Biology subjects

Wenzel, J.

Publications and source records attributed to Wenzel, J..

6 recordsLinked to original sources

bioRxiv2025

Machine Learning-Driven Discovery of Synergistic Protein Interactions Identifies ATL3 as a Putative Biomarker for Cancer Drug Response

BackgroundResistance to targeted molecular therapies--both primary and acquired--remains a major obstacle to effective cancer treatment. Despite extensive research, the molecular determinants of treatment resistance are still incompletely understood, underscoring the need to identify robust resistance drivers to improve therapeutic outcomes. Recently, the ProCan and Wellcome Sanger Institute released the worlds largest pan-cancer proteomic dataset to date, comprising 949 cancer cell lines treated with 625 anti-cancer agents. Despite progress in identifying single protein markers, scalable methods for detecting synergistic protein interactions driving drug susceptibility remain limited. Machine learning models such as random forests may offer a robust framework for capturing non-linear protein interactions across diverse cancer types. ResultsOur study presents synerOmics, a scalable framework for identifying putative synergistic protein interactions by leveraging parent-child co-occurrences in random forest regression trees to reduce the interaction search space. We validated our approach using simulated data and two independent cancer proteomic datasets, identifying both pan-cancer and breast cancer-specific markers associated with drug susceptibility. Synergistic interactions that consistently replicated across datasets were enriched for endoplasmic reticulum stress pathways. Notably, shared targets included established sensitivity markers for tyrosine kinase inhibitors (TKIs) and revealed a resistance-associated network centred on ATL3, which demonstrated both prognostic and predictive relevance. ConclusionsApplying synerOmics to the largest cancer cell line proteomic dataset to date, we identified ATL3 as a strong candidate biomarker for lapatinib resistance in breast cancer, with superior predictive performance compared to the current gold standard sensitivity biomarker, ERBB2. HighlightsO_LIWe present a machine learning framework for drug response biomarker discovery, leveraging the largest proteomic cancer cell line dataset, ProCan-DepMapSanger C_LIO_LIATL3 is proposed as a candidate predictive biomarker for lapatinib resistance in breast cancer C_LIO_LIElevated expression of a novel resistance-conferring subcluster centered on ATL3 is associated with poor prognosis across 11 TCGA cancer types C_LIO_LIBaseline drug resistance may be broadly driven by stress pathways, with ER stress and protein ATL3 implicated in ER-phagy in response to TKIs. C_LI

cancer biology↗

bioRxiv2025

Gαq/11 signaling counteracts endothelial dysfunction in the brain and protects cognition in aged mice

BackgroundCerebral small vessel disease (cSVD) is a major cause of stroke and dementia, and is associated with increased blood-brain barrier permeability, neuroinflammation, and endothelial dysfunction. Endothelial Gq/11 proteins are involved in vascular tone regulation and have been shown to affect capillary blood flow in the brain. Since factors downstream of activated Gq/11 proteins, such as endothelial NO synthase (eNOS) activity are discussed in cSVD, we wondered whether the brain endothelial Gq/11 signalling pathway might influence cSVD-related pathology. MethodsHere, we generated mice carrying a brain endothelial-specific deletion of the Gq/11 signalling and characterised these mice using different imaging and staining techniques, as well as behaviour tests measuring cognition in adult and aged mice. Immunoblots, electrophysiology, perfusion measurements, and in vitro experiments complemented those techniques. FindingsThe brain endothelial Gq/11 signalling pathway preserves normal vascular reactivity, and its loss resembles mild endothelial dysfunction in the brain. While the vessel structure was maintained in adult mice, a deletion of the Gq/11 signalling led to capillary rarefaction and blood-brain barrier disruption in aged mice. These effects were accompanied by disturbed VEGF signalling and an increase in senescence markers and oxidative stress in the vasculature, culminating in cognitive impairment with increased tau phosphorylation in the cortex and hippocampus, and decreased myelination in the white matter. InterpretationThese findings reflect the main hallmarks of cSVD and demonstrate a protective role of Gq/11 in endothelial cells in ageing. Furthermore, our results show that the combination of cerebral endothelial dysfunction and ageing accelerates cognitive impairment. FundingResearch was supported by grants from the European Research Council (2019-WATCH-810331 to R.N., V.P., and M.S.), the Deutsche Forschungsgemeinschaft (SCHW 416/12-1 to M.S.; WE 6456/1-1 to J.W.; GRK1957 to M.S., H.M.-F., and J.W.), the institutional priority program MI-VascAD of the University of Lubeck (to H.M.-F. and J.W.), and the Marie-Sklodowska-Curie European Unions Horizon 2020 research program (ENTRAIN-813294 to M.S. and J.W.). RESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSCerebral small vessel disease (cSVD) is associated with advanced age, hypertension, and metabolic diseases. It is considered causal for a substantial part of stroke and dementia cases. Endothelial dysfunction is described as being present in all of the diseases mentioned, and it is discussed to play a role in the development of cSVD. However, most of the evidence is correlational rather than causal, and studies are usually carried out on subjects with an underlying disease for which endothelial dysfunction is a side effect. Added value of this studyHere, we describe a novel brain endothelial signalling pathway that protects against endothelial dysfunction and loss of cerebrovascular reactivity. Without Gq/11 signalling exclusively in the brain endothelium, mice show an impaired ability to increase brain perfusion in response to vasodilatory stimuli, such as neuronal activity. These mice, combined with an older age, develop vessel rarefaction and cognitive dysfunction, which can be explained by increased tau phosphorylation and white matter alteration. Implications of all the available evidenceThese findings, in the context of the existing studies, suggest that endothelial dysfunction per se is sufficient to induce cognitive impairment. They imply that the diagnoses and treatments for diseases associated with cognitive impairment should focus more on a dysfunctional endothelium. The Gq/11 signalling pathway offers a new approach to address treatment endeavours in cSVD and, more broadly, in all diseases associated with a higher risk of vascular dementia and stroke.

neuroscience↗

bioRxiv2025

Isotropic, aberration-corrected light sheet microscopy for rapid high-resolution imaging of cleared tissue

Light sheet microscopy is the ideal technique for multiscale imaging of large and cleared tissues, and it is desirable to achieve the highest possible isotropic resolution across the entire sample. However, isotropic resolution for a centimeter-sized sample has only been achieved with slow and often aberrated, axially scanned light sheets, resulting in a low resolution of several micrometers. Here, we introduce a compact, high-speed light sheet fluorescence microscope with isotropic sub-micron resolution optimized for cleared tissue. We introduce three major opto-mechanical innovations using off-the-shelf optics to achieve an isotropic resolution of 850 nm across samples up to 1 cm3 and refractive indices ranging from 1.33 to 1.56, using mechanical tiling with a field of view of 800 {micro}m x 800 {micro}m. We show that combining an air objective and a meniscus lens achieves an axially swept light sheet with sub-micron diffraction-limited resolution and aberration correction. The effective field of view is increased 2-fold by correcting the field curvature of the light sheet with a concave mirror in the remote focusing unit. Furthermore, the imaging speed is enhanced 10-fold by adapting the light sheets motion with a closed-loop feedback, reaching 100 frames per second while maintaining isotropic resolution across the large field of view. Finally, we showcase the performance of our light sheet system for imaging from subcellular up to centimeter scale in cleared zebrafish, mouse cochlea, and mouse brain using various clearing methods.

developmental biology↗

bioRxiv2024

varVAMP: automated pan-specific primer design for tiled full genome sequencing and qPCR of highly diverse viral pathogens.

Time- and cost-saving surveillance of viral pathogens is achieved by tiled sequencing in which a viral genome is amplified in overlapping PCR amplicons and qPCR. However, designing pan-specific primers for viral pathogens that have high genomic variability represents a major challenge. Here, we present a bioinformatics command-line tool, called varVAMP (variable virus amplicons). It relies on multiple sequence alignments of highly variable virus sequences and enables automatic pan-specific primer design for qPCR or tiled amplicon whole genome sequencing. The varVAMP software guarantees pan-specificity by two means: it designs primers in regions with minimal variability and introduces degenerate nucleotides into primer sequences to compensate for common sequence variations. We demonstrate varVAMPs utility by designing and evaluating novel pan-specific primer schemes suitable for sequencing the genomes of SARS-CoV-2, Hepatitis E virus, rat Hepatitis E virus, Hepatitis A virus, Borna-disease-virus-1, and Poliovirus. Moreover, we established highly sensitive and specific Poliovirus qPCR assays that could potentially simplify current Poliovirus surveillance. Importantly, wet-lab and bioinformatic techniques established for SARS-CoV-2 tiled amplicon sequencing were readily transferable to these new primer schemes and will allow sequencing laboratories to extend their established methodology to other human pathogens.

bioinformatics↗

bioRxiv2022

Melatonin drugs inhibit SARS-CoV-2 entry into the brain and virus-induced damage of cerebral small vessels

COVID-19 is a complex disease with short- and long-term respiratory, inflammatory and neurological symptoms that are triggered by the infection with SARS-CoV-2. Invasion of the brain by SARS-CoV-2 has been observed in humans and is postulated to be involved in post COVID condition. Brain infection is particularly pronounced in the K18-hACE2 mouse model of COVID-19. Here, we show that treatment of K18-hACE2 mice with melatonin and two melatonin-derived marketed drugs, agomelatine and ramelteon, prevent SARS-CoV-2 entry in the brain thereby reducing virus-induced damage of small cerebral vessels, immune cell infiltration and brain inflammation. Brain entry of SARS-CoV-2 through endothelial cells is prevented by melatonin through allosteric binding to human angiotensin-converting enzyme 2 (ACE2), which interferes with the cell entry receptor function of ACE2 for SARS-CoV-2. Our findings open new perspectives for the repurposing of melatonergic drugs in the prevention of brain infection by SARS-CoV-2 and COVID-19-related long-term neurological symptoms.

pharmacology and toxicology↗

bioRxiv2020

Multivariate pattern analysis of brain structure predicts functional outcome after auditory-based cognitive training interventions

BackgroundCognitive gains following cognitive training interventions (CT) are associated with improved functioning in people with schizophrenia (SCZ). However, considerable inter-individual variability is observed. Here, we evaluate the sensitivity of brain structural features to predict functional response to auditory-based cognitive training (ABCT) at a single subject level. MethodsWe employed whole-brain multivariate pattern analysis (MVPA) with support vector machine (SVM) modeling to identify grey matter (GM) patterns that predicted higher vs. lower functioning after 40 hours of ABCT at the single subject level in SCZ patients. The generalization capacity of the SVM model was evaluated by applying the original model through an Out-Of-Sample Cross Validation analysis (OOCV) to unseen SCZ patients from an independent sample that underwent 50 hours of ABCT. ResultsThe whole-brain GM volume-based pattern classification predicted higher vs. lower functioning at follow-up with a balanced accuracy (BAC) of 69.4% (sensitivity 72.2%, specificity 66.7%) as determined by nested cross-validation. The neuroanatomical model was generalizable to an independent cohort with a BAC of 62.1% (sensitivity 90.9%, specificity 33.3%). ConclusionsIn particular, greater baseline GM volume in regions within superior temporal gyrus, thalamus, anterior cingulate and cerebellum -- predicted improved functioning at the single-subject level following ABCT in SCZ participants.

neuroscience↗