Modeling calcium signaling dynamics in the liver: from single cell to multi-scale
Date
2019
Authors
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Journal ISSN
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Publisher
University of Delaware
Abstract
Free Ca2+ within the intracellular compartments plays a vital role in regulating a wide array of hepatocyte functions such as glucose metabolism, bile secretion, proliferation, and apoptosis. Ca2+ agonists in the blood stream evoke cytosolic Ca2+ spikes in individual hepatocytes. Under circulating stimuli, hepatocytes in liver lobules exhibit spatially organized, sequential spiking, which propagate through liver lobules in a wave-like fashion. Ca2+ waves are hypothesized to synchronize hepatocyte response to extracellular stimuli throughout liver lobules and coordinate intracellular processes at the lobular scale. Wave-like propagation of Ca2+ signals in the liver lobules is shaped by a combination of systemic signals, lobular morphology, zonation and intercellular communication. Disruption of intra- and intercellular Ca2+ signaling dynamics are associated with pathological conditions such as cholestasis and metabolic syndrome. ☐ Although Ca2+ dynamics and their features have been studied extensively, the understanding of how the spatial organization of intracellular Ca2+ signaling components and the intercellular interactions that regulate lobular-scale Ca2+ signal propagation and hepatic function remains incomplete. Furthermore, how inherent lobular heterogeneity and inter-hepatocyte communication affect the whole body through multi-organ interactions remains poorly investigated. ☐ In this thesis, we present a combined computational modeling and high throughput data analysis approach towards exploring Ca2+ signaling and its effects different spatial scales – single cell, liver lobule, and multi-organ. Current technologies have enabled the study of hepatic function at the cellular and tissue level in great detail. However, experimental procedures that can simultaneously elucidate the combinatorial effects of structure-function relationships of hepatocytes within the complex lobular organization, single cell and lobular scale Ca2+ dynamics, and multi-organ interactions on short time scale signaling events such as intracellular signaling cascades and protein function regulation are lacking. Computational modeling and high throughput data analysis serve as ideal tools to investigate complex biological processes across different spatial and temporal scales and generate experimentally testable hypotheses. We therefore adopted a combined ODE-based dynamic cell network modeling and data-driven analysis to identify spatial features of lobular scale Ca2+ signal propagation and its effects on the whole organism. ☐ We first developed a computational model for Ca2+ spiking in single cells that captures dynamic features of cytosolic Ca2+ signaling observed experimentally. We analyzed this model of the single cell Ca2+ spiking model to identify the relative effects of extracellular stimulus and intracellular Ca2+ signaling components on Ca2+ spiking response in hepatocytes. Our analysis pointed towards a greater role of cell-intrinsic Ca2+ signaling machinery in regulating intracellular Ca2+ spiking frequency as compared to extracellular stimulus. ☐ We extended this single hepatocyte model to the lobular context by incorporating gap junction-mediated molecular exchange between adjacent hepatocytes. Simulations of our lobular scale model revealed that gap junction coupling overrides cell-to-cell heterogeneity in Ca2+ response in heterogeneous cells and synchronizes intracellular Ca2+ spikes across liver lobules. We next explored the effects of organized spatial heterogeneity in shaping lobular scale Ca2+ signal propagation. Our simulations revealed that spatially organized gradients of intracellular Ca2+ signaling components in liver lobules lead to wave-like propagation of Ca2+ signals. Our simulations also showed that enhanced gap junction coupling can rescue lobular scale function through neighbor-driven induction of Ca2+ spiking in hepatocytes that exhibit aberrant Ca2+ signaling. ☐ We next used a data-driven approach to identify the features of lobular morphology and cell-cell contacts on Ca2+ signal propagation in liver lobules. We used transfer entropy, information theoretic measures of directed information transfer, to identify causal networks between hepatocytes in a high throughput imaging dataset acquired by exposure of intact, perfused mouse livers to vasopressin. Our analysis revealed that liver lobules are divided into causally connected sub-domains even though Ca2+ signal is experimentally observed to propagate through entire liver lobules in a wave-like fashion. Within these “Ca2+ active” sub-domains, hepatocytes showed heterogeneity in number of co-localized hepatocytes they are causally connected with. Additionally, causal information flow between hepatocyte pairs within the Ca2+ active subdomains are not consistently aligned in a unidirectional fashion. We hypothesized that these observations could be due to complex organization of hepatocytes in lobules, noisy spatial gradients of intracellular Ca2+ signaling components, and heterogeneity in intercellular communication. We projected the findings of this analysis on lobular scale Ca2+ signal propagation using computational modeling. Our simulations revealed that despite noisy gradients and heterogeneity of cell-cell communication, Ca2+ waves propagate through liver lobules. Furthermore, the multiplicity of causal connections makes lobular scale Ca2+ signal propagation robust. ☐ We next explored the significance of inter-hepatocyte communication in the whole-body context. We developed a multi-scale, multi-organ model of hepatic metabolism incorporating intracellular metabolism, liver zonation, lobular scale Ca2+ signaling by systemic hormones, hepatic innervation, and direct and peripheral organ-mediated communication between the liver and the central nervous system. We focused our model simulations on the analysis of hepatic glucose output – a Ca2+ dependent process, under periods of high systemic glycemic demand. Our model simulations showed that coordination of Ca2+ signaling across liver lobules by intercellular communication and subsequent synchronization of downstream metabolic processes enhance hepatic glucose production rates. ☐ Although intercellular communication and homogeneity of response on short time scales is crucial for hepatic function, long term exposure to perturbations can alter intracellular function permanently. These are reflected in changes in single cell molecular states, defined by mRNA and protein content. Analysis of heterogeneity in molecular states of cell populations can reveal valuable information about the mechanisms that underlie aberrant function under pathological conditions. We acquired and analyzed a high throughput single cell transcriptomic data set to characterize single hepatocyte molecular states in acute liver injury and chronic alcohol adaptation in the context of liver regeneration. Liver regeneration is suppressed in chronic alcohol adapted livers. Our analysis revealed that although single hepatocyte belonged to the same set of molecular states irrespective of perturbation, their proportions in these molecular states were perturbation dependent. Based on functional classification of molecular states, our analysis suggested that hepatocytes in chronic ethanol adapted livers exhibit slower progression through cell cycle, which likely leads to suppressed liver regeneration.