sensory input but also by the history of previous stimuli, choices, or outcomes. Such history-dependent biases evolve across multiple timescales ranging from seconds to minutes. Synaptic plasticity is one possible mechanism mediating such effects. The by N-methyl-aspartate (NMDA) glutamate receptor is critical for synaptic plasticity, and indirect evidence points to its role in the generation of history-dependent biases. Here, we pharmacologically blocked NMDA receptors in healthy human participants performing a two-alternative visual decision-making task. Participants choices were biased by the accumulation of fluctuating sensory evidence within each trial as well as the accumulation of across-trial sequences of stimuli, which enabled them to adapt to changing stimulus statistics across blocks. NMDA receptor blockade reduced the task-adaptive across trials, history-dependent biases. In contrast, enhancing GABA-A receptor activity in the same participants increased the transiency of the within-trial evidence accumulation dynamics. Our findings provide direct evidence for the importance of NMDA receptor function in history-dependent biases in the human brain.

neuroscience↗

bioRxiv2025

Lamin B1 Safeguards the B Cell Genome and Shapes Lymphoma Outcome

Lamin B1 is a structural component of the nuclear lamina that participates in diverse cellular processes, including genome regulation and cellular senescence. During adaptive immune responses, B lymphocytes in germinal centres (GCs) undergo clonal expansion and programmed DNA damage at immunoglobulin loci, while simultaneously downregulating Lamin B1. Likewise, Lamin B1 downregulation has been observed in GC-derived lymphomas and myeloid malignancies, yet the functional consequences of Lamin B1 loss during B cell development remain poorly understood. Here, we used in vivo and in vitro B cell models of conditional hypomorphic expression of Lamin B1, which showed elevated DNA damage, altered chromatin accessibility, and disrupted transcriptional profiles. Using sBLISS (in situ labelling and sequencing of double-strand breaks), we identified non-random double-strand break hotspots in both mouse and human GC B cells, depleted of Lamin B1. These breaks are preferentially located near transcriptional start sites (TSSs) and regulatory elements that control translation and mRNA fate, implicating Lamin B1 in protecting fragile regulatory regions. Moreover, low LMNB1 expression correlated with poor clinical outcomes in patients with diffuse large B cell lymphoma (DLBCL). Together, this study reveals a crucial role for Lamin B1 in preserving genomic stability in B cells, underscoring its impact on the pathogenesis of B cell-derived malignancies.

cancer biology↗

bioRxiv2025

A transgenic mouse allows to capture the HLA-C*06:02 immunopeptidome in a model of psoriasis

Psoriasis vulgaris is a T cell-mediated autoimmune skin condition affecting around one in fifty people worldwide. Whilst advanced immunomodulatory therapeutic options have become available in recent years, ongoing disease suppression is still required with no curative treatment available to date. The human leukocyte antigen class I allele HLA-C*06:02 is the main genetic risk determinant of psoriasis. Its function is to present peptide antigens to CD8+ T cells and natural killer cells which in turn elicit and perpetuate the immune response, yet little is known about ligands presented by HLA-C*06:02. To gain an understanding which HLA-C*06:02-restricted peptides are presented by epidermal cell populations and might be initiators of the autoimmune response in psoriasis, we have conducted an in depth immunopeptidomics analysis of HLA-C*06:02+ keratinocyte and melanocyte cell lines. Furthermore, we introduce a HLA-C*06:02 transgenic mouse which, in conjunction with the imiquimod model of psoriasis, allowed us to assess the ex vivo immunopeptidome of HLA-C*06:02 in psoriasiform skin. Overall, we detected 20,812 high confidence HLA-C*06:02 bound peptide ligands. Thus, we present a comprehensive coverage HLA-C in vitro immunopeptidomics dataset and the first HLA-C*06:02 ex vivo dataset of psoriasis-relevant peptide antigens that may inform the development of antigen-specific, novel curative therapeutic approaches in psoriasis.

immunology↗

bioRxiv2025

Neuronal networks in the dorsal hippocampus causally regulate rescue behavior in mice

Prosocial behaviors, such as rescuing individuals in need, are crucial for social cohesion across species. While key brain regions involved in rescue behavior have been identified, the underlying neural mechanisms remain unclear. The hippocampus (HPC), known for its role in memory and spatial navigation, also contributes to emotional and social processing. However, its specific involvement in prosocial behavior is not well understood. Here, we investigate the causal role of the HPC in learning and executing rescue behavior in mice. Using chemogenetics, we show that the dorsal HPC (dHPC), but not the ventral HPC (vHPC), is essential for acquiring rescue behavior. Calcium imaging of the dHPC reveals network consolidation during successful rescues, with distinct synchronized ensembles and activity patterns linked to liberations of an individual in need. These findings establish a novel role for the dHPC in prosocial behavior, providing insights into the neural mechanisms underlying empathy-driven actions.

neuroscience↗

bioRxiv2025

Human Lung Alveolar Model with an Autologous Innate and Adaptive Immune Compartment

Lung-resident immune cells, spanning both innate and adaptive compartments, preserve the integrity of the respiratory barrier, but become pathogenic if dysregulated1. Current in vitro organoid models aim to replicate interactions between the alveolar epithelium and immune cells but have not yet incorporated lung-specific immune cells critical for tissue residency2. Here we address this shortcoming by describing human lung alveolar immuno-organoids (LIO) that contain an autologous tissue-resident lymphoid compartment, primarily composed of tissue-resident memory T cells (TRMs). Additionally, we introduce lung alveolar immuno-organoids with myeloid cells (LIOM), which include both TRMs and a macrophage-rich alveolar myeloid compartment. The resident immune cells formed a stable immune-epithelial system, frequently interacting with the epithelium and promoting a regenerative alveolar transcriptomic profile. To understand how dysregulated inflammation perturbed the respiratory barrier, we simulated T-cell-mediated inflammation in LIOs and LIOMs and used single-cell transcriptomic analyses to uncover the molecular mechanisms driving immune responses. The presence of innate cells induced a shift in T cell identity from cytotoxic to immunosuppressive, reducing epithelial cell killing and inflammation. Based on insights obtained with bulk RNA-seq data from the phase 3 IMpower150 trial, we tested whether LIOM cultures could model clinically-relevant but poorly understood pulmonary side effects caused by immunotherapies such as the checkpoint inhibitor atezolizumab3. We observed a decrease in immunosuppressive T cells and identified gene signatures that matched the transcriptomic profile of patients with drug-induced pneumonitis. Given its effectiveness in capturing outcomes and mechanisms associated with a prevalent pulmonary disease, this system unlocks opportunities for studying a wide range of immune-related pathologies in the lung.

cell biology↗

bioRxiv2024

Catecholamines reduce choice history biases

Theoretical accounts postulate that the catecholaminergic neuromodulator noradrenaline shapes cognition and behavior by reducing the impact of prior expectations on learning, inference, and decision-making. A ubiquitous effect of dynamic priors on perceptual decisions under uncertainty is choice history bias: the tendency to systematically repeat, or alternate, previous choices, even when stimulus categories are presented in a random sequence. Here, we directly test for a causal impact of catecholamines on these priors. We pharmacologically elevated catecholamine levels in human participants through the application of the noradrenaline reuptake inhibitor atomoxetine. We quantified the resulting changes in observers history biases in a visual perceptual decision task. Choice history biases in this task were highly idiosyncratic, tending toward choice repetition or alternation in different individuals. Atomoxetine decreased these biases (toward either repetition or alternation) compared to placebo. Behavioral modeling indicates that this bias reduction was due to a reduced bias in the accumulation of sensory evidence, rather than of the starting point of the accumulation process. Atomoxetine had no significant effect on other behavioral measures tested, including response time and choice accuracy. Atomoxetine and variations of pupil-linked arousal at slower and faster timescales had analogous effects on choice history bias. We conclude that catecholamines reduce the impact of a specific form of prior on perceptual decisions.

neuroscience↗

bioRxiv2024

Dynamic metal coordination controls chemoselectivity in radical halogenases

The activation of inert C(sp3)-H bonds by non-heme Fe enzymes plays a key role in metabolism, epigenetics, and signaling, while providing a powerful biocatalytic platform for the chemical synthesis of molecules with increased sp3 complexity. In this context, FeII/-ketoglutarate-dependent radical halogenases represent a broadly interesting system, as they are uniquely capable of carrying out transfer of a diverse array of bound anions following C-H activation. Here, we provide the first experimental evidence that bifurcation of H-atom abstraction and radical rebound is driven both by the ability of a dynamic metal coordination sphere to reorganize as well as by a second-sphere hydrogen-bond network where only two residues (Asn224 and Ile151) are necessary and sufficient. The identification of this minimal motif provides a paradigm for understanding the evolution of catalytic plasticity in these enzymes and yields new insight into the design principles by which to expand their reaction scope.

biochemistry↗

bioRxiv2024

Metastasis founder cells activate immunosuppression early in human melanoma metastatic colonization

The earliest steps of lethal metastasis in patients are incompletely understood. To dissect them, we prospectively searched for the earliest detectable disseminated cancer cells (DCC) in sentinel lymph node biopsies of 492 stage I-III patients. By visually-controlled, micromanipulator-assisted isolation and single cell transcriptome analysis of these extremely rare DCC, we identified MCSP+ melanoma cells as strong candidates for metastasis founder cells (MFC) in lymph nodes. Based on a median follow-up time of 6 years, their detection was the strongest predictor of systemic metastasis and death upon multivariable analysis. During transition from single cells to metastasis-initiating clusters, melanoma DCC were exposed to CD8 T cell attack, activated the extracellular vesicular exosomal pathway, and expressed the immunomodulatory proteins CD155 and CD276, but rarely PD-L1. CD155 and CD276-positive extracellular vesicles from patient-derived DCC models exhibited an immunosuppressive activity on CD8 T cells. Our data indicate that either direct targeting of MFC employing MCSP or their immune escape mechanisms might be key for cure of early-stage melanoma.

cancer biology↗

bioRxiv2024

SARS-CoV-2 modulates NK cell responses via induction of HLA-E and triggers expansion of adaptive NK cells during acute infection

HLA-E expression plays a central role for modulation of NK cell function by interaction with inhibitory NKG2A and stimulatory NKG2C receptors on canonical and adaptive NK cells, respectively. Here, we demonstrate that infection of human primary lung tissue with SARS-CoV-2 leads to increased HLA-E expression and show that processing of the peptide YLQPRTFLL from the spike protein is primarily responsible for the strong, dose-dependent increase of HLA-E. Targeting the peptide site within the spike protein revealed that a single point mutation was sufficient to abrogate the increase in HLA-E expression. Spike-mediated induction of HLA-E differentially affected NK cell function: whereas degranulation, IFN-{gamma} production, and target cell cytotoxicity were enhanced in NKG2C+ adaptive NK cells, effector functions were inhibited in NKG2A+ canonical NK cells. Analysis of a cohort of COVID-19 patients in the acute phase of infection revealed that adaptive NK cells were induced irrespective of the HCMV status, challenging the paradigm that adaptive NK cells are only generated during HCMV infection. During the first week of hospitalization, patients exhibited a selective increase of early NKG2C+CD57- adaptive NK cells whereas mature NKG2C+CD57+ cells remained unchanged. Further analysis of recovered patients suggested that the adaptive NK cell response is primarily driven by a wave of early adaptive NK cells during acute infection that wanes once the infection is cleared. Together, this study suggests that NK cell responses to SARS-CoV-2 infection are majorly influenced by the balance between canonical and adaptive NK cells via the HLA-E/NKG2A/C axis.

immunology↗

bioRxiv2024

A Simple and Rapid Protocol for the Isolation of Murine Bone Marrow Suitable for the Differentiation of Dendritic Cells

The generation of bone marrow-derived dendritic cells is a widely used approach in immunological research to study antigen processing and presentation as well as T cell activation responses. However, the initial step of isolating the bone marrow can be time-consuming, especially when larger numbers of precursor cells are required. Here, we assessed whether an accelerated bone marrow isolation method using centrifugation is suitable for the differentiation of FMS-like tyrosine kinase 3 ligand-driven dendritic cells. Compared to the conventional flushing method, the centrifugation-based isolation method resulted in a similar bone marrow cell yield on day 0, increased cell numbers by day 8, similar proportions of dendritic cell subsets, and consequently a higher number of type 1 conventional dendritic cells (cDC1) from the culture. Although the primary purpose of the method optimization was to improve experimental efficiency and increase the output of cDC1s, the protocol is also compatible with the differentiation of other dendritic cell subsets such as cDC2 and plasmacytoid dendritic cells, with an improved output cell count and a consistent phenotype.

immunology↗

bioRxiv2023

40 Hz Steady-State Responses in Human Auditory Cortex Depend on GABAergic Neuronal Inhibition

The 40 Hz auditory steady-state response (ASSR), an oscillatory brain response to periodically modulated auditory stimuli, is a promising, non-invasive physiological biomarker for schizophrenia and related neuropsychiatric disorders. The 40 Hz ASSR might be amplified by synaptic interactions in cortical circuits, which are, in turn, disturbed in neuropsychiatric disorders. Here, we tested whether the 40 Hz ASSR in human auditory cortex depends on two key synaptic components of neuronal interactions within cortical circuits: excitation via N-methyl-aspartate glutamate (NMDA) receptors and inhibition via gamma-amino-butyric acid (GABA) receptors. We combined magnetoencephalography (MEG) recordings with placebo-controlled, low-dose pharmacological interventions in the same healthy human participants. All participants exhibited a robust 40 Hz ASSR in auditory cortices, especially in the right hemisphere, under placebo. The GABAA receptor-agonist lorazepam increased the amplitude of the 40 Hz ASSR, while no effect was detectable under the NMDA-blocker memantine. Our findings indicate that the 40 Hz ASSR in auditory cortex involves synaptic (and likely intracortical) inhibition via the GABA-A receptor, thus highlighting its utility as a mechanistic signature of cortical circuit dysfunctions involving GABAergic inhibition. Significance statementThe 40 Hz auditory steady-state response is a candidate non-invasive biomarker for schizophrenia and related neuropsychiatric disorders. Yet, the understanding of the synaptic basis of this neurophysiological signature in humans has remained incomplete. We combined magnetoencephalography (MEG) recordings with placebo-controlled pharmacological interventions in healthy human subjects to test the modulation of the 40 Hz ASSR in auditory cortex by two synaptic components that have been implicated in the generation of neuronal oscillations in cortical microcircuits: glutamate N-methyl-aspartate glutamate (NMDA) receptors and gamma-amino-butyric acid (GABA) -A receptors. Boosting GABAergic transmission, but not blocking NMDA-receptors, increased the amplitude of this ASSR. Thus, GABAergic inhibition modulates 40 Hz steady-state responses in auditory cortex.

neuroscience↗

bioRxiv2023

REM-like Oscillatory Theta Activity Predicts a Reduction in the Recuperative Value of Natural Human Sleep

Here, using data from two independent studies, we examine whether all of sleep is restorative or paradoxically whether some sleep processes incur a sleep debt that impacts next-day wakefulness. Specifically, we examine whether rapid eye movement (REM) sleep is such a process due to its similarity to wake activity, which is causal for sleep debt. To investigate this, we first develop a novel measure of REM neural activity (REM-like oscillatory theta activity (OTA)), overcoming limitations of current sleep scoring. We find that naturally occurring average REM-like OTA across individuals: 1) is associated with increased neurobehavioral sleep debt; 2) explains 25-38% (p [≤] 0.001) of sleep debt differences across individuals the following day; 3) occurs throughout sleep to various degrees, contrary to current sleep scoring; and 4) can be measured automatically, without cumbersome manual scoring.

physiology↗

bioRxiv2023

Computational principles of adaptive multisensory combination in the Drosophila larva

Many sensory systems have evolved to optimally combine signals from multiple sensory modalities to improve perception. While theories have been proposed to explain how this process is accomplished through probabilistic inference using large neural populations in vertebrates, how animals with dramatically smaller nervous systems such as the Drosophila melanogaster larva achieve multisensory combination remains elusive. Here, we systematically characterize larval navigation in different configurations of odor and temperature gradients with optogenetically-controlled noise. Using a data-driven agent-based model, we find that larvae adapt to the reliability of individual sensory signals, and in some cases minimize the variance of the combined signal. Besides firmly establishing that probabilistic inference directs natural orientation behaviors in the Drosophila larva, our results indicate that the exact mechanism underlying the combination of sensory information may be modality-dependent. By underscoring that probabilistic inference is inherent to insect nervous systems, our work opens the way for studying its neural implementation.

neuroscience↗

bioRxiv2022

Adaptive biasing of action-selective cortical build-upactivity by choice history

Decisions under uncertainty are often biased by the history of preceding sensory input, behavioral choices, or received outcomes. Behavioral studies of perceptual decisions suggest that such history-dependent biases affect the accumulation of evidence and can be adapted to the correlation structure of the sensory environment. Here, we systematically varied this correlation structure while human participants performed a canonical perceptual choice task. We tracked the trial-by-trial variations of history biases via behavioral modeling and of a neural signature of decision formation via magnetoencephalography (MEG). The history bias was flexibly adapted to the environment and exerted a selective effect on the build-up (not baseline level) of action-selective motor cortical activity during decision formation. This effect added to the impact of the current stimulus. We conclude that the build-up of action plans in human motor cortical circuits is shaped by dynamic prior expectations that result from an adaptive interaction with the environment.

neuroscience↗