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Basílio J, Hochreiter B, Hoesel B, Sheshori E, Mussbacher M, Hanel R, Schmid JA. Antagonistic Functions of Androgen Receptor and NF-κB in Prostate Cancer-Experimental and Computational Analyses. Cancers (Basel) 2022; 14:cancers14246164. [PMID: 36551650 PMCID: PMC9776608 DOI: 10.3390/cancers14246164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 12/15/2022] Open
Abstract
Prostate cancer is very frequent and is, in many countries, the third-leading cause of cancer related death in men. While early diagnosis and treatment by surgical removal is often curative, metastasizing prostate cancer has a very bad prognosis. Based on the androgen-dependence of prostate epithelial cells, the standard treatment is blockade of the androgen receptor (AR). However, nearly all patients suffer from a tumor relapse as the metastasizing cells become AR-independent. In our study we show a counter-regulatory link between AR and NF-κB both in human cells and in mouse models of prostate cancer, implying that inhibition of AR signaling results in induction of NF-κB-dependent inflammatory pathways, which may even foster the survival of metastasizing cells. This could be shown by reporter gene assays, DNA-binding measurements, and immune-fluorescence microscopy, and furthermore by a whole set of computational methods using a variety of datasets. Interestingly, loss of PTEN, a frequent genetic alteration in prostate cancer, also causes an upregulation of NF-κB and inflammatory activity. Finally, we present a mathematical model of a dynamic network between AR, NF-κB/IκB, PI3K/PTEN, and the oncogene c-Myc, which indicates that AR blockade may upregulate c-Myc together with NF-κB, and that combined anti-AR/anti-NF-κB and anti-PI3K treatment might be beneficial.
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Affiliation(s)
- José Basílio
- Center for Physiology and Pharmacology, Institute of Vascular Biology and Thrombosis Research, Medical University Vienna, Schwarzspanierstraße 17, 1090 Vienna, Austria
- INESC ID—Instituto de Engenharia de Sistemas e Computadores, Investigação e Desenvolvimento em Lisboa, Universidade de Lisboa, Rua Alves Redol 9, 1000-029 Lisboa, Portugal
| | - Bernhard Hochreiter
- Center for Physiology and Pharmacology, Institute of Vascular Biology and Thrombosis Research, Medical University Vienna, Schwarzspanierstraße 17, 1090 Vienna, Austria
| | - Bastian Hoesel
- Center for Physiology and Pharmacology, Institute of Vascular Biology and Thrombosis Research, Medical University Vienna, Schwarzspanierstraße 17, 1090 Vienna, Austria
| | - Emira Sheshori
- Center for Physiology and Pharmacology, Institute of Vascular Biology and Thrombosis Research, Medical University Vienna, Schwarzspanierstraße 17, 1090 Vienna, Austria
| | - Marion Mussbacher
- Center for Physiology and Pharmacology, Institute of Vascular Biology and Thrombosis Research, Medical University Vienna, Schwarzspanierstraße 17, 1090 Vienna, Austria
- Department of Pharmacology and Toxicology, University of Graz, 8010 Graz, Austria
| | - Rudolf Hanel
- Complexity Science Hub Vienna, Josefstaedter Strasse 39, 1080 Vienna, Austria
- Section for Science of Complex Systems, Medical University of Vienna, Spitalgasse 23, 1090 Vienna, Austria
| | - Johannes A. Schmid
- Center for Physiology and Pharmacology, Institute of Vascular Biology and Thrombosis Research, Medical University Vienna, Schwarzspanierstraße 17, 1090 Vienna, Austria
- Correspondence: ; Tel.: +43-1-40160-31155
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Gecow A, Iantovics LB, Tez M. Cancer and Chaos and the Complex Network Model of a Multicellular Organism. BIOLOGY 2022; 11:biology11091317. [PMID: 36138796 PMCID: PMC9495805 DOI: 10.3390/biology11091317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 08/14/2022] [Accepted: 08/30/2022] [Indexed: 11/28/2022]
Abstract
Simple Summary Currently, knowledge on chaos has developed rapidly, and the link between cancer and “genomic chaos” seems obvious. Hopes for a deeper understanding of cancer, allowing cancer modeling, therefore relate to the meaning of the term “chaos”. It has many meanings, however. Chaos theory and medicine are conceptually quite distant, requiring the comparison and agreement of terms. This article was written by three authors whose fields cover both medical problems and complex dynamic networks suitable for modeling cancer, including chaotic phenomena. The article provides, first of all, a coherent, common interpretative basis linking chaos with modeling tools, which should significantly facilitate teams of specialists from various fields to undertake specific work on simulating cancer-related phenomena. Abstract In the search of theoretical models describing cancer, one of promising directions is chaos. It is connected to ideas of “genome chaos” and “life on the edge of chaos”, but they profoundly differ in the meaning of the term “chaos”. To build any coherent models, notions used by both ideas should be firstly brought closer. The hypothesis “life on the edge of chaos” using deterministic chaos has been radically deepened developed in recent years by the discovery of half-chaos. This new view requires a deeper interpretation within the range of the cell and the organism. It has impacts on understanding “chaos” in the term “genome chaos”. This study intends to present such an interpretation on the basis of which such searches will be easier and closer to intuition. We interpret genome chaos as deterministic chaos in a large module of half-chaotic network modeling the cell. We observed such chaotic modules in simulations of evolution controlled by weaker variant of natural selection. We also discuss differences between free and somatic cells in modeling their disturbance using half-chaotic networks.
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Affiliation(s)
| | - Laszlo Barna Iantovics
- Electrical Engineering and Information Technology, Engineering and Information Technology, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Targu Mures, 540139 Târgu Mureș, Romania
- Correspondence:
| | - Mesut Tez
- Ankara Numune Training and Research Hospital, 06100 Ankara, Turkey
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Rabajante JF, Babierra AL. Branching and oscillations in the epigenetic landscape of cell-fate determination. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 117:240-249. [DOI: 10.1016/j.pbiomolbio.2015.01.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 01/05/2015] [Accepted: 01/18/2015] [Indexed: 12/15/2022]
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Tran V, McCall MN, McMurray HR, Almudevar A. On the underlying assumptions of threshold Boolean networks as a model for genetic regulatory network behavior. Front Genet 2013; 4:263. [PMID: 24376454 PMCID: PMC3859184 DOI: 10.3389/fgene.2013.00263] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2013] [Accepted: 11/15/2013] [Indexed: 11/13/2022] Open
Abstract
Boolean networks (BoN) are relatively simple and interpretable models of gene regulatory networks. Specifying these models with fewer parameters while retaining their ability to describe complex regulatory relationships is an ongoing methodological challenge. Additionally, extending these models to incorporate variable gene decay rates, asynchronous gene response, and synergistic regulation while maintaining their Markovian nature increases the applicability of these models to genetic regulatory networks (GRN). We explore a previously-proposed class of BoNs characterized by linear threshold functions, which we refer to as threshold Boolean networks (TBN). Compared to traditional BoNs with unconstrained transition functions, these models require far fewer parameters and offer a more direct interpretation. However, the functional form of a TBN does result in a reduction in the regulatory relationships which can be modeled. We show that TBNs can be readily extended to permit self-degradation, with explicitly modeled degradation rates. We note that the introduction of variable degradation compromises the Markovian property fundamental to BoN models but show that a simple state augmentation procedure restores their Markovian nature. Next, we study the effect of assumptions regarding self-degradation on the set of possible steady states. Our findings are captured in two theorems relating self-degradation and regulatory feedback to the steady state behavior of a TBN. Finally, we explore assumptions of synchronous gene response and asynergistic regulation and show that TBNs can be easily extended to relax these assumptions. Applying our methods to the budding yeast cell-cycle network revealed that although the network is complex, its steady state is simplified by the presence of self-degradation and lack of purely positive regulatory cycles.
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Affiliation(s)
- Van Tran
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center Rochester, NY, USA
| | - Matthew N McCall
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center Rochester, NY, USA
| | - Helene R McMurray
- Department of Biomedical Genetics, University of Rochester Medical Center Rochester, NY, USA
| | - Anthony Almudevar
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center Rochester, NY, USA
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Biondo AE, Pluchino A, Rapisarda A, Helbing D. Reducing financial avalanches by random investments. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 88:062814. [PMID: 24483518 DOI: 10.1103/physreve.88.062814] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Indexed: 06/03/2023]
Abstract
Building on similarities between earthquakes and extreme financial events, we use a self-organized criticality-generating model to study herding and avalanche dynamics in financial markets. We consider a community of interacting investors, distributed in a small-world network, who bet on the bullish (increasing) or bearish (decreasing) behavior of the market which has been specified according to the S&P 500 historical time series. Remarkably, we find that the size of herding-related avalanches in the community can be strongly reduced by the presence of a relatively small percentage of traders, randomly distributed inside the network, who adopt a random investment strategy. Our findings suggest a promising strategy to limit the size of financial bubbles and crashes. We also obtain that the resulting wealth distribution of all traders corresponds to the well-known Pareto power law, while that of random traders is exponential. In other words, for technical traders, the risk of losses is much greater than the probability of gains compared to those of random traders.
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Affiliation(s)
- Alessio Emanuele Biondo
- Dipartimento di Economia e Impresa, Universitá di Catania, Corso Italia 55, 95129 Catania, Italy
| | - Alessandro Pluchino
- Dipartimento di Fisica e Astronomia, Universitá di Catania and INFN sezione di Catania, Via S. Sofia 64, 95123 Catania, Italy
| | - Andrea Rapisarda
- Dipartimento di Fisica e Astronomia, Universitá di Catania and INFN sezione di Catania, Via S. Sofia 64, 95123 Catania, Italy
| | - Dirk Helbing
- ETH Zurich, Clausiustrasse 50, 8092 Zurich, Switzerland
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Stationary distribution of self-organized states and biological information generation. Sci Rep 2013; 3:3329. [PMID: 24281357 PMCID: PMC3839033 DOI: 10.1038/srep03329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 11/08/2013] [Indexed: 11/08/2022] Open
Abstract
Self-organization, where spontaneous orderings occur under driven conditions, is one of the hallmarks of biological systems. We consider a statistical mechanical treatment of the biased distribution of such organized states, which become favored as a result of their catalytic activity under chemical driving forces. A generalization of the equilibrium canonical distribution describes the stationary state, which can be used to model shifts in conformational ensembles sampled by an enzyme in working conditions. The basic idea is applied to the process of biological information generation from random sequences of heteropolymers, where unfavorable Shannon entropy is overcome by the catalytic activities of selected genes. The ordering process is demonstrated with the genetic distance to a genotype with high catalytic activity as an order parameter. The resulting free energy can have multiple minima, corresponding to disordered and organized phases with first-order transitions between them.
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Eukaryotic mRNA decay: methodologies, pathways, and links to other stages of gene expression. J Mol Biol 2013; 425:3750-75. [PMID: 23467123 DOI: 10.1016/j.jmb.2013.02.029] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 02/24/2013] [Accepted: 02/26/2013] [Indexed: 01/15/2023]
Abstract
mRNA concentration depends on the balance between transcription and degradation rates. On both sides of the equilibrium, synthesis and degradation show, however, interesting differences that have conditioned the evolution of gene regulatory mechanisms. Here, we discuss recent genome-wide methods for determining mRNA half-lives in eukaryotes. We also review pre- and posttranscriptional regulons that coordinate the fate of functionally related mRNAs by using protein- or RNA-based trans factors. Some of these factors can regulate both transcription and decay rates, thereby maintaining proper mRNA homeostasis during eukaryotic cell life.
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Broderick G, Craddock TJA. Systems biology of complex symptom profiles: capturing interactivity across behavior, brain and immune regulation. Brain Behav Immun 2013; 29:1-8. [PMID: 23022717 PMCID: PMC3554865 DOI: 10.1016/j.bbi.2012.09.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2012] [Revised: 09/13/2012] [Accepted: 09/14/2012] [Indexed: 12/15/2022] Open
Abstract
As our thinking about the basic principles of biology and medicine continue to evolve, the importance of context and regulatory interaction is becoming increasingly obvious. Biochemical and physiological components do not exist in isolation but instead are part of a tightly integrated network of interacting elements that ensure robustness and support the emergence of complex behavior. This integration permeates all levels of biology from gene regulation, to immune cell signaling, to coordinated patterns of neuronal activity and the resulting psychosocial interaction. Systems biology is an emerging branch of science that sits as a translational catalyst at the interface of the life and computational sciences. While there is no universally accepted definition of systems biology, we attempt to provide an overview of some the basic unifying concepts and current efforts in the field as they apply to illnesses where brain and subsequent behavior are a chief component, for example autism, schizophrenia, depression, and others. Methods in this field currently constitute a broad mosaic that stretches across multiple scales of biology and physiological compartments. While this work by no means constitutes an exhaustive list of all these methods, this work highlights the principal sub-disciplines presently driving the field as well as future directions of progress.
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Affiliation(s)
- Gordon Broderick
- Department of Medicine, University of Alberta, Edmonton, Canada.
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Pluchino A, Rapisarda A, Tsallis C. Noise, synchrony, and correlations at the edge of chaos. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 87:022910. [PMID: 23496594 DOI: 10.1103/physreve.87.022910] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 01/23/2013] [Indexed: 06/01/2023]
Abstract
We study the effect of a weak random additive noise in a linear chain of N locally coupled logistic maps at the edge of chaos. Maps tend to synchronize for a strong enough coupling, but if a weak noise is added, very intermittent fluctuations in the returns time series are observed. This intermittency tends to disappear when noise is increased. Considering the probability distribution functions (pdfs) of the returns, we observe the emergence of fat tails which can be satisfactorily reproduced by q-Gaussians' curves typical of nonextensive statistical mechanics. The interoccurrence times of these extreme events are also studied in detail. Similarities with the recent analysis of financial data are also discussed.
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Affiliation(s)
- Alessandro Pluchino
- Dipartimento di Fisica e Astronomia, Università di Catania and Istituto Nazionale di Fisica Nucleare sezione di Catania, Via S. Sofia 64, 95123 Catania, Italy
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