Biology subjects

Knaus, P.

Publications and source records attributed to Knaus, P..

7 recordsLinked to original sources

bioRxiv2026

Assessing State-Specific Accuracy of Cofolding Models for Kinases and GPCRs

AI-driven cofolding models have emerged as powerful tools for predicting protein-ligand complexes, yet whether ligand placement faithfully captures the conformational states of dynamic proteins remains unclear. Here we show that cofolding adaptively remodels binding pockets around bound ligands, but that this local accuracy is frequently decoupled from recovery of the broader conformational state. We benchmark four models, AlphaFold3, RosettaFold3, Boltz-2, and Chai-1, against a set of kinases and class A G protein-coupled receptors (GPCRs), protein families whose pharmacology depends on well-defined structural states. We find that even when ligand root-mean-square deviation (RMSD) is low, critical state markers, including kinase activation-loop geometries and GPCR intracellular arrangements, are frequently mispredicted. Incorporating state-annotated templates and filtered multiple sequence alignments (MSAs) improves conformational recovery in selected cases, yet weakly impacts others. Furthermore, while orthosteric ligand placement is generally reliable, allosteric binders expose a consistent blind spot across all models. These findings establish conformational decoupling as a fundamental limitation of current cofolding approaches, with direct implications for state-selective drug design.

biochemistry↗

bioRxiv2025

TGFb-induced SMAD1/5 activation drives transient epithelial-to-mesenchymal transition in trophoblasts

Successful human placental development requires fetal trophoblasts to undergo epithelial-to-mesenchymal and mesenchymal-to-endothelial transitions, enabling invasion and remodeling of maternal spiral arteries for proper placental perfusion. These trans-differentiation processes are disrupted in preeclampsia, a major cause of maternal and fetal morbidity worldwide. Despite its clinical significance, the molecular mechanisms governing these differentiation trajectories at the fetal-maternal interface remain poorly defined. While Transforming Growth Factor-beta (TGF{beta}) has been implicated in trophoblast invasion, its role remains controversial. In this study, we report increased SMAD2/3 phosphorylation (pSMAD2/3), but reduced pSMAD1/5 and SNAIL levels in preeclamptic placentas. Mechanistically, we show that TGF{beta}1 induces transient SMAD1/5 phosphorylation via dual engagement of the TGF{beta} type I receptor ALK5 and the BMP type I receptor ALK2 in both HTR8/SVneo cells and human trophoblast stem cells. Moreover, single-nucleus transcriptomics of first-trimester placentas revealed co-expression of ACVR1, TGFBR1, SMAD1 and SMAD5 at the transition zone between cytotrophoblasts and extravillous trophoblasts. Our findings suggest that transient TGF{beta}-induced ALK5/ALK2-SMAD1/5 signaling is critical for EMT initiation, a prerequisite for proper placental differentiation.

molecular biology↗

bioRxiv2024

Atheroprone Flow Activates SMAD-FOXO1 to drive Endothelial-to-Mesenchymal Transition and Atherosclerosis

BackgroundCardiovascular diseases are the leading cause of death worldwide with atherosclerosis as the main underlying pathology. A hallmark of atherosclerotic lesion formation is endothelial-to-mesenchymal transition (EndoMT) triggered by perturbed blood flow patterns at arterial bifurcations and curvatures. SMAD transcription factors (TFs), activated by bone morphogenetic protein (BMP) 9/10 or transforming growth factor beta (TGF{beta}) signaling, are indispensable for endothelial homeostasis. Yet, they also play a significant role in stimulating EndoMT. How different interacting co-factors mediate the shift towards a pathological SMAD response remains elusive. MethodsWe generated endothelial cell (EC)-specific SMAD1/5 or SMAD2/3 knock-out mice and performed assay for transposase accessible chromatin sequencing (ATAC-Seq) of EC nuclei from regions of atheroprone (aortic arch) and atheroprotective (descending thoracic aorta) flow to identify transcriptional co-regulators of SMADs. We validated this using single-cell (sc)ATAC-Seq and immunofluorescence staining data from wild-type mice. To assess conservation of our findings for the human situation, we performed co-immunoprecipitation and proximity ligation assays in human aortic ECs (HAoECs). We exposed HAoECs to pathological or physiological (i.e. oscillatory or pulsatile) flow and performed ATAC- and RNA-Seq. Next, transcriptomic and chromatin accessibility data were integrated and motif enrichment and TF footprinting analysis were performed. Finally, we used siRNA-mediated approaches, TF inhibition, and luciferase-based reporter gene assays to analyze the transcriptional response of target TFs and explored their presence in plaques of atheroprone low-density lipoprotein receptor-deficient mice. ResultsWe observed enrichment of FOXO TF family motifs in DNA loci with increased accessibility in response to atheroprone flow in vitro and in vivo. These motifs were associated with genes displaying enhanced mRNA expression. We observed that FOXO motifs are enriched in peaks lost upon EC-specific SMAD KO in mice. We identified SMADs and FOXO1 as interacting partners that form complexes upon atheroprone flow stimulation. Inhibitor experiments revealed that FOXO1 and SMADs mediate EndoMT upon atheroprone flow exposure by upregulating SNAI2. ConclusionWe identified SMAD/FOXO1 complexes that mediate EndoMT in response to atheroprone flow. Targeting this interaction can potentially reduce atherosclerotic burden by interfering with pathological flow-induced EndoMT and thus disease progression.

genomics↗

bioRxiv2024

Gut microbial metabolite imidazole propionate impairs endothelial cell function and promotes the development of atherosclerosis

BackgroundThe microbially generated amino acid-derived metabolite imidazole propionate (ImP) contributes to the pathogenesis of type 2 diabetes. However, the effect of ImP on endothelial cell physiology and its role in atherosclerotic coronary artery disease (CAD) is unknown. Using both human and animal model studies, we investigated the potential contributory role of ImP in the development of atherosclerosis. MethodsPlasma levels of ImP were measured in patients undergoing elective cardiac angiography (n = 831) by means of ultra high-performance liquid chromatography coupled to tandem mass spectrometry. Odds ratios (ORs) and corresponding 95% confidence intervals for CAD were calculated based on the ImP quartiles using both univariable and multivariable logistic regression models. Atheroprone apolipoprotein E-/- (Apoe-/-) mice fed a high-fat diet were additionally treated with ImP (800 {micro}g) or vehicle and aortic atherosclerotic lesion area was evaluated after 12 weeks. In a mouse model of carotid artery injury, the effect of ImP on vascular regeneration was examined. Using human aortic endothelial cells (HAECs) the effect of ImP on functional properties of endothelial cells were assessed. Next-generation sequencing, western blot analysis, siRNA-based gene knockdown and tamoxifen-inducible Cre-loxP experiments were performed to investigate ImP-mediated molecular mechanisms. ResultsPlasma ImP levels in subjects undergoing cardiac evaluation were associated with increased risk for prevalent CAD. In atheroprone Apoe-/- mice ImP increased atherosclerotic lesion size. We found that ImP dose-dependently impaired migratory and angiogenic properties of human endothelial cells, and promoted an increased inflammatory response. Long-term exposure to ImP impaired the repair potential of the endothelium after an arterial insult. Mechanistically, ImP attenuated insulin receptor signaling by suppressing PI3K/AKT pathway leading to the sustained activation of the forkhead box protein O1 (FOXO1) transcription factor. Genetic inactivation of endothelial FOXO1 signaling in ImP-treated mice enhanced the angiogenic activity and preserved the vascular repair capacity of endothelial cells after carotid injury. ConclusionsOur findings reveal a hitherto unknown role of the microbially produced histidine-derived metabolite ImP in endothelial dysfunction and atherosclerosis, suggesting that ImP metabolism is a potential therapeutic target in atherosclerotic cardiovascular disease.

systems biology↗

bioRxiv2023

Reorganization of Septin structures regulates early myogenesis

Controlled myogenic differentiation is crucial for developmental formation, homeostatic maintenance and adult repair of skeletal muscle and relies on cell fate determinants in myogenic progenitors or resident stem cells. Proliferating muscle progenitors migrate, adopt spindle shape, align membranes and fuse into multinuclear syncytia. These processes are accompanied by cyto-architectural changes driven by rearranging of cytoskeletal components such as actin and microtubules. Here we highlight septins, the fourth component of the cytoskeleton, to represent an essential structural element of myoblasts. Specifically, Septin9 regulates myoblast differentiation during the early commitment process. Depletion of Septin9 in C2C12 cells and primary myoblasts led to a precocious switch from a proliferative towards a committed progenitor transcriptomic program. Additionally, we report Septin9 undergoing substantial reorganization and downregulation during myogenic differentiation. Together, we propose filamentous septin structures and their controlled reorganization in myoblasts to provide a key temporal regulation mechanism for the differentiation of myogenic progenitors.

cell biology↗

bioRxiv2022

Odd skipped-related 1 controls the pro-regenerative response of Fibro-Adipogenic Progenitors

Skeletal muscle regeneration requires the coordinated interplay of diverse tissue-resident- and infiltrating cells. Fibro-adipogenic progenitors (FAPs) are an interstitial cell population that provides a beneficial microenvironment for muscle stem cells (MuSCs) during muscle regeneration. Here we show that the transcription factor Osr1 is essential for FAPs to communicate with MuSCs and infiltrating macrophages, thus coordinating muscle regeneration. Conditional inactivation of Osr1 impaired muscle regeneration with reduced myofiber growth and formation of excessive fibrotic tissue with reduced stiffness. Osr1-deficient FAPs acquired a fibrogenic identity with altered matrix secretion and cytokine expression resulting in impaired MuSC viability, expansion and differentiation. Immune cell profiling suggested a novel role for Osr1-FAPs in macrophage polarization. In vitro analysis suggested that increased TGF{beta} signaling and altered matrix deposition by Osr1-deficient FAPs actively suppressed regenerative myogenesis. In conclusion, we show that Osr1 is central to FAP function orchestrating key regenerative events such as inflammation, matrix secretion and myogenesis.

developmental biology↗

bioRxiv2022

A versatile Halo- and SNAP-tagged BMP/TGFβ receptor library for quantification of cell surface ligand binding

The TGF{beta} superfamily of secreted growth factors comprises more than 30 members including TGF{beta}s, BMPs and Activins. While all TGF{beta} superfamily members signal through heteromeric receptor complexes to regulate a plethora of developmental and homeostatic processes, each ligand possesses a unique affinity towards a subset of BMP and TGF{beta} type I and type II receptors. Whereas the Activin and TGF{beta} class display a higher affinity towards type II receptors, BMPs and GDFs preferentially bind to type I receptors. Sofar, the lack of specific antibodies and chemical biology tools hampered simultaneous testing of ligand binding towards all BMP and TGF{beta} receptors. Here we present a N-terminally Halo- and SNAP-tagged TGF{beta}/BMP receptor library to visualize the receptor complexes in dual color. In combination with novel fluorescently labeled TGF{beta} superfamily ligands, we established a Ligand Surface Binding Assay (LSBA) for optical quantification of receptor-dependent growth factor binding for Activin A, TGF{beta}1 and BMP9 in a cellular context. We confirm ligand-receptor interface specificity by identifying BMPR2- or ALK2-mutants that switch from a low-affinity Activin A- or BMP9-receptor to a high-affinity receptor, respectively.

cell biology↗