Biology subjects

Becker, S.

Publications and source records attributed to Becker, S..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

LOX inhibition disrupts a collagen-integrin-MYC axis as a translatable targeting strategy in invasive lobular carcinoma

Invasive lobular carcinoma (ILC) accounts for 15% of breast cancers yet lacks specific therapy because ILCs are underrepresented in clinical trials and preclinical models are lacking. We established intraductal xenograft models to test whether the clinical pan-lysyl-oxidase PXS-5505, now in phase trials for myelofibrosis can exploit the collagen-rich matrix dependency created by CDH1 loss. PXS-5505 remodels fibrillar collagen, and halts tumor expansion and metastatic seeding across ER+ and triple negative models without systemic toxicity. Genome-wide CRISPR screens reveal ITGAV and ITGB5 as synthetic lethal partners of CDH1 and LOX inhibition downregulates their expression together with MYC, NF-{kappa}B, and AP-1 transcriptional programmes. Collagen fibre density/alignment, and MYC/AP-1 gene signatures serve as pharmacodynamic readouts of drug activity. These data uncover a tractable ECM-integrin-MYC axis in ILC and nominate PXS-5505, alone or with endocrine therapy, for window of opportunity trials in this understudied breast cancer subtype. One Sentence SummaryTargeting matrix remodelling in ILC inhibits ILC progression and alters multiple molecular endpoints, providing a translatable therapeutic strategy for this understudied subtype that requires better treatments.

cancer biology↗

bioRxiv2025

Side-by-side evaluation of two mouse models for Crimean-Congo Hemorrhagic Fever Virus infection.

Crimean-Congo hemorrhagic fever virus (CCHFV) is the causative agent of a severe hemorrhagic fever in humans, associated with case fatality rates ranging from 10 to 40%. Due to the lack of approved vaccines or specific antiviral treatments, CCHFV is classified as a biosafety level 4 (BSL4) pathogen in most countries and designated a priority pathogen by the World Health Organization (WHO). To facilitate the preclinical assessment of medical countermeasures, we have established two murine models using C57BL/6J IFNAR-/- mice, which lack the IFN/{beta} receptor, infected with the phylogenetically distinct CCHFV strains Afghanistan09-2990 (Afg09) and Kosovo Hoti (Hoti). Infection with both CCHFV strains in IFNAR-/- mice resulted in significant weight loss, with Afg09 infection leading to more severe clinical disease. Quantitative analysis of viral RNA revealed widespread viral dissemination across multiple organs in both models. Detection of infectious virus varied by organ and strain. These results confirm and extend previous findings, providing a deeper understanding of CCHFV strain-specific pathogenesis in IFNAR-/- mice. Thereby, these mouse models represent valuable tools for the evaluation of antiviral therapeutics and vaccine candidates, enabling the investigation of cross-lineage protection against genetically diverse CCHFV isolates.

microbiology↗

bioRxiv2025

Hierarchically ordered multi-timescale structural dynamics of the intrinsically disordered p53 transactivation domain

Intrinsically disordered proteins (IDPs) exhibit pronounced structural dynamics, which is crucial for their functional versatility. Yet their dynamics slower than nanoseconds remain largely elusive. We combined high-power relaxation dispersion nuclear magnetic resonance spectroscopy with molecular dynamics simulations to characterize these kinetics and the underlying structural interconversions of a prototypical IDP, the N-terminal transactivation domain of the tumor suppressor p53 (p53-TAD). We find a complex hierarchy of structural dynamics on timescales covering over seven orders of magnitude, ranging from fast nanoseconds backbone re-orientations, via sub-microsecond helix-formation dynamics involving many structural sub-states and transition times, to transient tertiary structure formation slower than 25 microseconds. These rich structural dynamics of p53-TAD, and likely those of other IDPs, parallel the timescale hierarchy of the conformational dynamics of folded proteins. One-Sentence summaryA hierarchical energy landscape governs kinetics and structural dynamics of the disordered p53 transactivation domain.

biophysics↗

bioRxiv2025

Accumulation of SA-βGal High Cells in Human Naive T Cell Compartments Reveals a Stress-Adapted, Senescent-Like State

Aging is associated with a decline in immune function termed immunosenescence, characterized by accumulation of senescent-like immune cells and chronic inflammation, known as inflammaging. While senescence-associated {beta}-galactosidase (SA-{beta}Gal) activity is a well-established senescence marker, its functional significance and the precise cellular subsets affected within the T cell compartment remain unclear. Here, we identify and characterize a previously unrecognized subset of naive CD4 and CD8 T cells displaying high SA-{beta}Gal activity that significantly increases with age. Despite exhibiting hallmark features of senescence such as DNA damage, nuclear envelope disruption, loss of heterochromatin, and pronounced dysregulation of autophagy and lysosomal pathways, these SA-{beta}Gal-high naive T cells notably lack the canonical senescence marker p21CIP1 and retain robust proliferative capacity upon activation. Remarkably, naive CD4 SA-{beta}Gal-high T cells acquire cytotoxic properties including NK-like features, granzyme secretion, and the ability to induce paracrine DNA damage in endothelial cells. Mechanistically, we demonstrate that impaired autophagic flux contributes significantly to this phenotype. Our findings address critical knowledge gaps regarding the nature and functional plasticity of senescence-like states in naive T cells, highlighting a novel link between lysosomal-autophagic dysfunction, cellular stress adaptation, and inflammaging. Understanding this unique T cell population provides important insights into immune aging and offers potential targets to mitigate age-associated immune dysfunction and chronic inflammation.

immunology↗

bioRxiv2025

The clinical drug candidate anle138b binds predominantly to the central cavity in lipidic Aβ fibrils and modulates fibril formation.

Alzheimers disease is a specific neurodegenerative disorder, distinct from normal aging, with a growing unmet medical need. It is characterized by the accumulation of amyloid plaques in the brain, primarily consisting of amyloid beta (A{beta}) fibrils. Therapeutic antibodies can slow down the disease, but are associated with potential severe side effects, motivating the development of small molecules to halt disease progression. This study investigates the interaction between the clinical drug candidate small molecule anle138b and lipidic A{beta}40 fibrils of type 1 (L1). L1 fibrils were previously shown to closely resemble fibrils from Alzheimers patients18. Using high-resolution structural biology techniques, including cryo-electron microscopy (cryo-EM), nuclear magnetic resonance (NMR) spectroscopy enhanced by dynamic nuclear polarization (DNP), and molecular dynamics (MD) simulations, we find that anle138b selectively binds to a cavity within the fibril. This structural insight provides a deeper understanding of a potential drug-binding mechanism at the atomic level and may inform the development of novel therapies and diagnostic approaches. In addition, anle138b reduces fibril formation in the presence of lipids by approximately 75%. This may suggest a mechanistic connection to its previously reported activity in animal models of Alzheimers disease15.

biochemistry↗

bioRxiv2025

The synovial lining macrophage layer develops in the first weeks of life in a CSF1- and TGFβ- dependent but monocyte-independent process.

Synovial joints harbor a protective lining layer, consisting of fibroblasts and macrophages, which form an epithelial-like barrier. In inflamed joints, lining macrophages regulate both early inflammatory cell influx and resolution. Despite these critical functions, it is currently unknown at what stage during development the synovial macrophage lining is established, and which signals drive this process. Here, we use a combination of genetic models and in vivo perturbations, single cell transcriptomics and imaging to delineate the process of lining formation in mice. We find that the synovial lining is immature at birth and becomes established within the first 3 weeks of life. In this window, the lining is gradually populated with macrophages that originate from fetal sources, proliferate and acquire the lining-specific transcriptional identity. In contrast, monocytes contribute only minimally to the developing lining, and their input remains limited in healthy adulthood. We identify CSF1 and TGF{beta} as key signals in this process, which also involves mechanosensing through PIEZO1. Our study thus identifies the early postnatal window as a critical period for lining macrophage development, with potential lifelong impact on joint health and disease.

immunology↗

bioRxiv2025

Human- and Rodent-derived Extracellular Vesicles Mediate the Spread of Pathology in MSA-like Models

Multiple system atrophy (MSA) is characterized by the presence of protein-rich inclusions mainly within oligodendrocytes, comprised primarily by the neuronal protein Synuclein and the oligodendroglial-specific phosphoprotein TPPP/p25. Mature oligodendrocytes do not normally express detectable Synuclein levels, suggesting that its oligodendroglial accumulation may arise from intercellular transfer, potentially via extracellular vesicles (EVs); however the precise role of oligodendroglial-derived EVs in MSA progression remains relatively understudied. Herein, we characterized the cargo/features and pathogenic potential of EVs released by oligodendrocytes treated with human Synuclein fibrils amplified from MSA or Parkinsons disease patient brains (or human recombinant Synuclein fibrils) and EVs isolated from murine and human MSA (or respective control) brains. Our findings reveal that both oligodendroglial cell- and brain-derived EVs harbor pathological Synuclein and TPPP/p25 conformations, similar to those accumulating in human MSA brains. These EVs are readily taken up by both neurons and oligodendrocytes, driving Synuclein propagation in vitro. Importantly, inoculation of these MSA-like EVs in animal models induce robust pSer129-Synuclein accumulation along the nigrostriatal axis, colocalizing with markers of mature oligodendrocytes and dopaminergic neurons. These findings underscore the pivotal role of oligodendroglial-derived EVs in pathology progression and neuronal-oligodendroglial communication, positioning them as promising targets for therapeutic strategies aimed at combating alpha-Synucleinopathies.

neuroscience↗

bioRxiv2025

Discovery of an Antiviral PROTAC Targeting the SARS-CoV-2 Main Protease Using an Allosteric Warhead

Targeted protein degradation represents a new paradigm in drug development. By hijacking the cellular ubiquitin-proteasome-system pathogenic proteins are degraded via heterobifunctional molecules, referred to as proteolysis targeting chimeras (PROTACs). However, to date, only few PROTACs targeting viral or proviral proteins have been developed. To explore the possibilities and advantages of antiviral PROTACs, we have developed an antiviral PROTAC against the SARS-CoV-2 main protease (MPro) using an allosteric warhead. Here, we present the design of ten MPro degraders that were developed using pelitinib as a warhead, an allosteric binder of MPro. Among several candidates, LLP019 emerged as the most potent molecule, capable of degrading up to 90% of MPro after ectopic expression in HEK293F cells. LLP019 displayed significant antiviral activity against several variants of concern of SARS-CoV-2 in infected Calu3 cells. In conclusion, we show that the development of antiviral PROTACs using an allosteric warhead represents a promising antiviral strategy, expanding the range of possible target proteins and ligands. SYNPOSISWe present a proof-of-concept study to construct a PROTAC targeting the SARS-CoV-2 main protease (MPro) using a warhead that binds outside the catalytic pocket.

microbiology↗

bioRxiv2025

Structural insight into binding of novel PET tracer MODAG-005 to lipidic ????-Synuclein fibrils

Accumulation of -synuclein (Syn) aggregates in the human brain is the major hallmark of synucleinopathies such as Parkinsons Disease, Multiple System Atrophy, and Dementia with Lewy bodies. Positron Emission Tomography (PET) plays a vital role in diagnosing these diseases and monitoring their progression by enabling the non-invasive and sensitive detection of Syn aggregates in the brain. However, developing PET tracers with specific target binding, as well as identifying the binding site and complex structure present significant challenges. Here, we investigated the interaction between lipidic Syn aggregates and MODAG-005, a new Syn PET tracer candidate, using nuclear magnetic resonance spectroscopy, cryogenic electron microscopy and molecular dynamics (MD) simulations. Two binding sites of MODAG-005 were found, one on the surface and one in a tubular cavity of the fibril, of which the occupancies were found to depend on the preparation protocols. The cavity binding site is thermodynamically more stable than the external binding site and is the only site occupied when MODAG-005 is applied with liposome as carriers to the aggregates. This is corroborated by MD simulations in which stable interactions between MODAG-005 and glycine containing backbone motifs of the tubular cavity of the aggregates are observed.

biochemistry↗

bioRxiv2025

CellFlow enables generative single-cell phenotype modeling with flow matching

High-content phenotypic screens provide a powerful strategy for studying biological systems, but the scale of possible perturbations and cell states makes exhaustive experiments unfeasible. Computational models that are trained on existing data and extrapolate to correctly predict outcomes in unseen contexts have the potential to accelerate biological discovery. Here, we present CellFlow, a flexible framework based on flow matching that can model single cell phenotypes induced by complex perturbations. We apply CellFlow to various phenotypic screens, accurately predicting expression responses to a wide range of perturbations, including cytokine stimulation, drug treatments and gene knockouts. CellFlow successfully modeled developmental perturbations at the whole-embryo scale and guided cell fate and organoid engineering by predicting heterogeneous cell populations arising from combinatorial morphogen treatments and by performing a virtual organoid protocol screen. Taken together, CellFlow has the potential to accelerate discovery from phenotypic screens by learning from existing data and generating phenotypes induced by unseen conditions.

bioinformatics↗

bioRxiv2025

Methylglyoxal mutagenizes single-stranded DNA via Rev1-associated slippage and mispairing

Methylglyoxal (MG) is a highly reactive aldehyde that is produced endogenously during metabolism and is derived from exogenous sources such as sugary food items and cigarette smoke. Unless detoxified by glyoxalases (Glo1 and Glo2), MG can readily react with all major biomolecules, including DNA and proteins, generating characteristic lesions and glycation-derived by- products. As a result, MG exposure has been linked to a variety of human diseases, including cancers. Prior studies show that MG can glycate DNA, preferentially on guanine residues, and cause DNA damage. However, the mutagenicity of MG is poorly understood in vivo. In the context of cancer, it is essential to comprehend the true contribution of MG to genome instability and global mutational burden. In the present study, we show that MG can robustly mutagenize induced single-stranded DNA (ssDNA) in yeast, within a guanine centered mutable motif. We demonstrate that genome-wide MG mutagenesis in ssDNA is greatly elevated throughout the genome in the absence of Glo1, and abrogated in the presence of the aldehyde quencher aminoguanidine. We uncovered strand slippage and mispairing as the predominant mechanism for generation of all MG-associated mutations, and demonstrate that the translesion polymerase Rev1 is necessary in this pathway. Finally, we find that the primary MG-associated mutation is enriched in a variety of sequenced tumor datasets. We discuss the genomic impact of methylglyoxal exposure in the context of mutagenesis, DNA damage, and carcinogenesis.

genetics↗

bioRxiv2025

Nora virus proliferates in dividing intestinal stem cells and sensitizes flies to intestinal infection and oxidative stress

The digestive tract represents the most complex interface of an organism with its biotope. Food may be contaminated by pathogens and toxicants while an abundant and complex microbiota thrives in the gut lumen. The organism must defend itself against potentially noxious biotic or abiotic stresses while preserving its microbiota, provided it plays a beneficial role. The presence of intestinal viruses adds another layer of complexity. Starting from a differential sensitivity of two lines from the same Drosophila wild-type strain to ingested Pseudomonas aeruginosa, we report here that the presence of Nora virus in the gut epithelium promotes the sensitivity to this bacterial pathogen as well as to an ingested oxidizing xenobiotic. The genotype, age, nature of the ingested food and, to a limited extent, the microbiota are relevant parameters that influence the effects of Nora virus on host fitness. Mechanistically, we detect the initial presence of the virus essentially in progenitor cells. Upon stress such as infection, exposure to xenobiotics, aging or feeding on a rich-food diet, the virus is then detected in enterocytes, which correlates with a disruption of the intestinal barrier function in aged flies. Finally, we show that the virus proliferates only when ISCs are induced to divide. We propose that enterocytes essentially get infected through lineage from progenitor cells and are not directly infected. In conclusion, it is important to check that experimental strains are devoid of intestinal viruses when monitoring survival/life span of fly lines or when investigating the homeostasis of the intestinal epithelium as these viruses can constitute significant confounding factors.

immunology↗

bioRxiv2025

Lymphoid-tissue-on-chip recapitulates human antibody responses in vitro

In the past decades, vaccine development has made great strides. Nevertheless, more often than not, vaccine candidates fail in advanced stages of development and clinical trials. A key reason is the poor predictive value of non-clinical in vivo and in vitro models, due to either species-specific differences in the immune response or insufficient reflection of physiological vaccine mechanisms. Reliable modeling of human adaptive immune responses is a prerequisite to understand processes leading to vaccine-induced protective immunization and to drive informed decisions in vaccine development pipelines. Here, we present a centrifugal microfluidics based organ-on-chip approach to generate an organotypic high density lymphoid tissue on-chip. The model enables long-term culture of lymphoid tissue and raised antigen-specific antibody responses against influenza vaccines even after four weeks on-chip. Antibody response of different magnitude and quality could be induced both by direct antigen exposure as well as by recruitment of antigen-presenting cells from the periphery. The model represents an attractive approach to evaluate the impact of the mode of antigen delivery on adaptive immune responses. Beyond applications in vaccine development, the lymphoid-tissue-on-chip provides a platform to study cellular interactions during homeostasis, immune responses and long-term impact of immunomodulators over several weeks.

bioengineering↗

bioRxiv2025

Loss of Effort in Chronic Low-Back Pain Patients: Motivational Anhedonia in Chronic Pain

The motivational and affective properties of chronic pain significantly impact patients lives and response to treatment but remain poorly understood. Most available phenotyping tools of chronic pain affect rely on patients self-report. Here we instead directly studied the willingness of chronic low-back pain (CLBP) patients to expend effort to win monetary rewards available for wins at different probabilities and different levels of difficulties in comparison to matched pain free controls and obtained functional brain imaging on a sub-group of our sample to link behavior to brain properties. We aimed to specifically test for a differential relationship of the functional connectivity in reward and effort related brain networks, and measures of effort in patients and pain free controls. Consistent with the hypothesis of "negative hedonic shift" in chronic pain we observed that CLBP patients are significantly less willing than pain free controls to expend effort to go for high cost/high reward choices and their reported low-back pain intensity predicted increased effort discounting. Furthermore, patients task performance was directly correlated to functional connectivity between the ventral striatum and ventro-medial prefrontal cortex, which are major nodes in the reward processing network. Patients performance was not explained by their self-reported depressive symptoms. Our results present new behavioral evidence characterizing the nature of anhedonia in chronic pain and links it directly to cortico-striatal connectivity highlighting the role of this circuitry in the pathophysiology of chronic pain.

neuroscience↗

bioRxiv2024

Restoring and sustaining human postmortem retinal light responses with scalable methods for testing degenerative disease therapies

Neuro- and retinal degenerative diseases, including Alzheimers, age-related macular degeneration, stroke, and central retinal artery occlusion, rob millions of their independence. Studying these diseases in human retinas has been hindered by the immediate loss of neuronal activity postmortem. While recent studies restored limited activity in postmortem CNS tissues, synchronized neuronal transmission >30 minutes postmortem remained elusive. Our study overcomes this barrier by reviving and sustaining light signal transmission in human retinas recovered up to four hours and stored 48 hours postmortem. We also establish infrared-based ex vivo imaging for precise sampling, a closed perfusion system for drug testing, and an ex vivo ischemia-reperfusion model in mouse and human retina. This platform enables testing of neuroprotective and neurotoxic effects of drugs targeting oxidative stress and glutamate excitotoxicity. Our advances question the irreversibility of ischemic injury, support preclinical vision restoration studies, offer new insights into treating ischemic CNS injuries, and pave the way for transplantation of human donor eyes. TeaserReviving light signaling in postmortem human retinas challenges the irreversibility of ischemic injury and advances research to restore vision.

neuroscience↗

bioRxiv2024

Many transcription factor families have evolutionarily conserved binding motifs in plants

Transcription factors control gene expression during development and in response to a broad range of internal and external stimuli. They regulate promoter activity by directly binding cis- regulatory elements in DNA. The angiosperm Arabidopsis thaliana contains more than 1,500 annotated transcription factors, each containing a DNA-binding domain that is used to define transcription factor families. Analyzing binding motifs of 686 and the binding sites of 335 A. thaliana transcription factors as well as motifs of 92 transcription factors from other plants, we identified a constrained vocabulary of 74 conserved motifs spanning 50 families in plants. Among 21 transcription factor families, we found one core motif for all analyzed members and between 2 and 72% overlapping binding sites. Five families show conservation of the motif along phylogenetic clades. Five families including the C2H2 zinc finger family show high diversity among motifs in plants, suggesting potential for neofunctionalization of duplicated transcription factors based on the motif recognized. For conserved motifs we tested if they remained conserved since at least 450 million years ago by determining the binding motifs of 17 orthologous transcription factors from 11 families in M. polymorpha using amplified DNA affinity purification sequencing. We detected nearly identical binding motifs as predicted from the angiosperm data. Taken together, the results show a large repertoire of overlapping binding sites within a TF family and species and a high degree of binding motif conservation for at least 450 million years. The results indicate more potential for evolution in cis- rather than trans-regulatory elements.

plant biology↗

bioRxiv2024

Mast cells are not essential for pubertal mammary gland branching.

Mast cells are long-lived, tissue-resident immune cells of the myeloid lineage with cardinal functions in allergy and atopic disease. They are now increasingly recognized also for protective roles e.g. against infections and venoms. Other functions originally assigned to mast cells in development and physiology, however, have been refuted, and for yet others, their true contribution remains uncertain. Mast cells have been implicated in promoting ductal branching in the pubertal mammary gland, the organ that produces and secretes milk in mammals, but these findings are based on mouse models that are not mast cell-specific. In this study, we therefore re-addressed the impact of mast cells on mammary gland branching using several complementary genetic models, including a new transgenic line. We report that neither constitutive deficiency of mast cells, nor their conditional ablation induced at puberty affected mammary gland branching. Our results thus dispute that mast cells promote this process in mice, at least in a unique and non-redundant manner. This study adds to a growing body of work clarifying the biological roles of mast cells, and further expands the toolbox available to the field of mast cell research.

developmental biology↗

bioRxiv2024

Representational similarity modulates neural and behavioral signatures of novelty

Novelty signals in the brain modulate learning and drive exploratory behaviors in humans and animals. While the perceived novelty of a stimulus is known to depend on previous experience, the effect of stimulus representations on novelty computation remains elusive. In particular, existing models of novelty computation fail to account for the effects of stimulus similarities that are abundant in naturalistic environments and tasks. Here, we present a unifying, biologically plausible model that captures how stimulus representations modulate novelty signals in the brain and influence novelty-driven learning and exploration. By applying our model to two publicly available data sets, we quantify and explain (i) how generalization across similar visual stimuli affects novelty responses in the mouse visual cortex, and (ii) how generalization across nearby locations impacts mouse exploration in an unfamiliar environment. Our model unifies and explains distinct neural and behavioral signatures of novelty, and enables theory-driven experiment design to investigate the neural mechanisms of novelty computation.

neuroscience↗