Biology subjects

Hatcher, C.

Publications and source records attributed to Hatcher, C..

10 recordsLinked to original sources

bioRxiv2026

Coordinated microRNA-mRNA regulatory remodelling across the compressed maturation of the African killifish (Nothobranchius furzeri)

The turquoise killifish (Nothobranchius furzeri) is an emerging vertebrate model for development and ageing due to its exceptionally rapid maturation and short lifespan. However, how microRNA (miRNA) regulation coordinates gene expression across its compressed developmental trajectory remains poorly understood. Here, we integrated miRNA and mRNA expression from the same unexposed animals across three developmental stages: newly hatched fry (4 weeks total age), juveniles (~8 weeks total age), and aged adults (~8 months of age). Developmental stage was the dominant source of variation in both datasets, with miRNA and mRNA profiles independently resolving a consistent progression from newly hatched fry to juveniles and adults. Transcriptomic changes reflected ongoing tissue maturation, including increased expression of crystallin genes associated with lens development, while more than 2,000 genes were differentially expressed during the juvenile transition. Integration of 398 developmentally dynamic miRNAs with predicted mRNA targets identified specific miRNAs whose developmental changes were significantly enriched for opposing changes in their target genes. These included conserved developmental regulators from the miR-200/141, miR-29, let-7, and miR-34 families, which increased toward adulthood as their predicted target cohorts decreased. Stage-controlled analyses further identified miR-34a, miR-29a, miR-29b, miR-15a, and a novel candidate whose target relationships persisted independently of the overall developmental trajectory. Notably, miR-29 showed particularly strong induction during maturation, consistent with its conserved roles in extracellular-matrix remodeling, differentiation, and vertebrate ageing. Together, these findings reveal coordinated remodeling of conserved miRNA-mRNA regulatory programs across the rapid maturation of N. furzeri and establish a framework for investigating post-transcriptional regulation during vertebrate development in a species with limited miRNA annotation.

genomics↗

bioRxiv2026

Low-Dose Microcystin-LR Elicits Sex-Dimorphic Transcriptomic Responses in Senescent Nothobranchius furzeri: Implications for Cyanotoxin Vulnerability in Aging Vertebrates

Microcystin-LR (MC-LR), a cyanobacterial toxin produced during harmful algal blooms, is an increasing environmental and public health concern as the frequency and intensity of harmful algal blooms continue to rise globally. While the effects of MC-LR have been extensively studied in young organisms, much less is known about how aging influences susceptibility to cyanotoxin exposure. Here, we used the naturally short-lived turquoise killifish, Nothobranchius furzeri, to investigate transcriptional responses to low-level MC-LR exposure in a senescent vertebrate. Approximately 8-month-old GRZ killifish were exposed to a low dose of 0.5 g/L MC-LR, followed by whole-body RNA sequencing and sex-stratified differential expression analysis. Despite identical experimental conditions and exposure, males and females exhibited strikingly distinct transcriptional responses, with 313 differentially expressed genes (DEGs) in males and 263 in females and only 27 DEGs shared between the sexes. Among the shared responses, pck1, a key regulator of gluconeogenesis, was strongly downregulated in both sexes, accompanied by altered expression of genes associated with mitochondrial function, metabolic regulation, extracellular matrix remodeling, and genome maintenance. Males exhibited prominent remodeling of skeletal muscle and contractile programs, supported by enrichment of sarcomeric, myofilament, and contractile-fiber-associated genes. In contrast, females showed pronounced alterations in reproductive and metabolic programs, including vitellogenin- and zona pellucida-associated transcripts. Cell/tissue associated marker-module analysis further revealed distinct sex-dependent shifts in structural, neural, immune, metabolic, and reproductive transcriptional signatures. Together, these findings demonstrate that MC-LR elicits a broad but strongly sex-dependent transcriptional response in senescent N. furzeri, involving responses in multiple physiological systems. Our study identifies biological sex as an important determinant of cyanotoxin responses in an aging context and establishes naturally aged N. furzeri as a tractable vertebrate model for investigating interactions between environmental exposure and biological aging.

pharmacology and toxicology↗

bioRxiv2026

PFOA exposure amplifies normal developmental gene expression programs in the African Killifish, Nothobranchius furzeri

Per- and polyfluoroalkyl substances (PFAS) are persistent environmental contaminants associated with developmental abnormalities and adverse health outcomes, yet it remains unclear whether PFAS exposure imposes novel transcriptional programs during development or perturbs endogenous developmental processes. Here, we continuously exposed African killifish (Nothobranchius furzeri) to an environmentally relevant concentration of perfluorooctanoic acid (PFOA) from egg laying through juvenile development to mimic prenatal-to-adolescent exposure and performed whole-transcriptome sequencing at two developmental stages. Despite four weeks of embryonic exposure, newly hatched juveniles, approximately equivalent to human infants, exhibited remarkably limited transcriptional responses, with only a few differentially expressed genes identified. In contrast, older juveniles, equivalent to human adolescents, exposed for eight weeks displayed a dramatic expansion of transcriptional perturbation, with approximately 30-fold more differentially expressed genes spanning pathways involved in cell-cycle regulation, endocrine signaling, immune function, oxidative stress, and lipid metabolism. Unexpectedly, more than half of the PFOA-induced genes were the same genes that normally increase during juvenile maturation, representing a highly significant enrichment of the endogenous developmental program. These findings indicate that the embryonic transcriptome is largely buffered against chronic PFOA exposure, whereas post-hatch stages exhibit heightened vulnerability. Rather than inducing a distinct toxicological state, PFOA predominantly acted by amplifying existing developmental gene regulatory programs. Our results identify the juvenile stage following hatching, equivalent to human neonatal and adolescent developmental stages, as a critical window of PFAS susceptibility and suggest that environmental contaminants may exert their effects by exaggerating normal developmental trajectories, with potential consequences for growth, maturation, and long-term health.

Developmental Biology↗

bioRxiv2026

Environmental PFOA Exposure Alters Early Developmental Programming during the Maternal Zygotic Transition

Early embryogenesis is governed by precisely timed gene regulatory programs that coordinate cell fate specification, tissue patterning, and morphogenesis. The maternal-to-zygotic transition (MZT) represents a pivotal developmental milestone during which regulatory control shifts from maternally deposited transcripts to activation of the zygotic genome. Disruption of this transition has the potential to alter developmental trajectories with lasting consequences. Per- and polyfluoroalkyl substances (PFAS), environmentally persistent contaminants, have been linked to developmental abnormalities, yet their impact on core embryonic gene regulatory networks especially during MZT is not well understood. Using zebrafish (Danio rerio), a tractable vertebrate model and New Approach Methodology (NAM), we investigated how PFAS exposure during the MZT alters early developmental programming. Embryos were exposed starting at different times within the 8-hour MZT window and collected at 24 hours post-fertilization (hpf) for transcriptomic analysis. Targeted qRT-PCR revealed dysregulation of genes controlling transcriptional activation, lineage specification, proliferation, and differentiation. Whole-transcriptome RNA sequencing (RNA-seq) further identified widespread perturbations in gene networks governing transcriptional regulation, cell signaling, and embryonic morphogenesis. Temporal analysis revealed that exposure beginning at 3.5 hpf, followed by 8 hpf, corresponding to early zygotic genome activation and near completion of zygotic activation, respectively, resulted in the greatest differential gene expression changes. Consistent with these early gene regulatory perturbations, larvae exposed at 8 hpf also exhibited altered behavior at 5 days post-fertilization. Together, these findings demonstrate that PFAS exposure during MZT disrupts the establishment of embryonic gene regulatory networks, linking environmental toxicant exposure to altered developmental patterning and organismal outcomes. This work underscores the vulnerability of early developmental transitions to environmental perturbation and positions MZT as a critical window of susceptibility during development.

developmental biology↗

bioRxiv2026

Short-chain PFAS exposure alters embryonic development and behavior in zebrafish

Per- and polyfluoroalkyl substances (PFAS) are manmade chemicals that are persistent in the environment and have been linked to various physiological and neurobehavioral outcomes, including anxiety disorders. Trifluoroacetic acid (TFA), a short chain PFAS and the most common PFAS degradation product, is increasingly detected in water, soil, and human blood, raising significant concerns about its developmental toxicity. However, the impact of early-life TFA exposure on neurodevelopment and behavior remain insufficiently characterized. In this study, we employed Zebrafish (Danio rerio) embryos as a New Approach Methodology (NAM), to evaluate the development, behavior, and protein expression changes in response to early-life TFA exposure. Embryos were exposed to environmentally relevant low and high concentrations of TFA beginning at one-cell stage. Early developmental physiology was assessed by measuring viability, tail twitch response, hatching rates, and chorion diameters during embryogenesis. Anxiety-like behaviors were evaluated at 5- and 6-days post-fertilization using validated behavioral assays such as the Light-Dark Test and Startle Response. Each test evaluates distinct anxiety-related behaviors by measuring locomotor activity, thigmotaxis (wall preference), and stimulus reactivity, with anxious zebrafish larvae showing increased movement in light and greater wall preference. Then to identify molecular pathways underlying observed developmental phenotypes with TFA exposure, proteomic analyses were performed on embryos at 24- and 48-hours post-fertilization. Our results indicate that TFA exposure altered developmental physiology, evidenced by reduced chorion diameters, and lead to increased anxiety-like behaviors with larvae exhibiting thigmotaxis. These phenotypic changes were accompanied by detectable alterations in the embryonic proteome. Collectively, our findings provide insight into how short-chain PFAS exposure during critical windows of development may contribute to neurobehavioral dysfunction, highlighting potential risks relevant to inform public health policies and environmental regulations.

developmental biology↗

bioRxiv2026

Sub-second Extracellular Impedance Measurement of Epithelial Cell Monolayers using Step Excitations and Time-domain Analysis

Extracellular electrochemical impedance spectroscopy (EIS) is emerging as a powerful technique in in vitro epithelial research, offering quantitative insights into barrier integrity, morphology, and apical-basolateral polarity noninvasively through metrics such as transepithelial electrical resistance (TER/TEER), transepithelial capacitance (TEC), and membrane ratio (), respectively. However, due to the broad range of frequencies probed, EIS typically requires tens of seconds per measurement, limiting its ability to capture more rapid biological phenomena. We present Time-domain Epithelial Impedance Measurement (TEIM), a method for sub-second extracellular impedance measurements of epithelial cell monolayers based on step (Heaviside function) current excitation and time-domain analysis of the voltage transients, without the need for Fourier transforms. We experimentally demonstrate TEIM measuring TER, TEC, , and model-derived impedance spectrum at [~]0.3 s sampling rate, which represents a 100- fold improvement in time resolution compared with traditional EIS. The accuracy and precision of TEIM were benchmarked against EIS on both electrical circuits and epithelial cell monolayers of immortalized Human Bronchial Epithelial (16HBE) and Human Colorectal Adenocarcinoma (Caco-2) (n = 3 for each), and average percent errors for TER, TEC, and ranged from 0.17-3.55%, 1.13-8.96%, and 0.59-26.35%, respectively. Application of TEIM to monitor Caco-2 responses to saponin, a quick-acting pore-forming detergent, revealed smoothly gated double-exponential transient TER and TEC dynamics that were too rapid to be adequately captured previously using EIS. Overall, TEIM enables electrophysiology studies of rapid changes in epithelial cell culture models and possibly more complex in vitro models, holding promise for future applications in areas such as disease modeling, therapeutic development, and beyond.

bioengineering↗

bioRxiv2026

Early exposure to PFAS disrupts neuro-muscular development in zebrafish embryos

Development is a tightly regulated process that establishes body axes and orchestrates the spatial organization of tissues and organs. Although developmental programs contain inherent redundancies, they remain highly sensitive to environmental cues. Among environmental contaminants, per- and polyfluoroalkyl substances (PFAS), chemicals that resist degradation and bioaccumulate in the body, are of particular concern. These "forever chemicals" are widespread in our household products, including non-stick and waterproof materials, and drinking water remains a major source of exposure. PFAS accumulate in specific tissues and have been associated with developmental delays, childhood leukemia, and other adverse health outcomes, yet the cellular and molecular mechanisms by which they disrupt early development remain largely unknown. To address this, we employ zebrafish embryos as a New Approach Methodology (NAM) to investigate how perfluorooctanoic acid (PFOA), a prevalent environmental PFAS, alters early embryogenesis. Embryos were exposed to physiologically relevant low and high doses of PFOA and analyzed at 24 hours post-fertilization (hpf), a key stage of organogenesis. We also included a parental exposure group, in which adults were treated with PFOA and their offspring were collected to assess whether the effects of exposure were transmitted to the next generation. Developmental processes are inherently plastic, and we wanted to understand the extent to which PFOA impacts normal cellular processes as well as the redundancy in the system (different developmental signaling pathways) which ensures that an embryo develops properly. Towards this, we performed single-nucleus RNA sequencing at 24 hpf, and it revealed that neuronal and muscle tissue clusters are particularly sensitive to PFOA exposure. These molecular perturbations correspond with anxiety-like behavioral phenotypes we observed in the exposed larvae, linking early developmental disruptions to organism-level outcomes. Overall, our findings provide mechanistic insight into the way in which PFAS exposure alters development, disrupting gene expression patterns and chromatin organization in developing tissues, revealing how early molecular perturbations can give rise to long-term behavioral consequences. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=61 SRC="FIGDIR/small/700343v1_ufig1.gif" ALT="Figure 1"> View larger version (11K): org.highwire.dtl.DTLVardef@1fec69aorg.highwire.dtl.DTLVardef@1a0b3beorg.highwire.dtl.DTLVardef@17883e2org.highwire.dtl.DTLVardef@11a7571_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2021

Evidence of positive and negative selection associated with DNA methylation

Signatures of negative selection are pervasive amongst complex traits and diseases. However, it is unclear whether such signatures exist for DNA methylation (DNAm) that has been proposed to have a functional role in disease. We estimate polygenicity, SNP-based heritability and model the joint distribution of effect size and minor allele frequency (MAF) to estimate a selection coefficient (S) for 2000 heritable DNAm sites in 1774 individuals from the Avon Longitudinal Study of Parents and Children. Additionally, we estimate S for meta stable epi alleles and DNAm sites associated with aging and mortality, birthweight and body mass index. Quantification of MAF-dependent genetic architectures estimated from genotype and DNAm reveal evidence of positive (S > 0) and negative selection (S < 0) and confirm previous evidence of negative selection for birthweight. Evidence of both negative and positive selection highlights the role of DNAm as an intermediary in multiple biological pathways with competing function.

genetics↗

bioRxiv2021

Antibodies with potent and broad neutralizing activity against antigenically diverse and highly transmissible SARS-CoV-2 variants

The emergence of highly transmissible SARS-CoV-2 variants of concern (VOC) that are resistant to therapeutic antibodies highlights the need for continuing discovery of broadly reactive antibodies. We identify four receptor-binding domain targeting antibodies from three early-outbreak convalescent donors with potent neutralizing activity against 12 variants including the B.1.1.7 and B.1.351 VOCs. Two of them are ultrapotent, with sub-nanomolar neutralization titers (IC50 <0.0006 to 0.0102 g/mL; IC80 < 0.0006 to 0.0251 g/mL). We define the structural and functional determinants of binding for all four VOC-targeting antibodies, and show that combinations of two antibodies decrease the in vitro generation of escape mutants, suggesting potential means to mitigate resistance development. These results define the basis of therapeutic cocktails against VOCs and suggest that targeted boosting of existing immunity may increase vaccine breadth against VOCs. One Sentence SummaryUltrapotent antibodies from convalescent donors neutralize and mitigate resistance of SARS-CoV-2 variants of concern.

immunology↗

bioRxiv2018

Leveraging brain cortex-derived molecular data to elucidate epigenetic and transcriptomic drivers of neurological function and disease

Integrative approaches which harness large-scale molecular datasets can help develop mechanistic insight into findings from genome-wide association studies (GWAS). We have performed extensive analyses to uncover transcriptional and epigenetic processes which may play a role in neurological trait variation.\n\nThis was undertaken by applying Bayesian multiple-trait colocalization systematically across the genome to identify genetic variants responsible for influencing intermediate molecular phenotypes as well as neurological traits. In this analysis we leveraged high dimensional quantitative trait loci data derived from prefrontal cortex tissue (concerning gene expression, DNA methylation and histone acetylation) and GWAS findings for 5 neurological traits (Neuroticism, Schizophrenia, Educational Attainment, Insomnia and Alzheimers disease).\n\nThere was evidence of colocalization for 118 associations suggesting that the same underlying genetic variant influenced both nearby gene expression as well as neurological trait variation. Of these, 73 associations provided evidence that the genetic variant also influenced proximal DNA methylation and/or histone acetylation. These findings support previous evidence at loci where epigenetic mechanisms may putatively mediate effects of genetic variants on traits, such as KLC1 and schizophrenia. We also uncovered evidence implicating novel loci in neurological disease susceptibility, including genes expressed predominantly in brain tissue such as MDGA1, KIRREL3 and SLC12A5.\n\nAn inverse relationship between DNA methylation and gene expression was observed more than can be accounted for by chance, supporting previous findings implicating DNA methylation as a transcriptional repressor. Our study should prove valuable in helping future studies prioritise candidate genes and epigenetic mechanisms for in-depth functional follow-up analyses.

genetics↗