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Ziegler, S.

Publications and source records attributed to Ziegler, S..

18 recordsLinked to original sources

Rational scaffold design mitigates mitochondrial complex I off-target inhibition in bifunctional degraders

Chemical inducers of proximity have transformed small-molecule pharmacology, but the large, bifunctional architectures they often employ introduce new and poorly understood off-target risks. During a targeted protein degrader synthesis project, we identified a subset of compounds that cause rapid and unexpected ATP depletion in cells. Mechanistic studies traced this effect to inhibition of mitochondrial complex I, a central component of oxidative phosphorylation. This inhibition does not stem from off-target binding by either of the two target ligands, but from the overall long, linear architecture of the bifunctional molecules, which renders them effective ligands of the narrow ubiquinone binding tunnel of complex I. Strikingly, this liability extends to structurally unrelated bifunctional molecules, including six androgen receptor PROTACs including the clinical candidate ARV-110, which inhibits complex I at low nanomolar concentrations. To mitigate complex I inhibition, we established a generalizable design strategy to disrupt linear molecular geometry through the introduction of structural "bumps" or "kinks". In a proof-of-concept study, we successfully apply this strategy to the ARV-110 scaffold, discovering potent AR-degrading ARV-110 analogs that do not inhibit complex I. These findings uncover a previously underappreciated structural determinant of off-target mitochondrial toxicity and establish new design principles for safer proximity-inducing therapeutics.

cancer biology↗

Coordinated IFN-γ/TNF Axis Drives Selective Loss of Activated Enteric Glia in Inflammatory Bowel Diseases

BackgroundEnteric glial cells (EGC) play a crucial role in maintaining gut homeostasis, but their dysregulation in inflammatory bowel diseases (IBD) remains poorly understood. Emerging preclinical data suggests activated EGC have beneficial roles in controlling gut pathophysiology. ObjectiveUnderstanding EGC activation and adaptation during experimental and clinical IBD. DesignWe provide the first highly integrated approach to identify EGC activation signature in IBD. Profiling 390 samples from IBD patients via bulk and single-nucleus (sn) transcriptomics and replicate the findings on publicly available bulk and single-cell (sc) datasets from 1160 patients and 19,000 single EGC. Preclinical modelling of Th1/Th17 inflammation, reporter-assisted EGC sorting, analysis of regulated cell death, and Casp8 ablation in EGC was performed ResultsWe identified novel IBD type and sampling associated EGC activation signature. Specific EGC activation markers were shared in biopsies and resection specimens, and were divergent between Crohns disease and Ulcerative colitis. Preclinical modelling of intestinal inflammation identified combinatorial TNF and IFN-{gamma}-driven activation of EGC, associated with elevated necroptosis, and negatively impacting gut motility. Genetic-reporter-enabled sorting and downstream analyses confirmed TNF and IFN-{gamma}-driven EGC necroptosis, potentiated by Casp8 deficiency. Furthermore, snRNA-Seq from IBD patient samples confirmed elevated cell death signature in activated but not in rare neuroglia progenitor-like cluster. ConclusionOur findings identify IBD type-associated activated EGC markers involved in immune and epithelial homeoastasis. We uncover necroptosis of activated EGCs as a constituent of intestinal inflammation. Advancing our understanding of activated EGC survival is pivotal in elucidating their complex roles in maintaining gut immune-epithelial homeostasis. What is already known on this topicActivated EGC have emerged as important contributors in maintaining epithelial, immune and neuronal homeostasis. Increasing evidence from mouse studies points to the role of activated EGC in epithelial regeneration, tolerogenic T-cell activation, relaying psychological stress to the enteric nervous system, post-injury neurogenesis, and helminth clearance. Nevertheless, no consensus has emerged on what might define activated EGC in the context of IBD and how EGC turnover is affected in gut inflammation, limiting translation of their disease associated roles. What this study addsBy combining bulk with single cell and single nucleus transcriptomes from IBD patients we identified new IBD type- and location-associated EGC activation signatures. Some of these are conserved with mouse EGC in gut inflammation models. We identified osteopontin an immunomodulator and Wnt6 an epithelial morphogen elevated in IBD EGC. We also identified IBD-associated EGC cell clusters, which display higher expression of cell death pathway transcripts. To investigate EGC turnover, we utilized preclinical models and found rapid EGC activation upon Th1/Th17 inflammation. This was associated with elevated EGC activation and caspase-independent necroptotic cell death. Ex vivo experiments showed a combinatorial requirement of IFN-{gamma} and TNF in mediating EGC necroptosis. Our findings were replicated on multiple publicly available sc-RNA sequencing datasets from IBD patients. How this study might affect research, practice or policyExpanding on the available repertoire of EGC activation markers in IBD, both shared and unique to sampling procedure, disease type, and location will provide researchers with tools to identify EGC homeostasis during IBD. Moreover, the nature of the identified markers will stimulate research into specific EGC pathways triggered in inflammation. Adding to this, the rapid induction in pathological death of activated but not naive EGC upon IFN-{gamma} and TNF stimulation will shed light on EGC adaptation and turnover. Our identification of markers of activated EGC with immuno-modulatory and epithelial-regenerative properties, including osteopontin and wingless family of morphogenes will stimulate further research in EGC-immune and EGC-epithelial communication in the context of IBD.

neuroscience↗

Understanding the Dynamics of Biomass Deconstruction by the Cellulolytic Anaerobe C. thermocellum

Clostridium thermocellum is one of the most efficient microorganisms for the deconstruction of cellulosic biomass. To achieve this high level of cellulolytic activity, C. thermocellum uses large multienzyme complexes known as cellulosomes to break down complex polysaccharides, notably cellulose, found in plant cell walls. The attachment of bacterial cells to the nearby substrate via the cellulosome has been hypothesized to be the reason for this high efficiency. The region lying between the cell and the substrate has shown great variation and dynamics that are affected by the growth stage of cells and the biomass used for growth. Here, we utilized both photoactivation localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM) in combination with Density-Based Spatial Clustering of Applications with Noise (DBSCAN) to study the distribution of C. thermocellum cellulosomes at different stages of growth when actively growing on soluble and insoluble substrates, providing a clearer picture of the dynamics of cellulosome populations at the enzyme microbe substrate interface. This research demonstrates the promising application of novel optical methodologies in tandem with targeted mutations within C. thermocellum to test the prevailing theories regarding the mechanisms of cellulosomes and their potential to shuttle onto the biomass for the attachment of C. thermocellum to improve biomass deconstruction.

microbiology↗

Identification of small molecule enhancers of NK cell tumoricidal activity via a tumor microenvironment-mimicking co-culture assay

The tumor microenvironment (TME) is a pro-cancerous niche harboring immunosuppressive factors that are secreted by cancer cells and the surrounding cancer-supportive tissue, such as kynurenine, prostaglandin E2 and transforming growth factor {beta} (TGF{beta}). These factors dampen the activity of cytotoxic lymphocytes like natural killer (NK) cells, allowing evasion of immune cell-mediated killing. To identify small molecules that counteract the immunosuppressive effect of the TME and restore NK cell-mediated cytotoxicity, we developed a phenotypic co-culture assay of cancer cells and primary lymphocytes suitable for medium-throughput screening. We discovered small molecules that restore NK cell-mediated cytotoxicity through diverse mechanisms. The potent TGF{beta} type I receptor (TGF{beta}R-1) inhibitor, RepSox, stood out as superior to other TGF{beta}R-1 inhibitors due to its ability to abolish the effects of both inhibitory factors used in our setup. This mode of action goes beyond TGF{beta}R-1 inhibition and is related to the simultaneous abrogation of cyclooxygenase 1 (COX1) activity.

immunology↗

Monovalent Pseudo-Natural Product Degraders Supercharge the Native Degradation of IDO1 by KLHDC3

Targeted protein degradation (TPD) modulates protein function beyond inhibition of enzyme activity or protein-protein interactions. Most degrader drugs function by directly mediating proximity between a neosubstrate and hijacked E3 ligase. Here, we identified pseudo-natural products derived from (-)-myrtanol, termed iDegs that inhibit and induce degradation of the immunomodulatory enzyme indoleamine-2,3-dioxygenase 1 (IDO1) by a distinct mechanism. iDegs boost IDO1 ubiquitination and degradation by the cullin-RING E3 ligase CRL2KLHDC3, which we identified to natively mediate ubiquitin-mediated degradation of IDO1. Therefore, iDegs increase IDO1 turnover using the native proteolytic pathway. In contrast to clinically explored IDO1 inhibitors, iDegs reduce formation of kynurenine by both inhibition and induced degradation of the enzyme and, thus, would also modulate non-enzymatic functions of IDO1. This unique mechanism of action may open up new therapeutic opportunities for the treatment of cancer beyond classical inhibition of IDO1.

cell biology↗

Emergence of bluetongue virus serotype 3 in western Germany, October 2023, and ad-hoc monitoring in Culicoides biting midges

Bluetongue virus serotype 3 emerged in October 2023 in Germany, where Schmallenberg virus is enzootic. BTV-3 was detected in a pool of Culicoides biting midges at the same time as infections were reported from ruminants. Schmallenberg virus was frequently found in vector pools, reflecting the epidemiological situation. One sentence summary lineCoinciding with the emergence and low-level circulation of bluetongue virus serotype 3 in ruminants in Germany in October 2023, the virus was detected in a pool of Culicoides biting midges of the Obsoletus Group, while enzootic Schmallenberg virus was found in numerous midge pools.

microbiology↗

MemBrain v2: an end-to-end tool for the analysis of membranes in cryo-electron tomography

Cryo-electron tomography (cryo-ET) provides unique insights into macromolecular complexes in their native environments, yet membrane analysis remains a major bottleneck due to low signal-to-noise ratios, missing wedge artifacts, and the complexity of membrane-associated proteins. Existing tools often require extensive manual annotation, struggle with generalization across datasets, and lack integrated solutions for segmentation, protein localization, and quantitative analysis. We introduce MemBrain v2, a deep learning-enabled framework that unifies these tasks into a streamlined pipeline. MemBrain-seg leverages a diverse, collaboratively generated training dataset and specialized model training strategies to achieve generalizable membrane segmentation across variable tomographic conditions. MemBrain-pick enables data-efficient localization of membrane-bound proteins by integrating geometric constraints with deep learning, reducing the need for extensive manual annotation. MemBrain-stats provides quantitative insights into protein distributions, computing spatial metrics to analyze intra-membrane particle organization. MemBrain v2 integrates seamlessly into cryo-ET workflows, providing an accessible and structured approach to membrane analysis. The full package is available at https://github.com/CellArchLab/MemBrain-v2.

bioinformatics↗

Genome-wide association study of delay discounting in Heterogenous Stock rats

Delay discounting refers to the behavioral tendency to devalue rewards as a function of their delay in receipt. Heightened delay discounting has been associated with substance use disorders, as well as multiple co-occurring psychopathologies. Genetic studies in humans and animal models have established that delay discounting is a heritable trait, but only a few specific genes have been associated with delay discounting. Here, we aimed to identify novel genetic loci associated with delay discounting through a genome-wide association study (GWAS) using Heterogenous Stock rats, a genetically diverse outbred population derived from eight inbred founder strains. We assessed delay discounting in 650 male and female rats using an adjusting amount procedure in which rats chose between smaller immediate sucrose rewards or a larger reward at variable delays. Preference switch points were calculated for each rat and both exponential and hyperbolic functions were fitted to these indifference points. Area under the curve (AUC) and the discounting parameter k of both functions were used as delay discounting measures. GWAS for AUC, exponential k, and indifference points for a short delay identified significant loci on chromosomes 20 and 14. The gene Slc35f1, which encodes a member of the solute carrier family of nucleoside sugar transporters, was the only gene within the chromosome 20 locus. That locus also contained an eQTL for Slc35f1, suggesting that heritable differences in the expression of that gene might be responsible for the association with behavior. The gene Adgrl3, which encodes a member of the latrophilin family of G-protein coupled receptors, was the only gene within the chromosome 14 locus. These findings implicate novel genes in delay discounting and highlight the need for further exploration.

genomics↗

Discovery of the sEH Inhibitor Epoxykynin as Potent Kynurenine Pathway Modulator

Disease-related phenotypic assays enable unbiased discovery of novel bioactive small molecules and may provide novel insights into physiological systems and unprecedented molecular modes-of-action (MMOA). Herein we report the identification and characterization of epoxykynin, a potent inhibitor of the soluble epoxide hydrolase (sEH). Epoxykynin was discovered by means of a cellular assay monitoring modulation of kynurenine (Kyn) levels in BxPC-3 cells upon stimulation with the cytokine interferon-{gamma} (IFN-{gamma}) and subsequent target identification employing affinity-based chemical proteomics. Increased Kyn levels are associated with immune suppression in the tumor microenvironment and, thus, the Kyn pathway and its key player indoleamine 2,3-dioxygenase 1 (IDO1) are appealing targets in immuno-oncology. However, targeting IDO1 directly has led to limited success in clinical investigations, demonstrating that alternative approaches to reduce Kyn levels are in high demand. We uncover a cross-talk between sEH and the Kyn pathway that may provide new opportunities to revert cancer-induced immune tolerance.

cell biology↗

Detection of a Mitochondrial Stress Phenotype using the Cell Painting Assay

Mitochondria are cellular powerhouses and crucial for cell function. However, these organelles are vulnerable to internal and external perturbagens that may impair mitochondrial function and eventually lead to cell death. In particular, small molecules may impact mitochondrial function and cardio- or hepatotoxicity caused by numerous drugs links mitochondrial toxicity to these adverse effects. Therefore, the influence of small molecules on mitochondrial homeostasis is at best assessed early on in the characterization of biologically active small molecules and drug discovery. We demonstrate that unbiased morphological profiling by means of the Cell Painting assay (CPA) can detect mitochondrial stress coupled to the induction of integrated stress response. This activity is common for compounds addressing different targets, is not shared by direct inhibitors of the electron transport chain and enables prediction of mitochondrial stress induction for small molecules that are profiled using CPA.

cell biology↗

Illuminating Dark Chemical Matter using the Cell Painting Assay

The identification of bioactive small molecules is at the heart of chemical biology and medicinal research. The screening for modulators of disease-relevant targets and phenotypes is the first step on the way to new drugs. Therefore, large compound libraries have been synthesized and employed by academia and, particularly, pharmaceutical companies to meet the need for chemical entities that are as diverse as possible. Extensive screening of these compound libraries revealed a portion of small molecules that is inactive in more than 100 different assays and was therefore termed dark chemical matter (DCM). Deorphanization of DCM promises to yield very selective compounds as they, by definition, should have less off-target effects. We employed morphological profiling using the Cell painting assay (CPA) to detect bioactive DCM compounds. CPA is not biased to a given target or phenotype and can detect various unrelated mechanisms and modes of action. Within the DCM collection, we identified bioactive compounds and confirmed several modulators of microtubules, DNA synthesis and pyrimidine biosynthesis. Profiling approaches are therefore powerful tools to probe compound collections for bioactivity in an unbiased manner and particularly suitable for deorphanization of DCM.

cell biology↗

Deciphering sources of PET signals in the tumor microenvironment of glioblastoma at cellular resolution

Various cellular sources hamper interpretation of positron-emission-tomography (PET) biomarkers in the tumor microenvironment (TME). We developed immunomagnetic cell sorting after in vivo radiotracer injection (scRadiotracing) in combination with 3D-histology via tissue clearing to dissect the cellular allocation of PET signals in the TME. In SB28 glioblastoma mice, translocator protein (TSPO) radiotracer uptake per tumor cell was higher compared to tumor-associated microglia/macrophages (TAMs). Cellular radiotracer uptake was validated by proteomics and confirmed for in vitro samples of patients with glioblastoma. Regional agreement between PET signals and single cell tracer uptake predicted the individual cell distribution in 3D-histology. In consideration of cellular tracer uptake and cell type abundance, tumor cells were the main contributor to TSPO enrichment in glioblastoma, however proteomics identified potential PET targets highly specific for TAMs. Combining cellular tracer uptake measures with 3D-histology facilitates precise allocation of complex PET signal sources and will serve to validate novel TAM-specific radioligands.

neuroscience↗

GPR183 targets lung-resident CD301b+ conventional dendritic cells type 2 to a subtissular TSLP-TSLP receptor-mediated survival niche within the adventitial cuff

Conventional dendritic cells (cDCs) are strategically localized throughout non-lymphoid tissues. How such spatially regulated subtissular placement is achieved remains largely elusive. Here, we reveal that GPR183 targets CD301b+ cDC2 to a TSLP-dependent survival niche within the adventital cuff. We identified a close association of CD301b+ cDC2 with PDGFR+ fibroblasts within the adventitial region of the lung. Genetic ablation of GPR183 within the cDC lineage leads to a selective loss of CD301b+ cDC2 in conjunction with the loss of CD301b+ cDC2 : fibroblast colocalization. Next bone marrow chimeric experiments and expression studies suggested adventitial fibroblasts as the main source of 7,25 hydroxycholesterol, the natural ligand of GPR183. Single cell transcriptomic receptor ligand inference and subsequent genetic validation revealed TSLP receptor signalling as a crucial fibroblast derived CD301b+ cDC2 survival factor. These data expose a subtissular localization mechanism for tissue-specific functionalization of CD301b+ cDC2.

immunology↗

Morphological Subprofile Analysis for Bioactivity Annotation of Small Molecules

Fast prediction of mode of action for bioactive compounds would immensely foster bioactivity annotation in compound collections and may early on reveal off-targets in chemical biology research and drug discovery. A variety of target-based assays is available for addressing the modulation of druggable proteins. However, they cannot precisely predict how a compound would influence cellular processes due to polypharmacology. Furthermore, non-protein targets are often not considered. Morphological profiling, e.g., using the Cell Painting assay that monitors hundreds of morphological features upon compound perturbation and staining of cellular components, offers a fast, unbiased assessment of compound activity on various targets and cellular processes in one single experiment. However, due to incomplete bioactivity annotation and unknown activities of reference (landmark) compounds, prediction of bioactivity is not straightforward. Here we introduce the concept of subprofile analysis to map the mode of action for both reference and unexplored compounds. We defined mode-of-action clusters for a group of reference compounds and extracted cluster subprofiles that contain only a subset of morphological features (i.e., subprofiles) to represent a consensus profile. Subprofile analysis allows for assignment of compounds to, currently, ten different targets or modes of action in one single assay and bypasses the need of exploring all biosimilar reference compounds for the generation of target hypothesis. This approach will enable rapid bioactivity annotation of compound collections, particularly of uncharacterized small molecules, and will be extended to further bioactivity clusters in future. The data is public accessible via https://github.com/mpimp-comas/2022_pahl_ziegler_subprofiles and the web app tool http://cpcse.pythonanywhere.com/.

cell biology↗

Active Translation Control of CD4 T Cell Activation by Regulatory T Cells

Increased protein synthesis is a hallmark of lymphocyte activation. Regulatory T cells (Tregs) suppress the activation and subsequent effector functions of CD4 effector T cells (Teffs). However, molecular mechanisms that enforce Treg-mediated suppression in CD4 Teff are not fully clear. Control of CD4 Teff activation by Tregs has largely been defined at the transcriptional level, which does not reflect changes in post-transcriptional control. We found that Tregs suppressed activation-induced global protein synthesis in CD4 Teffs prior to cell division. We analyzed genome-wide changes in the transcriptome and translatome of activated CD4 Teffs using two independent approaches. We show that mRNAs encoding for the protein synthesis machinery are regulated at the level of translation in activated Teffs. Strikingly, Tregs suppressed global protein synthesis of CD4 Teffs by specifically inhibiting mRNAs of the translation machinery at the level of mTORC1-mediated translation control. Lastly, we found that the RNA helicase eIF4A inhibitor rocaglamide A (RocA) can suppress CD4 Teff activation in vitro to alleviate inflammatory CD4 Teff activation caused by acute Treg depletion in vivo. These data provide evidence that peripheral tolerance is enforced by Tregs through mRNA translational control in CD4 Teffs. Therefore, therapeutic targeting of the protein synthesis machinery can be expected to mitigate inflammatory responses invoked by Treg loss of function.

immunology↗

A scalable, clinically severe pig model for Duchenne muscular dystrophy

Large animal models for Duchenne muscular dystrophy (DMD) are crucial for preclinical evaluation of novel diagnostic procedures and treatment strategies. Pigs cloned from male cells lacking DMD exon 52 (DMD{Delta}52) resemble molecular, clinical and pathological hallmarks of DMD, but cannot be propagated by breeding due to death before sexual maturity. Therefore, female DMD+/- carriers were generated. A single founder animal had 11 litters with 29 DMDY/-, 34 DMD+/- as well as 36 male and 29 female wild-type (WT) offspring. Breeding with F1 and F2 DMD+/- carriers resulted in additional 114 DMDY/- piglets. The majority of them survived for 3-4 months, providing large cohorts for experimental studies. Pathological investigations and proteome studies of skeletal muscles and myocardium confirmed the resemblance of human disease mechanisms. Importantly, DMDY/- pigs reveal progressive fibrosis of myocardium and increased expression of connexin-43, associated with significantly reduced left ventricular fractional shortening and ejection fraction already at age 3 months. Furthermore, behavioral tests provided evidence for impaired cognitive ability of DMDY/- pigs. Our breeding cohort of DMD{Delta}52 pigs and standardized tissue repositories from DMDY/- pigs, DMD+/- carriers, and WT littermate controls provide important resources for studying DMD disease mechanisms and for testing novel diagnostic procedures and treatment strategies.

pathology↗

Spatial multi-omic map of human myocardial infarction

Myocardial infarction is a leading cause of mortality. While advances in the acute treatment have been made, the late-stage mortality is still high, driven by an incomplete understanding of cardiac remodeling processes1,2. Here we used single-cell gene expression, chromatin accessibility and spatial transcriptomic profiling of different physiological zones and timepoints of human myocardial infarction and human control myocardium to generate an integrative high-resolution map of cardiac remodeling. This approach allowed us to increase spatial resolution of cell-type composition and provide spatially resolved insights into the cardiac transcriptome and epigenome with identification of distinct cellular zones of injury, repair and remodeling. We here identified and validated mechanisms of fibroblast to myofibroblast differentiation that drive cardiac fibrosis. Our study provides an integrative molecular map of human myocardial infarction and represents a reference to advance mechanistic and therapeutic studies of cardiac disease.

systems biology↗

Cortico-thalamic dysconnectivity links with aberrant striatal dopamine in schizophrenia. A simultaneous 18F-DOPA-PET/resting-state fMRI study

In schizophrenia, among the most consistent brain changes are both aberrant dopamine function in the dorsal striatum and aberrant intrinsic functional connectivity (iFC) between distinct cortical networks and thalamic nuclei; however, it is unknown whether these changes are pathophysiologically related. Such a relationship is expected because cortico-thalamic-connectivity is modulated by striatal dopamine within topographically distinct, parallel but interacting cortico-basal-ganglia-thalamic circuits. We hypothesized: (1) Within-circuits, aberrant striatal dopamine contributes to aberrant cortico-thalamic-iFC, specifically, associative-striatum dopamine contributes to salience-network-thalamic-iFC, and sensorimotor-striatum dopamine to auditory-sensorimotor-network-thalamic-iFC. (2) Due to between-circuits interactions following an anterior-to-posterior gradient, salience-network-centered-system changes contribute to auditory-sensorimotor-network-centered-system changes. To test these hypotheses, 19 patients with schizophrenia during symptomatic remission of positive symptoms and 19 age- and sex-comparable controls underwent simultaneous fluorodihydroxyphenyl-L-alanine positron emission tomography (18F-DOPA-PET) and resting-state functional magnetic resonance imaging (rs-fMRI). The influx constant kicer based on 18F-DOPA-PET was used to measure dopamine synthesis capacity (DSC), indicating striatal dopamine function; correlation coefficients between rs-fMRI time-series of cortical networks and thalamic regions-of-interest were used to measure iFC. In the salience-network(SAL)-centered-system, patients had reduced associative-striatum-DSC, which correlated positively with SAL-mediodorsal-thalamus-iFC and mediated the reduction of SAL-thalamic-iFC in patients. In the auditory-sensorimotor-network(ASM)-centered-system, patients had reduced sensorimotor-striatum-DSC, which correlated positively with ASM-ventrolateral-thalamus-iFC, but did not mediate increased ASM-thalamic-iFC in patients. Finally, aberrant DSC and iFC of the SAL-centered-system mediated corresponding changes in the ASM-centered-system. Results demonstrate that cortico-thalamic-dysconnectivity links with aberrant striatal dopamine in schizophrenia - in a topographically distinct way, with an anterior-to-posterior gradient, and primary changes in the SAL-centered system.

neuroscience↗