Biology subjects

Bauer, B.

Publications and source records attributed to Bauer, B..

10 recordsLinked to original sources

bioRxiv2026

Glioblastoma-derived extracellular vesicles released after radiation promote cognitive impairment through NFκB-mediated microglial activation

Glioblastoma (GBM) is the most aggressive primary brain tumor in adults. Cognitive impairment is a common sequela in glioblastoma survivors, yet the underlying mechanisms remain poorly understood. Extracellular vesicles (EVs) derived from glioblastoma are established mediators of intercellular signaling within the tumor microenvironment. Here, we investigated whether GBM-derived EVs released after radiation treatment (RT-EVs) regulate cognitive function. Treatment with RT-EVs was associated with cognitive deficits and neuroinflammatory responses in vivo. In vitro, RT-EVs activated the NF{kappa}B pathway and induced the release of neurotoxic H2O2. Importantly, NF{kappa}B p50 knockdown abolished the H2O2 release previously triggered by RT-EVs, demonstrating mechanistic dependence on NF{kappa}B signaling. Collectively, these findings identify GBM-derived RT-EVs as critical mediators of cognitive impairment through NF{kappa}B-dependent redox imbalance. EV-driven redox dysregulation may therefore represent a therapeutic target to mitigate GBM-associated cognitive dysfunction. Highlights- Radiation induces the release of glioblastoma-derived EVs that are biologically different from those released under non-irradiated conditions. - EVs released from glioblastoma after radiation are sufficient to impair cognition - EVs from irradiated glioblastoma can activate microglia via NF{kappa}B and induce production of neurotoxic H2O2 Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=52 SRC="FIGDIR/small/730969v1_ufig1.gif" ALT="Figure 1"> View larger version (11K): org.highwire.dtl.DTLVardef@e57bcborg.highwire.dtl.DTLVardef@228862org.highwire.dtl.DTLVardef@127dd13org.highwire.dtl.DTLVardef@232ddd_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2026

A chimeric, half-life extended lysin with a unique mode of action

Anti-staphylococcal lytic agents, such as lysostaphin (LSN), a glycyl-glycyl (Gly-Gly) peptidase, have long been considered for the management of chronic and complicated bacterial infections typically resistant to conventional antibiotics, but their use is restricted by poor pharmacokinetic properties. We generated half-life extended lysostaphin constructs by fusing the lysin - either alone or chimerized with an additional enzymatic cysteine, histidine-dependent amidohydrolases/peptidase (CHAP) domain - to the human IgG1 Fc fragment. The Fc-CHAP-LSN constructs retain high potency against Staphylococcus aureus and coagulase negative staphylococcal strains in vitro and are efficacious in S. aureus ex vivo biofilm models and in vivo sepsis models. A detailed investigation of the Fc-CHAP-LSN mode of action revealed that upon binding to the bacterial cell, but not in solution, LSN mediates its own release by cleaving the Gly-Gly CHAP-LSN linker. The bactericidal activity of Fc-CHAP-LSN is driven by the LSN-catalyzed and target cell-dependent release of free LSN. The half-life extended lysin acts as a pro-drug, unveiling a novel mechanism of targeted release and an alternative approach to half-life extension.

bioengineering↗

bioRxiv2026

Multi-dimensional optimization of a lysin towards a ribolysin against life-threatening S. aureus infections: Fc-LysM-CHAP and its strong synergy with standard of care antibiotics

Bacterial lysins are promising novel antimicrobials but are limited by poor pharmacokinetics and challenging manufacturability. We developed a lysin discovery platform tailored for lysin delivery via mRNA: staphylococcal LysM-CHAP (cysteine, histidine-dependent amidohydrolases/peptidase) autolysin was selected and its serum half-life extended via Immunoglobulin G1-Fc-fusion. The Fc-induced drop in lysin potency was rescued by the concerted optimization of linkers, binding kinetics and catalytic activity, using a combination of rational and AI-guided approaches. The engineered Fc-LysM-CHAP was active against planktonic bacteria (minimum inhibitory concentration of 1 - 2 {micro}g/mL) and simulated endocardial vegetations and synergized strongly (Fractional eradication concentration index FECI = 0.06) with cell wall active antibiotics in vitro. In mouse models of Staphylococcus aureus sepsis, the recombinant Fc-LysM-CHAP - antibiotic combination was superior to single agent treatments and mRNA-delivered Fc-LysM-CHAP showed single agent activity at a mRNA-lipid nanoparticle dose as low as 0.2 mg/kg.

microbiology↗

bioRxiv2026

TAX1BP1 recruitment reactivates autophagy of Tau aggregates through ULK1 and TBK1

The accumulation of protein aggregates is a hallmark of numerous neurodegenerative diseases. These aggregates frequently accumulate ubiquitin and the early autophagy factor p62 yet fail to undergo degradation. Whether such aggregates are principally susceptible to autophagic clearance is unknown. Here, we show that Tau aggregates associated with Alzheimers disease (AD) and other tauopathies persist due to defective autophagy initiation. This autophagy resistance correlates with a block in the recruitment of the autophagy receptor TAX1BP1 and the downstream machinery to the aggregates. Artificial targeting of TAX1BP1 to Tau aggregates restores their autophagic turnover. Mechanistically, TAX1BP1 co-activates ULK1- and TBK1-dependent signaling, thereby enabling aggregate sequestration by autophagosomes. We identify exclusion of the TAX1BP1 receptor as a breaking point at which pathological Tau aggregates evade autophagy. Furthermore, we show that Tau aggregates can be rendered susceptible to autophagy, revealing therapeutic strategies for their clearance in disease.

cell biology↗

bioRxiv2024

Mechanism of TAX1BP1 recruitment in aggrephagy to switch from cargo collection to sequestration

Autophagy mediates the degradation of harmful material within lysosomes. In aggrephagy, the pathway mediating the degradation of aggregated, ubiquitinated proteins, this cargo material is collected in larger condensates prior to its sequestration by autophagosomes. In this process, SQSTM1/p62 and NBR1 drive cargo condensation, while TAX1BP1, which binds to NBR1 recruits the autophagy machinery to facilitate autophagosome biogenesis at the condensates. The mechanistic basis for the TAX1BP1 mediated switch from cargo collection to its sequestration is unclear. Here we show that TAX1BP1 is not a constitutive component of the condensates. Its recruitment correlates with the induction of autophagosome biogenesis. TAX1BP1 is sufficient to recruit the TBK1 kinase via the SINTBAD adapter. We define the NBR1 - TAX1BP1 binding site, which is adjacent to the GABARAP/LC3 interaction site and demonstrate that the recruitment of TAX1BP1 to cargo mimetics can be enhanced by an increased ubiquitin load. Our study suggests that autophagosome biogenesis is initiated once sufficient cargo is collected in the condensates.

cell biology↗

bioRxiv2024

Cohesin supercoils DNA during loop extrusion

Cohesin extrudes genomic DNA into loops that promote chromatin assembly, gene regulation and recombination. Here we show that cohesin introduces negative supercoils into extruded DNA. Supercoiling requires engagement of cohesins ATPase heads, DNA clamping by these heads, and a DNA binding site on cohesins hinge, indicating that cohesin supercoils DNA when constraining it between the hinge and the clamp. Our results suggest that DNA extrusion stops once cohesin reaches its stall torque during supercoiling, and a cohesin mutant predicted to stall at lower torque forms shorter loops in cells. These results indicate that supercoiling is an integral part of the loop extrusion mechanism and that cohesin controls genome architecture not only by looping DNA but also by supercoiling it.

biochemistry↗

bioRxiv2022

Somatic hypermutation spectra are independent of the local transcriptional and epigenetic landscape

Somatic hypermutation (SHM) of immunoglobulin variable (V) regions modulates antibody-antigen affinity is initiated by activation-induced cytidine deaminase (AID) on single-stranded DNA (ssDNA). Transcription is essential for SHM and AID target genes harbor activating chromatin marks and RNA polymerase II (Pol II) stalling, leading to the model that these features favor higher rates of mutagenesis. However, whether such relationships exist within V regions is undetermined. Here, we directly compared SHM and nascent transcription across four V regions and 275 non-immunoglobulin SHM targets at single-nucleotide resolution using precision run-on sequencing (PRO-seq). Although locales of Pol II enrichment and zones of Pol II stalling were detected within V regions, their correlation with SHM was not statistically significant. Moreover, SHM was robust against major reductions of activating epigenetic marks and transcription. This data suggests that SHM patterns and spectra are established independently of specific local nascent transcriptional features.

immunology↗

bioRxiv2021

SMC complexes can traverse physical roadblocks bigger than their ring size

The ring-shaped structural-maintenance-of-chromosomes (SMC) complexes condensin and cohesin extrude loops of DNA as a key motif in chromosome organization. It remains, how ever, unclear how these SMC motor proteins can extrude DNA loops in chromatin that is bound with proteins. Here, using in vitro single-molecule visualization, we show that nucleosomes, RNA polymerase, and dCas9 pose virtually no barrier to DNA loop extrusion by yeast condensin. Strikingly, we find that even DNA-bound nanoparticles as large as 200 nm, much bigger than the SMC ring size, can be translocated into DNA loops during condensin-driven extrusion. Similarly, human cohesin can pass 200 nm particles during loop extrusion, which even occurs for a single-chain version of cohesin in which the ring-forming subunits are covalently linked and cannot open up to entrap DNA. These findings disqualify all common loop-extrusion models where DNA passes through the SMC rings (pseudo)topologically, and instead point to a nontopological mechanism for DNA loop extrusion. One-sentence summaryHuge DNA-bound roadblocks can be incorporated into SMC-extruded DNA loops, pointing to a nontopological mechanism for loop extrusion.

biophysics↗

bioRxiv2021

Structures of active melanocortin-4 receptor--Gs-protein complexes with NDP-α-MSH and setmelanotide

The melanocortin-4 receptor (MC4R), a hypothalamic master regulator of energy homeostasis and appetite, is a G-protein coupled receptor and a prime target for the treatment of obesity. Here, we present cryo-electron microscopy structures of MC4R- Gs-protein complexes with two recently FDA-approved drugs, the peptide agonists NDP--MSH and setmelanotide, with 2.9 [A] and 2.6 [A] resolution. Together with signaling data, the complex structures reveal the agonist-induced origin of transmembrane helix (TM) 6 regulated receptor activation. In both structures, different ligand binding modes of NDP--MSH, a high-affinity variant of the endogenous agonist, and setmelanotide, an anti-obesity drug with biased signaling, underline the key role of TM3 for ligand-specific interactions and of calcium ion as a ligand-adaptable cofactor. The agonist-TM3 interplay subsequently impacts the receptor- Gs-protein interfaces, mainly at intracellular loop 2. These structures reveal mechanistic details of MC4R activation or inhibition and provide important insights into receptor selectivity that will facilitate the development of tailored anti-obesity drugs.

biochemistry↗

bioRxiv2019

Quantifying the heterogeneity of macromolecular machines by mass photometry

Sample purity is central to in vitro studies of protein function and regulation, as well as to the efficiency and success of structural studies requiring crystallization or computational alignment of individual molecules. Here, we show that mass photometry (MP) accurately reports on sample heterogeneity using minimal volumes with molecular resolution within minutes. We benchmark our approach by negative stain electron microscopy (nsEM), including workflows involving chemical crosslinking and multi-step purification of a multi-subunit ubiquitin ligase. When applied to proteasome stability, we detect and quantify assemblies invisible to nsEM. Our results illustrate the unique advantages of MP for rapid sample characterization, prioritization and optimization.

biophysics↗