Biology subjects

Fritsche, E.

Publications and source records attributed to Fritsche, E..

6 recordsLinked to original sources

bioRxiv2026

ToxCastLite: A portable semantic evidence graph linking in vitro bioactivity, in vivo toxicity, and exposure-use context

MotivationThe ToxCast database is a valuable resource for computational toxicology and new approach methodologies (NAMs), but the approximately 100 GB MySQL distribution is difficult to use for portable local analysis and cross-domain evidence mining. Many practical questions concern chemicals, in vitro bioactivity, in vivo toxicological evidence, and exposure-relevant product-use context rather than raw database keys. ResultsWe present ToxCastLite, a portable semantic evidence-access system that combines assay-scoped SQLite databases with a compact RDF layer for GraphDB-based querying. The system streams large ToxCast/invitrodb MySQL dumps into curated SQLite profiles, reducing the footprint to approximately 3 GB for focused use cases such as developmental neurotoxicity. Dense numerical evidence, including concentration-response rows, remains in SQLite, while the RDF projection exposes linked semantic entities such as chemicals, assays, endpoints, model results, potency parameters (AC50), and MC6 quality flags. We further extend the graph with CPDat v4.0 product-use and functional-use evidence and ToxRefDB v3.0 in vivo toxicity evidence, including processed studies, point-of-departure records, effect summaries, and observation summaries. These layers are linked through DSSTox Substance Identifiers, enabling integrated queries across NAM bioactivity, curated animal-study evidence, and exposure/use context. A Streamlit prototype supports exploration through a locally deployed LLM that translates natural-language questions into SPARQL, grounded by a versioned RDF schema to reduce hallucination risk. Case studies in developmental neurotoxicity demonstrate how ToxCastLite identifies concordance between high-confidence in vitro DNT activity and positive in vivo apical evidence, detects in vitro DNT activity beyond available DNT-specific in vivo evidence, and prioritizes chemicals where NAM signals, ToxRefDB evidence, and CPDat product-use context intersect. For selected results, users can drill down from the semantic graph to the underlying SQLite records and retrieve concentration-response curves for expert inspection without manually writing SQL or SPARQL. AvailabilityProject website at toxcast-lite.github.io/. Contactarif.doenmez@iuf-duesseldorf.de

bioinformatics↗

bioRxiv2024

Multi-behavioral phenotyping in zebrafish identifies a novel disruptor of non-associative learning with environmental and human relevance

BackgroundThe vertebrate nervous system is vulnerable to chemical toxicity and the widespread release of chemicals into the environment outstrips the capacity to assess their safety. The zebrafish (Danio rerio) is a powerful vertebrate model that can bridge the gap between in vitro and mammalian-based in vivo studies. However, the behavior-rich repertoire of larval zebrafish, a 3R-compliant model amenable to higher-throughput chemical screens, has yet to be fully deployed to identify and characterize chemical compounds that cause neurotoxicity. ObjectiveWe sought to establish a multi-behavioral phenotyping approach in larval zebrafish to identify and mechanistically elucidate neuroactive chemicals, with particular focus on chemical compounds that affect non-associative habituation learning. MethodsWe devised a battery of automated behavior assays in larval zebrafish. The battery captures stereotypical visual and acoustic behaviors including habituation, a form of non-associative learning. To elucidate mechanisms underlying exposure-induced behavioral alterations in zebrafish, in silico target predictions, pharmacological interventions, patch-clamp recordings in cultured mouse cortical neurons, and human multi-neurotransmitter (hMNR) assay in 3D BrainSpheres were used. ResultsKnown pharmacological modulators of habituation in zebrafish evoked distinct behavioral patterns. By screening chemicals positive for ex vivo N-methyl-D-aspartate receptor (NMDAR) modulation, we identified chlorophene, a biocide that caused sedation, paradoxical excitation, and reduced habituation in zebrafish. Using in silico target predictions and pharmacological interventions, we discovered that chlorophene acts via gamma-aminobutyric acid A receptors (GABAARs), a previously unknown target site. Orthogonal validation in cultured mouse cortical neurons and human stem cell-derived BrainSpheres confirmed chlorophenes interaction with GABAARs. Chlorophenes behavioral profile resembled that of flupirtine, a Kv7 potassium channel (M-current) activator, suggesting that habituation deficits stem from M-current rather than GABAAR modulation. ConclusionsThese studies combined a series of behavior assays in a phenotypically rich, rapid, and inexpensive non-mammalian vertebrate test system to screen chemicals for neurotoxicity. Together with in silico target predictions and mouse- and human-based models, our findings establish multi-behavioral phenotyping in zebrafish as a powerful toolkit for neurotoxicity testing and mechanism identification, with relevance for humans.

pharmacology and toxicology↗

bioRxiv2023

Cockayne syndrome patient iPSC-derived brain organoids and neurospheres show early transcriptional dysregulation of biological processes associated with brain development and metabolism.

Cockayne syndrome is a rare hereditary autosomal recessive disorder characterized by diverse neurological afflictions. However, little is known about the cerebral development in CS patients. We generated neurospheres and cerebral organoids utilizing Cockayne Syndrome B Protein (CSB) deficient induced pluripotent stem cells derived from two patients with distinct severity levels of CS and healthy controls. The transcriptome of both developmental timepoints was explored using RNA-Seq and bioinformatic analysis to identify dysregulated biological processes common to both CS patients in comparison to control. CSB-deficient neurospheres displayed upregulation of VEGFA-VEGFR2 signaling pathway, Vesicle-Mediated transport and head development. CSB-deficient cerebral organoids exhibited downregulation of brain development, neuron projection development and synaptic signalling. We further identified upregulation of Steroid Biosynthesis as common to both timepoints, in particular upregulation of the Cholesterol Biosynthesis branch. Our results provide insights into the neurodevelopmental dysregulation in CS patients and strengthen the theory, that CS is not only a neurodegenerative, but also a neurodevelopmental disorder.

neuroscience↗

bioRxiv2023

Molecular and functional characterization of different BrainSphere models for use in neurotoxicity testing on microelectrode arrays

The currently accepted methods for neurotoxicity (NT) testing rely on animal studies. However, high costs and low testing throughput hinder their application for large numbers of chemicals. To overcome these limitations, in vitro methods are currently developed which are based on human induced pluripotent stem cells (hiPSC) that allow higher testing throughput at lower costs. We applied six different protocols to generate 3D BrainSphere models for acute NT evaluation. These include three different media for 2D neural induction and two media for subsequent 3D differentiation resulting in self-organized, organotypic neuron/astrocyte microtissues. All induction protocols yielded nearly 100 % nestin-positive hiPSC-derived neural progenitor cells (hiNPCs) yet with different gene expression profiles concerning regional patterning. Moreover, gene expression and immunocytochemistry analyses revealed that the choice of media determines neural differentiation patterns. On the functional level, BrainSpheres exhibited different levels of electrical activity on microelectrode arrays (MEA). Spike sorting allowed BrainSphere functional characterization with the mixed cultures consisting of GABAergic, glutamatergic, dopaminergic, serotonergic, and cholinergic neurons. A test method for acute NT testing, the human multi-neurotransmitter receptor (hMNR) assay, was proposed applying such MEA-based spike sorting. These models are not only promising tools in toxicology but also for drug development and disease modeling.

neuroscience↗

bioRxiv2023

A human iPSC-based in vitro neural network formation assay to investigate neurodevelopmental toxicity of pesticides

Proper brain development is based on the orchestration of key neurodevelopmental processes, including the formation and function of neural networks. If at least one key neurodevelopmental process is affected by a chemical, an adverse outcome is expected. To allow a higher testing throughput than the guideline animal experiments, a developmental neurotoxicity (DNT) in vitro testing battery (DNT IVB) has been set up that includes a variety of assays, which model several key neurodevelopmental processes. Gap analyses of the DNT IVB revealed the need of a human-based assay to assess neural network formation and function (NNF). Therefore, here we established the human NNF (hNNF) assay. A co-culture comprised of human-induced pluripotent stem cell (hiPSC)- derived excitatory and inhibitory neurons, as well as primary human astroglia, was differentiated for 35 days on micro-electrode arrays (MEA) and spontaneous electrical activity, together with cytotoxicity, was assessed on a weekly basis after washout of the compounds 24 h prior to measurements. In addition to the characterization of the test system, the assay was challenged with 28 compounds, mainly pesticides, identifying their DNT potential by evaluation of specific spike-, burst- and network parameters. This approach confirmed the suitability of the assay for screening environmental chemicals. Comparison of benchmark concentrations (BMC) with an NNF in vitro assay (rNNF) based on primary rat cortical cells, revealed differences in sensitivity. Together with the successful implementation of hNNF data into a postulated stressor-specific adverse outcome pathway (AOP) network associated with a plausible molecular initiating event for deltamethrin, this study suggests the hNNF assay as a useful complement to the current DNT IVB.

pharmacology and toxicology↗

bioRxiv2022

Biostatistics and its impact on hazard characterization using in vitro developmental neurotoxicity assays

In the field of hazard assessment, Benchmark concentrations (BMC) and their associated uncertainty are of particular interest for regulatory decision making. The BMC estimation consists of various statistical decisions to be made, which depend largely on factors such as experimental design and assay endpoint features. In current data practice, the experimenter is often responsible for the data analysis and therefore relies on statistical software without being aware about the software default settings and how they can impact the outputs of data analysis. To provide more insight into how statistical decision making can influence the outcomes of data analysis and interpretation, we have used case studies on a large dataset produced by a developmental neurotoxicity (DNT) in vitro battery (DNT IVB). Here we focused on the BMC and its confidence interval (CI) estimation, as well as on the final hazard classification. We identified five crucial statistical decisions experimenter have to face during data analysis: choice of replicate averaging, response data normalization, regression modelling, BMC and CI estimation, as well as choice of benchmark response levels. In addition, the strength of our data evaluation platform is the integration of endpoint-specific hazard classifications, including flagging systems for uncertain cases, which none of the so far existing statistical data analysis platforms provide. The insights gained in this study demonstrate how important fit-for-purpose, internationally harmonized and accepted data evaluation and analysis procedures are for an objective hazard classification.

bioinformatics↗