Circadian clocks are intrinsic molecular oscillators present in cells across prokaryotes and eukaryotes that synchronize physiological processes with external cues, enabling organismal adaptation and survival. These clocks regulate crucial biological functions, including sleep-wake cycles, thermoregulation, hepatic metabolism, and hormonal secretion, through the rhythmic expression of clock-controlled genes. The mammalian liver comprises structural units called lobules, with hepatocytes arranged in a hexagonal pattern along a pericentral-to-periportal axis extending from the central vein to the portal triad. Perturbations in the circadian clock network can contribute to the pathogenesis of various disorders, such as obesity, diabetes, inflammatory conditions, and certain cancers.2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is an exogenous ligand that binds to the aryl hydrocarbon receptor (AHR), eliciting diverse toxic effects by disrupting the circadian clock mechanism. To investigate whether TCDD-activated AHR disrupts the intrahepatic circadian clock by interfering with genome-wide CLOCK:BMAL1 binding, potentially leading to a reduction or loss of rhythmicity in clock-controlled genes, interpretable machine learning models were developed to predict BMAL1 binding to DNA in liver, kidney, and heart tissues using genetic and epigenetic features (binding sequence, DNA shape, and histone modifications). Thus, TCDD-activated AHR has been proposed to bind to the E-box binding motifs to disrupt the regulation of circadian clock genes. The findings demonstrated that BMAL1 binding to DNA is tissue-specific, and the combination of sequence, DNA shape, and histone modification features yielded the highest binding prediction accuracy. Additionally, the flanking sequences upstream and downstream of the binding motifs played a crucial role in BMAL1 binding to DNA. Furthermore, a spatiotemporal multicellular mathematical model of the mammalian circadian clock in the liver lobule was developed to investigate intercellular coupling for the synchronization of circadian clock expression across the portal-to-central axis. The analysis revealed that similar to the coupling of autonomous circadian oscillators in the suprachiasmatic nucleus (SCN), hepatic clock rhythms are likely synchronized by an unknown coupling factor. Sensitivity analysis, bifurcation analysis, and parameter estimation from the model provided insights into the physiology of the hepatic clock and potential mechanisms of alteration. Lastly, to understand the interplay between the spatial and temporal axes of gene expression in the liver, particularly in drug metabolism pathways, the existence of a third axis, chemical perturbation, and its implications for hepatic function were uncovered. We developed a non-linear mixed effect model to investigate the effect of acute TCDD perturbation on the spatial and temporal axes of gene expression in the liver lobule. The analysis revealed a distortion of the spatial axis of gene expression but a low significant effect on the temporal axis. These findings provide a comprehensive examination of circadian rhythms and their disruption by TCDD in the liver, encompassing molecular mechanisms, predictive modeling, and spatiotemporal dynamics. The study offers valuable insights into the intricate regulatory mechanisms governing circadian rhythms, the significance of zonation in hepatic functions, and the interplay between spatial and temporal gene expression. The findings have the potential to contribute significantly to our understanding of circadian resilience and the mitigation of pathological conditions, particularly in the context of drug metabolism pathways and hepatic function.
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