Biology subjects

Winkler, T.

Publications and source records attributed to Winkler, T..

14 recordsLinked to original sources

bioRxiv2026

Mapping chromothripsis across human cancer cell lines reveals genome evolution and therapeutic vulnerabilities

Chromothripsis is a catastrophic chromosomal rearrangement found in ~40% of primary tumors, yet its landscape in cancer cell lines (CCLs) remains uncharacterized. To address this gap, we developed a pipeline to detect chromothripsis-like events from copy-number data alone, and mapped their occurrence across 1,646 human CCLs. Chromothripsis patterns were broadly conserved between primary tumors and CCLs, but CCLs displayed some distinct features and a significantly higher prevalence of chromothripsis. Chromothripsis continued to emerge during culture propagation, likely contributing to its increased prevalence in CCLs. Integrating genomic and functional data revealed selective vulnerabilities: chromothriptic cells were resistant to DNA damage-inducing agents but highly sensitive to histone deacetylase inhibitors (HDACi). Using isogenic models, we validated that HDACi could synergistically sensitize chromothriptic cells to DNA damage-inducing agents. Our study establishes the first comprehensive resource of chromothripsis in CCLs and reveals functional consequences and therapeutic vulnerabilities of chromothripsis-positive cancers.

cancer biology↗

bioRxiv2026

TLR-mediated activation of synovial fibroblasts from osteoarthritis patients promotes chondrocyte dysfunction

Objective: Toll like receptor (TLR) activation by cartilage derived damage-associated molecular patterns contributes to osteoarthritis (OA) pathogenesis, but the role of synovial fibroblasts in this process remains incompletely understood. We investigated the TLR responsiveness of human OA synovial fibroblasts and determined how TLR activation influences fibroblast-mediated regulation of chondrocyte function. Design: Primary synovial fibroblasts isolated from OA patients were characterized for TLR expression and stimulated with agonists targeting TLR1/2 to TLR9. Inflammatory mediator production, matrix metalloproteinase expression, mitochondrial respiration, and transcriptomic responses were assessed. Functional effects on cartilage homeostasis were evaluated using autologous chondrocyte spheroid co-cultures. Results: Approximately 50% of cells within OA synovial membranes were fibroblasts (CD45-CD31-PDPN+). Synovial fibroblasts expressed multiple TLRs at both the transcript and protein levels. Activation of TLR1/2, TLR4, TLR5, and TLR2/6 induced robust expression of IL-6, IL-8, G-CSF, MMP3, and MMP10, with minimal effects on mitochondrial respiratory function. Transcriptomic analysis revealed activation of inflammatory pathways together with enrichment of antigen presentation and protein translation programs. In autologous co-culture, TLR1/2-activated synovial fibroblasts promoted inflammatory and catabolic gene expression, suppressed anabolic gene expression, and impaired chondrocyte spheroid growth. Conclusions: Human OA synovial fibroblasts are highly responsive to TLR activation and acquire a pro-inflammatory, cartilage-degrading phenotype that directly impairs chondrocyte homeostasis. These findings identify synovial fibroblasts as key effectors of innate immune signalling within the OA joint and support targeting shared TLR-mediated pathways in joint-resident cells as a potential disease-modifying therapeutic strategy.

immunology↗

bioRxiv2025

Chromosome-arm 17p Loss Renders Breast Cancer Cells Vulnerable to AURKB Inhibition

Loss of chromosome-arm 17p (Del17p) is a genetic hallmark of breast cancer. While TP53 loss is an established driver of Del17p, the potential therapeutically-relevant cellular vulnerabilities of this common aneuploidy remain unexplored. Here, we first analyzed genomic and clinical data from breast cancer patients using METABRIC and TCGA datasets. Del17p was prevalent across molecular subtypes and correlated with higher tumor grade, advanced stage, and worse survival. Gene expression profiling revealed reduced expression and activity of the chromosome 17p-residing gene Aurora Kinase B (AURKB) in Del17p tumors and cell lines. Moreover, functional dependency screens across breast cancer cell lines identified increased sensitivity of Del17p cells to genetic inhibition of AURKB, which we validated using chemical inhibition in matched breast cancer cell lines. Next, we generated an isogenic model of CAL51 breast cancer cells with/without heterozygous AURKB loss in TP53-WT and TP53-null backgrounds, and confirmed that heterozygous loss of AURKB resulted in its reduced expression and in increased sensitivity to the AURKB inhibitor barasertib. Notably, p53 inactivation increased AURKB expression and reduced drug sensitivity, as previously reported, but AURKB heterozygous knockout reverted these phenotypes, revealing opposite effects of common modes of p53 inactivation (Del17p vs. point mutations). Mechanistically, the phenotypes associated with barasertib treatment - mitotic aberrations, cytokinesis failure, whole-genome doubling and apoptosis - were exacerbated in Del17p cells. Our findings therefore suggest Del17p as a potential biomarker for identifying breast cancer patients who may benefit from AURKB inhibition and highlight its potential as a therapeutic target in Del17p breast tumors. SignificanceBreast cancer tumors with loss of chromosome-arm 17p (Del17p) exhibit reduced AURKB expression and increased sensitivity to AURKB inhibition, suggesting Del17p as a biomarker for AURKB-targeted therapy.

cancer biology↗

bioRxiv2025

Transcriptional Profiling of Commonly Used Liver Cancer Cell Lines Reveals Disease-Specific Modeling Potential and Authentication Concerns

Cell lines are essential tools for liver cancer research, yet their molecular fidelity to primary tumors remains incompletely characterized. Here we comprehensively evaluated transcriptomic similarities between commonly used liver cancer cell lines and primary tumor subtypes to guide optimal model selection. We analyzed RNA sequencing data from 541 samples spanning primary HCC, HPBL, CHOL, and FLC tumors, alongside 21 liver cancer cell lines and primary human hepatocytes. Through systematic variance analysis, we identified 2,523 highly variable genes distinguishing cancer subtypes and cell lines, then performed correlation analyses, unsupervised clustering, and pathway enrichment to assess molecular similarities. Molecular subtypes within each cancer type were identified through hierarchical clustering and characterized using pathway analysis. HepG2 cells showed strongest correlation with HPBL (r=0.62), confirming their hepatoblastoma origin despite frequent HCC misclassification. This correlation was driven by shared Wnt pathway dysregulation signatures. Huh7 cells best represented HCC, particularly the immune-modulatory, MYC-activated subtype with the highest median correlation. RBE cells optimally modeled CHOL, specifically the dedifferentiated, immune-evasive subtype. Several commonly used cell lines (LO2, SMMC-7721, MHCC97L) and specific publicly available samples demonstrated likely HeLa contamination. Primary human hepatocytes cultured under physioxic conditions better preserved liver-specific transcriptional programs compared to standard culture. No established cell line analyzed represented FLC strongly, identifying the need for a standard, available model. This transcriptomic framework provides evidence-based guidance for selecting appropriate liver cancer cell line models and highlights the critical need for rigorous cell line validation to improve experimental design and translational relevance of liver cancer research.

cancer biology↗

bioRxiv2025

Endophytes induce systemic spatial reprogramming of metabolism in poplar roots under drought

Beneficial endophytes help plants thrive in challenging environments by altering their hosts metabolism, but how these cellular scale metabolic changes propagate to the systems biology scale is unknown. In this work, we employed a high-resolution chemical imaging approach to map metabolic changes at the root zone and cell type levels and found that a 9-strain consortium of beneficial endophytes differentially altered the metabolome of droughted root tissues according to cell types and locations along the root system architecture. Using machine learning (ML) models, we identified root metabolites and exudates that have predictive power over treatment class and could therefore be used as systems biology indicators of drought and endophyte inoculation status. We calculated the correlation between each endophyte and metabolite and found that this relationship shifts under drought conditions, indicating the dynamic role endophytes play in a plants microbiome and metabolism in response to environmental changes.

plant biology↗

bioRxiv2025

A recombinant hybrid provides insights into gene regulation, pathogenesis and tumorigenesis of phytopathogenic smut fungi

The maize smut fungi Ustilago maydis and Sporisorium reilianum are closely related and have similar genomes in terms of size and synteny. While U. maydis induces tumors locally at sites of infection, S. reilianum systemically colonizes the host and causes symptoms in the inflorescences. To investigate the genetic basis of these differences, an interspecific recombinant hybrid (rUSH) with the mating type system of S. reilianum was generated. rUSH exhibited extensive in-planta proliferation, showing a S. reilianum-like phenotype at all developmental stages except teliospore formation. Transcriptome profiling revealed that expression of pathogenicity-related effector gene orthologs was induced in rUSH, but not in a wild-type hybrid control. Multiple transcriptome comparisons identified 253 differentially expressed one-to-one effector orthologs with distinct regulatory patterns, including cis-, trans-, and rUSH-specific regulation. Functional analysis via CRISPR/Cas9 mutagenesis uncovered three novel virulence factors among the rUSH-specific regulated effectors. Ultimately, rUSH facilitated to identify the transcription factor UmHdp2 as key regulator of U. maydis-induced tumorigenesis. Together, these findings highlight the utility of a recombinant, interspecific hybrid in unraveling the molecular mechanisms underlying pathogenic differences in closely related fungal pathogens.

microbiology↗

bioRxiv2023

Inactivation of p53 drives breast cancer brain metastasis by altering fatty acid metabolism

Brain metastasis (BM) is a dire prognosis across cancer types. It is largely unknown why some tumors metastasize to the brain whereas others do not. We analyzed genomic and transcriptional data from clinical samples of breast cancer BM (BCBM) and found that nearly all of them carried p53-inactivating genetic alterations through mutations, copy-number loss, or both. Importantly, p53 pathway activity was already perturbed in primary tumors giving rise to BCBM, often by loss of the entire 17p chromosome-arm. This association was recapitulated across other carcinomas. Experimentally, p53 knockout was sufficient to drastically increase BCBM formation and growth in vivo, providing a causal link between p53 inactivation and brain tropism. Mechanistically, p53-deficient BC cells exhibited altered lipid metabolism, particularly increased fatty acid (FA) synthesis and uptake, which are characteristic of brain-metastasizing cancer cells. FA metabolism was further enhanced by astrocytes in a p53-dependent manner, as astrocyte-conditioned medium increased FASN, SCD1, and CD36 expression and activity, and enhanced the survival, proliferation and migration of p53-deficient cancer cells. Consequently, these cells were more sensitive than p53-competent cells to FA synthesis inhibitors, in isogenic cell cultures, in BCBM-derived spheroids, and across dozens of BC cell lines. Lastly, a significant association was observed between p53 inactivation, astrocyte infiltration, and SCD1 expression in clinical human BCBM samples. In summary, our study identifies p53 inactivation as a driver of BCBM and potentially of BM in general; suggests a p53-dependent effect of astrocytes on BC cell behavior; and reveals FA metabolism as an underlying, therapeutically-targetable molecular mechanism.

cancer biology↗

bioRxiv2023

Regional pulmonary perfusion, blood volume, and their relationship change during early ARDS in an experimental study

Regional pulmonary perfusion (Q) has been investigated using blood volume (Fb) imaging as an easier-to-measure surrogate. However, it is unclear if changing pulmonary conditions could affect their relationship. We hypothesized that vascular changes in early acute respiratory distress syndrome (ARDS) affect Q and Fb differently. Five sheep were anesthetized and received protective mechanical ventilation for 20 hours while endotoxin was continuously infused. Using dynamic 18F-FDG and 13NN Positron Emission Tomography (PET), regional Fb and Q were analysed in 30 regions of interest (ROIs) and normalized by tissue content (Fbn and Qn, respectively). After 20 hours, the animals lung injury showed characteristics of early ARDS, including gas exchange and lung mechanics. PET images of Fbn and Qn showed substantial differences between baseline and lung injury. Lung injury caused a significant change in the Fbn-Qn relationship compared to baseline (p<0.001). The best models at baseline and lung injury were Fbn=0.32+0.690Qn and Fbn=1.684Qn-0.538Qn2, respectively. Early ARDS changed the relationship between Fb and Q from linear to curvilinear. Effects of endotoxin exposure on the vasoactive blood flow regulation were most likely the key factor for this change limiting the quantitative accuracy of Fb imaging as a surrogate for regional Q.

physiology↗

bioRxiv2023

Modulation of Polar Auxin Transport Identifies the Molecular Determinants of Source-Sink Carbon Relationships and Sink Strength in Poplar

Source-to-sink carbon (C) allocation driven by the sink strength, i.e., the ability of a sink organ to import C, plays a central role in tissue growth and biomass productivity. However, molecular drivers of sink strength have not been thoroughly characterized in trees. Auxin, as a major plant phytohormone, regulates the mobilization of photoassimilates in source tissues and elevates the translocation of carbohydrates toward sink organs, including roots. In this study, we used an auxin-stimulated carbon sink approach to understand the molecular processes involved in the long-distance source-sink C allocation in poplar. Poplar cuttings were foliar sprayed with polar auxin transport modulators, including auxin enhancers (AE) (i.e., IBA and IAA) and auxin inhibitor (AI) (i.e., NPA), followed by a comprehensive analysis of leaf, stem, and root tissues using biomass evaluation, phenotyping, C isotope labeling, metabolomics, and transcriptomics approaches. Auxin modulators altered root dry weight and branching pattern, and AE increased photosynthetically fixed C allocation from leaf to root tissues. The transcriptome analysis identified highly expressed genes in root tissue under AE condition including transcripts encoding polygalacturonase and {beta}-amylase that could increase the sink size and activity. Metabolic analyses showed a shift in overall metabolism including an altered relative abundance levels of galactinol, and an opposite trend in citrate levels in root tissue under AE and AI conditions. In conclusion, we postulate a model suggesting that the source-sink C relationships in poplar could be fueled by mobile sugar alcohols, starch metabolism-derived sugars, and TCA-cycle intermediates as key molecular drivers of sink strength.

plant biology↗

bioRxiv2020

Elevated expression of ACE2 in tumor-adjacent normal tissues of cancer patients

The rapidly developing COVID-19 pandemic has raised a concern that cancer patients may have increased susceptibility to SARS-CoV-2 infection. This discussion has mostly focused on therapy-induced immune suppression. Here, we examined the expression patterns of ACE2, the receptor through which SARX-CoV2 enters human cells, and found that ACE2 mRNA levels are elevated in tumor-adjacent normal tissues of cancer patients, including in normal-adjacent lung tissues of lung cancer patients. These observations raise the possibility that the elevated COVID-19 risk of cancer patients may not be limited to those undergoing immune-suppressing treatment.

cancer biology↗

bioRxiv2019

Maximum likelihood method quantifies the overall contribution of gene-environment interaction to complex traits: an application to obesity traits

As genome-wide association studies (GWAS) increased in size, numerous gene-environment interactions (GxE) have been discovered, many of which however explore only one environment at a time and may suffer from statistical artefacts leading to biased interaction estimates. Here we propose a maximum likelihood method to estimate the contribution of GxE to complex traits taking into account all interacting environmental variables at the same time, without the need to measure any. This is possible because GxE induces fluctuations in the conditional trait variance, the extent of which depends on the strength of GxE. The approach can be applied to continuous outcomes and for single SNPs or genetic risk scores (GRS). Extensive simulations demonstrated that our method yields unbiased interaction estimates and excellent confidence interval coverage. We also offer a strategy to distinguish specific GxE from general heteroscedasticity (scale effects). Applying our method to 32 complex traits in the UK Biobank reveals that for body mass index (BMI) the GRSxE explains an additional 1.9% variance on top of the 5.2% GRS contribution. However, this interaction is not specific to the GRS and holds for any variable similarly correlated with BMI. On the contrary, the GRSxE interaction effect for leg impedance [Formula] is significantly (P < 10-56) larger than it would be expected for a similarly correlated variable [Formula]. We showed that our method could robustly detect the global contribution of GxE to complex traits, which turned out to be substantial for certain obesity measures.

epidemiology↗

bioRxiv2019

Chemical biofilm dislodgement with chelating and reducing agents in comparison to sonication: implications for the diagnosis of implant associated infection

Sonication of removed devices improved the microbiological diagnosis of infection. Recently, chemical agents have been investigated for dislodgement of biofilms, including the chelating agent ethylenediaminetetraacetic acid (EDTA) and the reducing agent dithiothreitol (DTT). We compared the efficacy of chemical methods (EDTA and DTT) to sonication for biofilm dislodgement. Staphylococcus epidermidis (ATCC 35984) and Pseudomonas aeruginosa (ATCC 53278) biofilms were grown on porous glass beads for 3 days. After biofilm formation, beads were exposed to 0.9% saline, sonication and/or chemical agents. Quantitative and qualitative biofilm analyses were performed by colony counting (CFU/ml), isothermal microcalorimetry and scanning electron microscopy. The colony counts after treatment with EDTA and DTT were similar to those after exposure to 0.9% saline (6.3, 6.1 and 6.0 log CFU/ml, respectively) for S. epidermidis biofilms, and (5.1, 5.2 and 5.0 log CFU/ml, respectively) for P. aeruginosa biofilm. Sonication detected higher CFU counts (7.5 log CFU/ml) for S. epidermidis; (p<0.05) and 6.5 log for P. aeruginosa biofilm (p <0.05). Concordant results were detected with isothermal microcalorimetry and scanning electron microscopy. In conclusion, the CFU count after treatment of S. epidermidis or P. aeruginosa biofilms with EDTA and DTT was similar to those observed after 0.9% saline used as control. In contrast, sonication was superior to chemical methods for biofilm dislodgment and detection of microorganisms in sonication fluid. In conclusion, our study showed that sonication is superior to chemical method to dislodge bacterial biofilm from artificial surface and should be considered as standard diagnostic method for biofilm detection in implant-associated infections.

microbiology↗

bioRxiv2018

Placental-expanded, mesenchymal cells improve muscle function following hip arthroplasty

BackgroundNo regenerative approach has thus far been shown to be effective in skeletal muscle injuries, despite high frequency and associated functional deficits. We sought to address surgical trauma related muscle injuries using local intraoperative application of allogeneic placenta-derived, mesenchymal-like adherent cells (PLX-PAD), using hip arthroplasty as a standardized injury model, because of the high regenerative and immunomodulatory potency of this cell type.\n\nMethodsOur pilot phase I/IIa study was prospective, randomized, double blind and placebo-controlled. Twenty patients undergoing hip arthroplasty via a direct lateral approach were injected with 3.0x108 or 1.5x108 PLX-PAD or a placebo into the gluteus medius muscle.\n\nResultsWe did not observe any relevant PLX-PAD-related adverse events at the 2-year follow-up. Improved gluteus medius strength was noted as early as week 6 in the treatment-groups. Surprisingly, until week 26 the low-dose outperformed the high-dose group and reached significantly improved strength compared to placebo, mirrored by an increase in muscle volume. Histology indicated accelerated healing after cell therapy. Biomarker studies revealed that low-dose treatment reduced the surgery-related immunological stress reaction more than high-dose. Signs of late-onset immune reactivity after high-dose treatment corresponded to reduced functional improvement.\n\nConclusionAllogeneic PLX-PAD therapy improved strength and volume of injured skeletal muscle with a reasonable safety profile. Outcomes could be positively correlated with the modulation of early postoperative stress-related immunological reactions.\n\nTrial RegistrationClinicalTrials.gov (number NCT01525667) and EudraCT (number 2011-003934-16)\n\nFundingThe study was funded by the Sponsor, Pluristem Therapeutics, the Israeli innovation authority and the German Federal Ministry of Education and Research.\n\nConflict of interestT. Winkler, C. Perka and G.N. Duda are members of a clinical advisory board of Pluristem Ltd for future indications. T. Winkler, C. Perka, G.N. Duda, P. von Roth filed a patent together with Pluristem Ltd. E. Lukasiewicz Hagai, R. Ofir, L. Pinzur and E. Eyal are current or former employees of Pluristem Ltd. T. Winkler, P. Reinke and H.-D. Volk received in the past consulting fees from Pluristem Ltd. but not for this project.

clinical trials↗

bioRxiv2017

VarExp: Estimating variance explained by Genome-Wide GxE summary statistics

Many genomic analyses, such as genome-wide association studies (GWAS) or genome-wide screening for Gene-Environment (GxE) interactions have been performed to elucidate the underlying mechanisms of human traits and diseases. When the analyzed outcome is quantitative, the overall contribution of identified genetic variants to the outcome is often expressed as the percentage of phenotypic variance explained. In practice, this is commonly estimated using individual genotype data. However, using individual-level data faces practical and ethical challenges when the GWAS results are derived in large consortia through meta-analysis of results from multiple cohorts. In this work, we present a R package, \"VarExp\", that allows for the estimation of the percentage of phenotypic variance explained by variants of interest using summary statistics only. Our package allows for a range of models to be evaluated, including marginal genetic effects, GxE interaction effects, and main genetic and interaction effects jointly. Its implementation integrates all recent methodological developments on the topic and does not need external data to be uploaded by users.\n\nThe R source code, tutorial and associated example are available at https://gitlab.pasteur.fr/statistical-genetics/VarExp.git.

bioinformatics↗