Biology subjects

Lopez Rodriguez, D.

Publications and source records attributed to Lopez Rodriguez, D..

4 recordsLinked to original sources

bioRxiv2025

A chemical space model for the exploration of eco-toxicological data

With over 350000 chemicals and mixtures currently registered for production and use worldwide, up to 90% of authorized chemicals lack adequate toxicity data, leaving the majority of chemicals poorly characterized. International agencies urge scientists to develop screening methods to explore, identify, and predict chemical hazards, supporting the prioritization of chemical risk assessment. Here, Tree Manifold Approximation and Projection (TMAP) were applied, with the aim of reducing the dimensionality of large toxicological dataset, providing the foundations to data imputation methods allowing to get an understanding of chemical modes of action. Specifically, TMAP was implemented using MHFP6 fingerprints and the NORMAN SusDat database, containing over 100000 compounds. Physicochemical properties and CTD toxicogenomic data were retrieved and a graph-based spatial imputation function was generated to obtain insights into the potential ecotoxicity mechanisms of data poor chemicals. The relevance and meaningfulness of TMAP chemical space was explored for Daphnia magna, Pimephales promelas and Algae. Chemical classes known to be structurally similar were found to be grouped together in the TMAP chemical space, while heterogeneous classes were found to be sparse. Data imputation allowed for the identification of known and potential chemical mechanisms of action. Indeed, acethylcolinesterase and transthyretin were confirmed as major mechanisms of action of organothiophosphate and brominated flame retardant toxicity in Daphnia magna and Pimephales promelas, respectively. Overall, transdisciplinary toxicological databases combined with TMAP, stand out as a powerful, fast and scalable method to explore large datasets, allowing for meaningful and interpretable associations between chemical structures and chemical hazard identification. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=82 SRC="FIGDIR/small/677052v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@153d3bborg.highwire.dtl.DTLVardef@71a801org.highwire.dtl.DTLVardef@1cce83dorg.highwire.dtl.DTLVardef@1a3330f_HPS_FORMAT_FIGEXP M_FIG C_FIG Highlights- Transdisciplinary toxicological datasets are unique resources for hazard identification. - TMAP is a powerful tool for the visualization of very large ecotoxicological datasets. - Graph-based imputation helps to identify targets for additional toxicological evaluation.

pharmacology and toxicology↗

bioRxiv2025

Multiomics profiling of zebrafish embryonic cell line PAC2 across growth phases to assess its relevance for toxicological studies

Permanent fish cell lines offer promising alternatives to traditional animal models for environmental risk assessment of chemicals. However, to facilitate their broader uptake into toxicity testing practice, a better understanding of functional capacities and expression of toxicologically relevant molecular targets is needed. Here, we present an extensive molecular profiling of the zebrafish embryonic cell line PAC2, combining global proteomics across cell population growth phases (over 7300 protein groups) with matched transcriptomics at exponential and stationary phase (over 14500 transcripts). Proteome coverage was sufficiently deep to reveal functional insights consistent with those derived from transcriptomics data, despite differences in the total number of measured genes. Major gene expression shifts detected upon transition from exponential to stationary cell population growth phase indicated reduction in DNA replication, translation, metabolism, and cell cycle regulation, along with increased stress responses, immune system responses, and extracellular matrix remodeling. Functional annotation revealed expression of core cellular processes along with a number of toxicologically relevant pathways, including xenobiotic metabolism, stress signaling, and nuclear receptors responsive to important chemical classes, such as steroids (e.g., estrogens, glucocorticoids) and chemicals known to disrupt lipid metabolism, e.g., through interaction with peroxisome proliferation activating receptors. These findings reinforce the potential of PAC2 cells to offer a versatile in vitro model for studying fish cell biology and omics-enhanced exploration of chemical toxicity mechanisms, aided by the well-developed molecular annotation in zebrafish. Moreover, the analysis approaches developed in this work offer a blueprint for molecular baseline characterization of other fish cell lines. This work thus strengthens the mechanistic foundation supporting the use of fish cell lines as alternative models in aquatic toxicity testing and risk assessment.

molecular biology↗

bioRxiv2025

Neurotoxicity of Propylene Glycol Butyl Ether: Multiomic Evidence from Human BrainSpheres

Exposure to solvents may contribute to the development of neurodevelopmental and neurodegenerative diseases. Glycol ethers consist in a widely used class of organic solvents leading to workers and consumers exposure via many different applications. Ethylene glycol ethers are gradually being replaced by propylene glycol ethers thought to be less toxic. However, their neurotoxicity is not systematically assessed prior to placing them on the market. Therefore, this study investigated the potential neurotoxicity of propylene glycol butyl ether (PGBE) for which no official occupational limit has been established. To this aim, new approach methodologies have been used. Human induced pluripotent stem cells-derived BrainSpheres model was exposed to PGBE and to its main metabolite, 2-butoxypropanoic acid (2BPA). An integrative multiomic approach (transcriptomics, proteomics, metabolomics and lipidomics) was adopted to assess molecular alterations, derive benchmark concentrations and define potential mechanisms of action. PGBE was neurotoxic at occupationally relevant exposure concentrations. This was shown for the first time in human cells. And, although PGBE was more cytotoxic than 2BPA, both compounds showed very similar neurotoxicity. PGBE and 2BPA strongly affected the cell cycle, induced oxidative stress and perturbed energy and lipid metabolism. They also targeted specific nervous system processes, such as axon guidance and synapse organization. Finally, 2BPA may trigger ferroptosis by increased iron uptake. Our results show an urgent need for public health authorities to carefully assess the risk glycol ethers pose to humans, to properly protect the workers as well as individuals in the general population unknowingly exposed from indoor air contaminations.

pharmacology and toxicology↗

bioRxiv2020

Multi- and transgenerational disruption of maternal behavior and female puberty by Endocrine Disrupting Chemical (EDC) mixture exposure

Female reproductive development and maternal behavior are two intertwined phenotypes centrally controlled by the hypothalamus. Endocrine disrupting chemicals (EDC) can alter these processes especially when animals are exposed during development. We propose the concept that developmental exposure to a low environmentally relevant dose of EDC mixture induces a transgenerational alteration of female rat pubertal timing and ovarian physiology throughout epigenetic reprograming of hypothalamic Kiss1, Esr1 and Oxt1 loci. Such exposure also caused a multigenerational reduction of maternal behavior induced by the loss in hypothalamic dopaminergic signaling. Our results identify the hypothalamic Polycomb Group of epigenetic repressors as actors of this mechanism of transgenerational reproductive disruption. Using a cross-fostering approach, we identified that while the reduction in maternal phenotype was normalized in EDC exposed pups raised by unexposed dams, no reversal of the pubertal phenotype was achieved, suggesting a germline transmission of the reproductive phenotype.

neuroscience↗