Biology subjects

Bauer, S.

Publications and source records attributed to Bauer, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Prospective pan-cancer phosphoproteomics at clinical scale extends therapeutic options in precision oncology

Genomics-guided precision oncology has improved survival in cancer entities with actionable mutations but cannot capture oncogenic signaling that manifests at the protein level. Here, we report a prospective, real-world pan-cancer study profiling proteomes and phosphoproteomes of 1,998 tumor samples from adults and children with rare or advanced cancers enrolled in the German precision oncology programs DKFZ/NCT/DKTK MASTER, CATCH and INFORM and their molecular tumor boards (MTBs). We developed tumor proteome activity status (TOPAS) scores for 46 clinically relevant kinases, an immune activity score capturing antigen presentation and T-cell activation and identified therapeutically targetable cell-surface proteins for 94% of patients. These readouts enhance MTB recommendations by exposing actionable non-genomic kinase activity, refining interpretation of oncogenic genome alterations, and highlighting cell-surface treatment options. Three proof-of-concept analyses indicate clinical utility including kinase activity-stratified pazopanib response in sarcoma, immune activity score-tracked checkpoint-inhibitor outcomes pan-cancer, and a phosphoproteomic biomarker distinguishing EGFR-inhibitor response in chordoma.

cancer biology↗

bioRxiv2026

SMLMFlow: Improving Structural Resolution in Single Molecule Localization Microscopy with Flow Matching

While Single Molecule Localization Microscopy (SMLM) aims to generate precise coordinates of molecular targets in cells, the resulting point clouds are inherently blurred by additive noise sources across the experimental, imaging, and processing workflow. This blurring often limits SMLMs ability to accurately quantify complex assembled structures required to address biological issues, despite reported localization precision down to a couple of nanometers. Here, we present SMLMFlow, a machine learning framework for improving structural resolution in SMLM datasets that combines a graph neural network and a hierarchical transformer with flow matching. We show that SMLMFlow improves structural resolution and downstream quantification across different structures, including filaments and protein nano-clusters, and generalizes to new unseen photophysics models.

bioinformatics↗

bioRxiv2026

DeepDiffusion: a Physics-Informed Neural Network for Heterogeneous Facilitated 1D Diffusion

Single-molecule fluorescence microscopy combined with optical tweezers has enabled the direct observation of diffusing proteins on tethered DNA. These and complementary techniques reveal facilitated one-dimensional diffusion as a common functional mechanism for numerous DNA-binding proteins, with a wide range of heterogeneous diffusive behaviours arising from different DNA-binding modes. However, detailed investigations have been limited by the lack of methods to detect such heterogeneous diffusion. We have developed DeepDiffusion, a physics-informed neural network model for estimating the instantaneous diffusion at each point along a single-molecule trajectory. We show, using synthetic trajectories, that DeepDiffusion can accurately detect subtle changes in diffusion even when challenged with large underlying errors. DeepDiffusion can recapitulate previously characterised heterogeneity in experimental data and reveal mechanistic details of facilitated diffusion that are inaccessible to current methods. We expect DeepDiffusion to become a powerful tool for single-molecule researchers, allowing them to investigate the diffusion of their proteins of interest in unprecedented detail.

biophysics↗

bioRxiv2026

Alternative lengthening of telomeres stratifies complex karyotype sarcomas into distinct genomic and transcriptomic states

Complex karyotype sarcomas (CKS) are heterogeneous mesenchymal malignancies that typically lack recurrent actionable oncogenic drivers and remain therapeutically challenging. Loss of ATRX is a recurrent feature of CKS and defines a particularly high-risk subgroup. ATRX loss is also associated with activation of the alternative lengthening of telomeres (ALT) pathway, and ALT-positive sarcomas have been linked to poor clinical outcomes. However, the molecular underpinnings underlying ALT-status-dependent differences in CKS, as well as the therapeutic vulnerabilities associated with ALT, remain poorly defined. By integrating C-circle-based ALT detection across 776 sarcoma samples with multi-modal sequencing of five CKS subtypes, we find that ALT activity is associated with enriched hallmarks of genomic instability. ALT-positive transcriptomes are dominated by a coordinated DNA damage response and mitotic program, in contrast to oncogenic signaling pathways that drive TERT activation in ALT-negative tumors. Long-read sequencing reveals telomere repeat clusters and telomere-mediated healing at structural breakpoints in ALT-positive tumors. These events also occur on extrachromosomal DNA (ecDNA), linking ALT activity to ecDNA biology. Together, our findings position ALT status as an important stratifying feature of CKS and identify ALT-associated transcriptional programs as potential therapeutic targets.

cancer biology↗

bioRxiv2026

Quantifying Treatment Resistance in Mixtures of Gastrointestinal Stromal Tumor Cells with BARMIX

Targeted therapies in gastrointestinal stromal tumors (GIST) often fail due to heterogeneous resistance mutations arising across metastatic sites. Efficient, rational design of mutation-specific therapies requires the ability to quantify treatment resistance across many genotypes in parallel. Here, we present BARcode MIXture analysis (BARMIX), a platform combining multiplexed experiments with DNA-barcoded cancer cell mixtures in vitro and in vivo, and a probabilistic framework for quantitative assessment of genotype-specific treatment resistance. BARMIX efficiently and accurately recapitulated known clinical resistance patterns in GIST and matched resistance measurements from individual cell lines in vitro and in vivo. This experimental-computational approach provides a scalable and broadly applicable strategy for quantifying treatment responses in complex cell populations, enabling systematic preclinical testing of new drugs and combinations to identify mutation-specific therapeutic options for precision oncology in GIST and beyond.

systems biology↗

bioRxiv2026

A hidden biomass flow - 10,000 tons of insects fly over Switzerland

Flying insects are the most diverse and abundant group of animals using the airspace to travel and spread across regions. Through movements that can span multiple life stages and generations, aerial insect migrations shape the ecosystems where they emerge but also connect ecosystems across sometimes vast distances. Yet even basic data on the abundance of aerial insects is still scarce. Their small sizes and often high-altitude movements make it challenging to describe flyways or measure this transport of biomass within or between regions. We used a remote-sensing approach with vertical looking radars to quantify insect migration across Switzerland. Switzerland harbours complex terrain, with the Alps, Jura mountains, and pre-Alpine lowlands featuring starkly contrasting topography. At three locations within these three main habitats, we recorded a total of 6.6 million medium- to large-sized individual insects during the 8-month study period. Extrapolating this to the whole of Switzerland results in an estimated number of 21 billion insects. Adding the presumed additional proportion of small insects, this translates to a rough estimate of 10,000 tons of insect biomass across Switzerland per year. Our results show that insect migration remains substantial even in topographically complex landscapes and seems strikingly synchronized over a relatively wide area. Mountain passes in particular act as key conduits for insects traversing the Alps, with many crossings occurring at high altitudes and with air temperatures below 10 {degrees}C. Nevertheless, our study is only a first step unraveling insect movements across space and time and their large-scale synchronicity. Significance StatementInsect abundance is of great importance for most terrestrial food chains, including human agriculture. While ground-based studies have elucidated many relationships within trophic systems, very little is known about the effects of their large-scale movements through the airspace. We show how insect movements, dispersal and migration, are spatially and temporarily correlated across a wide area of complex terrain and provide a rough estimate of the insect biomass involved. Temperature is a crucial factor in the extent of activity; however, our results show that low temperatures (<10{degrees}C) do not prevent massive insect migrations when crossing mountain ranges. Our results demonstrate the large, coordinated flow of insect biomass across the landscape, which needs to be studied in much more detail to better understand the spread of pests and beneficial insects, their impact on local communities, and the transmission of diseases.

ecology↗

bioRxiv2026

Inositol hexakisphosphate Functions as a Cofactor and Modulator of ADAR1 Activity

Adenosine-to-inosine (A-to-I) RNA editing by ADAR1 is a key post-transcriptional modification, and mutations in ADAR1 lead to Aicardi-Goutieres syndrome (AGS), an autoimmune disorder. Despite its biological and clinical relevance, the regulation of ADAR1 activity remains incompletely understood. Using a combination of biochemical approaches, inositol-pentakisphosphate 2-kinase (IPPK)-knockout cells, molecular dynamics simulations, and a cell-permeable inositol hexakisphosphate (IP6) prodrug (Pro-IP6), we demonstrate that IP6 depletion drastically reduces global RNA editing, while supplementation with Pro-IP6 restores and even enhances editing levels. Furthermore, we identify the C6-phosphate of IP6 as a critical determinant of ADAR1 catalytic efficiency, functioning within a hydrogen-bonding network that indirectly coordinates a Zn{superscript 2}-ion. Finally, we show that the AGS-associated ADAR1 mutation N907S impairs RNA editing activity, most likely by altering the hydrogen-bond interaction network linking IP6 to the ADAR1 catalytic center. Together, these findings identify IP6 as an essential cofactor and regulator of ADAR1 activity and highlight cofactor availability and interaction networks as strategies for therapeutically modulating RNA editing.

molecular biology↗

bioRxiv2025

Hippocampal network activity changes during early epileptogenesis predict subsequent epilepsy

The circuit mechanisms underlying focal epileptogenesis are, despite of decades of epilepsy research, still incompletely understood. In this study, we aimed to characterize the changes in hippocampal network activity induced by a potentially epileptogenic insult. In rats, long-lasting electrical perforant pathway stimulation leads in a high percentage of animals to the development of temporal lobe epilepsy. However, a subset of animals remains resilient against the stimulation. We monitored alterations of neuronal activity by chronically recording the local field potential (LFP) from the hippocampal dentate gyrus before, during and after the potentially epileptogenic insult. Intriguingly, epilepsy animals identified by subsequent spontaneous epileptic seizures were characterized by a transient increase in the aperiodic exponent suggesting a shift towards a reduced local excitation-to-inhibition (E/I) ratio during the first days after the perforant path stimulation. Furthermore, these animals developed a strong impairment of theta oscillation prevalence and regularity during early epileptogenesis. In contrast, resilient non-epilepsy animals without spontaneous seizures neither showed this modulation in E/I ratio nor a corruption of hippocampal theta activity. In fact, the increase in the aperiodic exponent on the first day after completion of the electrical stimulation paradigm could predict epileptogenesis with very high fidelity (AUC 0.92) and correlated significantly with later seizure rate. This finding opens the opportunity to dissect mechanisms of epileptogenesis and to test the effectiveness of anti-epileptogenesis treatment in very early disease stages by allowing identification of individuals at high risk. Furthermore, it might offer a potential explanation for the frequently observed failure of anti-epileptogenesis drugs boosting GABAergic inhibition.

neuroscience↗

bioRxiv2025

Murine Toll-like receptor 8 is a nucleic acid multi-sensor detecting 2',3'-cyclic monophosphate guanosine as well as combinations of ribo-, deoxy-, cyclic nucleotides, and nucleosides

Toll-like receptor 8 (TLR8) in humans senses RNA degradation products and elicits an inflammatory immune response. In contrast, the ligand specificity and function of its murine counterpart mTLR8, long considered non-functional, remain poorly defined. Here, we established an agonist combination model of poly-deoxythymidine (poly-dT) DNA and TLR7/8 binding site 1 agonists such as uridine or the benzazepine compound TL8-506, which activates mTLR8, while suppressing mTLR7 signaling. Extensive agonist analysis based on this model revealed that 2,3-cyclic guanosine monophosphate (2,3-cGMP) serves as a natural ligand for mTLR8, suggesting functionality of its binding site 1 without engagement of site 2. In addition, 2,3-cyclic uridine monophosphate, bacterial single-stranded (ss) DNA, double-stranded (ds) DNA fragments, microRNAs, ssRNA derived from HIV1, SARS-CoV-2, or bacterial sources all potentiate mTLR8 sensing of site 1 agonists. All these stimuli induce distinct inflammatory responses from murine macrophages and microglia via TLR8. In vivo, intrathecal administration of TL8-506 and poly-dT led to microglial accumulation and neuronal injury in the murine cerebral cortex through TLR8, highlighting the potential neuropathological consequences of mTLR8 activation. Taken together, our study defines mTLR8 as a nucleic acid sensor detecting 2,3-cGMP as well as combinations of ssDNA, dsDNA, ssRNA fragments, 2,3-cyclic nucleotide monophosphates, and nucleosides, with implications for host defense and neuroinflammation.

immunology↗

bioRxiv2025

Dual-color expansion microscopy of membrane proteins using bioorthogonal labelling

Site-specific incorporation of non-canonical amino acids (ncAAs) combined with bioorthogonal click chemistry provides a powerful tool for fluorescent protein labeling, overcoming the linkage error inherent to antibody-based probes. In this study, we present the development of dual-color super-resolution imaging utilizing ncAA labeling together with expansion microscopy (ExM). After optimizing the labeling procedures and fluorophore selection, we visualize and resolve the nanoscale distribution of Na,K-ATPase 1 and {beta}1 subunits in expanded HEK 293T cells. We validate our approach by super-resolution STED imaging of ncAA labeled {beta}1 subunit in unexpanded cells. This work establishes a robust framework for multiplexed, high-resolution imaging and suggests that the combination of ncAA labeling with ExM has the potential to push biological imaging toward [A]ngstrom-level resolution.

biophysics↗

bioRxiv2025

6S RNA facilitates bacterial virulence and adaptation at the epithelial barrier

Enteropathogenic bacteria must adapt dynamically to the complex gastrointestinal environment to successfully colonize host tissue and evade immune defenses. Using Yersinia pseudotuberculosis as a model, we performed in vivo spatial transcriptomics to investigate bacterial gene expression as it translocates from cecal lumen to associated lymphoid tissue in the mouse intestine. By optimizing bacterial RNA enrichment, we achieved near-complete transcriptome coverage and identified compartment-specific transcriptional profiles. Bacteria in lymphoid tissue exhibited elevated expression of virulence-associated type III secretion system (T3SS) genes and markers of increased replication, alongside a higher plasmid copy number. Oxygen availability emerged as an environmental cue for T3SS induction. Importantly, we discovered a role for the non-coding 6S RNA in accelerating virulence gene expression. Tissue-localized bacteria had significantly upregulated 6S RNA levels, and deletion of the ssrS gene encoding 6S RNA impaired T3SS gene expression and effector secretion. Further, spatial analyses of bacterial gene expression in foci of infected lymphoid tissue revealed heterogeneous expression patterns with significantly elevated expression of T3SS and 6S RNA in bacteria located close to surrounding phagocytes. Together these findings demonstrate that Y. pseudotuberculosis undergoes rapid transcriptional reprogramming upon epithelial barrier crossing coordinated by environmental sensing, where 6S RNA accelerates tissue colonization by promoting efficient expression of T3SS.

microbiology↗

bioRxiv2025

Pattern separation in cerebellar-targeted whisking pre-motor nuclei

The cerebellar output can trigger whisker movement through indirect projections that pass via several brainstem pre-motor nuclei before reaching the facial nucleus, which directly controls whisker movements in rodents. Although the central pattern generator function of the intermediate reticular formation has been recently clarified, the roles of the other whisker pre-motor nuclei remain unclear. Here, we set out to compare the whisker movement kinematics of the main pre-motor whisker nuclei connecting the cerebellum and the facial nucleus. We optogenetically stimulated neurons located in the cerebellar cortex Purkinje cells (PCs), the cerebellar nuclei (CN), the red nucleus (RN), the superior colliculus (SC), the spinal trigeminal nucleus (SV), and the reticular formation (RF); in head-fixed awake mice while monitoring the bilateral whisker movement. Here, we find that optogenetic stimulation of the RN, SC, and SV resulted in a predominant midpoint change, whereas optogenetic stimulation of the PCs, CN, and RF resulted in faster whisker movements. In addition, the excitation of PCs, the RN, and SC resulted in symmetric bilateral whisking. In contrast, the excitation of CN, the RF, and SV resulted in initial asymmetric movement, followed by a more dominantly symmetrical bilateral whisking. Our results suggest that several pre-motor nuclei receiving cerebellar output modulate different aspects of whisking, suggesting pattern separation takes place in the brain-wide network downstream of the cerebellum.

neuroscience↗

bioRxiv2025

AI4CellFate: Interpretable Early Cell Fate Prediction with Generative AI

Live-cell imaging provides a unique insight into complex cellular processes including single cell fate, but remains limited by both low-throughput and the lack of generalisable analytics for the multidimensional datasets it produces. This work introduces AI4CellFate, an interpretable and data-driven machine learning framework for predicting cell fate from microscopy timelapses, applied here to cancer therapy. By integrating generative AI and contrastive learning, AI4CellFate enables early fate prediction as well as visualisation of biologically relevant features, with limited annotation.

bioinformatics↗

bioRxiv2025

Proteins are a source of glycans found in preparations of glycoRNA

Recent discoveries show that RNA can be modified with sialylated glycans (termed glycoRNA), thus broadening our understanding of cellular glycosylation beyond traditional proteins and lipids. However, the pathway of RNA-glycosylation and its biological function remain elusive. Following the original glycoRNA isolation protocol, we also detect labelled glycans in small RNA preparations. However, glycosylated molecules showed resistance to treatment with RNase A/T1 but were sensitive to proteinase K digestion under denaturing conditions. Using liquid chromatography-mass spectrometry (LC-MS) based proteomics, we detect various proteins that co-purify with small but not large RNA preparations isolated from human or murine cells, including the glycosylated membrane protein LAMP1. Importantly, we further demonstrate that recombinant soluble LAMP1 can be purified following the glycoRNA isolation method. These findings suggest that glycoproteins co-purify with RNA using current glycoRNA purification protocols, thus representing a considerable source of glycans in samples of glycoRNA.

molecular biology↗

bioRxiv2025

Precision in Spinal Cord Injury Research: A Novel Electromagnetic Impactor for a Consistent Porcine Model

PurposeReplicating spinal cord injury (SCI) in large animals is necessary for evaluating therapeutics for potential human translation, yet there is currently no commercial, standardized device for inducing SCI. We present the fabrication and testing of a custom impactor device for producing repeatable contusion SCI in porcine models. MethodsWe first designed and built the device. Mechanical modeling was subsequently utilized to calibrate our benchtop testing setup. Benchtop verification was performed to measure impact force post calibration. We then used the device to generate a contusion SCI model in 2 pigs and the results were compared to an uninjured pig. Intraoperative ultrasound was used to visualize a hematoma in the injured spinal cord. Hematoxylin-eosin (H&E) and Massons trichrome staining were used to confirm injury presence on ex vivo spinal cord samples. ResultsMechanical modeling forces matched benchtop impact forces within 1.4 N, indicating successful calibration of the testing setup. Our device demonstrated repeatability and the potential for modulating injury severity on the benchtop. Impactor forces were demonstrated across a range from 12.8 to 67.6 N, with variability remaining within 0.2 to 0.7 N standard deviation. The device induced two contusion injuries of different severity in vivo, confirmed by intraoperative ultrasound imaging and post-excision histology of the spinal cord. ConclusionOur impactor device is a major advancement towards producing repeatable and titratable contusions in large animal SCI models.

bioengineering↗

bioRxiv2025

Virus-against-virus dominant-negative interference strategy targeting a viral CC chemokine prevents cytomegalovirus-related neurodevelopmental pathogenesis

BackgroundCongenital cytomegalovirus (CMV) infections are one leading cause of human neurodevelopmental disorders. Increasing evidence for the pathogenic involvement of brain immune alterations was obtained in the recent years. Host and virus-encoded chemokines might play important roles in CMV-related neuropathogenesis by regulating leukocyte trafficking and microglia recruitment in the CMV-infected brains, and by interfering with key neurodevelopmental steps. In a rat model of CMV infection of the fetal brain in utero that leads to detrimental neurologic and other severe phenotypes postnatally, we reported on the early alteration of microglia and on the infiltration of the infected brains by lymphoid and myeloid cells. Particularly, expression of the r129 gene encoding the viral chemokine RCK3 was detected as early as 24h post-infection; together with the previously reported chemotaxis properties exerted by RCK3 on lymphocytes and on macrophages in vitro, this suggested that RCK3 might be involved in the brain immune cell alterations seen in the CMV-infected developing brains, and in the related neuropathogenesis. MethodsInfection of the rat fetal brain was done by intracerebroventricular injections in utero of either rat CMV encoding wild-type (wt) RCK3 (RCMV-wt), or a mutant CMV counterpart encoding RCK3 with a deletion in its chemokine domain (RCMV-r129{Delta}NT). As RCMV-r129{Delta}NT had shown dominant-negative effects on the chemotaxis properties of RCK3 in vitro, simultaneous and successive co-infection rescue assays were also performed. The detrimental postnatal phenotypes in vivo and the epileptiform activity ex vivo usually detected after infection of the rat developing brain with RCMV-wt were monitored in the RCMV-r129{Delta}NT condition and in co-infection assays. ResultsIn sharp contrast with RCMV-wt whose infection of the fetal brain led to decreased postnatal survival, impaired sensorimotor development, hindlimb hyperextension and epileptic seizures in neonatal pups, RCMV-r129{Delta}NT infection was not associated with any severe postnatal phenotype in vivo. Consistently, the epileptiform activity recorded in most neocortical slices from RCMV-wt-infected pups was not detected in any slice from RCMV-r129{Delta}NT-infected pups. Simultaneous co-infection assays led to dramatic prevention against the postnatal phenotypes in vivo and the altered network activity ex vivo, revealing a dose-dependent rescuing effect exerted by RCMV-r129{Delta}NT on RCMV-wt. Importantly, successful rescue was also obtained when the mutant RCMV-r129{Delta}NT was inoculated in the fetal brains either before or after infection with RCMV-wt. SignificanceOur data demonstrate the crucial neuropathogenic role of RCK3 CMV chemokine in vivo. The dramatic success and apparent safety of the dominant-negative RCK3 rescue assays in vivo provide a proof-of-principle for the beneficial use of a virus-against-virus approach against CMV-related pathogenesis.

neuroscience↗

bioRxiv2024

Longitudinal blood microsampling and proteome monitoring facilitate timely intervention in experimental type 1 diabetes

Symptoms of immune-mediated diseases (IMIDs) typically appear after irreversible tissue damage, making early interventions based on pre-symptomatic indicators crucial. Current efforts to identify molecular markers of early disease lack the resolution, convenience and cost efficiency required to prevent irreversible tissue damage. Analyzing frequently self-collected samples, such as dried blood spots (DBS), could enable the earlier detection of diseases, identify disease-predictive markers and facilitate tailored interventions. To test this, we regularly microsampled a mouse model infected with a type 1-diabetes (T1D)-associated virus. This longitudinal DBS sample collection was analyzed for 92 circulating proteins, revealing transient molecular changes in virus-infected animals that would have been missed with less frequent sampling. Machine learning predicted infection status after day 2 post-infection with >90% accuracy, enabling well-timed treatment of virus-infected animals and diabetes prevention. Our study demonstrates the utility of frequent blood microsampling to monitor disease during the pre-symptomatic phase, allowing for timely interventions. TeaserFrequent blood microsampling detects early biomarkers, enabling timely intervention in immune-mediated diseases

systems biology↗

bioRxiv2024

Decomposition of L-glutamine and accumulation of ammonium in cell culture media inhibit infectivity of influenza viruses

Cationic lysosomotropic molecules such as ammonium salts and chloroquine inhibit influenza A virus (IAV) infection in cell culture by counteracting endosomal acidification and hampering viral-endosomal fusion. Here, we studied the effects of storage of L-glutamine-supplemented cell culture media on accumulation of ammonium and inhibition of IAV infection. The storage-related inhibitory effect was observed in the case of DMEM and OptiMEM media, but not RPMI medium, and was more pronounced for the IAV with pH-stable hemagglutinin. Our results highlight the importance to consider potential presence of virus-inhibiting lysosomotropic agents and/or their production in culture media with negative effect on influenza virus infection.

microbiology↗