Dataset Information

Causality Analysis and Cell Network Modeling of Spatial Calcium Signaling Patterns in Liver Lobules.

ABSTRACT: Dynamics as well as localization of Ca²⁺ transients plays a vital role in liver function under homeostatic conditions, repair, and disease. In response to circulating hormonal stimuli, hepatocytes exhibit intracellular Ca²⁺ responses that propagate through liver lobules in a wave-like fashion. Although intracellular processes that control cell autonomous Ca²⁺ spiking behavior have been studied extensively, the intra- and inter-cellular signaling factors that regulate lobular scale spatial patterns and wave-like propagation of Ca²⁺ remain to be determined. To address this need, we acquired images of cytosolic Ca²⁺ transients in 1300 hepatocytes situated across several mouse liver lobules over a period of 1600 s. We analyzed this time series data using correlation network analysis, causal network analysis, and computational modeling, to characterize the spatial distribution of heterogeneity in intracellular Ca²⁺ signaling components as well as intercellular interactions that control lobular scale Ca²⁺ waves. Our causal network analysis revealed that hepatocytes are causally linked to multiple other co-localized hepatocytes, but these influences are not necessarily aligned uni-directionally along the sinusoids. Our computational model-based analysis showed that spatial gradients of intracellular Ca²⁺ signaling components as well as intercellular molecular exchange are required for lobular scale propagation of Ca²⁺ waves. Additionally, our analysis suggested that causal influences of hepatocytes on Ca²⁺ responses of multiple neighbors lead to robustness of Ca²⁺ wave propagation through liver lobules.

SUBMITTER: Verma A

PROVIDER: S-EPMC6180170 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Causality Analysis and Cell Network Modeling of Spatial Calcium Signaling Patterns in Liver Lobules.

Verma Aalap A Antony Anil Noronha AN Ogunnaike Babatunde A BA Hoek Jan B JB Vadigepalli Rajanikanth R

Frontiers in physiology 20181004

Dynamics as well as localization of Ca2+ transients plays a vital role in liver function under homeostatic conditions, repair, and disease. In response to circulating hormonal stimuli, hepatocytes exhibit intracellular Ca2+ responses that propagate through liver lobules in a wave-like fashion. Although intracellular processes that control cell autonomous Ca2+ spiking behavior have been studied extensively, the intra- and inter-cellular signaling factors that regu ...[more]

PMID: 30337879

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Project description:Expression profiles of 22 reference Arabidopsis immunity mutants were collected using the Arabidopsis Pathoarray 464_001 (GPL3638) in order to build a network model predicting the Arabidopsis immune signaling network. Biological signaling processes may be mediated by complex networks in which network components and network sectors interact with each other in complex ways. Studies of complex networks benefit from approaches in which the roles of individual components are considered in the context of the network. The plant immune signaling network, which controls inducible responses to pathogen attack, is such a complex network. Here, we demonstrate that use of mRNA profiling to collect and analyze detailed descriptions of changes in the network state resulting from specific network perturbations is a powerful and economical strategy to elucidate regulatory relationships among the components of a complex signaling network. Specifically, we studied the Arabidopsis immune signaling network upon challenge with a strain of the bacterial pathogen Pseudomonas syringae expressing the effector protein AvrRpt2 (Pto DC3000 AvrRpt2). This bacterial strain feeds multiple inputs into the signaling network, allowing many parts of the network to be activated at once. mRNA profiles of 22 Arabidopsis immunity mutants and wild type were collected 6 hours after inoculation with the Pto DC3000 AvrRpt2 and used as detailed descriptions of the network states resulting from specific genetic perturbations. Regulatory relationships among the genes corresponding to the mutations were inferred by recursively applying a non-linear dimensionality reduction procedure to the mRNA profile data. The resulting network model accurately predicted 22 of 23 regulatory relationships reported in the literature, suggesting that predictions of novel regulatory relationships are also accurate. The network model revealed two striking features: (i) the components of the network are highly interconnected; (ii) negative regulatory relationships are common between signaling sectors. One case of a novel negative regulatory relationship, between the early microbe-associated molecular pattern (MAMP)-activated sector and the salicylic acid (SA)-mediated sector, was further validated. We propose that prevalent negative regulatory relationships among the signaling sectors make the plant immune signaling network a "sector-switching" network, which effectively balances two apparently conflicting demands, robustness against pathogenic perturbations and moderation of negative impacts of immune responses on plant fitness. Keywords: Responses of reference Arabidopsis immunity mutants to Pseudomonas syringae pv. tomato DC3000 carrying avrRpt2 This experiment consists of two (group00) or three (group01-04) biological replicates of each genotype (total 25 genotypes [3 are multiple mutants, which were removed for the network modeling, but were used for normalization]). For each genotype, two leaves per plant were pooled from three pots to prepare total RNA.

Dataset Information

Causality Analysis and Cell Network Modeling of Spatial Calcium Signaling Patterns in Liver Lobules.

Publications

Causality Analysis and Cell Network Modeling of Spatial Calcium Signaling Patterns in Liver Lobules.

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