Biology subjects

Krauss, S.

Publications and source records attributed to Krauss, S..

18 recordsLinked to original sources

bioRxiv2026

Modelling mechanisms and treatment of cholangiopathies with a bile duct on a chip

Background and aims Model systems for bile duct disorders are needed for testing therapeutic interventions. Current models have poor human relevance or limited potential for recreating the complex bile duct microenvironment at scale. We aimed to generate a humanized microphysiological system to model and treat cholangiopathies. Methods An in vitro bile duct was created using 3D printed microfluidic chips containing a collagen-embedded canal seeded with patient-derived primary human cholangiocytes. Barrier permeability and compound transport across the epithelium was measured, and disruption of the barrier was performed with lipopolysaccharide treatment. The duct was challenged with the known hepatotoxicant Chlorpromazine. Biliatresone was used to model biliary-atresia and treated using N-acetyl-L-cysteine. Results Cholangiocytes in the bile duct chip established a tight, polarized epithelial barrier. Verapamil and Linerixibat inhibited transport of rhodamine 123 and cholyl-lys-fluorescein respectively with 66 % (p = 0.0004) and 57 % (p = 0.03) reduction. 10 g/mL lipopolysaccharide led to a loss of epithelial barrier integrity, measured by an increase of over 1000 % in leakage of both 3 kDa (p = 0.0002) and 10 kDa dextran (p = 0.0001) along with upregulation of cytokines. Chlorpromazine displayed dose-dependent toxicity with EC50 values of 84, 140 and 96 M for three patient lines. Biliatresone induced a dose-dependent abnormal phenotype with loss of viability. The induced phenotype could be treated with N-acetyl-L-cysteine, improving viability from 23 % to 59 % (p < 0.0001) with treatment of 2 g/mL Biliatresone. Conclusions Our novel platform allows complex studies of bile duct biology, testing of off-target effects from drugs and treatment of a disease phenotype.

cell biology↗

bioRxiv2025

Tankyrase inhibition demonstrates anti-fibrotic effects in preclinical pulmonary fibrosis models

BackgroundIdiopathic pulmonary fibrosis (IPF) is a progressive and fatal lung disease with limited treatment options. Although transforming growth factor beta 1 (TGFB1, TGF{beta}) is a key driver of fibrosis, additional signaling pathways, including wingless-type mammary tumor virus integration site (WNT)/{beta}-catenin and yes-associated protein 1 (YAP), contribute to IPF pathogenesis. Clinical data indicate that inhibition of TGF{beta} alone provides limited efficacy or is associated with toxicity, underscoring the need for alternative therapeutic approaches. Tankyrase (TNKS) 1 and 2 are post-translational regulators of WNT/{beta}-catenin and YAP signaling and therefore represent promising antifibrotic targets. OM-153, a potent and selective TNKS inhibitor, exhibits pharmacological properties suitable for preclinical development in IPF. MethodsPrimary normal human lung fibroblasts (NHLF), Scar-in-a-Jar assays, lung-on-a-chip models, and precision-cut lung slices (PCLS) from non-pulmonary fibrosis (non-PF) tissue were stimulated with an IPF-relevant cytokine cocktail (IPF-RC) designed to accurately recapitulate the pro-fibrotic environment and compared to TGF{beta}. These models, with bleomycin-challenged mice and PCLS from end-stage pulmonary fibrosis (PF) patients, were treated with OM-153. Fibrosis markers, extracellular matrix (ECM) components, and signaling pathway-specific gene expression or protein markers were assessed by real-time qRT-PCR, RNA sequencing, immunoblotting, ELISA, and immunofluorescence. ResultsOM-153 stabilized the direct TNKS targets axin 1 (AXIN1) and angiomotin-like 1 (AMOTL1), suppressed WNT/{beta}-catenin and YAP signaling. In parallel, it reduced profibrotic ECM expression across in vitro, in vivo, and ex vivo IPF models. ConclusionsSelective TNKS inhibition by OM-153 demonstrates broad antifibrotic activity in multiple preclinical models, supporting further development as a potential disease-modifying strategy for IPF. Shareable abstractOur findings show that the potent and selective TNKS inhibitor OM-153 suppresses WNT/{beta}-catenin and YAP signaling, reducing pro-fibrotic ECM expression in preclinical IPF models, supporting TNKS inhibition as a novel antifibrotic strategy.

cell biology↗

bioRxiv2025

Reconstituting epiblast-extraembryonic endoderm interactions restores anterior-ventral patterning in stem cell-based embryo models.

During mammalian embryogenesis, reciprocal interactions between the epiblast and extraembryonic endoderm are critical for germ layer specification and body plan development during gastrulation. Gastruloids recapitulate aspects of gastrulation in the absence of extraembryonic cues, resulting in a predominantly posteriorized and dorsalized phenotype with a limited lineage diversity. Here, we establish a modular co-aggregation ("aggregoid") strategy that spatially couples embryonic and extraembryonic endoderm-like cells to reconstruct key interactions in vitro. This drives self-organized anterior-ventral patterning together with the emergence of node- and notochord-like structures, enriched endodermal populations, and increased mesodermal diversity, including cardiopharyngeal lineages and vascular endothelium. Our findings demonstrate that modular engineering of lineage interactions can direct self-organized patterning in stem-cell-based embryo models and provide a versatile framework for generating defined morphotypes.

developmental biology↗

bioRxiv2025

Data-driven model reveals increased stability of CAG-expanded huntingtin RNA due to MID1 binding

RNA-binding proteins (RBP) are important regulators of RNA metabolism. In neurode-generative disorders such as Huntingtons Disease (HD), disrupted RBP-RNA interactions contribute to neuronal dysfunction. One such RBP, Midline 1 (MID1), has been shown to aberrantly associate with mutant huntingtin (Htt) RNA, enhancing its translation, yet the mechanism driving this effect remains unknown. Here, we develop a computational model to understand the role of MID1. Based on previously published data, our model predicts that MID1 increases the stability of the Htt RNA. We experimentally validate this prediction, showing that overexpression of MID1 significantly prolongs the half-life of mutant Htt RNA. Furthermore, we evaluate model refinements, including clustering of MID1-bound RNA, which allow capturing all key observations in the data. Together, we provide a data-driven framework that underlines the importance of RBP-RNA interaction in post-transcriptional regulation. This framework also shows how individual molecular reactions jointly determine RNA stability and protein levels in HD.

systems biology↗

bioRxiv2025

Uncovering the transcriptional hallmarks of endothelial cell aging via integrated single-cell analysis

Endothelial cells (ECs) are critical regulators of vascular function and exhibit specialized, organ-specific roles across tissues. During aging, these cells become dysfunctional, resulting in increased susceptibility to cardiovascular disease and its associated mortality. While single-cell transcriptomics studies have revealed extensive endothelial heterogeneity across tissues and conditions, a comprehensive atlas of human EC transcriptomes over the course of the adult human lifespan is still lacking. Here, we present the Human Aging Endothelial Cell Atlas (HAECA), a harmonized single-cell transcriptomic compendium of over 375,000 ECs from 12 human tissues throughout adulthood. Using HAECA, we identified age-associated transcriptional shifts, including a decline in angiogenic gene expression in venous ECs and widespread alterations in extracellular matrix (ECM)- and mechanotransduction-associated pathways. We validated these findings in aging human skin and further uncovered a p21-linked transcriptional program in ECs, confirmed in both in vitro and in vivo models and linked to cellular senescence. Together, our study provides a high-resolution transcriptome reference across spatial as well as temporal axes of the human endothelium.

cell biology↗

bioRxiv2025

Genetic modification of intractable staphylococcal clones by heat-shock facilitated phage transduction

Increasing recognition of commensal bacteria as a requirement for microbiome integrity and pathogen exclusion puts urgency to the molecular characterization of commensal interactions. However, many commensals cannot be transformed with available methodology because of potent restriction barriers. We developed a new method for the introduction of plasmid DNA into otherwise intractable non-Staphylococcus aureus (NAS) staphylococci, important commensal members of human nose and skin microbiomes, by phage transduction. We demonstrate that a precise pulse of recipient bacteria with elevated temperatures prior to exposure to transducing phages renders NAS isolates effectively and transiently amenable to transduction. Transduction of NAS mutants lacking restriction-modification (RM) systems did not profit from a heat shock indicating that it is the transient deactivation of RM enzymes that permit transduction. Our method also facilitated the transduction of other Bacillota from the genera Bacillus and Listeria indicating that it will support research on different bacterial groups from diverse ecosystems. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/647181v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@233348org.highwire.dtl.DTLVardef@fbf57corg.highwire.dtl.DTLVardef@1b1abadorg.highwire.dtl.DTLVardef@17e283f_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2024

msiFlow: Automated Workflows for Reproducible and Scalable Multimodal Mass Spectrometry Imaging and Immunofluorescence Microscopy Data Processing and Analysis

Multimodal imaging by matrix-assisted laser desorption ionisation mass spectrometry imaging (MALDI MSI) and immunofluorescence microscopy holds great potential for understanding pathological mechanisms by mapping molecular signatures from the tissue microenvironment to specific cell populations. However, existing open-source software solutions for analysis of MALDI MSI data are incomplete, require programming skills and contain laborious manual steps, hindering broadly applicable, reproducible, and high-throughput analysis to generate impactful biological discoveries across interdisciplinary research fields. Here we present msiFlow, an accessible open-source, platform-independent and vendor-neutral software for end-to-end, high-throughput, transparent and reproducible analysis of multimodal imaging data. msiFlow integrates all necessary steps from import and pre-processing of raw MALDI MSI data to visual analysis output, as well as registration, along with state-of-the-art and newly developed algorithms, into automated workflows. Using msiFlow, we unravel the molecular heterogeneity of leukocytes in infected tissues by spatial regulation of ether-linked phospholipids containing arachidonic acid. We anticipate that msiFlow will facilitate the broad applicability of MSI in the emerging field of multimodal imaging to uncover context-dependent cellular regulations in disease states.

bioinformatics↗

bioRxiv2023

Acoustic wave-induced stroboscopic optical mechanotyping of adherent cells

In this study, we present a novel, high content technique using an innovative cylindrical acoustic transducer, stroboscopic fast imaging and homodyne detection to recover the mechanical properties (dynamic shear modulus) of living adherent cells at low ultrasonic frequencies. By analyzing the micro-oscillations of cells we were able to simultaneously mechanotype whole populations of cells with sub-cellular resolution. The technique can be combined with standard fluorescence imaging allowing to further cross-correlate biological and mechanical information. We demonstrate the potential of the technique by mechanotyping co-cultures of different cell types with significantly different mechanical properties.

biophysics↗

bioRxiv2023

Simultaneous LC-MS determination of glucose regulatory peptides secreted by stem cell-derived islet organoids

For studying stem cell-derived islet organoids (SC-islets) in an organ-on-chip platform, we have developed a reversed phase liquid chromatography tandem mass spectrometry (RPLC-MS/MS) method allowing for simultaneous determination of insulin, somatostatin-14, and glucagon, with improved matrix robustness compared to earlier methodology. Combining phenyl/hexyl-C18 separations using 2.1 mm inner diameter LC columns and triple quadrupole mass spectrometry, identification and quantification were secured with negligible variance in retention time and quantifier/qualifier ratios, negligible levels of carry-over (< 2%), and sufficient precision ({+/-} 10% RSD) and accuracy ({+/-} 15% relative error) with and without use of internal standard. The here developed RPLC-MS/MS method showed that the SC-islets have an insulin response dependent on glucose concentration, and the SC-islets produce and release somatostatin-14 and glucagon. The RPLC-MS/MS method for these peptide hormones was compatible with an unfiltered off-line sample collection from SC-islets cultivated on a pump-less, recirculating organ-on-chip (rOoC) platform. The SC-islets background secretion of insulin was not significantly different on the rOoC device compared to a standard cell culture well-plate. Taken together, RPLC-MS/MS is well suited for multi-hormone measurements of SC-islets on an organ-on-chip platform.

biochemistry↗

bioRxiv2023

Mass Spectrometry Reveals that Oxysterols are Secreted from Non-Alcoholic Fatty Liver Disease Induced Organoids

Oxysterols are potential biomarkers for liver metabolism that are altered under disease conditions such as non-alcoholic fatty liver disease (NAFLD). We here apply sterolomics to organoids used for disease modeling of NAFLD. Using liquid chromatography-mass spectrometry with on-line sample clean-up and enrichment, we establish that liver organoids produce and secrete oxysterols. We find elevated levels of 26-hydroxycholesterol, an LXR agonist and the first oxysterol in the acidic bile acid synthesis, in medium from steatotic liver organoids compared to untreated organoids. Other upregulated sterols in medium from steatotic liver organoids are dihydroxycholesterols, such as 7,26-dihydroxycholesterol, and 7,25-dihydroxycholesterol. Through 26-hydroxycholesterol exposure to human stem cell-derived hepatic stellate cells, we observe a trend of expressional downregulation of the pro-inflammatory cytokine CCL2, suggesting a protective role of 26-hydroxycholesterol during early-phased NAFLD disease development. Our findings support the possibility of oxysterols serving as NAFLD indicators, demonstrating the usefulness of combining organoids and mass spectrometry for disease modeling and biomarker studies. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=118 SRC="FIGDIR/small/529551v2_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@9de7fdorg.highwire.dtl.DTLVardef@e9b328org.highwire.dtl.DTLVardef@f14101org.highwire.dtl.DTLVardef@e2e9c3_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2022

Pump-less, recirculating organ-on-a-chip (rOoC) platform

Current organ-on-a-chip (OoC) systems mimic important aspects of specific organ and tissue functions, however, many commercial and academic devices are either too simple for advanced assays or require a complicated support set-up including external driving systems such as pumps and tubing that hamper scalability and robustness. We have developed a novel, pump-less directional flow recirculating organ-on-a-chip (rOoC) platform that creates continuous or pulsed directional gravity-driven flow by a combination of a 3D-tilting system and an optimized microfluidic layout. The rOoC platform allows growing and connecting tissue or organ representations on-chip with the possibility of incorporating barrier functions, gradients, and circulating cells. Using the rOoC platform we demonstrate simple and reproducible endothelialisation, hepatic organoid integration, and the first steps of vascularization of 3D organ representations on-chip.

bioengineering↗

bioRxiv2022

Horizontal transfer of bacteriocin biosynthesis genes requires metabolic adaptation to improve compound production and cellular fitness

Biosynthetic gene clusters (BGCs) encoding the production of bacteriocins are widespread amongst bacterial isolates and are important genetic determinants of competitive fitness within a given habitat. Staphylococci produce a tremendous diversity of compounds and the corresponding BGCs are frequently associated with mobile genetic elements, suggesting gain and loss of biosynthetic capacity. Pharmaceutical biology has shown that compound production in heterologous hosts is often challenging and many BGC recipients produce initially low compound amounts or show reduced growth rates. To assess whether transfer of BGCs between closely related S. aureus strains can be instantly effective or requires elaborate metabolic adaptation, we investigated the intra species transfer of a BGC encoding the ribosomally synthesized and post-translationally modified peptide (RiPP) micrococcin P1 (MP1). We found that acquisition of the BGC by S. aureus RN4220 enabled immediate MP1 production but also imposed a metabolic burden, which was relieved after prolonged cultivation by adaptive mutation. We used a multiomics approach to study this phenomenon and found adaptive evolution to select for strains with increased activity of the tricarboxylic acid cycle (TCA), which enhanced metabolic fitness and levels of compound production. Metabolome analysis revealed increases of central metabolites including citrate and -ketoglutarate in the adapted strain, suggesting metabolic adaptation to overcome the BGC-associated growth defects. Our results indicate that BCG acquisition requires genetic and metabolic predispositions allowing the integration of bacteriocin production into the cellular metabolism. Inappropriate metabolic characteristics of recipients can entail physiological burdens, negatively impacting the competitive fitness of recipients within natural bacterial communities. ImportanceHuman microbiomes are critically associated with human health and disease. Importantly, pathogenic bacteria can hide in human associated communities and can cause disease when the composition of the community becomes dysbalanced. Bacteriocin producing commensals are able to displace pathogens from microbial communities, suggesting that their targeted introduction in human microbiomes might prevent pathogen colonisation and infection. However, in view of future probiotic approaches, strains are needed that produce high levels of bioactive compounds and retain cellular fitness within mixed bacterial communities. Our work offers insights into the metabolic burdens associated with the production of the bacteriocin micrococcin P1 and highlights evolutionary strategies that increase cellular fitness in the context of production. Most likely metabolic adaptations are broadly relevant for bacteriocin producers and need to be considered for the future development of effective microbiome editing strategies.

microbiology↗

bioRxiv2022

Adipose-derived stromal cells preserve pancreatic islet function in a transplantable 3D bioprinted scaffold

Intra-portal islet transplantation is the method of choice for treatment of insulin dependent type 1 diabetes, but its outcome is hindered by limited islet survival due to the immunological and metabolic stress post transplantation. Adipose-derived stromal cells (ASCs) promise to improve significantly the islet micro-environment but an efficient long-term delivery method has not been achieved. We therefore explore the potential of generating ASC enriched islet transplant structure by 3D bioprinting. Here, we fabricate a double-layered 3D bioprinted scaffold for islets and ASCs by using alginate-nanofibrillated cellulose bioink. We demonstrate the diffusion properties of the scaffold and report that human ASCs increase the islet viability, preserve the endocrine function, and reduce pro-inflammatory cytokines secretion in vitro. Intraperitoneal implantation of the ASCs and islets in 3D bioprinted scaffold improve the long-term function of islets in diabetic mice. Our data reveals an important role for ASCs on the islet micro-environment. We suggest a novel cell therapy approach of ASCs combined with islets in a 3D structure with a potential for clinical beta cell replacement therapies at extrahepatic sites.

cell biology↗

bioRxiv2021

Host diversity and behavior determine patterns of interspecies transmission and geographic diffusion of avian Influenza A subtypes among North American wild reservoir species

Wild birds can carry avian influenza viruses (AIV), including those with pandemic or panzootic potential, long distances. Even though AIV has a broad host range, few studies account for host diversity when estimating AIV spread. We analyzed AIV genomic sequences from North American wild birds, including 303 newly sequenced isolates, to estimate interspecies transmission and geographic diffusion patterns among multiple co-circulating subtypes. Our results show high transition rates within Anseriformes and Charadriiformes, but limited transitions between these orders. Patterns of interspecies transmission were positively associated with breeding habitat range overlap, and negatively associated with host genetic distance. Distance between regions (negative correlation) and summer temperature at origin (positive correlation) were strong predictors of diffusion. Taken together, this study demonstrates that host diversity and ecology can determine evolutionary processes that underlie AIV natural history and spread. Understanding these processes can provide important insights for effective control of AIV.

evolutionary biology↗

bioRxiv2021

The adenoviral E1B-55k protein introduced to immortalize HEK293 cells mediates accumulation of key WNT/β-catenin signaling proteins in large cytoplasmic aggregates and influences the activity of WNT/β-catenin signaling.

HEK293 cells are one of the most widely used cell lines in research and HEK293 cells are frequently used as an in vitro model for studying the WNT signaling pathway. The HEK293 cell line was originally established by transfection of human embryonic kidney cells with sheared adenovirus 5 DNA and it is known that that HEK293 cells stably express the adenoviral E1A and E1B-55k proteins. Here we show that HEK293 cells display an unexpected distribution of key components of the WNT/{beta}-catenin signaling pathway where AXIN1, APC, DVL2 and tankyrase are all co-localized in large spherical cytoplasmic aggregates. The cytoplasmic aggregates are enclosed by a narrow layer of the adenoviral E1B-55k protein. Reduction of E1B-55k protein levels leads to disappearance of the cytoplasmic aggregates thus corroborating an essential role of the E1B-55k protein in mediating the formation of the aggregates. Furthermore, HEK293 cells with reduced E1B-55k protein levels display reduced levels of transcriptional activation of WNT/{beta}-catenin signaling upon stimulation by the Wnt3A agonist. The demonstrated influence of the E1B-55k protein on the cellular localization of WNT/{beta}-catenin signaling components and on transcriptional regulation of WNT/{beta}-catenin signaling asks for caution in the interpretation of data derived from the HEK293 cell line.

cell biology↗

bioRxiv2020

Organoid-in-a-column coupled on-line with liquid chromatography-mass spectrometry

Organoids, i.e. laboratory-grown organ models developed from stem cells, are emerging tools for studying organ physiology, disease modeling and drug development. On-line analysis of organoids with mass spectrometry would provide analytical versatility and automation. To achieve these features with robust hardware, we have loaded liquid chromatography column housings with induced pluripotent stem cell (iPSC) derived liver organoids and coupled the "organ-in-a-column" units on-line with liquid chromatography-mass spectrometry (LC-MS). Liver organoids were co-loaded with glass beads to achieve an even distribution of organoids throughout the column while preventing clogging. The liver organoids were interrogated "on column" with heroin, followed by on-line monitoring of the drugs phase 1 metabolism. Enzymatic metabolism of heroin produced in the "organ-in-a-column" units was detected and monitored using a triple quadrupole MS instrument, serving as a proof-of-concept for on-line coupling of liver organoids and mass spectrometry. Taken together, the technology allows direct integration of liver organoids with LC-MS, allowing selective and automated tracking of drug metabolism over time.

bioengineering↗

bioRxiv2020

Electromembrane extraction and mass spectrometry for liver organoid drug metabolism studies

Liver organoids are emerging tools for precision drug development and toxicity screening. We demonstrate that electromembrane extraction (EME) based on electrophoresis across an oil membrane is suited for segregating selected organoid-derived drug metabolites prior to mass spectrometry (MS)-based measurements. EME, allowed drugs and drug metabolites to be separated from cell medium components (albumin, etc.) that could interfere with subsequent measurements. Multi-well EME (Parallel-EME) holding 100 L solutions allowed for simple and repeatable monitoring of heroin phase I metabolism kinetics. Organoid Parallel-EME extracts were compatible with ultrahigh-performance liquid chromatography (UHPLC) used to separate the analytes prior to detection. Taken together, liver organoids are well-matched with EME followed by MS-based measurements.

biochemistry↗

bioRxiv2019

Tankyrase inhibition sensitizes melanoma to PD-1 immune checkpoint blockade in syngeneic mouse models

The development of immune checkpoint inhibitors represents a major breakthrough in cancer therapy. Nevertheless, a substantial number of patients fail to respond to checkpoint pathway blockade. {beta}-catenin is the key transcriptional regulator of WNT/{beta}-catenin signaling. Evidence for {beta}-catenin-mediated immune evasion is found in 13% of all cancers, 42% of primary cutaneous melanoma and a mouse melanoma model. Currently, there are no therapeutic strategies available for targeting WNT/{beta}-catenin signaling to counteract checkpoint inhibitor resistance in melanoma. Here we report that a specific small-molecule tankyrase inhibitor, G007-LK, attenuates WNT/{beta}-catenin and YAP signaling pathways in the syngeneic murine B16-F10 melanoma model enabling sensitivity to anti-PD-1 immune checkpoint therapy. RNA sequencing of 18 tankyrase inhibitor-treated human melanoma cell lines and B16-F10 cells revealed a transcriptional response profile for a subpopulation. This cell line sub-group displayed elevated baseline YAP signaling activity and was susceptible to reduce melanocyte inducing transcription factor (MITF) expression upon tankyrase inhibition.

cancer biology↗