Biology subjects

Sadler, K. C.

Publications and source records attributed to Sadler, K. C..

9 recordsLinked to original sources

bioRxiv2026

Hepatocyte Embryonic Ectoderm Development (Eed) Deficiency Causes Liver Injury, Fibrosis and Impacts Liver Regeneration

Regeneration depends on tightly coordinated transcriptional programs governed by a dynamic epigenetic landscape to regulate cell identity, proliferation, and tissue remodelling following injury. The liver is highly regenerative due to its ability to rapidly upregulate genes that drive the cell cycle and other genes important for hepatocyte proliferation. In the uninjured liver, many of these genes are poised for activation based on promoter occupancy of trimethylated histone 3 lysine 27 (H3K27me3) and regenerative stimulus provided by partial hepatectomy leads to evacuation of this mark, suggesting this is a key component of proregenerative gene regulation in the liver. H3K27me3 is deposited by the polycomb repressive complex 2 (PRC2). Were we deplete H3K27me3 using hepatocyte specific deletion of key component of PRC2, Embryonic Ectoderm Development (EedHepKO). This results in reduced liver size, increased hepatocyte death, proliferation, and fibrosis associated with upregulation of cell cycle and fibrogenic genes. Though these mice are less likely to survive two-thirds partial hepatectomy than WT (WT) controls, those that do survive increase liver mass faster than WTs. Importantly, genes occupied by H3K27me3 in uninjured WT livers are upregulated in EEDHepKO livers, and become further induced following PH. This demonstrates that PRC2 loss induces liver injury and dysregulates pro-regenerative gene expression, highlighting that epigenetic modulation depends requires precise targeting to achieve enhanced regenerative

pathology↗

bioRxiv2025

UHRF1 Overexpression Generates Distinct Senescent States with Different Tp53 Dependencies

SummarySenescence is a pleiotropic phenotype that alternatively suppresses or promotes cancer. The tumor suppressive roles are linked to clearance of damaged cells by the immune system, while cells with tumor promoting functions resist apoptosis, evade immune clearance and either persist and support the tumor microenvironment, or escape and proliferate. What generates these diverse populations is unclear. We investigated this in preneoplastic zebrafish livers where the epigenetic regulator, UHRF1, is overexpressed in hepatocytes. Double strand breaks, DNA methylation repatterning, retrotransposon expression, cell cycle withdrawal and activation of Atm and Tp53 dependent senescence were early responses to UHRF1 overexpression. This evolved to generate diverse populations of senescent cells, some which expressed immune and senescence signatures plus anti-apoptotic markers, and others co-expressed proliferative genes. The fate of these populations was dictated by UHRF1 levels and Tp53, as Tp53 loss enabled proliferation of cells with reduced UHRF1 expression but not in cells expressing high UHRF1. The senolytic Navitoclax targeted only a subset of senescent cells. Thus, the diversity of senescent cells driven by epigenetic changes can generate divergent outcomes. Short summaryUHRF1 overexpression in zebrafish hepatocytes induces DNA damage leading to Atm-tp53-dependent senescence with UHRF1 levels dictating whether hepatocytes remain senescent, escape, or undergo senolytic elimination.

cancer biology↗

bioRxiv2024

Epigenetic Disordering Drives Stemness, Senescence Escape and Tumor Heterogeneity

Tumor heterogeneity is the substrate for tumor evolution and the linchpin of treatment resistance. Cancer cell heterogeneity is largely attributed to distinct genetic changes within each cell population. However, the widespread epigenome repatterning that characterizes most cancers is also highly heterogenous within tumors and could generate cells with diverse identities and malignant features. We show that high levels of the epigenetic regulator and oncogene, UHRF1, in zebrafish hepatocytes rapidly induced methylome disordering, loss of heterochromatin, and DNA damage, resulting in cell cycle arrest, senescence, and acquisition of stemness. Reducing UHRF1 expression transitions these cells from senescent to proliferation-competent. The expansion of these damaged cells results in hepatocellular carcinomas (HCC) that have immature cancer cells intermingled with fibroblasts, immune and senescent cells expressing high UHRF1 levels, which serve as reservoirs for new cancer cells. This defines a distinct and heterogenous HCC subtype resulting from epigenetic changes, stemness and senescence escape.

cancer biology↗

bioRxiv2023

Sustained Effects of Developmental Exposure to Inorganic Arsenic on Hepatic Gene 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 was 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. Developmental exposure to iAs has massive effects on the hepatic transcriptome, with 23% of genes differentially expressed at the end of exposure at 120 hpf, and some of these genes remain deregulated in the liver 9 months after iAs was removed. Developmental exposure to 1.5 mM iAs, but not 0.5 mM, increased mortality through 3 months by over 50%. 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 gene expression in the liver. SUMMARY STATEMENTThis work investigates the long-term effects of developmental exposure to inorganic arsenic (iAs) using zebrafish. Months after iAs-exposure was terminated, we found increased mortality, changes in gene expression in the liver and decreased mating success.

pharmacology and toxicology↗

bioRxiv2023

Cdk4/6 is activated by DNA hypomethylation to cause DNA rereplication and organ outgrowth defects

Coordinating epigenomic inheritance and cell cycle progression is essential for organogenesis. UHRF1 connects these functions by facilitating maintenance of DNA methylation and cell cycle progression. Here, we provide evidence resolving the paradoxical phenotype of uhrf1 mutant zebrafish embryos that have both activation of pro-proliferative E2F target genes and increased number of hepatocytes in S-phase, but the liver fails to grow. We find that Atr inhibition reduces DNA replication and increases liver size in uhrf1 mutants, suggesting that uhrf1 mutant hepatocytes have replication stress leading to Atr-mediated cell cycle inhibition and dormant origin firing. We uncover persistent Cdk4/6 activation as the mechanism driving uhrf1 mutant hepatocytes into S-phase, activating Atr and restricting hepatic outgrowth. Palbociclib treatment of uhrf1 mutant embryos prevented aberrant S-phase entry, and the DNA damage response. Palbociclib rescued most cellular and developmental phenotypes in uhrf1 mutants, except DNA hypomethylation, transposon activation and the interferon response. Pro-proliferative genes were also activated in a Cdk4/6 dependent fashion in the liver of dnmt1 mutants, suggesting DNA hypomethylation as a mechanism of Cdk4/6 activation. Thus, the developmental defects caused by DNA hypomethylation are attributed to persistent Cdk4/6 activation leading to DNA replication stress, dormant origin firing and cell cycle inhibition, preventing hepatic outgrowth.

developmental biology↗

bioRxiv2023

Arsenite methyltransferase 3 regulates hepatic energy metabolism which dictates the hepatic response to arsenic exposure

Inorganic arsenic (iAs(III)) is among the most pervasive environmental toxicants in the world. The iAs metabolizing enzyme, arsenite methyltransferase (AS3MT), is a key mediator of iAs(III) toxicity and has been almost exclusively investigated in the context of iAs(III) exposure. We use functional genomics approach with zebrafish as3mt mutants which lack arsenite methyltransferase activity to uncover novel, arsenic-independent functions for As3mt. Transcriptomic analysis of untreated whole larvae, and the larval and adult livers from as3mt mutants revealed thousands of differentially expressed genes (DEGs) compared to wild-type controls. These were enriched for genes functioning in the ribosome or mitochondria. Nearly all genes in the citric acid cycle and mitochondrial transport were downregulated in as3mt mutant livers. This resulted in reduction in reactive oxygen species levels by half and fatty liver in 81% of as3mt mutant larvae. An inverse expression pattern was detected for over 2,000 of the As3mt regulated DEGs in the liver of larvae with transgenic overexpression of As3mt in hepatocytes. Replacing as3mt expression in hepatocytes of as3mt mutants prevented fatty liver, demonstrating that As3mt has novel, cell-autonomous and arsenic-independent functions regulating mitochondrial metabolism. We suggest that these functions contribute to iAs toxicity, as the mitochondrial function genes that were downregulated in the liver of unexposed as3mt mutants were further downregulated upon iAs exposure and as3mt mutants were sensitized to iAs. This indicates that As3mt regulates hepatic energy metabolism and demonstrates that, in addition to its role in iAs detoxification, the physiological functions of As3mt contribute to arsenic toxicity. SIGNIFICANCEArsenic is an endemic environmental toxicant, and the current paradigm is that susceptibility to arsenic toxicity is dictated by levels of expression of the arsenite 3 methyltransferase gene (As3mt), which is dedicated enzyme involved in arsenic detoxification. Our data showing that As3mt serves arsenic-independent functions in energy metabolism challenge this paradigm. We show that zebrafish as3mt mutants have loss of mitochondrial function and develop fatty liver and suggest that as3mt mutants are sensitized to arsenic toxicity due, in part, to impaired mitochondrial function. This finding opens an entirely new area of study to identify the cellular function of As3mt and further advances the understanding of how genetic variants in As3mt confer sensitivity arsenic toxicology.

genetics↗

bioRxiv2021

Epigenetic machinery is functionally conserved in cephalopods

Epigenetic regulatory mechanisms are divergent across the animal kingdom, yet little is known about the epigenome in non-model organisms. Unique features of cephalopods make them attractive for investigating behavioral, sensory, developmental and regenerative processes, but using molecular approaches in such studies is hindered by the lack of knowledge about genome organization and gene regulation in these animals. We combined bioinformatic and molecular analysis of Octopus bimaculoides to identify gene expression signatures for 12 adult tissues and a hatchling, and investigate the presence and pattern of DNA methylation and histone methylation marks across tissues. This revealed a dynamic gene expression profile encoding several epigenetic regulators, including DNA methylation maintenance factors that were highly conserved and functional in cephalopods, as shown by detection of 5-methyl-cytosine in multiple tissues of octopus, squid and bobtail squid. WGBS of octopus brain and RRBS from a hatchling revealed that less than 10% of CpGs are methylated, highlighting a non-random distribution in the genome of all tissues, with enrichment in the bodies of a subset of 14,000 genes and absence from transposons. Each DNA methylation pattern encompassed genes with distinct functions and, strikingly, many of these genes showed similar expression levels across tissues. In contrast to the static pattern of DNA methylation, the histone marks H3K27me3, H3K9me3 and H3K4me3 were detected at different levels in diverse cephalopod tissues. This suggests the methylome and histone code cooperate to regulate tissue specific gene expression in a way that may be unique to cephalopods.

genomics↗

bioRxiv2021

Permissive epigenetic landscape facilitates distinct transcriptional signatures of activating transcription factor 6 in the liver

Proteostatic stress initiates a transcriptional response that is unique to the stress condition, yet the regulatory mechanisms underlying the distinct gene expression patterns observed in stressed cells remains unknown. Using a functional genomic approach, we investigated how activating transcription factor 6 (ATF6), a key transcription factor in the unfolded protein response (UPR), regulates target genes. We first designed a computational strategy to define Atf6 target genes based on the evolutionary conservation of predicted ATF6 binding in gene promoters, identifying 652 conserved putative Atf6 target (CPAT) genes. CPATs were overrepresented for genes functioning in the UPR, however, the majority functioned in cellular processes unrelated to proteostasis, including small molecule metabolism and development. Functional studies of stress-independent and toxicant based Atf6 activation in zebrafish livers showed that the pattern of CPAT expression in response to Atf6 overexpression, alcohol and arsenic was unique. Only 34 CPATs were differentially expressed in all conditions, indicating that Atf6 is sufficient to regulate a small subset of CPATs. Blocking Atf6 using Ceapins in zebrafish demonstrated that Atf6 is necessary for activation of these genes in response to arsenic. We investigated CPAT during physiologically mediated hepatocyte stress using liver regeneration in mice as a model. Over half of all CPATs were differentially expressed during this process. This was attributed to the permissive chromatin environment in quiescent livers on the promoters of these genes, characterized by the absence of H3K27me3 and enrichment of H3K4me3. Taken together, these data uncover a complex transcriptional response to Atf6 activation and implicate a permissive epigenome as a mechanism by which distinct transcriptional responses are regulated by Atf6.

genomics↗

bioRxiv2020

Rearing medium dictates variability across replicates in untreated and arsenic challenged zebrafish larvae

Reproducibility and consistency are hallmarks of scientific integrity. Biological systems are inherently noisy, posing a challenge to reproducibility. This is particularly relevant to the field of environmental toxicology, where many unaccounted experimental parameters can have a marked influence on the biological response to exposure. Here, we extend the use of zebrafish as a robust toxicological model for studying the effects of inorganic arsenic (iAs) on liver biology. We observed that iAs toxicity in this system is not influenced by important parameters including genetic background, rearing container material or rearing volume but the dose response to iAs is influenced by the rearing medium. We compared mortality as a measure of iAs toxicity to embryos cultured in two standard rearing media: egg water made from dehydrated ocean salts dissolved in water and a defined embryo medium which is a pH adjusted, buffered salt solution. Larvae reared in egg water were more susceptible to iAs compared to those reared in embryo medium. This effect was independent of the pH differences between these solutions. These culture conditions did not cause any difference in the global hepatic transcriptome of control zebrafish. Further, no difference in the expression of genes involved in the unfolded protein response (UPR) in larvae exposed to iAs treatment or in a stress independent system to activate UPR genes by transgenic overexpression of activating transcription factor 6 (nAtf6) in hepatocytes was observed. However, the clutch-to-clutch variation in gene expression was significantly greater in larvae reared in egg water compared to those in embryo medium. These data demonstrate that egg water affects reproducibility across replicates in terms of gene expression and exacerbates iAs mediated toxic response. This highlights the importance of rigorous evaluation of experimental conditions to assure reproducibility.

pharmacology and toxicology↗