Perfluorooctane sulfonate (PFOS) is a persistent and bioaccumulative member of the per- and polyfluoroalkyl substances (PFAS) family widely used in various industrial applications and consumer products. In this study we present a comprehensive analysis of the effects of PFOS exposure on zebrafish embryos with respect to possible role of the organic anion transporting polypeptide 1d1 (Oatp1d1) membrane transporter, focusing on the differential responses between wild-type (WT) and Oatp1d1 mutant embryos. Significant differences in mortality rates were observed, with LC50 values of 23.57 μM for WT and 16.71 μM for oatp1d1 mutants, indicating a higher susceptibility of the mutants to PFOS toxicity. Developmental abnormalities, particularly in the swim bladder, were more pronounced in mutant embryos. In addition, gene expression analysis showed changes in expression of genes involved in biotransformation processes, including members of the cytochrome P450 and glutathione S-transferase families. In summary, results of this study emphasize the complexity of PFOS-induced developmental toxicity mechanisms, implying important protective role of the Oatp1d1 transporter possibly related to detoxification processes or regulation of bioavailability. The findings improve our understanding of the toxicokinetic and toxicodynamic mechanisms of PFOS, emphasizing potential need for additional regulatory measures to address PFOS contamination and protect both aquatic life and human populations.

DNA-protein crosslinks (DPCs) are toxic DNA lesions that block all DNA transactions including replication and transcription, and the consequences of impaired DNA-protein crosslink repair (DPCR) are severe. At the cellular level, impaired DPCR leads to the formation of double strand breaks, genomic instability, and cell death, while at the organismal level, it is associated with cancer, aging, and neurodegeneration. Despite its importance, the mechanisms of DPCR at the organismal level are largely unknown. Proteases play a central role in DPCR, as they remove proteinaceous part of the DPCs, while the peptide remnant crosslinked to DNA is subsequently removed by other repair factors. We characterized the role of putative protease ACRC/GCNA (ACidic Repeat Containing/Germ Cell Nuclear Antigen) in DPCR at the organismal level. For this purpose, we have created new animal models with CRISPR/Cas system: two zebrafish lines with inactive Acrc. We were able to overcome the early embryonic lethality caused by Acrc inactivation by injecting Acrc-WT messenger RNA and have created a viable animal model to study the role of Acrc in adult tissues. We identified histone H3, topoisomerases 1 and 2, Dnmt1, Parp1, Polr3a, and Mcm2 as putative DPC substrates of Acrc. We have shown that Acrc is essential for vertebrate development, and that the mechanism behind it is DPC removal.

As a member of the ABC transporter superfamily, ABCG2 is a half transporter that mediates the translocation of various xenobiotic substrates across cell membranes, playing an essential role in cellular detoxification. With the aim of developing a reliable in vivo model to study the role of ABCG2 and its interaction with drugs and environmental contaminants, in this study we used the CRISPR/Cas9 gene-editing technology to develop a zebrafish (Danio rerio) Abcg2a mutant line. The generated Abcg2a mutants developed normally to adulthood with no visible phenotype changes, abcg2a gene expression was reduced by more than 90% in the mutant larvae up to 5 days-post-fertilization, and overexpression of transcripts of functionally related ABC genes was detected in three out of eight monitored genes. The accumulation pattern of the specific Abcg2 fluorescent substrate pheophorbide A differed between mutants and wildtypes with a dominant signal in the gallbladder and intestine, respectively. Upon exposure to the model toxicants MLN7243 and mitoxantrone, the mutant larvae showed increased mortality compared to the wildtypes. The addition of the specific inhibitor Ko143 increased the mortality rate of the wildtype larvae to that of the mutants, indicating that the protective effect of Abcg2a had been abolished. The developed Abcg2a mutant line could be used as a reliable in vivo model in both pharmacology and ecotoxicology to further elucidate the function of Abcg2a in different tissues and cell compartments and to better understand the interaction of Abcg2a with different physiological or xenobiotic compounds.

DNA repair and autophagy are distinct biological processes vital for cell survival. Although autophagy helps maintain genome stability, there is no evidence of its direct role in the repair of DNA lesions. We discovered that lysosomes process Topoisomerase 1-cleavage complexes (TOP1cc) DNA lesions in human cancer cell. TOP1 resolves DNA topological stress ahead of DNA replication and transcription. If not promptly repaired, TOP1cc hinder the progression of DNA replication and transcription fostering genomic instability. Thus, stabilising TOP1cc with TOP1 poisons, such as Camptothecin or its analogue, is highly effective and widely used in cancer therapy. Proteolysis of TOP1cc by the proteasome is described at excessively high doses of CPT that are not relevant in a clinical setting, calling into question the relevance of the proteasome role in TOP1cc repair for cancer therapy and patient response. Here we described that repair of TOP1cc induced by clinically relevant dose of Camptothecin depends on selective autophagy. Proteomics, sequencing, biochemistry techniques and live imaging all demonstrate the lysosomal uptake of TOP1cc upon induction of replication stress. Selective degradation of TOP1cc by autophagy directs DNA damage repair and cell survival. TOP1cc are exported from the nucleus to lysosomes through transient alteration of the nuclear envelope and independent of the proteasome. Mechanistically, the autophagy receptor TEX264 acts as a TOP1cc sensor at DNA replication forks, triggering TOP1cc processing by the p97 ATPase and mediating the delivery of TOP1cc to lysosomes in an MRE11 nuclease and ATR kinase-dependent manner. We found an evolutionarily conserved role for selective autophagy in DNA damage repair that enables cell survival, protects genome stability, and is clinically relevant for colorectal cancer patients. Pauline Lascaux, Gwendoline Hoslett, Sara Tribble, Ivan Antičević, Cecile Otten, Ignacio Torrecilla, Yichen Zhao, Wei Song, Cristiano Peron, Giulio Deangeli, Enric Domingo, James Bancroft, Loïc Carrique, Errin Johnson, Alvin Wei Tian Ng, Joanne Ngeow, Nuno Raimundo, Tim Maughan, Marta Popović, Ira Milošević, and Kristijan Ramadan. TEX264 DRIVES SELECTIVE AUTOPHAGY OF DNA LESIONS TO PROMOTE DNA REPAIR AND CELL SURVIVAL [abstract]. In: Proceedings of Frontiers in Cancer Science 2024; 2024 Nov 13-15; Singapore. Philadelphia (PA): AACR; Cancer Res 2025;85(15_Suppl):Abstract nr P11.

DNA repair and autophagy are distinct biological processes vital for cell survival. Although autophagy helps maintain genome stability, there is no evidence of its direct role in the repair of DNA lesions. We discovered that lysosomes process topoisomerase 1 cleavage complexes (TOP1cc) DNA lesions in vertebrates. Selective degradation of TOP1cc by autophagy directs DNA damage repair and cell survival at clinically relevant doses of topoisomerase 1 inhibitors. TOP1cc are exported from the nucleus to lysosomes through a transient alteration of the nuclear envelope and independent of the proteasome. Mechanistically, the autophagy receptor TEX264 acts as a TOP1cc sensor at DNA replication forks, triggering TOP1cc processing by the p97 ATPase and mediating the delivery of TOP1cc to lysosomes in an MRE11-nuclease- and ATR-kinase-dependent manner. We found an evolutionarily conserved role for selective autophagy in DNA repair that enables cell survival, protects genome stability, and is clinically relevant for colorectal cancer patients.

DNA-protein crosslinks pose a significant challenge to genome stability and cell viability. Efficient repair of DPCs is crucial for preserving genomic integrity and preventing the accumulation of DNA damage. Despite recent advances in our understanding of DPC repair, many aspects of this process, especially at the organismal level, remain elusive. In this study, we used zebrafish as a model organism to investigate the role of TDP2 (Tyrosyl-DNA phosphodiesterase 2) in DPC repair. We characterized the two tdp2 orthologs in zebrafish using phylogenetic, syntenic and expression analysis and investigated the phenotypic consequences of tdp2 silencing in zebrafish embryos. We then quantified the effects of tdp2a and tdp2b silencing on cellular DPC levels and DSB accumulation in zebrafish embryos. Our findings revealed that tdp2b is the main ortholog during embryonic development, while both orthologs are ubiquitously present in adult tissues. Notably, the tdp2b ortholog is phylogenetically closer to human TDP2. Silencing of tdp2b, but not tdp2a, resulted in the loss of Tdp2 activity in zebrafish embryos, accompanied by the accumulation of DPCs and DSBs. Our findings contribute to a more comprehensive understanding of DPC repair at the organismal level and underscore the significance of TDP2 in maintaining genome stability.

DNA-protein crosslinks (DPCs) are frequent and damaging DNA lesions that affect all DNA transactions, which in turn can lead to the formation of double-strand breaks, genomic instability and cell death. At the organismal level, impaired DPC repair (DPCR) is associated with cancer, ageing and neurodegeneration. Despite the severe consequences of DPCs, little is known about the processes underlying repair pathways at the organism level. SPRTN is a protease that removes most cellular DPCs during replication, whereas tyrosyl-DNA phosphodiesterase 1 repairs one of the most abundant enzymatic DPCs, topoisomerase 1-DPC (TOP1-DPC). How these two enzymes repair DPCs at the organism level is currently unknown. We perform phylogenetic, syntenic, structural and expression analysis to compare tyrosyl-DNA phosphodiesterase 1 (TDP1) orthologues between human, mouse and zebrafish. Using the zebrafish animal model and human cells, we demonstrate that TDP1 and SPRTN repair endogenous, camptothecin- and formaldehyde-induced DPCs, including histone H3- and TOP1-DPCs. We show that resolution of H3-DNA crosslinks depends on upstream proteolysis by SPRTN and subsequent peptide removal by TDP1 in RPE1 cells and zebrafish embryos, whereas SPRTN and TDP1 function in different pathways in the repair of endogenous TOP1-DPCs and total DPCs. Furthermore, we have found increased TDP2 expression in TDP1-deficient cells and embryos. Understanding the role of TDP1 in DPCR at the cellular and organismal levels could provide an impetus for the development of new drugs and combination therapies with TOP1-DPC inducing drugs.

Summary DNA-protein crosslinks (DPCs) are frequent DNA lesions associated with cancer, neurodegeneration and premature aging. These bulky lesions are an obstacle to all DNA transactions, but the mechanisms of DPC repair (DPCR) at the organism level are largely unknown. Because proteases play a central role in DPCR, we investigate the function of the putative protease ACRC/GCNA (ACidic Repeat Containing/Germ Cell Nuclear Antigen) which has recently been linked to DPCR, in a zebrafish model. Using a newly created fish line with a mutation in the protease core, we show for the first time that the proteolytic function of Acrc is critical for DPCR during early vertebrate development and that Acrc deficiency leads to DPC accumulation and embryonic death. We also show that Sprt domain rather than IDR domain of Acrc is essential and that Sprtn protease cannot compensate for the absence of Acrc. We identified histone H3-DPC as a novel Acrc substrate.

The capillary-venous pathology cerebral cavernous malformation (CCM) is caused by loss of CCM1/Krev interaction trapped protein 1 (KRIT1), CCM2/MGC4607, or CCM3/PDCD10 in some endothelial cells. Mutations of CCM genes within the brain vasculature can lead to recurrent cerebral hemorrhages. Pharmacological treatment options are urgently needed when lesions are located in deeply-seated and in-operable regions of the central nervous system. Previous pharmacological suppression screens in disease models of CCM led to the discovery that treatment with retinoic acid improved CCM phenotypes. This finding raised a need to investigate the involvement of retinoic acid in CCM and test whether it has a curative effect in preclinical mouse models. Here, we show that components of the retinoic acid synthesis and degradation pathway are transcriptionally misregulated across disease models of CCM. We complemented this analysis by pharmacologically modifying retinoic acid levels in zebrafish and human endothelial cell models of CCM, and in acute and chronic mouse models of CCM. Our pharmacological intervention studies in CCM2-depleted human umbilical vein endothelial cells (HUVECs) and krit1 mutant zebrafish showed positive effects when retinoic acid levels were increased. However, therapeutic approaches to prevent the development of vascular lesions in adult chronic murine models of CCM were drug regiment-sensitive, possibly due to adverse developmental effects of this hormone. A treatment with high doses of retinoic acid even worsened CCM lesions in an adult chronic murine model of CCM. This study provides evidence that retinoic acid signaling is impaired in the CCM pathophysiology and suggests that modification of retinoic acid levels can alleviate CCM phenotypes.

The increasing use of the zebrafish model in biomedical and (eco)toxicological studies aimed at understanding the function of various proteins highlight the importance of optimizing existing methods to study gene and protein expression and localization in this model. In this context, zebrafish cryosections are still underutilized compared with whole‐mount preparations. In this study, we used zebrafish embryos (24–120 hpf) to determine key factors for the preparation of high‐quality zebrafish cryosections and to determine the optimal protocol for (immuno)fluorescence analyses of Na+/K+‐ATPase and F‐actin, across developmental stages from 1 to 5 dpf. The results showed that the highest quality zebrafish cryosections were obtained after the samples were fixed in 4% paraformaldehyde (PFA) for 1 h, incubated in 2.5% bovine gelatin/25% sucrose mixture, embedded in OCT, and then sectioned to 8 μm thickness at −20°C. Fluorescence microscopy analysis of phalloidin‐labeled zebrafish skeletal muscle revealed that 1‐h‐4% PFA‐fixed samples allowed optimal binding of phalloidin to F‐actin. Further immunofluorescence analyses revealed detailed localization of F‐actin and Na+/K+‐ATPase in various tissues of the zebrafish and a stage‐dependent increase in their respective expression in the somitic muscles and pronephros. Finally, staining of zebrafish cryosections and whole‐mount samples revealed organ‐specific and zone‐dependent localizations of the Na+/K+‐ATPase α1‐subunit.

Background and Purpose— Cerebral cavernous malformations (CCMs) are vascular malformations of the brain that lead to cerebral hemorrhages. A pharmacological treatment is needed especially for patients with nonoperable deep-seated lesions. We and others obtained CCM mouse models that were useful for mechanistic studies and rapid trials testing the preventive effects of candidate drugs. The shortened lifespan of acute mouse models hampered evaluation of compounds that would not only prevent lesion appearance but also cure preexisting lesions. Indirubin-3′-monoxime previously demonstrated its efficacy to reverse the cardiac phenotype of ccm2 m201 zebrafish mutants and to prevent lesion development in an acute CCM2 mouse model. In the present article, we developed and characterized a novel chronic CCM2 mouse model and evaluated the curative therapeutic effect of indirubin-3′-monoxime after CCM lesion development. Methods— The chronic mouse model was obtained by a postnatal induction of brain-endothelial-cell-specific ablation of the Ccm2 gene using the inducible Slco1c1 -CreER T2 mouse line. Results— We obtained a fully penetrant novel CCM chronic mouse model without any obvious off-target phenotypes and compatible with long-term survival. By 3 months of age, CCM lesions ranging in size from small isolated lesions to multiple caverns developed throughout the brain. Lesion burden was quantified in animals from 1 week to 5 months of age. Clear signs of intracerebral hemorrhages were noticed in brain-endothelial-cell-specific ablation of the Ccm2 gene. In contrast with its preventive effect in the acute CCM2 mouse model, a 20 mg/kg indirubin-3′-monoxime treatment for 3 weeks in 3-month old animals neither had any beneficial effect on the lesion burden nor alleviated cerebral hemorrhages. Conclusions— The brain-endothelial-cell-specific ablation of the Ccm2 gene chronic model is a strongly improved disease model for the CCM community whose challenge today is to decipher which candidate drugs might have a curative effect on patients’ preexisting lesions. Visual Overview— An online visual overview is available for this article.

The Hippo-Yap pathway regulates multiple cellular processes in response to mechanical and other stimuli. In Drosophila, the polarity protein Lethal (2) giant larvae [L(2)gl], negatively regulates Hippomediated transcriptional output. However, in vertebrates, little is known about its homolog Llgl1. Here, we define a novel role for vertebrate Llgl1 in regulating Yap stability in cardiomyocytes, which impacts heart development. In contrast to the role of Drosophila L(2)gl, Llgl1 depletion in cultured rat cardiomyocytes decreased Yap protein levels and blunted target gene transcription without affecting Yap transcript abundance. Llgl1 depletion in zebrafish resulted in larger and dysmorphic cardiomyocytes, pericardial effusion, impaired blood flow and aberrant valvulogenesis. Cardiomyocyte Yap protein levels were decreased in llgl1 morphants, whereas Notch, which is regulated by hemodynamic forces and participates in valvulogenesis, was more broadly activated. Consistent with the role of Llgl1 in regulating Yap stability, cardiomyocytespecific overexpression of Yap in Llgl1-depleted embryos ameliorated pericardial effusion and restored blood flow velocity. Altogether, our data reveal that vertebrate Llgl1 is crucial for Yap stability in cardiomyocytes and its absence impairs cardiac development.

Endothelial cells respond to different levels of fluid shear stress through adaptations of their mechanosensitivity. Currently, we lack a good understanding of how this contributes to sculpting of the cardiovascular system. Cerebral cavernous malformation (CCM) is an inherited vascular disease that occurs when a second somatic mutation causes a loss of CCM1/KRIT1, CCM2, or CCM3 proteins. Here, we demonstrate that zebrafish Krit1 regulates the formation of cardiac valves. Expression of heg1, which encodes a binding partner of Krit1, is positively regulated by blood-flow. In turn, Heg1 stabilizes levels of Krit1 protein, and both Heg1 and Krit1 dampen expression levels of klf2a, a major mechanosensitive gene. Conversely, loss of Krit1 results in increased expression of klf2a and notch1b throughout the endocardium and prevents cardiac valve leaflet formation. Hence, the correct balance of blood-flow-dependent induction and Krit1 protein-mediated repression of klf2a and notch1b ultimately shapes cardiac valve leaflet morphology.

Cerebral cavernous malformations (CCMs) are vascular lesions in the central nervous system causing strokes and seizures which currently can only be treated through neurosurgery. The disease arises through changes in the regulatory networks of endothelial cells that must be comprehensively understood to develop alternative, non-invasive pharmacological therapies. Here, we present the results of several unbiased small-molecule suppression screens in which we applied a total of 5,268 unique substances to CCM mutant worm, zebrafish, mouse, or human endothelial cells. We used a systems biology-based target prediction tool to integrate the results with the whole-transcriptome profile of zebrafish CCM2 mutants, revealing signaling pathways relevant to the disease and potential targets for small-molecule-based therapies. We found indirubin-3-monoxime to alleviate the lesion burden in murine preclinical models of CCM2 and CCM3 and suppress the loss-of-CCM phenotypes in human endothelial cells. Our multi-organism-based approach reveals new components of the CCM regulatory network and foreshadows novel small-molecule-based therapeutic applications for suppressing this devastating disease in patients.

The zebrafish embryonic heart is composed of only a few hundred cells, representing only a small fraction of the entire embryo. Therefore, to prevent the cardiac transcriptome from being masked by the global embryonic transcriptome, it is necessary to collect sufficient numbers of hearts for further analyses. Furthermore, as zebrafish cardiac development proceeds rapidly, heart collection and RNA extraction methods need to be quick in order to ensure homogeneity of the samples. Here, we present a rapid manual dissection protocol for collecting functional/beating hearts from zebrafish embryos. This is an essential prerequisite for subsequent cardiac-specific RNA extraction to determine cardiac-specific gene expression levels by transcriptome analyses, such as quantitative real-time polymerase chain reaction (RT-qPCR). The method is based on differential adhesive properties of the zebrafish embryonic heart compared with other tissues; this allows for the rapid physical separation of cardiac from extracardiac tissue by a combination of fluidic shear force disruption, stepwise filtration and manual collection of transgenic fluorescently labeled hearts.

Mechanotransduction pathways are activated in response to biophysical stimuli during the development or homeostasis of organs and tissues. In zebrafish, the blood-flow-sensitive transcription factor Klf2a promotes VEGF-dependent angiogenesis. However, the means by which the Klf2a mechanotransduction pathway is regulated to prevent continuous angiogenesis remain unknown. Here we report that the upregulation of klf2 mRNA causes enhanced egfl7 expression and angiogenesis signaling, which underlies cardiovascular defects associated with the loss of cerebral cavernous malformation (CCM) proteins in the zebrafish embryo. Using CCM-protein-depleted human umbilical vein endothelial cells, we show that the misexpression of KLF2 mRNA requires the extracellular matrix-binding receptor β1 integrin and occurs in the absence of blood flow. Downregulation of β1 integrin rescues ccm mutant cardiovascular malformations in zebrafish. Our work reveals a β1 integrin-Klf2-Egfl7-signaling pathway that is tightly regulated by CCM proteins. This regulation prevents angiogenic overgrowth and ensures the quiescence of endothelial cells.