Biology subjects

Guenther, C.

Publications and source records attributed to Guenther, C..

10 recordsLinked to original sources

bioRxiv2026

A Framework for NGN1-Induced Sensory Neuron Differentiation for Disease Modelling and Drug Screening

Background: Neuropathic pain is a burdensome, difficult-to-treat, and highly heterogeneous condition with limited therapeutic options, underscoring the need for robust and reproducible human disease models. Human induced pluripotent stem cell (iPSC)-derived sensory neurons provide a promising platform for patient specific disease modelling and drug screening; however, their translational use is hampered by variability in differentiation efficiency, cellular composition, and functional maturation across protocols and cell lines. Methods: Here, we present a standardized and potentially scalable framework for NGN1 driven differentiation of human iPSCs into sensory neurons. Building on a previously published two step protocol (1), we systematically deconstructed and optimized each stage of differentiation across a large panel of genetically diverse iPSC lines. Results: We identified robust parameters for neural crest like cell (NCLC) generation, established a flow cytometry-based quality control strategy for NCLCs, and defined optimal combinations of seeding density and lentiviral multiplicity of infection to maximize sensory neuron progenitor yield. To improve culture homogeneity, we compared antimitotic selection strategies and demonstrated that tightly timed Ara-C treatment combined with low progenitor seeding density yields consistently pure sensory neuron cultures. We further evaluated maturation under physiologically relevant glucose conditions and performed a systematic review of media compositions to derive two defined maturation media. Morphological, immunocytochemical, transcriptomic, and electrophysiological analyses revealed that time in culture is a major determinant of maturation, while specific supplements such as prostaglandin E2; (PGE2) selectively enhance transcriptional signatures associated with nociceptor identity without substantially altering global network activity. Bulk RNA sequencing demonstrated broad expression of sensory neuron and pain related markers and gene programs across conditions, with long term maturation and PGE2; treatment showing the highest similarity to human dorsal root ganglion reference data. Functional assessment using multi electrode arrays enabled the detection of donor specific electrophysiological phenotypes, including reproducible hyperexcitability in small fiber neuropathy patient derived lines. Conclusions: This study establishes a modular, reproducible NGN1 based differentiation workflow with integrated quality checkpoints that accommodates iPSC line to line variability. The framework provides a practical foundation for translational sensory neuron research, patient specific disease modelling, and scalable drug screening applications.

neuroscience↗

bioRxiv2026

Host-derived bile acids drive dysbiosis by selecting bile-resistant epimerizing bacteria in inflammatory bowel disease

Microbial dysbiosis is a hallmark of inflammatory bowel diseases (IBD); however, its drivers and impact on disease pathophysiology are poorly understood. Applying neural network-based feature attribution to metabolomics and metagenomics datasets from >5000 individuals, we identified epimerized host derived bile acids (BAs) produced by microbial hydroxysteroid dehydrogenases (HSDHs) as a novel hallmark of IBD-associated dysbiosis. Epimerized BAs reduce FXR activity in intestinal epithelial cells and dampen their production of FGF19, a negative feedback regulator of host-derived bile acid (HBA) production in the liver. Increased HBA levels drive colonic epithelial remodeling by impacting goblet cell maturation and select for HSDH-carrying bacteria that transform bactericidal HBA into less toxic, epimerized forms. Confirming the translational relevance of these findings, we demonstrated that high HBA levels limit fecal microbiota transplant engraftment and show that BA sequestering drugs support microbiome recovery in patients with high HBA levels. Together, we discover that elevated HBAs deplete BA-sensitive commensals and favor the growth of HSDH-encoding pathobionts that disrupt host BA feedback signaling, establishing a causal link between changes in microbial ecology and IBD pathophysiology.

microbiology↗

bioRxiv2026

Natural microbial exposure imposes layered constraints on epithelial and type 2 immunity

The tuft cell-ILC2 amplification circuit has emerged as a central paradigm of anti-helminth immunity in laboratory animals, driving the so-called weep and sweep response, required for parasite expulsion. Yet soil-transmitted helminths (STHs) commonly establish chronic infections in humans. Whether tuft cell expansion is required for parasite clearance under naturalistic conditions remains unknown. Here, using wildlings, a naturalized mouse model exposed from birth to complex microbial communities and pathogens, we re-investigated anti-STH immunity in the context of ecological realism. Following infection with Nippostrongylus brasiliensis, specific pathogen-free (SPF) mice mounted markedly amplified type 2 responses in both lung and intestine compared to wildlings. In the intestine, SPF mice mounted robust tuft cell expansion, IL-25 production, ILC2 accumulation, and goblet cell hyperplasia. In contrast, infected wildlings exhibited delayed parasite expulsion, limited tuft cell expansion, reduced IL-25 and ILC2 responses, and attenuated goblet cell expansion. Wildling tuft cells, but not goblet cells, displayed markedly reduced expansion in response to succinate or exogenous IL-13, indicating selective hypo-responsiveness of the epithelial sensory compartment. Microbial transfer into adult SPF mice selectively conferred tuft cell hypo-responsiveness without impairing ILC2 accumulation or goblet cell expansion. Tuft cell hypo-responsiveness in wildlings and FMT recipients was associated with enrichment of fermentative bacteria and increased levels of the short chain fatty acids acetate and propionate. Together, these findings indicate that ecological microbial exposure imprints systemic type 2 immunity during early-life, whereas epithelial responsiveness remains plastic and microbiome-dependent, thereby revealing regulatory constraints not evident under SPF conditions. One Sentence SummaryOur findings reveal that in a naturalized immune-microbiome context, intestinal tuft cells are surprisingly hypo-responsive, highlighting how environmental microbial exposure can calibrate type 2 immunity and helminth resistance.

immunology↗

bioRxiv2026

Csf1r-mediated depletion of midbrain microglia prevents dopaminergic neuron loss during chronic colitis

Inflammatory bowel disease (IBD) predisposes to neuropsychiatric comorbidity and particularly increases the risk of Parkinsons Disease (PD) in later life. Although the gut-immune-brain axis was proposed as a link between IBD and PD and a driver of PD immunopathogenesis, the regional pattern and single-cell landscape of the brain immune response during colitis and its contribution to PD pathology remain poorly defined. Here, we observe a loss of dopaminergic neurons in the substantia nigra pars compacta of adult mice with chronic colitis. By confocal microscopy and integrated multi-omics, we reveal a complex midbrain-centered immune response to chronic colitis in comparison to the cortex, hippocampus, and striatum. Single-cell mapping of the midbrain immune landscape showed an inflammatory shift of microglial clusters including an expansion of interferon-response microglia, CD8+ T cell extravasation, and increased numbers of vessel-associated neutrophils. Selective myeloid cell depletion using a colony stimulating factor 1 receptor (Csf1r) inhibitor after colitis onset reduced midbrain microglia by 67% and led to a complete rescue of dopaminergic neuron loss, without affecting mucosal pathology or T cell and neutrophil migration to the midbrain. Collectively, within the complex innate and adaptive midbrain immune response to chronic colitis, we demonstrate a causal role of Csf1r-dependent microglia for dopaminergic neurodegeneration. Thus, Csf1r inhibition in IBD may not locally ameliorate colitis, but provide neuroprotection to dopaminergic neurons. These results reveal a novel cellular link between chronic gut-derived peripheral inflammation and midbrain vulnerability and thereby substantially enhance our understanding of the risk for PD related to the gut-immune-brain axis. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=174 SRC="FIGDIR/small/700559v1_ufig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@1bf7217org.highwire.dtl.DTLVardef@1db66c0org.highwire.dtl.DTLVardef@136ef2eorg.highwire.dtl.DTLVardef@190f641_HPS_FORMAT_FIGEXP M_FIG Graphical abstract. C_FIG

neuroscience↗

bioRxiv2025

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↗

bioRxiv2025

Deciphering Brain Organoids Heterogeneity by Identifying Key Quality Determinants

Brain organoids derived from human pluripotent stem cells (hPSCs) hold immense potential for modeling neurodevelopmental processes and disorders. However, their experimental variability and undefined organoid selection criteria for analysis hinder reproducibility. As part of the Bavarian ForInter consortium, we generated 72 brain organoids from distinct hPSC lines. We conducted a comprehensive analysis of their morphological and cellular characteristics at an early stage of their development. In our assessment, the Feret diameter emerged as a reliable, single parameter that characterizes brain organoid quality. Transcriptomic analysis further confirmed the reliability of this marker and identified a negative impact of mesenchymal cells on the abundance of organoid formation. High-quality organoids consistently displayed a lower mesenchymal cell presence. These findings offer a framework for enhancing brain organoid standardization and reproducibility, underscoring the need for morphological quality controls and the consideration of mesenchymal cell influence on organoid-based modeling. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=186 HEIGHT=200 SRC="FIGDIR/small/632763v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@11c214org.highwire.dtl.DTLVardef@1dcb643org.highwire.dtl.DTLVardef@1420141org.highwire.dtl.DTLVardef@6074e6_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2024

Integrated multi-model analysis of intestinal inflammation exposes key molecular features of preclinical and clinical IBD

BackgroundInflammatory bowel disease (IBD) is a chronic inflammatory condition of the intestine with a complex and multifaceted pathogenesis. While various animal models exist to study specific disease mechanisms relevant to human IBD, a comprehensive comparative framework linking these to IBD pathophysiology is lacking. ObjectiveIn our study, we aimed at providing a framework that delineates common and unique features encountered in 13 widely used mouse models comparing them with human IBD to identify translatable pathways in model-cohort pairs. Another aim of our study was to provide an explorable resource for looking up gene and pathway level changes in mouse models assisting in hypothesis testing and minimizing animal burden abiding by the 3R principals. DesignWe employed comparative transcriptomic analyses with curated and a priori statistical correlative methods between mouse models versus established as well as own patient datasets at both bulk and single cell levels. ResultsWe identify IBD-related pathways, ontologies, and cellular processes that are translatable between mouse models and patient cohorts. Moreover, we identify, known and novel IBD-associated subcellular mechanisms and how they are recapitulated in specific mouse models. ConclusionOur findings provide a valuable resource for selecting the most appropriate experimental paradigm to model unique features of IBD pathomechanisms, allowing analysis at the tissue, cellular, and subcellular levels. What is already known on this topicPreclinical modelling of IBD is key to the discovery of pathomechanisms and the evaluation of therapeutic approaches. However, individual models do not recapitulate the complexity of the disease and comprehensive studies comparing modelling paradigms with human IBD are lacking. What this study addsOur study provides a comparative analysis of thirteen commonly used intestinal inflammation models, identifying core-conserved pathways between mouse models and IBD patient cohorts. In addition, our study shows how specific pathways involved in IBD are recapitulated in specific mouse models and introduces a web tool to analyse the models. How this study might affect research, practice or policyBy identifying conserved and discrepant pathways between specific mouse models and IBD patient cohorts, our analysis platform provides an invaluable resource for translational IBD research.

systems biology↗

bioRxiv2024

Stiffness regulates dendritic cell and macrophage subtype development and increased stiffness induces a tumor-associated macrophage phenotype in cancer co-cultures

Mechanical properties of tissues including their stiffness change throughout our lives, during both healthy development but also during chronic diseases like cancer (1-4). How changes to stiffness, occurring during cancer progression, impact leukocytes is unknown. To address this, myeloid phenotypes resulting from mono- and cancer co-cultures of primary murine and human myeloid cells on 2D and 3D hydrogels with varying stiffnesses were analyzed. On soft hydrogels, conventional DCs (cDCs) developed, whereas on stiff hydrogels plasmacytoid DCs (pDCs) developed. Cell populations expressing macrophage markers CD14, Ly6C, and CD16 also increased on stiff hydrogels. In cancer co-cultures, CD86+ populations decreased on higher stiffnesses across four different cancer types. High stiffness also led to increased vascular endothelial growth factor A (VEGFA), matrix metalloproteinases (MMP) and CD206 expression; M2 markers expressed by tumour-associated macrophages (TAMs) (5). Indeed, the majority of CD11c+ cells expressed CD206 across human cancer models. Targeting the PI3K/Akt pathway led to a decrease in CD206+ cells in murine cultures only, while human CD86+ cells increased. Increased stiffness in cancer could, thus, lead to the dysregulation of infiltrating myeloid cells and shift their phenotypes towards a M2-like TAM phenotype, thereby actively enabling tumor progression. Additionally, stiffness-dependent signaling appears species-dependent, potentially contributing to the high failure rate of clinical trials (6).

immunology↗

bioRxiv2022

Human Dectin-1 is O-glycosylated and serves as a ligand for C-type lectin receptor CLEC-2

C-type lectin receptors (CLRs) elicit immune responses upon recognition of glycoconjugates present on pathogens and self-components. While Dectin-1 is the best-characterized CLR recognizing {beta}-glucan on pathogens, the endogenous targets of Dectin-1 are not fully understood. Herein, we report that human Dectin-1 is a ligand for CLEC-2, another CLR expressed on platelets. Biochemical analyses revealed that Dectin-1 is a mucin-like protein as its stalk region is highly O-glycosylated. A sialylated core 1 glycan attached to the EDxxT motif of human Dectin-1, which is absent in mouse Dectin-1, provides a ligand moiety for CLEC-2. Strikingly, the expression of human Dectin-1 in mice rescued the lethality and lymphatic defect resulting from a deficiency of Podoplanin, a known CLEC-2 ligand. This finding is the first example of an innate immune receptor also functioning as a physiological ligand to regulate ontogeny upon glycosylation.

immunology↗

bioRxiv2022

Validation of an RNase H2 activity assay suitable for clinical screening

As the key enzyme mediating ribonucleotide excision repair, RNase H2 is essential for the removal of single ribonucleotides from DNA in order to prevent genome damage. Loss of RNase H2 activity directly contributes to the pathogenesis of autoinflammatory and autoimmune diseases and might further play a role in ageing and neurodegeneration. Moreover, RNase H2 activity is a potential diagnostic and prognostic marker in several types of cancer. Until today, no method for quantification of RNase H2 activity has been validated for the clinical setting. Herein, validation and benchmarks of a FRET-based whole-cell lysate RNase H2 activity assay are presented, including standard conditions and procedures to calculate standardized RNase H2 activity. Spanning a wide working range, the assay is applicable to various human cell or tissue samples with overall methodological assay variability from 8.6% to 16%. The assay readily detected reduced RNase H2 activity in lymphocytes of a patient with systemic sclerosis carrying a RNASEH2C variant. Implementation of larger control groups will help to assess the diagnostic and prognostic value of clinical screening for RNase H2 activity in the future.

immunology↗