Biology subjects

Buettner, M.

Publications and source records attributed to Buettner, M..

12 recordsLinked to original sources

bioRxiv2026

A gut-on-chip model reveals architecture-dependent epithelial responses to microbial challenge

Advanced in vitro models that better recapitulate human intestinal physiology are needed to improve translational relevance and reduce reliance on animal experimentation. Microfluidic gut-on-chip systems provide controlled architectural and mechanical microenvironments that more closely resemble native tissue than conventional static cultures. However, how these features influence epithelial responses to microbial stimuli remains incompletely understood. In this study, we compared conventional two-dimensional (2D) Caco-2 monolayers with a perfused three-dimensional (3D) gut-on-chip model exhibiting crypt-like epithelial organization. Microbial challenge was employed as a biologically relevant perturbation to investigate barrier-associated responses under distinct culture conditions. Following exposure to the probiotic Escherichia coli Nissle 1917 (EcN), epithelial morphology, barrier-associated gene expression, inflammatory signaling, and temporal response patterns were assessed over time. In a complementary approach, susceptibility to bacterial stress was examined using increasing doses of Citrobacter rodentium (C. rodentium). Both culture systems responded dynamically to microbial exposure; however, differences in response patterns were observed between static and perfused cultures. EcN induced transient alterations in epithelial organization followed by recovery-associated responses, while C. rodentium caused dose-dependent structural and transcriptional changes. Notably, epithelial damage became apparent at lower bacterial loads in conventional 2D cultures, whereas the chip-based model maintained tissue integrity under comparable conditions. Together, these findings indicate that epithelial architecture and the surrounding culture environment influence barrier-associated responses to microbial challenge. The study highlights the utility of gut-on-chip systems for investigating host-microbe interactions and provides a framework for functional comparison of advanced intestinal in vitro models.

cell biology↗

bioRxiv2026

Rapid estimation of receptive fields across stages of the early visual system

Estimating receptive fields in large neural populations is often limited by experimental time: stimuli with theoretically favorable statistics for receptive-field estimation may, in practice, evoke too few informative spikes in neurons with high specificity for structured features, requiring impracticably long recordings. Therefore, we asked whether a structured stimulus could broadly engage neural populations across stages of the early visual system while permitting a tractable and interpretable reverse-correlation analysis. To address this question, we developed "reverse correlation against stimulus elements (RCASE)", an analysis framework for stimuli that can be represented frame by frame through the presence or absence of specific stimulus elements. We then designed such a stimulus consisting of random moving objects (RMO) and compared RMO/RCASE with conventional spike-triggered averaging using a dense binary white noise (WN/STA) stimulus across different stages of the early visual system of the mouse, namely the retina, the nucleus of the optic tract, the superior colliculus and the primary visual cortex, and in the primate retina. To distinguish the contributions of spatial and temporal scales, motion, stimulus structure, and analysis choice, we additionally compared against WN/STA with different square sizes and frame rates, spike-triggered covariance analysis, as well as random static objects and spatially correlated cloud stimuli. RMO evoked stronger and more reliable responses than WN in the mouse retina and across the investigated mouse visual areas. RMO/RCASE yielded discernible receptive fields for a substantially larger proportion of neurons and in a fraction of the recording time. Although the stimulus objects featured localized moving contrast edges, this advantage was not restricted to direction-selective cell populations. In the primate retina, in contrast, WN/STA approached the performance of RMO/RCASE. RMO/RCASE also supported simultaneous estimation of stimulus direction, speed, and color tuning. Our approach enables rapid and interpretable functional characterization of large populations of visual neurons, enabling to simultaneously recover receptive fields and feature tuning, whenever a low-dimensional feature space can be specified beforehand.

neuroscience↗

bioRxiv2026

Longitudinal single-cell and spatial transcriptomics reveals intratumor heterogeneity, therapeutic response, and comparative value of canine marginal zone lymphoma

Diffuse B-cell lymphomas are the most prevalent canine hematologic malignancies, and their clinical presentation resembles that of human B-cell non-Hodgkin lymphomas (NHLs). However, a lack of a clear subtyping framework perpetuates imprecise treatment approaches that fail to address mechanisms of therapy resistance. Here, we employed deep phenotyping via serial sampling and longitudinal transcriptomics to evaluate intratumoral composition and therapy response in a 6-year-old neutered male goldendoodle with stage 5A marginal zone lymphoma (MZL). Following sequential treatment consisting of a single IV dose of oncolytic vesicular stomatitis virotherapy (VSV) and standard CHOP chemotherapy 30 days later, we performed scRNAseq on seven serial lymph node biopsies and spatial sequencing on a resection taken 10 days post-VSV treatment. B cells (>90%) comprised three transcriptionally distinct and temporally stable subpopulations, with specific copy number profiles and robust spatial organization despite disrupted lymph node architecture. Analysis across subpopulations revealed downregulation of the quiescence program including KLF2, suggesting similarity to KLF2-deficient human MZL. While VSV successfully reached target B cells, downstream transcriptional responses were predominantly localized to the T-cell compartment. T cells ([≤]6%) showed increased proliferation and upregulation of cytotoxicity markers post-VSV administration, enriching for leukocyte-mediated cytotoxicity pathways consistent with an anti-viral immune response. Ultimately, these results provide an in vivo proof-of-concept for the treatment paradigm in canine lymphoma, while emphasizing the need for improved subtyping frameworks and multidimensional treatment strategies targeting intratumoral heterogeneity.

cancer biology↗

bioRxiv2026

Activated macrophages restrict invasive bacterial infection in a human intestinal organoid co-culture model

Intestinal organoids provide physiologically relevant models of the epithelial barrier, but lack the immune compartment that critically shapes host responses to infection. Here, we established a human colon organoid-derived monolayer co-culture system with macrophage-like THP-1 cells positioned directly beneath the epithelial layer. The model enabled controlled apical infection with Listeria monocytogenes and Salmonella Typhimurium while preserving epithelial barrier integrity. PMA-differentiated THP-1 cells reduced intracellular L. monocytogenes burden, whereas additional activation with IFN-{gamma} and LPS resulted in a pronounced reduction of both L. monocytogenes and S. Typhimurium, accompanied by decreased infection-associated cytotoxicity. Bulk RNA sequencing revealed a distinct co-culture transcriptional signature characterized by coordinated changes in inflammatory, antimicrobial, and epithelial lineage-associated programs. These included reduced HLA-D/MHC class II-associated gene expression, altered S100A8/S100A9 expression, and changes in epithelial lineage markers indicating a shift in epithelial cellular composition and differentiation state. Together, these findings establish a versatile human organoid-macrophage platform for dissecting epithelial-immune interactions and macrophage-associated control of invasive bacterial infection.

immunology↗

bioRxiv2026

Mice and humans use ambiguous local motion to stabilize gaze

Animals need to infer properties of the environment that are only ambiguously encoded by neurons in the sensory periphery. In vision, local edge motion seen through small receptive fields does not uniquely specify the direction of global or object motion. Can these ambiguous local motion signals drive behavior directly, or must the ambiguity first be resolved? We addressed this question in reflexive gaze stabilization by tracing motion signals from the retina through the nucleus of the optic tract (NOT) to eye movements, combining retinal and in vivo electrophysiology, computational modelling, and eye tracking in mice and humans. By using stimuli that dissociate local edge motion from global, object motion, we found that NOT cell responses were strongly biased towards local motion and were largely explained by linear pooling of retinal inputs. This effect propagated to behavior: eye movements followed local motion, to the point that changing the edge orientation of vertically moving objects produced horizontal eye movements. Humans showed a qualitatively similar bias, which increased when central vision was masked. Thus, ambiguous local motion signals can drive effective behavior; a conserved sensorimotor strategy in which visually guided behavior relies on a heuristic rather than an accurate reconstruction of the external world.

neuroscience↗

bioRxiv2025

Intrinsic structure of lipoplexes embedded in polyelectrolyte multilayers

The functionalization of surfaces with therapeutically applicable nucleic acid carriers provides promising strategies in biomedical research to develop therapies which focus on local nucleic acid delivery. One such approach is the embedding of lipoplexes (LPXs) in polysaccharide-based polyelectrolyte multilayers (PEMs). PEMs based on hyaluronic acid and chitosan lead to efficient embedding of customized LPX connected with good biological activity. However, although quantitative evaluation demonstrates LPX embedding, information on the embedded LPXs has been missing. In this study we used synchrotron-based grazing-incidence small angle x-ray scattering to investigate the effects of the change in the chemical environment caused by the embedding into PEMs on the LPXs internal mesoscopic structure. While the lamellar character of the LPXs was preserved, the repeat distance was affected by the embedding into polysaccharide-based coatings.

biophysics↗

bioRxiv2025

A metabolism-chromatin axis promotes ribosome heterogeneity in the human malaria parasite

The transmission of the most virulent human malaria parasite, Plasmodium falciparum, relies on its survival in the contrasting environments of the human host and mosquito vector. One of the most fascinating adaptations to this lifestyle is the specific silencing of individual rDNA genes in the human host that are de-repressed following host-to-vector transmission. In this study, we defined the epigenetic signatures of rRNA transcription and found that rDNA silencing relies on aerobic glycolysis, the sole energy-generating pathway in the human host. We show that disruption of NAD+ regeneration during lactate fermentation promotes rDNA de-repression and identify the sirtuin histone deacetylase Sir2a as the mediator between fluctuating NAD+ levels and a functional transcriptional outcome. Hence, rDNA activation appears to be coupled to the metabolic state of the parasite as it transitions from aerobic glycolysis to mitochondrial respiration during host-to-vector transmission.

microbiology↗

bioRxiv2022

Rearing environment persistently modulates the phenotype of mice

The phenotype of an organism results from its genotype and the influence of the environment throughout development. Even when using animals of the same genotype, independent studies may test animals of different phenotypes, resulting in poor replicability due to genotype-by-environment interactions 1-4. Thus, genetically defined strains of mice may respond differently to experimental treatments depending on their rearing environment 5. However, the extent of such phenotypic plasticity and its implications for the replicability of research findings have remained unknown. Here, we examined the extent to which common environmental differences between rearing facilities modulate the phenotype of genetically homogeneous (inbred) mice. We conducted a comprehensive multi-center study, where inbred mice from the same breeding stock were reared in five different facilities throughout early life and adolescence, before being transported to a single test laboratory. We found persistent effects of rearing facility on the composition and heterogeneity of the gut microbial community. These effects were paralleled by persistent differences in body weight and in the behavioural phenotype of the mice. Furthermore, we show that common variation among rearing facilities is strong enough to influence epigenetic patterns in neurons at the level of chromatin organization. We detected changes in chromatin organization in the regulatory regions of genes involved in nucleosome assembly, neuronal differentiation, synaptic plasticity and regulation of behavior. Our findings demonstrate that common environmental differences between rearing facilities may produce facility-specific phenotypes, from the molecular to the behavioural level. We expect our findings to stimulate further research into the mechanisms and drivers of these epigenetic changes mediated by the laboratory environment. Furthermore, they highlight an important limitation of inferences from single-laboratory studies and a need to account for the animals environmental background in study design to produce robust and replicable findings.

neuroscience↗

bioRxiv2021

MYCN mediates cysteine addiction and sensitizes to ferroptosis

Aberrant expression of MYC family members predicts poor clinical outcome in many human cancers. Oncogenic MYC profoundly alters metabolism and mediates an antioxidant response to maintain redox balance. Here we show that MYC induces massive lipid peroxidation upon depletion of cysteine, the rate-limiting amino acid for glutathione biosynthesis and sensitizes cells to ferroptosis, an oxidative, non-apoptotic and irondependent type of cell death. In MYCN-amplified childhood neuroblastoma, MYCN mediates resistance to ferroptosis by activating transsulfuration of methionine to cysteine. MYCN may contribute to spontaneous tumor regression in low-risk neuroblastomas by promoting ferroptosis in cells with epigenetically silenced cystathionine-beta-synthase, the rate-limiting enzyme for transsulfuration. We identified enzymes and antiporter proteins crucial to ferroptotic escape, providing multiple previously unknown sites that may be acted on therapeutically.

cancer biology↗

bioRxiv2020

scCODA: A Bayesian model for compositional single-cell data analysis

Compositional changes of cell types are main drivers of biological processes. Their detection through single-cell experiments is difficult due to the compositionality of the data and low sample sizes. We introduce scCODA (https://github.com/theislab/scCODA), a Bayesian model addressing these issues enabling the study of complex cell type effects in disease, and other stimuli. scCODA demonstrated excellent detection performance and identified experimentally verified cell type changes that were missed in original analyses.

bioinformatics↗

bioRxiv2020

Wnt/PCP-primed intestinal stem cells directly differentiate into enteroendocrine or Paneth cells

A detailed understanding of intestinal stem cell (ISC) self-renewal and differentiation is required to better treat chronic intestinal diseases. However, different models of ISC lineage hierarchy1-6 and segregation7-12 are debated. Here we report the identification of Lgr5+ ISCs that express Flattop (Fltp), a Wnt/planar cell polarity (PCP) reporter and effector gene. Lineage labelling revealed that Wnt/PCP-activated Fltp+ ISCs are primed either towards the enteroendocrine or the Paneth cell lineage in vivo. Integration of time-resolved lineage labelling with genome-wide and targeted single-cell gene expression analysis allowed us to delineate the ISC differentiation path into enteroendocrine and Paneth cells at the molecular level. Strikingly, we found that both lineages are directly recruited from ISCs via unipotent transition states, challenging the existence of formerly predicted bi- or multipotent secretory progenitors7-12. Transitory cells that mature into Paneth cells are quiescent and express both stem cell and secretory lineage genes, indicating that these cells are the previously described Lgr5+ labelretaining cells7. Wnt/PCP-activated Lgr5+ ISCs are indistinguishable from Wnt/{beta}-catenin-activated Lgr5+ ISCs based on the expression of stem-cell signature or secretory lineagespecifying genes but possess less self-renewal activity. This suggests that lineage priming and cell-cycle exit is triggered at the post-transcriptional level by polarity cues and a switch from canonical to non-canonical Wnt/PCP signalling. Taken together, we identified the Wnt/PCP pathway as a new niche signal and polarity cue regulating stem cell fate. Active Wnt/PCP signalling represents one of the earliest events in ISC lineage priming towards the Paneth and enteroendocrine cell fate, preceding lateral inhibition and expression of secretory lineagespecifying genes. Thus, our findings provide a better understanding of the niche signals and redefine the mechanisms underlying ISC lineage hierarchy and segregation.

developmental biology↗

bioRxiv2019

Redox-mediated Kick-Start of Mitochondrial Energy Metabolism drives Resource-efficient Seed Germination

Seeds preserve a far developed plant embryo in a quiescent state. Seed metabolism relies on stored resources and is re-activated to drive germination when the external conditions are favorable. Since the switchover from quiescence to re-activation provides a remarkable case of a cell physiological transition we investigated the earliest events in energy and redox metabolism of Arabidopsis seeds at imbibition. By developing fluorescent protein biosensing in intact seeds, we observed ATP accumulation and oxygen uptake within minutes, indicating rapid activation of mitochondrial respiration, which coincided with a sharp transition from an oxidizing to a more reducing thiol redox environment in the mitochondrial matrix. To identify individual operational protein thiol switches, we captured the fast release of metabolic quiescence in organello and devised quantitative iodoacetyl tandem mass tag-based (iodoTMT) thiol redox proteomics. The redox state across all Cys-peptides was shifted towards reduction from 27.1 % to 13.0 %. A large number of Cys-peptides (412) were redox-switched, representing central pathways of mitochondrial energy metabolism, including the respiratory chain and each enzymatic step of the tricarboxylic acid cycle (TCA). Active site Cys-peptides of glutathione reductase 2, NADPH-thioredoxin reductase a/b and thioredoxin-o1 showed the strongest responses. Germination of seeds lacking those redox proteins was associated with markedly enhanced respiration and deregulated TCA cycle dynamics suggesting decreased resource efficiency of energy metabolism. Germination in aged seeds was strongly impaired. We identify a global operation of thiol redox switches that is required for optimal usage of energy stores by the mitochondria to drive efficient germination.

plant biology↗