Sustained effects of developmental exposure to inorganic arsenic on hepatic gsto2 expression and mating success in zebrafish.

The impacts of exposure to the pervasive environmental toxicant, inorganic arsenic (iAs), on human and fish health are well characterized and several lines of evidence suggest that some impacts can manifest years after exposure cessation. Using a developmental exposure protocol whereby zebrafish embryos were exposed to 0.5 and 1.5 mM iAs from 4-120 hours post fertilization (hpf) and then removed, we investigated the sustained effects of iAs on gene expression in the liver, survival, reproductive success, and susceptibility to iAs toxicity in the subsequent generation. Persistent exposure to iAs during development had substantial effects on the hepatic transcriptome, with 23% of all expressed genes significantly changed following developmental exposure. The gsto2 gene is involved in iAs metabolism and this gene was significantly downregulated in female livers 9 months after iAs was removed. Developmental exposure to 1.5 mM iAs, but not 0.5 mM, decreased survival by over 50% at 3 months of age. Adults that were developmentally exposed to 0.5 mM iAs had reduced mating success, but their offspring had no differences in observable aspects of development or their susceptibility to iAs toxicity. This demonstrates that developmental exposure of zebrafish to iAs reduces long-term survival, reproductive success and causes sustained changes to gsto2 expression in the liver.

DNA hypomethylation activates Cdk4/6 and Atr to induce DNA replication and cell cycle arrest to constrain liver outgrowth in zebrafish.

Coordinating epigenomic inheritance and cell cycle progression is essential for organogenesis. UHRF1 connects these functions during development by facilitating maintenance of DNA methylation and cell cycle progression. Here, we provide evidence resolving the paradoxical phenotype of uhrf1 mutant zebrafish embryos which have activation of pro-proliferative genes and increased number of hepatocytes in S-phase, but the liver fails to grow. We uncover decreased Cdkn2a/b and persistent Cdk4/6 activation as the mechanism driving uhrf1 mutant hepatocytes into S-phase. This induces replication stress, DNA damage and Atr activation. Palbociclib treatment of uhrf1 mutants prevented aberrant S-phase entry, reduced DNA damage, and rescued most cellular and developmental phenotypes, but it did not rescue DNA hypomethylation, transposon expression or the interferon response. Inhibiting Atr reduced DNA replication and increased liver size in uhrf1 mutants, suggesting that Atr activation leads to dormant origin firing and prevents hepatocyte proliferation. Cdkn2a/b was downregulated pro-proliferative genes were also induced in a Cdk4/6 dependent fashion in the liver of dnmt1 mutants, suggesting DNA hypomethylation as a mechanism of Cdk4/6 activation during development. This shows that the developmental defects caused by DNA hypomethylation are attributed to persistent Cdk4/6 activation, DNA replication stress, dormant origin firing and cell cycle inhibition.

atm Mutation and Oxidative Stress Enhance the Pre-Cancerous Effects of UHRF1 Overexpression in Zebrafish Livers.

The ataxia-telangiectasia mutated (atm) gene is activated in response to genotoxic stress and leads to activation of the tp53 tumor suppressor gene which induces either senescence or apoptosis as tumor suppressive mechanisms. Atm also serves non-canonical functions in the response to oxidative stress and chromatin reorganization. We previously reported that overexpression of the epigenetic regulator and oncogene Ubiquitin Like with PHD and Ring Finger Domains 1 (UHRF1) in zebrafish hepatocytes resulted in tp53-dependent hepatocyte senescence, a small liver and larval lethality. We investigated the role of atm on UHRF1-mediated phenotypes by generating zebrafish atm mutants. atm-/- adults were viable but had reduction in fertility. Embryos developed normally but were protected from lethality caused by etoposide or H2O2 exposure and failed to fully upregulate Tp53 targets or oxidative stress response genes in response to these treatments. In contrast to the finding that Tp53 prevents the small liver phenotype caused by UHRF1 overexpression, atm mutation and exposure to H2O2 further reduced the liver size in UHRF1 overexpressing larvae whereas treatment with the antioxidant N-acetyl cysteine suppressed this phenotype. We conclude that UHRF1 overexpression in hepatocytes causes oxidative stress, and that loss of atm further enhances this, triggering elimination of these precancerous cells, leading to a small liver.

The shifting culture of the scientific workforce - a change for women and girls in science.

Celebrating, educating and mobilizing the global community to achieve equality for women and girls in science is recognized worldwide each February 11 on the International Day of Women and Girls in Science. This day serves as a rousing call for people of all genders to gain unfettered access to opportunities to become successful, engaged and productive scientists. One strategy to achieve this is to develop policies to ensure that all people can pursue science education, training and careers, unimpeded by their sex, gender and gender identity. Another strategy is to assure representation of women and non-binary people at every level of the scientific workforce. Collectively, these strategies and other important efforts are shifting the global mindset to one where women and girls are recognized as vital, capable and innovative contributors to disciplines that have historically been dominated by men. These male-dominated disciplines have evolved cultural norms rooted in masculine stereotypes and the next challenge is to continue this shift away from a scientific culture in which hypercompetitive, individualistic, solo artists work alone in single-minded pursuit of a breakthrough. Instead, the reality is that contemporary biomedical scientific research is a cosmopolitan culture; one where breakthroughs depend on collaboration, where data sharing is the norm and where all are encouraged to contribute their best ideas to help solve science's most vexing and exciting problems.

Epigenetics across the evolutionary tree: New paradigms from non-model animals.

All animals have evolved solutions to manage their genomes, enabling the efficient organization of meters of DNA strands in the nucleus and allowing for nuanced regulation of gene expression while keeping transposable elements suppressed. Epigenetic modifications are central to accomplishing all these. Recent advances in sequencing technologies and the development of techniques that profile epigenetic marks and chromatin accessibility using reagents that can be used in any species has catapulted epigenomic studies in diverse animal species, shedding light on the multitude of epigenomic mechanisms utilized across the evolutionary tree. Now, comparative epigenomics is a rapidly growing field that is uncovering mechanistic aspects of epigenetic modifications and chromatin organization in non-model invertebrates, ranging from octopus to sponges. This review puts recent discoveries in the epigenetics of non-model invertebrates in historical context, and describes new insight into the patterning and functions of DNA methylation and other highly conserved epigenetic modifications.

Epigenetic machinery is functionally conserved in cephalopods.

BACKGROUND: Epigenetic regulatory mechanisms are divergent across the animal kingdom, yet these mechanisms are not well studied in non-model organisms. Unique features of cephalopods make them attractive for investigating behavioral, sensory, developmental, and regenerative processes, and recent studies have elucidated novel features of genome organization and gene and transposon regulation in these animals. However, it is not known how epigenetics regulates these interesting cephalopod features. We combined bioinformatic and molecular analysis of Octopus bimaculoides to investigate the presence and pattern of DNA methylation and examined the presence of DNA methylation and 3 histone post-translational modifications across tissues of three cephalopod species. RESULTS: We report a dynamic expression profile of the genes encoding conserved epigenetic regulators, including DNA methylation maintenance factors in octopus tissues. Levels of 5-methyl-cytosine in multiple tissues of octopus, squid, and bobtail squid were lower compared to vertebrates. Whole genome bisulfite sequencing of two regions of the brain and reduced representation bisulfite sequencing from a hatchling of O. bimaculoides revealed that less than 10% of CpGs are methylated in all samples, with a distinct pattern of 5-methyl-cytosine genome distribution characterized by enrichment in the bodies of a subset of 14,000 genes and absence from transposons. Hypermethylated genes have distinct functions and, strikingly, many showed similar expression levels across tissues while hypomethylated genes were silenced or expressed at low levels. Histone marks H3K27me3, H3K9me3, and H3K4me3 were detected at different levels across tissues of all species. CONCLUSIONS: Our results show that the DNA methylation and histone modification epigenetic machinery is conserved in cephalopods, and that, in octopus, 5-methyl-cytosine does not decorate transposable elements, but is enriched on the gene bodies of highly expressed genes and could cooperate with the histone code to regulate tissue-specific gene expression.

A permissive epigenetic landscape facilitates distinct transcriptional signatures of activating transcription factor 6 in the liver.

Restoring homeostasis following proteostatic stress hinges on a stress-specific transcriptional signature. How these signatures are regulated is unknown. We use functional genomics to uncover how activating transcription factor 6 (ATF6), a central factor in the unfolded protein response, regulates its target genes in response to toxicant induced and physiological stress in the liver. We identified 652 conserved putative ATF6 targets (CPATs), which functioned in metabolism, development and proteostasis. Strikingly, Atf6 activation in the zebrafish liver by transgenic nAtf6 overexpression, ethanol and arsenic exposure resulted in a distinct CPAT signature for each; with only 34 CPATs differentially expressed in all conditions. In contrast, during liver regeneration in mice resulted in a dynamic differential expression pattern of 53% of CPATs. These CPATs were distinguished by residing in open chromatin, H3K4me3 occupancy and the absence of H3K27me3 on their promoters. This suggests that a permissive epigenetic landscape allows stress-specific Atf6 target gene expression.

Systematic Evaluation of the Effects of Toxicant Exposure on Survival in Zebrafish Embryos and Larvae.

The use of whole animal models in toxicological studies is essential for understanding the physiological responses caused by chemical exposures. However, such studies can face reproducibility challenges due to unaccounted experimental parameters that can have a marked influence on toxicological outcomes. Zebrafish embryos and larvae are a popular vertebrate animal model for studying cellular, tissue, and organ responses to toxicant exposures. Despite the popularity of this system, standardized protocols that control for the influence of various experimental parameters and culture conditions on the toxicological response in these animals have not been widely adopted, making it difficult to compare findings from different laboratories. Here, we describe a detailed approach for designing and optimizing protocols to assess the impact of chemical exposures on the development and survival of zebrafish embryos and larvae. We first describe our standard procedure to determine two key toxicological thresholds, the maximum tolerable concentration (MTC) and the lethal concentration (LC50 , defined as that in which 50% of larvae die), in response to an exposure that persists from early development through larval maturation. We then describe two protocols to systematically test how key experimental parameters, including genetic background, culture media, animal density, volume, plate material, and developmental stage in which the embryos are exposed, alter the MTC and LC50 . Finally, we provide a step-by-step guide to assess the interaction between two chemicals using this model. These protocols will guide the standardization of toxicological studies using zebrafish and maximize reproducibility. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Zebrafish embryo collection and culture, and establishment of the MTC and LC50 Basic Protocol 2: Evaluation of the impact of culture conditions on toxicant responses of zebrafish embryo and larvae Basic Protocol 3: Identification of the developmental window of sensitivity to toxicant exposure Basic Protocol 4: Testing interaction between multiple toxicants.

Nuclear Organization during Hepatogenesis in Zebrafish Requires Uhrf1.

Acquisition of cellular fate during development is initiated and maintained by well-coordinated patterns of gene expression that are dictated by the epigenetic landscape and genome organization in the nucleus. While the epigenetic marks that mediate developmental gene expression patterns during organogenesis have been well studied, less is known about how epigenetic marks influence nuclear organization during development. This study examines the relationship between nuclear structure, chromatin accessibility, DNA methylation, and gene expression during hepatic outgrowth in zebrafish larvae. We investigate the relationship between these features using mutants that lack DNA methylation. Hepatocyte nuclear morphology was established coincident with hepatocyte differentiation at 80 h post-fertilization (hpf), and nuclear shape and size continued to change until the conclusion of outgrowth and morphogenesis at 120 hpf. Integrating ATAC-Seq analysis with DNA methylation profiling of zebrafish livers at 120 hpf showed that closed and highly methylated chromatin occupies most transposable elements and that open chromatin correlated with gene expression. DNA hypomethylation, due to mutation of genes encoding ubiquitin-like, containing PHD and RING Finger Domains 1 (uhrf1) and DNA methyltransferase (dnmt1), did not block hepatocyte differentiation, but had dramatic effects on nuclear organization. Hepatocytes in uhrf1 mutants have large, deformed nuclei with multiple nucleoli, downregulation of nucleolar genes, and a complete lack of the nuclear lamina. Loss of lamin B2 staining was phenocopied by dnmt1 mutation. Together, these data show that hepatocyte nuclear morphogenesis coincides with organ morphogenesis and outgrowth, and that DNA methylation directs chromatin organization, and, in turn, hepatocyte nuclear shape and size during liver development.

Chromatin states shaped by an epigenetic code confer regenerative potential to the mouse liver.

We hypothesized that the highly controlled pattern of gene expression that is essential for liver regeneration is encoded by an epigenetic code set in quiescent hepatocytes. Here we report that epigenetic and transcriptomic profiling of quiescent and regenerating mouse livers define chromatin states that dictate gene expression and transposon repression. We integrate ATACseq and DNA methylation profiling with ChIPseq for the histone marks H3K4me3, H3K27me3 and H3K9me3 and the histone variant H2AZ to identify 6 chromatin states with distinct functional characteristics. We show that genes involved in proliferation reside in active states, but are marked with H3K27me3 and silenced in quiescent livers. We find that during regeneration, H3K27me3 is depleted from their promoters, facilitating their dynamic expression. These findings demonstrate that hepatic chromatin states in quiescent livers predict gene expression and that pro-regenerative genes are maintained in active chromatin states, but are restrained by H3K27me3, permitting a rapid and synchronized response during regeneration.

uhrf1 and dnmt1 Loss Induces an Immune Response in Zebrafish Livers Due to Viral Mimicry by Transposable Elements.

Activation of transposable elements (TEs) can cause cellular damage. Cytoplasmic nucleic acid sensing pathways evolved to detect pathogens, but can also serve to cull cells with inappropriate TE activation as TEs can be viral mimetics. Epigenetic silencing of TEs is mediated in part by DNA methylation, but it is not clear if TE activation or the immune system contribute to the cellular damage caused by loss of DNA methylation. Here, we provide mechanistic insight into the observation of an activated interferon response in the liver of zebrafish larvae with deletion in critical components of the DNA methylation machinery, uhrf1 and dnmt1. We focus on dissecting the relationship between DNA methylation, TE activation and induction of an immune response through cytoplasmic DNA and double stranded RNA sensing pathways and identify tnfa as a mediator of cell death in the liver of these mutants. Integrated RNAseq and methylome analysis identified LTR transposons as the most upregulated in these mutants and also the most methylated in control larvae, indicating a direct role of DNA methylation in suppressing this TE subclass. RNAseq analysis from these same samples revealed expression signatures of a type-I interferon response and of tnfa activation, mimicking the pattern of gene expression in virally infected cells. CRISPR/Cas9 mediated depletion of the cellular antiviral sensors sting and mavs reduced expression of interferon response genes and tnfa depletion dramatically reduced cell death in uhrf1 mutant livers. This suggests that the antiviral response induced by DNA hypomethylation and TE activation in the liver is mediated by the signaling pathways activated by both cytoplasmic double stranded RNA and DNA and that tnfa mediates cell death as a potential mechanism to eliminate these damaged cells.

Manipulating and tracking single hepatocyte behavior during mouse liver regeneration by performing hydrodynamic tail vein injection.

Studies to identify genes relevant to mammalian hepatocyte biology in vivo are largely carried out using germline genetic-engineering approaches, which can be costly and time-consuming. We describe hydrodynamic tail vein injection as an alternative approach to introduce genetic elements into hepatocytes. Transfected hepatocytes can then be traced with a GFP reporter enabling the use of immunohistochemistry and FACS sorting to examine the changes in hepatocyte gene expression and proliferation during liver regeneration induced by 2/3 partial hepatectomy (PH). For complete details on the use and execution of this protocol, please refer to Wang et al. (2019).

Arsenic induced redox imbalance triggers the unfolded protein response in the liver of zebrafish.

Inorganic arsenic (iAs) is one of the most endemic toxicants worldwide and oxidative stress is a key cellular pathway underlying iAs toxicity. Other cellular stress response pathways, such as the unfolded protein response (UPR), are also impacted by iAs exposure, however it is not known how these pathways intersect to cause disease. We optimized the use of zebrafish larvae to identify the relationship between these cellular stress response pathways and arsenic toxicity. We found that the window of iAs susceptibility during zebrafish development corresponds with the development of the liver, and that even a 24-h exposure can cause lethality if administered to mature larvae, but not to early embryos. Acute exposure of larvae to iAs generates reactive oxygen species (ROS), an antioxidant response, endoplasmic reticulum (ER) stress and UPR activation in the liver. An in vivo assay using transgenic larvae expressing a GFP-tagged secreted glycoprotein in hepatocytes (Tg(fabp10a:Gc-EGFP)) revealed acute iAs exposure selectively decreased expression of Gc-EGFP, indicating that iAs impairs secretory protein folding in the liver. The transcriptional output of UPR activation is preceded by ROS production and activation of genes involved in the oxidative stress response. These studies implicate redox imbalance as the mechanism of iAs-induced ER stress and suggest that crosstalk between these pathways underlie iAs-induced hepatic toxicity.

Covalent Organic Framework Embedded with Magnetic Nanoparticles for MRI and Chemo-Thermotherapy.

Nanoscale imine-linked covalent organic frameworks (nCOFs) were first loaded with the anticancer drug Doxorubicin (Dox), coated with magnetic iron oxide nanoparticles (γ-Fe2O3 NPs), and stabilized with a shell of poly(l-lysine) cationic polymer (PLL) for simultaneous synergistic thermo-chemotherapy treatment and MRI imaging. The pH responsivity of the resulting nanoagents (γ-SD/PLL) allowed the release of the drug selectively within the acidic microenvironment of late endosomes and lysosomes of cancer cells (pH 5.4) and not in physiological conditions (pH 7.4). γ-SD/PLL could efficiently generate high heat (48 °C) upon exposure to an alternating magnetic field due to the nCOF porous structure that facilitates the heat conduction, making γ-SD/PLL excellent heat mediators in an aqueous solution. The drug-loaded magnetic nCOF composites were cytotoxic due to the synergistic toxicity of Dox and the effects of hyperthermia in vitro on glioblastoma U251-MG cells and in vivo on zebrafish embryos, but they were not significantly toxic to noncancerous cells (HEK293). To the best of our knowledge, this is the first report of multimodal MRI probe and chemo-thermotherapeutic magnetic nCOF composites.

Unraveling the Epigenetic Basis of Liver Development, Regeneration and Disease.

A wealth of studies over several decades has revealed an epigenetic prepattern that determines the competence of cellular differentiation in the developing liver. More recently, studies focused on the impact of epigenetic factors during liver regeneration suggest that an epigenetic code in the quiescent liver may establish its regenerative potential. We review work on the pioneer factors and other chromatin remodelers that impact the gene expression patterns instructing hepatocyte and biliary cell specification and differentiation, along with the requirement of epigenetic regulatory factors for hepatic outgrowth. We then explore recent studies involving the role of epigenetic regulators, Arid1a and Uhrf1, in efficient activation of proregenerative genes during liver regeneration, thus highlighting the epigenetic mechanisms of liver disease and tumor development.

Supercritical CO2 Processing Generates Aqueous Cisplatin Solutions with Enhanced Cancer Specificity.

Cisplatin is a highly toxic material used clinically as a potent chemotherapeutic. While effective against some cancers, toxicity limits widespread use and low solubility confounds delivery. To formulate a better tolerated and more water-soluble form of cisplatin, we designed a rapid expansion of supercritical solutions (RESS) technique with supercritical carbon dioxide (sc-CO2) to collect nanoclusters of cisplatin embedded in dry ice, in a dual-stage collection vessel cooled to liquid nitrogen temperature. These nanoclusters were solubilized in deionized water and further concentrated (up to 51.3 mM) by a Rotovap process, yielding stable cisplatin solutions with solubility up to 15 × (w/w) greater than that of normal cisplatin. Extensive material characterizations of the solutions were carried out to determine any chemical and/or structural changes of the RESS-processed cisplatin. In vitro cytotoxicity studies of these aqueous solutions showed increased cell viability and early apoptosis compared to equivalent concentrations of standard cisplatin solutions. In vivo studies using zebrafish embryos revealed that standard cisplatin solutions were acutely toxic and caused death of rapidly proliferating cells compared to RESS-processed cisplatin, which were better tolerated with reduced general cell death. Increased water solubility and matched chemical identity of RESS-processed aqueous cisplatin solutions indicate the potential to open up novel drug-delivery routes, which is beneficial for new pharmaceutical design and development.

Casting a wide net: use of diverse model organisms to advance toxicology.

Toxicology - the study of how chemicals interact with biological systems - has clear relevance to human health and disease. Persistent exposure to natural and synthetic chemicals is an unavoidable part of living on our planet; yet, we understand very little about the effects of exposure to the vast majority of chemicals. While epidemiological studies can provide strong statistical inference linking chemical exposure to disease, research in model systems is essential to elucidate the mechanisms of action and to predict outcomes. Most research in toxicology utilizes a handful of mammalian models that represent a few distinct branches of the evolutionary tree. This narrow focus constrains the understanding of chemical-induced disease processes and systems that have evolved in response to exposures. We advocate for casting a wider net in environmental toxicology research to utilize diverse model systems, including zebrafish, and perform more mechanistic studies of cellular responses to chemical exposures to shift the perception of toxicology as an applied science to that of a basic science. This more-inclusive perspective will enrich the field and should remain central to research on chemical-induced disease.

Aqueous Synthesis of Triphenylphosphine-Modified Gold Nanoparticles for Synergistic In Vitro and In Vivo Photothermal Chemotherapy.

Triphenylphosphine (TPP) surface-functionalized and F-108 Pluronic-stabilized gold nanoparticles (F-108@TPP-AuNPs) have been synthesized through a one-step approach, leading to well-defined (9.6±1.6 nm) and water-soluble nanoparticles by microwave heating an aqueous solution of TPP-AuI Cl in the presence of a Pluronic polymer under basic conditions. TPP release was negligible under physiological conditions, but enhanced significantly at an acidic pH (5.4) mimicking that of a cancer cell. Laser irradiation (532 nm) raised the temperature of an aqueous solution of F-108@TPP-AuNPs to 51.7 °C within 5 min, confirming efficient light-to-heat conversion capabilities without significant photodegradation. TEM confirmed intracellular localization of F-108@TPP-AuNPs in the cytosol, endosomes and lysosomes of HeLa cells. F-108@TPP-AuNPs were well tolerated by HeLa cells and zebrafish embryos at ambient temperatures and became toxic upon heat activation, suggesting synergistic interactions between heat and cytotoxic action by TPP.

Potent and selective in vitro and in vivo antiproliferative effects of metal-organic trefoil knots.

A set of metal-organic trefoil knots (M-TKs) generated by metal-templated self-assembly of a simple pair of chelating ligands were well tolerated in vitro by non-cancer cells but were significantly more potent than cisplatin in both human cancer cells--including those resistant to cisplatin--and in zebrafish embryos. In cultured cells, M-TKs generated reactive oxygen species that triggered apoptosis via the mitochondrial pathway without directly disrupting the cell-membrane or damaging nuclear DNA. The cytotoxicity and wide scope for structural variation of M-TKs indicate the potential of synthetic metal-organic knots as a new field of chemical space for pharmaceutical design and development.