Biology subjects

Hartmann, D.

Publications and source records attributed to Hartmann, D..

8 recordsLinked to original sources

bioRxiv2026

Host-derived lipids license proliferation of sterol-auxotrophic tick cells and promote flavivirus output

Sterol molecules play indispensable roles in the biology of cells and organisms. Yet, arthropods, including ticks, lack the capacity for de novo sterol biosynthesis and must rely on exogenous sources. How these organisms sense and utilise exogenous lipids at the cellular level remains poorly understood. Here, we show that host cholesterol and linoleic acid act as essential external signals that license proliferation of Ixodes ricinus tick cells. In lipid-depleted conditions, cells fail to proliferate despite retaining intracellular cholesterol, indicating that exogenous lipids function as regulatory cues rather than merely structural components. We further demonstrate that tick cells exhibit a non-canonical intracellular distribution of cholesterol, with predominant accumulation in lysosome-associated compartments, and that lipid availability induces a coordinated transcriptional program involving lipid uptake and trafficking machinery. Importantly, we find that limiting host lipid availability significantly reduces extracellular RNA output of tick-borne encephalitis virus (TBEV) from infected tick cells, indicating that viral production is affected by the metabolic state of the host cell. Together, our findings establish host-derived lipids as key regulators of cellular state in a sterol-auxotrophic organism and identify lipid availability as a determinant of flavivirus output. This work provides a conceptual framework linking nutrient sensing, cell proliferation, and vector-pathogen interactions.

microbiology↗

bioRxiv2026

Prolonged TGF-β locks NK cells in a dysfunctional state through persistent epigenetic remodeling of IRF, T-bet and EOMES binding sites

TGF-{beta} signaling is a major regulator of immune cell differentiation and function, yet whether prolonged signaling can durably imprint dysfunctional immune states independently of continued pathway engagement remains unclear. Here, we identify signal duration as a critical determinant of human natural killer (NK) cell fate: short-term TGF-{beta} exposure induces largely reversible transcriptional, chromatin and functional changes, whereas prolonged exposure establishes persistent effector dysfunction independent of continued signaling. Mechanistically, prolonged TGF-{beta} drives durable loss of chromatin accessibility at effector-associated regulatory elements, particularly those enriched for IRF, EOMES, and T-bet binding motifs, resulting in stable restriction of NK cell effector programs despite reversibility of active histone marks. In contrast, tissue residency-associated programs remain largely reversible, revealing that distinct NK cell fate programs differ fundamentally in their susceptibility to epigenetic fixation downstream of the same cytokine signal. SMAD4 CUT&RUN and knockout experiments further demonstrate that canonical TGF-{beta} signaling acts primarily through rewiring of upstream transcriptional regulatory networks rather than direct targeting of effector loci. Finally, NK cells from patients with hepatocellular carcinoma recapitulate key functional and epigenetic features of the persistent TGF-{beta}-associated state defined in vitro. Together, these findings identify signal duration as a critical determinant of TGF-{beta}-driven cell fate and demonstrate that prolonged TGF-{beta} exposure can induce epigenetically stabilized dysfunctional states that persist after signal withdrawal, with important implications for therapeutic strategies aimed at reversing chronic TGF-{beta}-mediated dysfunction.

immunology↗

bioRxiv2023

Adaptation of Graph Convolutional Neural Networks and Graph Layer-wise Relevance Propagation to the Spektral library with application to gene expression data of Colorectal Cancer patients

MotivationColorectal Cancer has the second-highest mortality rate worldwide, which requires advanced diagnostics and individualized therapies to be developed. Information about the interactions between molecular entities provides valuable information to detect the responsible genes driving cancer progression. Graph Convolutional Neural Networks are able to utilize the prior knowledge provided by interaction networks and the Spektral library adds a performance increase in contrast to standard implementations. Furthermore, machine learning technology shows great potential to assist medical professionals through guided clinical decision support. However, the deep learning models are limited in their application in precision medicine due to their lack to explain the factors contributing to a prediction. Adaption of the Graph Layer-Wise Relevance Propagation methodology to graph-based deep learning models allows to attribute the learned outcome to single genes and determine their relevance. The resulting patient-specific subnetworks then can be used to identify potentially targetable genes. ResultsWe present an implementation of Graph Convolutional Neural Networks using the Spektral library in combination with adapted functions for Graph Layer-Wise Relevance Propagation. Deep learning models were trained on a newly composed large gene expression dataset of Colorectal Cancer patients with different molecular interaction networks as prior knowledge: Protein-protein interactions from the Human Protein Reference Database and STRING, and pathways from the Reactome database. Our implementation performs comparably with the original implementation while reducing the computation time, especially for large networks. Further, the generated subnetworks are similar to those of the initial implementation and reveal possible, and even more distant, biomarkers and drug targets. AvailabilityThe implementation details and corresponding dataset including their visualizations can be found at https://github.com/frankkramer-lab/spektral-gcnn-glrp-on-crc-data Contactsebastian.lutz@uni-a.de

bioinformatics↗

bioRxiv2022

The gut microbiota promotes liver regeneration through hepatic membrane phospholipid synthesis

Background & AimsHepatocyte growth and proliferation is dependent on the synthesis of membrane phospholipids. Lipid synthesis, in turn, requires short chain fatty acids (SCFA) generated by bacterial fermentation, delivered through the gut- liver axis. We therefore hypothesized that dysbiotic insults like antibiotics treatment not only negatively affect gut microbiota, but also impair hepatic lipid synthesis and liver regeneration. MethodsStable isotope labelling and 70% partial hepatectomy (PHx) was carried out in C57Bl/6J wildtype mice, in mice treated with broad-spectrum antibiotics, in germfree mice and gnotobiotic mice colonized with minimal microbiota. Microbiome was analysed by 16S rRNA gene sequencing and microbial culture. Gut content, liver and blood were tested by lipidomics mass spectrometry, qRT-PCR, immunoblot and immunohistochemistry for expression of proliferative and lipogenic markers. Matched biopsies from hyperplastic and hypoplastic liver tissue of human patients subjected to portal vein embolization were analysed by qRT-PCR for lipogenic enzymes and results were correlated with liver volumetry. ResultsThree days of antibiotics treatment induced persistent dysbiosis with significantly decreased beta-diversity and richness, but massive increase of Proteobacteria, accompanied by decreased colonic SCFA. After PHx, antibiotics- treated mice showed delayed liver regeneration, increased mortality, impaired hepatocyte proliferation and decreased hepatic phospholipid synthesis. Expression of the key lipogenic enzyme SCD1 was upregulated after PHx, but delayed by antibiotics-treatment. Germfree mice essentially recapitulated the phenotype of antibiotics-treatment. Importantly, phospholipid synthesis, hepatocyte proliferation, liver regeneration and survival were rescued in gnotobiotic mice colonized with a minimal SCFA-producing microbial community. SCD1 was required for human hepatoma cell proliferation, and its hepatic expression was associated with liver regeneration and hyperproliferation in human patients. ConclusionGut microbiota are pivotal for hepatic membrane phospholipid synthesis and liver regeneration. Lay SummaryGut microbiota affects the liver lipid metabolism through the gut-liver axis, and microbial metabolites promote liver regeneration. Perturbations of the microbiome, e.g., by antibiotics treatment, impair the production of bacterial metabolites, which serve as building blocks for new membrane lipids in liver cells. As a consequence, hepatocyte growth and proliferation, and ultimately, liver regeneration and survival after liver surgery is impaired. HighlightsO_LIPartial hepatectomy in mice pretreated with antibiotics is associated with impaired hepatocyte proliferation and phospholipid synthesis, delayed liver regeneration and increased mortality C_LIO_LIThe delay in liver regeneration and impaired lipogenesis upon antibiotics treatment is preceded by dysbiosis of gut microbiota, increase of Proteobacteria and decreased short-chain fatty acids in the gut C_LIO_LIPartial hepatectomy in germfree mice essentially phenocopies the detrimental effects of antibiotic treatment C_LIO_LILiver regeneration and mortality, as well as phospholipid synthesis and hepatocyte proliferation in germfree mice are fully rescued upon colonisation with a minimal gut bacterial consortium capable of short-chain fatty acid production C_LIO_LIIn human patients, the intrahepatic expression of lipid synthesis enzymes positively correlates with proliferation and liver regeneration in the clinic C_LIO_LIThus, liver regeneration is affected by composition of gut microbiota C_LIO_LIClinically, pre-operative analysis of the gut microbiome may serve as biomarker to determine the extent of liver resections C_LI

cell biology↗

bioRxiv2022

Engineering cellular communication between light-activated synthetic cells and bacteria

Gene-expressing compartments assembled from simple, modular parts, are a versatile platform for creating minimal synthetic cells. In a manner synonymous with natural cells, these life-like assemblies utilise information encoded in DNA within the compartments interior to dictate which proteins are expressed and consequently the overall function of the synthetic cell. Hence, by incorporating gene regulatory motifs into the DNA templates, in situ gene expression can be controlled according to specific stimuli. In this work, cell-free protein synthesis within synthetic cells was controlled using light by encoding genes of interest on light-activated DNA templates. Light-activated DNA contained a photocleavable blockade within the T7 promoter region that tightly repressed transcription until the blocking groups were removed with UV light. In this way, synthetic cells were activated remotely, in a spatiotemporally controlled manner. By applying this strategy to the expression of an acyl homo-serine lactone synthetase, BjaI, quorum-sensing based communication between synthetic cells and bacteria was controlled with light. This work provides a framework for the remote-controlled production and delivery of small molecules from non-living matter to living matter, with applications in biology and medicine.

synthetic biology↗

bioRxiv2022

Integrative assessment of the transcriptome and virome of the poultry red mite Dermanyssus gallinae.

Dermanyssus gallinae is a blood-feeding mite that parasitises on wild birds and farmed poultry. The D. gallinae mite has a short life cycle of fewer than two weeks from the egg to an egg-laying female. The remarkably swift processing of blood, together with the capacity to blood-feed in most developmental stages, makes this mite a highly debilitating pest. We have constructed developmental stage-specific transcriptomes, through Illumina RNA-seq, to mine the repertoire of protein-encoding mRNA transcripts, products of which participate in key processes that ensure the success of blood digestion, rapid ontogeny, and immunity. As a result of high reproductive capacity, the prevalence of D. gallinae in egg-producing poultry farms globally causes significant economic losses. Acaricides that are used to limit the reproduction of D. gallinae mites target cys-loop ion channels, which are widely shared across the phylogeny of invertebrates. To catalogue a comprehensive list of potential invertebrate-specific ion channels, we have constructed and analysed an additional RNA-seq library of D. gallinae micro-dissected midguts, a tissue with direct exposure to host blood and potential anti-parasitics. We phylogenetically defined groups of cys-loop proteins and probed their sensitivity to selected acaricides. Ultimately, we have catalogued all assembled transcripts and their expression values in a hyper-linked excel sheet with available sequences of individual contigs. The transcriptomic data were complemented by mass-spectrometry (MS)-based metabolite identification and by viability assays using selected inhibitors applied either by microinjection or through artificial membrane feeding. Additionally, we have described the RNA-virome of D. gallinae and identified a novel virus dubbed Red Mite Quaranjavirus 1.

microbiology↗

bioRxiv2021

Precise, 3-D optogenetic control of the diameter of single arterioles

Modulation of brain arteriole diameter is critical for maintaining cerebral blood pressure and controlling regional hyperemia during neural activity. However, studies of hemodynamic function in health and disease have lacked a method to control arteriole diameter independently with high spatiotemporal resolution. Here, we describe an all-optical approach to manipulate and monitor brain arteriole contractility in 3-dimensions using combined in vivo two-photon optogenetics and imaging. The expression of the red-shifted excitatory opsin, ReaChR, in vascular smooth muscle cells enabled rapid and repeated vasoconstriction controlled by brief light pulses. Two-photon activation of ReaChR using a spatial light modulator produced highly localized constrictions when targeted to individual arterioles within the neocortex. We demonstrate the utility of this method for examining arteriole contractile dynamics and creating transient focal blood flow reductions. Additionally, we show that optogenetic constriction can be used to reshape vasodilatory responses to sensory stimulation, providing a valuable tool to dissociate blood flow changes from neural activity.

neuroscience↗

bioRxiv2018

A specific, glycomimetic Langerin ligand for human Langerhans cell targeting

Langerhans cells are a subset of dendritic cells residing in the epidermis of the human skin. As such, they are key mediators of immune regulation and have emerged as prime targets for novel transcutaneous cancer vaccines. Importantly, the induction of protective T cell immunity by these vaccines requires the efficient and specific delivery of both tumor-associated antigens and adjuvants. Langerhans cells uniquely express Langerin (CD207), an endocytic C-type lectin receptor. Here, we report the discovery of a specific, glycomimetic Langerin ligand employing a heparin-inspired design strategy that integrated NMR spectroscopy and molecular docking. The conjugation of these glycomimetics to liposomes enabled the specific and efficient targeting of Langerhans cells in the human skin. This delivery platform provides superior versatility and scalability over antibody-based approaches and thus addresses current limitations of dendritic cell-based immunotherapies.

immunology↗