Biology subjects

Wirth, J.

Publications and source records attributed to Wirth, J..

6 recordsLinked to original sources

bioRxiv2026

Modeling pancreatic cancer tumor stroma co-evolution in an in ovo model

Pancreatic ductal adenocarcinoma (PDAC) is characterized by a dense, desmoplastic microenvironment that drives disease progression, yet conventional models fail to capture this complex tumor-stroma coevolution. Here, we utilize the chick chorioallantoic membrane (CAM) platform to investigate tumor-stroma interactions using murine PDAC cell lines and patient-derived organoids (PDOs). Integrating single-cell RNA sequencing and spatial transcriptomics, we show that the CAM microenvironment supports the emergence of complex tumor ecosystems while preserving patient-specific characteristics. Within five days, in ovo tumors faithfully recapitulated the structural and molecular features of parental tumors. Histological analysis revealed the rapid recruitment and spatial organization of heterogeneous host cancer-associated fibroblast (CAF) populations, showcasing distinct myofibroblastic and inflammatory stromal states. Crucially, the model preserved intrinsic tumor heterogeneity and permitted functional interrogation of subtype-specific extracellular matrix remodeling and metastatic dissemination. Together, our findings demonstrate that the CAM provides a highly permissive niche for tumor-stroma coevolution. As a rapid, scalable, and biologically relevant platform, this in ovo model offers a powerful approach for studying stromal composition, metastatic progression, and patient-specific tumor biology in pancreatic cancer.

cancer biology↗

bioRxiv2025

Single cell spatial transcriptomics integration deciphers the morphological heterogeneity of atherosclerotic carotid arteries

The process of arterial atherosclerosis is characterised by accumulation of lipids and fibrous material with accompanying inflammation. As plaques progress, they restrict blood flow and cause rupture, which results in life threatening organ ischemia and dysfunction. Although extensively studied, a clear understanding of plaque heterogeneity and mechanisms that trigger their destabilization remains elusive. Our study reveals the molecular microarchitecture of human carotid artery plaques, using bulk and single-cell RNA sequencing combined with single cell spatial transcriptomics, for which we present optimized cell segmentation algorithms. We identified distinct plaque morphologies linked to different cell type compositions, impacting early and advanced lesion formation, as well as destabilization. Spatial transcriptomics enabled us further to determine an inflammatory smooth muscle cell subtype, localize regions of neovascularization, and assign hotspots for macrophage activity within distinct cellular neighbourhoods across lesions. For different macrophage substates, we propose gradual and locally contained transdifferentiation of subluminal inflammatory HMOX1+ macrophages into a lipid-handling TREM2+ phenotype within border zones of the fibrous cap and necrotic core. Our findings provide insight into the complex heterogeneity of human atherosclerosis by unravelling location and proximity of different mural and immune cell substates involved in plaque progression and vulnerability.

cell biology↗

bioRxiv2025

InSituPy -- A framework for histology-guided, multi-sample analysis of single-cell spatial transcriptomics data

Single-cell spatial transcriptomics (scST) methodologies allow, in combination with histological stainings, an unprecedented view on disease progression. To comprehensively analyze scST data, bioinformatic analysis frameworks need to integrate the diverse set of data modalities and, just as importantly, enable the joint analysis of multiple datasets from clinical or experimental cohorts together with its corresponding metadata. Here, we present the InSituPy framework to comprehensively analyze single-cell spatial transcriptomic data from a multi-sample level down to the cellular and subcellular level. The framework contains analysis workflows for the integration of image data as well as pathological and biological expert knowledge. Increasing the accessibility of the data for non-bioinformaticians, the framework opens new ways of generating hypotheses, especially in the context of translational research.

bioinformatics↗

bioRxiv2024

Characterization of root exudates of black oat in the presence of interspecific weed species neighbours and intraspecific neighbours, and their effects on root traits

Root exudates are composed of primary and secondary organic compounds that function as signalling molecules and play important roles in plant-environment interactions. The quantity and composition of root exudates vary depending on the species, genotype, and environmental conditions, including the presence and identity of neighbouring plants. Although cover crops are commonly used in agricultural practices for their ecosystem services, such as weed suppression, pathogen control, and soil structure improvement, studies on their root exudates are limited. Our study provides the first characterization of the root exudates of black oat interacting with weed neighbours, redroot pigweed and blackgrass, as well as with neighbours of the same species, black oat. We investigated how these interactions influence the black oat root exudation patterns. Furthermore, we investigated the impact of black oat presence on neighbours and how exposure to black oat root exudate treatments affects the root traits of weeds. The upregulated compounds detected in root exudates in response to neighbouring plants primarily belonged to the organic oxygen compounds superclass, with most of which identified as amino acids and carbohydrates. In the presence of redroot pigweed, a general increase in root exudation was observed, with amino acids and sugar sulphates being upregulated. The presence of black oat had varying effects among the neighbouring plants. While significant decreases observed and black oat in redroot pigweed root traits, an increase was observed in blackgrass. Similarly, more pronounced effects were observed in redroot pigweed compared to blackgrass upon root exudate application. This study provides a characterization and insights into the dynamic nature of root exudates and their influence on root traits and plant interactions.

plant biology↗

bioRxiv2022

Spatial Transcriptomics Using Multiplexed Deterministic Barcoding in Tissue

In this study, we present a multiplexed version of deterministic barcoding in tissue (xDbit) to acquire spatially resolved transcriptomes of nine tissue sections in parallel. New microfluidic chips were developed to spatially encode mRNAs over a total tissue area of 1.17 cm2 with spots of 50 mx50 m. Optimization of the biochemical protocol increased read and gene counts per spot by one order of magnitude compared with previous reports. Furthermore, the introduction of alignment markers allows seamless registration of images and spatial transcriptomic spot coordinates. Together with technological advances, we provide an open-source computational pipeline to transform raw sequencing data from xDbit experiments into the AnnData format. The functionality of xDbit was demonstrated by the acquisition of 18 spatially resolved transcriptomic datasets from five different murine organs, including cerebellum, liver, kidney, spleen, and heart. Factor analysis and deconvolution of xDbit spatial transcriptomes allowed for in-depth characterization of the murine kidney.

genomics↗

bioRxiv2020

A polycomb-independent role of EZH2 in TGFβ1-damaged epithelium triggers a fibrotic cascade with mesenchymal cells

To restore organ homeostasis, a myriad of cell types need to activate rapid and transient programs to adjust cell fate decisions and elicit a collective behaviour. Characterisation of such programs are imperative to elucidate an organs regenerative capacity and its aberrant repair in disease. By modelling epithelial-mesenchymal crosstalk, we provide direct evidence for transforming growth factor {beta}1 (TGF{beta}1)-damaged epithelium initiating a bi-directional fibrotic cascade with the mesenchyme. Strikingly, TGF{beta}1-damaged epithelia facilitates the release of Enhancer of Zester Homolog 2 (EZH2) from Polycomb Repressive Complex 2 (PRC2) to establish a novel fibrotic transcriptional complex of EZH2, RNA-polymerase II (POL2) and nuclear actin. Perturbing this complex by disrupting epithelial EZH2 or actomyosin remodelling abrogates the fibrotic crosstalk. The liberation of EZH2 from PRC2 is accompanied by an EZH2-EZH1 switch to preserve global H3K27me3 occupancy. Our results reveal an important non-canonical function of EZH2, paving the way for therapeutic interventions in fibrotic disease.

cell biology↗