Biology subjects

Wilhelm, C.

Publications and source records attributed to Wilhelm, C..

14 recordsLinked to original sources

bioRxiv2026

Micro-Cm: restrictase-free microbiome-wide chromosome conformation profiling

Mobile genetic elements like plasmids, viruses and transposons can considerably augment the genomic repertoire of individual bacterial members of a complex multi-species microbiome and influence community dynamics. As linking a mobile element to its bacterial host based on metagenome sequencing alone proves challenging, such assays have been augmented with high-throughput chromosome conformation capture (Hi-C). However, the efficacy of Hi-C metagenomics is constrained by the protocol limitations and a lack of ground-truth reference datasets. In order to overcome these limitations, we present Micro-C metagenomics (Micro-Cm) - an adaptation of a superior, restrictase-free Micro-C technique for processing microbiome samples and mapping plasmid-host associations. We validated the developed experimental protocol and bioinformatic workflow on a simulated, defined consortium of diverse gut bacterial species and applied them to a long-read human gut microbiome sample. The proportion of valid reads in the synthetic community was an order of magnitude higher than that observed in multiple Hi-C metagenomic studies. For both samples, we obtained high-quality contact maps, which in the case of the synthetic community revealed fine-scale chromosome interactions. Moreover, successful recovery of plasmid-host interactions in the simulated community validated the method, which we then applied to the real stool sample. Our plasmid-host association analysis in a complex bacterial community successfully identified bacterial hosts for most of the identified complete plasmids. Our results show that Micro-Cm method improves profiling of complex microbiomes, exploration of mobile genetic element dynamics and community-wide, detailed investigation of chromosomal conformation patterns.

microbiology↗

bioRxiv2025

Shaping and probing living tissues with magnetic bioprinting

Mechanical and geometric cues play a crucial role in vivo, regulating both morphogenetic processes and proper tissue function. This is particularly evident in skeletal muscle, where aligned architecture is essential for myogenesis and functional force generation. However, precisely engineering tissue geometry at both macroscopic and microscopic scales while simultaneously controlling internal mechanical forces remains a significant challenge. In this study, we introduce a magnetic tissue engineering platform based on a magnetic bioprinting technique, enabling precise control of biophysical cues that guide in vitro tissue morphogenesis. Applied here to skeletal muscle, this approach allows for the rapid fabrication of cohesive tissues in any desired shape using cells labeled with magnetic nanoparticles. Additionally, multiple cell types can be incorporated and spatially organized within the same construct through magnetic segregation. Optimizing tissue geometry further enables magnetic actuation, including the ability to trap and maintain tissue shape over time. Furthermore, this magnetic platform facilitates the investigation of how tissue architecture influences mechanical properties, such as resistance to rupture. Overall, this study highlights the significant potential of magnetic bioprinting and stimulation for controlling tissue morphology and advancing biomechanical research.

bioengineering↗

bioRxiv2025

Label-free Machine Learning Prediction of Chemotherapy on Tumor Spheroids using a Microfluidics Droplet Platform

To rapidly evaluate the effects of anticancer treatments in 3D models, an integrated approach is proposed, combining a droplet-based microfluidic platform for spheroid formation and single-spheroid chemotherapy application, label-free morphological analysis, and machine learning to assess treatment response. Morphological features of spheroids, such as size and color intensity, are extracted and selected using the Multivariate Information-based Inductive Causation (MIIC) algorithm, and used to train a neural network for spheroid classification into viability classes, derived from metabolic assays performed within the same platform as a benchmark. The model was tested on Ewing sarcoma cell line and patient-derived xenograft (PDX) cells, demonstrating robust performance across datasets. It accurately predicts spheroid viability, used to generate dose-response curves and to determine half-maximal inhibitory concentration (IC50) values comparable to traditional biochemical assays. Notably, a model trained on cell line spheroids successfully classifies PDX spheroids, highlighting its adaptability. Compared to convolutional neural network-based approaches, this method works with smaller training datasets and provides greater interpretability by identifying key morphological features. The droplet platform further reduces cell requirements, while single spheroid confinement enhances classification quality. Overall, this label-free experimental and analytical platform is confirmed as a scalable, efficient, and dynamic tool for drug screening.

bioengineering↗

bioRxiv2025

Magnetic printing and actuation of stretchable muscle tissue

While the link between tissue organization, stimulation, and function is now acknowledged as crucial for tissue development, engineering tissues with precise, long-lasting shapes and the capability for mechanical stimulation remains challenging. This study addresses this challenge by developing a next-generation magnetic bioprinting approach to create anisotropic, shape-controlled, scaffold-free, and stretchable skeletal muscle constructs. Murine skeletal muscle cells and human induced pluripotent stem cell-derived skeletal muscle cells, labeled with iron oxide nanoparticles, were magnetically bioprinted into wrench-shaped tissues. Their magnetic properties allowed these tissues to be clipped onto magnetic needles, preserving their shape over two weeks of culture while promoting anisotropic differentiation and myoblast fusion. Additionally, the magnetic tissues could be stretched by up to 100%, enhancing their anisotropy and improving muscle maturation. This magnetic toolbox demonstrates significant advancements in muscle tissue engineering, as evidenced by enhanced indicators of myoblast differentiation, including cell fusion, increased myogenic maturation and contractility. These findings highlight the potential of magnetic-based techniques for developing advanced muscle-on-chip systems and other complex tissue constructs.

bioengineering↗

bioRxiv2025

Magnetite Nanoparticle Photothermal Therapy in a Pancreatic Tumor-on-Chip: A Dual-Action Approach Targeting Cancer Cells and their Microenvironment

The application of magnetite nanoparticles (MagNPs) for photothermal therapy (MagNP-PTT) has recently expanded in cancer treatment. This study introduces MagNP-PTT in a tumor-on-chip model to target highly aggressive pancreatic ductal adenocarcinoma (PDAC). A tumor-on-chip system was developed using PANC-1 PDAC cells embedded in a collagen type I extracellular matrix and cultured for one week to form tumor spheroids. This platform serves as the foundation for applying PTT in a model system that is aimed to mimic the native tumor microenvironment. MagNPs efficiently penetrate the tumor spheroids, achieving controlled heating via near-infrared (NIR) light. By adjusting nanoparticle concentration and laser power, temperature increments of 2{degrees}C between 38-48{degrees}C were established. Temperatures above 44{degrees}C significantly increased cell death, while lower temperatures allowed partial recovery. Beyond inducing cancer cell death, MagNP-PTT altered the extracellular matrix, and triggered a slight epithelial-mesenchymal transition marked by increased vimentin expression. These findings highlight MagNP-PTT as a dual-action therapy, targeting both tumor cells and their microenvironment, offering a novel approach for overcoming stromal barriers in pancreatic cancer treatment. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=99 SRC="FIGDIR/small/636875v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@9b9c20org.highwire.dtl.DTLVardef@272c7aorg.highwire.dtl.DTLVardef@1d91021org.highwire.dtl.DTLVardef@1b1ea8d_HPS_FORMAT_FIGEXP M_FIG SYNOPSIS TABLE OF CONTENTS C_FIG

cancer biology↗

bioRxiv2025

Harnessing hydrodynamics for high-yield production of extracellular vesicles from stem cells spheroids with specific cargo profiling

This study presents a novel method and device for the hydrodynamic production of extracellular vesicles (EVs) derived from biomimetic multicellular 3D spheroids, enabling high-throughput particle release that is 10 to 20 times higher than in non-stimulated conditions. The device facilitates the formation of spheroids from human mesenchymal stem cells (hMSCs), offering an all-in-one approach for both spheroid generation and EV release. Production times are reduced to just a few hours, with yield further increased by alternating periods of high hydrodynamic flow and spheroid recovery in a sequential production approach. Using this system, we explored the impact of hydrodynamic and starvation conditions on the protein cargo of EVs, identifying distinct protein markers through proteomics. Specifically, hydrodynamic stimulation enriched EVs in plasma membrane-derived and mitochondrial proteins, revealing divergent biogenesis pathways. Importantly, the produced EVs exhibited therapeutic properties, with demonstrated effects in wound healing, angiogenesis, and anti-inflammatory responses, some showing enhanced efficacy under hydrodynamic stimulation.

bioengineering↗

bioRxiv2024

Mechanical constraints organize 3D tissues and orchestrate muscle differentiation

Biological tissues achieve proper shape and ordered structures during development through responses to internal and external signals, with mechanical cues playing a crucial role. These forces guide cellular organization, leading to complex self-organizing structures that are foundational to embryonic patterns. Emerging theories and experiments suggest that "topological morphogens" drive these processes. Despite the predominance of three-dimensional (3D) structures in biology, studying 3D tissues remains challenging due to limited model systems and the complexity of modeling. Here, we address these challenges by using self-organized cellular aggregates, specifically spindle-shaped C2C12 myoblasts, subjected to controlled mechanical stretching. Our findings reveal that these cells form a multilayered, actin-oriented tissue structure, where mechanical forces drive long-range 3D organization and muscle differentiation. Notably, tissue surface emerges as a hotspot for differentiation, correlating with directional order as shown by single molecule fluorescent in situ hybridization. Significance StatementWe explore how cells work together to form complex structures, particularly in 3D, using muscle precursors cells (C2C12 myoblasts) as a model. By applying controlled stretching forces, we found that these cells self-organize into layered tissues that guide their transformation into muscle. This research highlights the critical role of physical forces in shaping tissues, suggesting that the way cells are physically arranged and stretched in three dimensions can significantly influence their behavior and function. Our findings offer new insights into how tissues develop and could have implications for tissue engineering, where creating the right 3D environment is key to successful tissue growth and repair.

biophysics↗

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↗

bioRxiv2024

Anabolic lipid metabolism regulates adipose type 2 innate lymphoid cell differentiation to maintain metabolic health

Group 2 innate lymphoid cells (ILC2) residing in the adipose tissue play an important role in maintaining the metabolic health and energy balance of the organisms. In obesity ILC2 numbers are reduced and their function is impaired, leading to the progression of metabolic inflammation. However, which events impact on ILC2 biology in the adipose tissue in obesity remains unresolved. Here, we find that high fat diet (HFD)-induced obesity in mice results in the metabolic reprogramming of adipose ILC2, impairing mitochondrial function and the expression of the enzyme Acetyl-CoA carboxylase 1 (ACC1). Investigating a possible connection between ACC1 and obesity-induced changes in ILC2, we show that fatty acids directly reduce the expression of ACC1, while pharmacological inhibition of ACC1 diminishes mitochondrial function and ILC2 metabolism. Furthermore, deletion of ACC1 in ILC2 phenocopies the overall reduction and functional impairment of ILC2 observed in obesity, which ultimately leads to increased triglycerides in circulation, adipose tissue hypertrophy and inflammation, even in the absence of HFD. Through single-cell RNA sequencing analysis we uncover that HFD-feeding or deletion of ACC1 results in the accumulation of undifferentiated ILC2 and ILC progenitors in the adipose tissue, suggesting that ACC1 may primarily regulate the maturation of ILC2. Together, these results reveal that obesity could predominately impair adipose ILC2 differentiation and activation by impacting on the expression of ACC1, rather than inducing cell death through lipid overload and lipotoxicity.

immunology↗

bioRxiv2023

Imaging membrane damage in ferroptosis and necrosis by wash-free fluorogenic chemical probes

Selectively labelling cells with damaged membranes is needed in contexts as simple as identifying dead cells in culture, or as complex as imaging membrane barrier functionality in vivo. The commonly used dyes are permanently coloured/fluorescent dyes that are simply excluded by intact membranes, but to achieve good image contrast therefore requires removing their extracellular signal by washing or background subtraction, which are not possible in vivo. Here, we develop fluorogenic probes which sensitively and selectively reveal damaged cells, without needing washing steps since their fluorescence turns on from near-zero background. From a set of novel fluorogenic probes impermeabilised by sulfonations along different vectors, we identify a specific disulfonated fluorogenic scaffold that enters cells only upon membrane damage, where it is enzymatically activated to mark them. The esterase probe iPS-FS2 is a reliable tool to reveal live cells that have been permeabilised by biological, biochemical, or physical membrane damage; and it can be used in multicolour microscopy. We confirm the modularity of this approach by also adapting it for redox-unmasked cell-excluded probes with improved hydrolytic stability. This scaffold-based design thus provides tools for wash-free in vivo imaging of membrane damage, which is relevant across many pathologies. The insightss gained from these probes should also be translatable to damage-targeted prodrugs, for selective therapy of membrane-compromised cells. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=145 SRC="FIGDIR/small/543437v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@1594016org.highwire.dtl.DTLVardef@7e7053org.highwire.dtl.DTLVardef@1008cb0org.highwire.dtl.DTLVardef@1148bd7_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2023

Simple droplet microfluidics platform for drug screening on cancer spheroids

3D in vitro biological systems are progressively replacing 2D systems to increase the physiological relevance of cellular studies. Microfluidics-based approaches can be powerful tools towards such biomimetic systems, but often require high-end complicated and expensive processes and equipments for microfabrication. Herein, a drug screening platform is proposed, minimizing technicality and manufacturing steps. It provides an alternate way of spheroid generation in droplets in tubes. Droplets microfluidics then elicit multiple droplets merging events at programmable times, to submit sequentially the spheroids to chemotherapy and to reagents for cytotoxicity screening. After a comprehensive study of tumorigenesis within the droplets, the system is validated for drug screening (IC50) with chemotherapies in cancer cell lines as well as cells from patient-derived-xenografts (PDX). As compared to microtiter plates methods, our sytem reduces the initial amout of cell up to 10 times and opens new avenues towards primary tumors drug screening approaches.

cancer biology↗

bioRxiv2022

Magnetic bioprinting of stem-cell based tissues

An attractive approach in cell therapies and medically oriented nanotechnologies is to interface magnetic nanoparticles with cells. This will supply the cells with sufficient magnetization for theranostic applications and for external magnetic field manipulation. In tissue engineering, one challenge is to produce tissue analogues that are large, precisely organized, and responsive to stimuli, preferably without the need for an artificial supporting scaffold. One powerful tool for such biofabrication is certainly the bioprinting technology. In magnetic tissue engineering, it appears possible to use magnetic forces to manipulate cells, both individually and within aggregates, and thereby to produce three-dimensional artificial tissues with inherent capacities for further physical stimulation, a possibility that bioprinting does not offer yet. We here introduce the feasibility of using magnetic forces created by external (micro)magnets to form 3D tissue-like scaffold-free structures. Because stem cells are essential in tissue engineering, such magnetic technologies were developed with magnetized stem cells, and applied for instance to vascular or cartilage tissue engineering. One precondition to this approach, which lies in the magnetization of (stem) cells endowed through internalization of iron oxide magnetic nanoparticles, is to ensure the safety of magnetic nanoparticles with respect to cellular functions, which is initially discussed. Finally, we introduce a magnetic tissue stretcher which, in a single step, allows to create a tissue composed of any type of component cell, then to mature it, stimulate it by compression or stretching at any desired frequency, e.g. cyclically, opening new possibilities in the cardiac muscle tissue engineering field.

bioengineering↗

bioRxiv2022

Surface tension drives neuronal sorting in magnetically engineered brain-like tissue

Engineered 3D brain-like models have advanced the understanding of neurological mechanisms and disease, yet their mechanical signature, while fundamental for brain function, remains understudied. The surface tension for instance controls brain development and is a marker of cell-cell interactions. Here, we engineered 3D magnetic brain-like tissue spheroids composed of intermixed primary glial and neuronal cells at different ratios. Remarkably, the two cell types self-assemble into a functional tissue, with the sorting of the neuronal cells towards the periphery of the spheroids, whereas the glial cells constitute the core. The magnetic fingerprint of the spheroids then allows their deformation when placed under a magnetic field gradient, at a force equivalent to a 70 g increased gravity at the spheroid level. The tissue surface tension and elasticity can be directly inferred from the resulting deformation, revealing a transitional dependence on the glia/neuron ratio, with the surface tension of neuronal tissue being much lower. This provides the underlying mechanical explanation for the exclusion of the neurons towards the outer spheroid region, and depicts the glia/neuron organization as a surface tension-driven sophisticated mechanism that should in turn influence brain development and homeostasis.

bioengineering↗

bioRxiv2021

Multiparameters dependance of tissue shape maintenance in myoblasts multicellular aggregates: the role of intermediate filaments.

Liquid and elastic behavior of tissues drives their morphology and their response to the environment. They appear as the first insight on tissue mechanics. We explore the role of individual cell properties on spheroids of mouse muscle precursor cells by developing a fully automated surface tension and Youngs modulus measurement system. Flattening multicellular aggregates under magnetic constraint, we show that rigidity and surface tension act as highly sensitive macroscopic reporters closely related to microscopic local tension and effective adhesion. Shedding light on the major contributions of acto-myosin contractility, actin organization and intercellular adhesions, we reveal the role of desmin organization on the macroscopic mechanics of this tissue model.

biophysics↗