Studies on mechanisms of interferon-gamma action in pancreatic cancer using a data-driven and model-based approach

<p>Abstract</p> <p>Background</p> <p>Interferon-gamma (IFNγ) is a multifunctional cytokine with antifibrotic and antiproliferative efficiency. We previously found that pancreatic stellate cells (PSC), the main effector cells in cancer-associated fibrosis, are targets of IFNγ action in the pancreas. Applying a combined experimental and computational approach, we have demonstrated a pivotal role of STAT1 in IFNγ signaling in PSC. Using <it>in vivo </it>and <it>in vitro </it>models of pancreatic cancer, we have now studied IFNγ effects on the tumor cells themselves. We hypothesize that IFNγ inhibits tumor progression through two mechanisms, reduction of fibrogenesis and antiproliferative effects on the tumor cells. To elucidate the molecular action of IFNγ, we have established a mathematical model of STAT1 activation and combined experimental studies with computer simulations.</p> <p>Results</p> <p>In BALB/c-<it>nu/nu </it>mice, flank tumors composed of DSL-6A/C1 pancreatic cancer cells and PSC grew faster than pure DSL-6A/C1 cell tumors. IFNγ inhibited the growth of both types of tumors to a similar degree. Since the stroma reaction typically reduces the efficiency of therapeutic agents, these data suggested that IFNγ may retain its antitumor efficiency in PSC-containing tumors by targeting the stellate cells. Studies with cocultures of DSL-6A/C1 cells and PSC revealed a modest antiproliferative effect of IFNγ under serum-free conditions. Immunoblot analysis of STAT1 phosphorylation and confocal microscopy studies on the nuclear translocation of STAT1 in DSL-6A/C1 cells suggested that IFNγ-induced activation of the transcription factor was weaker than in PSC. The mathematical model not only reproduced the experimental data, but also underscored the conclusions drawn from the experiments by indicating that a maximum of 1/500 of total STAT1 is located as phosphorylated STAT1 in the nucleus upon IFNγ treatment of the tumor cells.</p> <p>Conclusions</p> <p>IFNγ is equally effective in DSL-6A/C1 tumors with and without stellate cells. While its action in the presence of PSC may be explained by inhibition of fibrogenesis, its efficiency in PSC-free tumors is unlikely to be caused by direct effects on the tumor cells alone but may involve inhibitory effects on local stroma cells as well. To gain further insights, we also plan to apply computer simulations to the analysis of tumor growth <it>in vivo</it>.</p

Longitudinal claudin gene expression analyses in canine mammary tissues and thereof derived primary cultures and cell lines

Human and canine mammary tumours show partial claudin expression deregulations. Further, claudins have been used for directed therapeutic approaches. However, the development of claudin targeting approaches requires stable claudin expressing cell lines. This study reports the establishment and characterisation of canine mammary tissue derived cell lines, analysing longitudinally the claudin-1, -3, -4 and -7 expressions in original tissue samples, primary cultures and developed cell lines. Primary cultures were derived from 17 canine mammary tissues: healthy, lobular hyperplasia, simple adenoma, complex adenoma, simple tubular carcinoma, complex carcinoma, carcinoma arising in a benign mixed tumour and benign mixed tissue. Cultivation was performed, if possible, until passage 30. Claudin mRNA and protein expressions were analysed by PCR, QuantiGene Plex Assay, immunocytochemistry and immunofluorescence. Further, cytokeratin expression was analysed immunocytochemically. Cultivation resulted in 11 established cell lines, eight showing epithelial character. In five of the early passages the claudin expressions decreased compared to the original tissues. In general, claudin expressions were diminished during cultivation. Three cell lines kept longitudinally claudin, as well as epithelial marker expressions, representing valuable tools for the development of claudin targeted anti-tumour therapies

Enabling multiscale modeling in systems medicine

CITATION: Wolkenhauer, O. et al. 2014. Enabling multiscale modeling in systems medicine. Genome Medicine, 6:21, doi:10.1186/gm538.The original publication is available at http://genomemedicine.biomedcentral.com[See article for abstract].Publisher's versio

Enabling multiscale modeling in systems medicine: From reactions in cells to organ physiology

International audienceSystems medicine is an interdisciplinary approach that integrates data from basic research and clinical practice to improve our understanding and treatment of diseases. Systems medicine can be seen as a further development of systems biology and bioinformatics towards applica-tions of clinical relevance. The term 'systems' refers to systems approaches, emphasizing a close integration of data generation with mathematical modeling [1-3]. The (mal)functioning of the human body is a complex process, characterized by multiple interactions between systems that act across multiple levels of structural and functional organization -from molecular reactions to cell-cell interac-tions in tissues to the physiology of organs and organ systems. Over the past decade, we have gained detailed insights into the structure and function of molecular, cellu-lar and organ-level systems, with technologies playing an important role in the generation of data at these different scales

Symbolic dynamics, entropy and complexity of the feigenbaum map at the accumulation point

This paper aims to make further contributions to the exploration of the symbolic dynamics generated by the logistic map at Feigenbaum accumulation point. In particular we are interested in the grammar of these sequences; completing earlier studies we study here arbitrary partitions also. Our main aim is the investigation of the special grammars which characterize the long-range correlations between letters. Considering these sequences as standard examples of a complex system, we introduce and discuss a complexity function derived from the conditional entropies. Further we discuss local predictabilities

Entropy analysis of noise contaminated sequences

The entropy analysis of symbol sequences created by symbolic dynamics reveals temporal correlations present in the stationary dynamics. We investigate how noise, introduced in different ways, affects temporal correlations found in the logistic map at the period doubling accumulation point. The deterministic system under consideration yields a highly structured spectrum of conditional entropies. We will discuss how additive noise, parametric noise, a fluctuating cell boundary and a noisy transmission channel modify the unperturbed entropy spectrum.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

Thermostating by deterministic scattering: the periodic Lorentz gas

info:eu-repo/semantics/publishe

Nucleo-cytoplasmic shuttling of APC can maximize β-catenin/TCF concentration

International audienceβ-catenin is the key player of the canonical Wnt pathway. Its activity is mainly regulated via protein degradation. In the nucleus, its interaction with TCF initiates target gene expression. Although the functional relevance is unclear, it has been shown that β-catenin antagonists are also capable of nucleo-cytoplasmic shuttling. The focus of our systems biology analysis lies on the β-catenin subcellular distribution regulated by the antagonist and scaffolding protein APC. We address the following questions: Can the concentration of the transcription factor complex [β-catenin/TCF], which is considered as the output of the pathway, be maximized by APC nucleo-cytoplasmic shuttling and how is retention of β-catenin by APC influencing this output? We established a mathematical model based on experimental findings to examine the influence of nucleo-cytoplasmic shuttling of APC and retention of β-catenin by APC on the output of the pathway. The model is based on ordinary differential equations and includes protein shuttling between the two compartments nucleus and cytoplasm as well as protein complex formation in each compartment. We discuss how the steady state concentration of [β-catenin/TCF] is influenced by APC shuttling and retention. The analysis of the model shows that the breakdown of β- catenin cytoplasmic retention induced by APC shuttling can enhance nuclear accumulation of β-catenin and hence maximize the output of the pathway. Using mathematical modelling, we demonstrate that in certain parameter ranges, the steady state concentration of [β-catenin/TCF] benefits from APC shuttling. The inhibitory effect of APC is alleviated due to shuttling of APC. Surprisingly, our study therefore indicates that the nucleo-cytoplasmic shuttling of APC can have a beneficial effect on the output of the pathway in steady state, although APC is in general a β-catenin antagonizing protein. Furthermore, we show that saturated protein translocation can under certain conditions be modelled by pure diffusion. A difference in the shuttling rate constants of sufficient orders of magnitude leads to an accumulation in either compartment, which corresponds to saturation in translocation

Anti-inflammatory effects of reactive oxygen species : a multi-valued logical model validated by formal concept analysis

CITATION: Wollbold, J. et al. 2015. Anti-inflammatory effects of reactive oxygen species : a multi-valued logical model validated by formal concept analysis. BMC Systems Biology, 8:101, doi:10.1186/s12918-014-0101-7.The original publication is available at http://bmcsystbiol.biomedcentral.comBackground: Recent findings suggest that in pancreatic acinar cells stimulated with bile acid, a pro-apoptotic effect of reactive oxygen species (ROS) dominates their effect on necrosis and spreading of inflammation. The first effect presumably occurs via cytochrome C release from the inner mitochondrial membrane. A pro-necrotic effect – similar to the one of Ca2+ – can be strong opening of mitochondrial pores leading to breakdown of the membrane potential, ATP depletion, sustained Ca2+ increase and premature activation of digestive enzymes. To explain published data and to understand ROS effects during the onset of acute pancreatitis, a model using multi-valued logic is constructed. Formal concept analysis (FCA) is used to validate the model against data as well as to analyze and visualize rules that capture the dynamics. Results: Simulations for two different levels of bile stimulation and for inhibition or addition of antioxidants reproduce the qualitative behaviour shown in the experiments. Based on reported differences of ROS production and of ROS induced pore opening, the model predicts a more uniform apoptosis/necrosis ratio for higher and lower bile stimulation in liver cells than in pancreatic acinar cells. FCA confirms that essential dynamical features of the data are captured by the model. For instance, high necrosis always occurs together with at least a medium level of apoptosis. At the same time, FCA helps to reveal subtle differences between data and simulations. The FCA visualization underlines the protective role of ROS against necrosis. Conclusions: The analysis of the model demonstrates how ROS and decreased antioxidant levels contribute to apoptosis. Studying the induction of necrosis via a sustained Ca2+ increase, we implemented the commonly accepted hypothesis of ATP depletion after strong bile stimulation. Using an alternative model, we demonstrate that this process is not necessary to generate the dynamics of the measured variables. Opening of plasma membrane channels could also lead to a prolonged increase of Ca2+ and to necrosis. Finally, the analysis of the model suggests a direct experimental testing for the model-based hypothesis of a self-enhancing cycle of cytochrome C release and ROS production by interruption of the mitochondrial electron transport chain.http://bmcsystbiol.biomedcentral.com/articles/10.1186/s12918-014-0101-7Publisher's versio