Pinning Control for the p53-Mdm2 Network Dynamics Regulated by p14ARF

p53 regulates the cellular response to genotoxic damage and prevents carcinogenic events. Theoretical and experimental studies state that the p53-Mdm2 network constitutes the core module of regulatory interactions activated by cellular stress induced by a variety of signaling pathways. In this paper, a strategy to control the p53-Mdm2 network regulated by p14ARF is developed, based on the pinning control technique, which consists into applying local feedback controllers to a small number of nodes (pinned ones) in the network. Pinned nodes are selected on the basis of their importance level in a topological hierarchy, their degree of connectivity within the network, and the biological role they perform. In this paper, two cases are considered. For the first case, the oscillatory pattern under gamma-radiation is recovered; afterward, as the second case, increased expression of p53 level is taken into account. For both cases, the control law is applied to p14ARF (pinned node based on a virtual leader methodology), and overexpressed Mdm2-mediated p53 degradation condition is considered as carcinogenic initial behavior. The approach in this paper uses a computational algorithm, which opens an alternative path to understand the cellular responses to stress, doing it possible to model and control the gene regulatory network dynamics in two different biological contexts. As the main result of the proposed control technique, the two mentioned desired behaviors are obtained.

[1]  Galit Lahav,et al.  Stimulus-dependent dynamics of p53 in single cells , 2011, Molecular systems biology.

[2]  Didier Lime,et al.  Hybrid Modelling and Dynamical Analysis of Gene Regulatory Networks with Delays , 2007, Complexus.

[3]  Voon Yee-Lin,et al.  Nutlin-3, A p53-Mdm2 Antagonist for Nasopharyngeal Carcinoma Treatment , 2018, Mini reviews in medicinal chemistry.

[4]  Frank L. Lewis,et al.  Cooperative Control of Multi-Agent Systems: Optimal and Adaptive Design Approaches , 2013 .

[5]  J. Elf,et al.  Probing Transcription Factor Dynamics at the Single-Molecule Level in a Living Cell , 2007, Science.

[6]  Arnold Kristjuhan,et al.  ARF and ATM/ATR cooperate in p53-mediated apoptosis upon oncogenic stress. , 2005, Biochemical and biophysical research communications.

[7]  L. Vassilev,et al.  In Vivo Activation of the p53 Pathway by Small-Molecule Antagonists of MDM2 , 2004, Science.

[8]  Ting Chen,et al.  Modeling Gene Expression with Differential Equations , 1998, Pacific Symposium on Biocomputing.

[9]  Wen-Xu Wang,et al.  Modeling and controlling the two-phase dynamics of the p53 network: a Boolean network approach , 2014 .

[10]  Andrea Ciliberto,et al.  Steady States and Oscillations in the p53/Mdm2 Network , 2005, Cell cycle.

[11]  Y. Shav-Tal,et al.  Dynamics of single mRNP nucleocytoplasmic transport and export through the nuclear pore in living cells , 2010, Nature Cell Biology.

[12]  K. Vousden,et al.  Stress Signals Utilize Multiple Pathways To Stabilize p53 , 2000, Molecular and Cellular Biology.

[13]  Ettore Appella,et al.  p300/CBP‐mediated p53 acetylation is commonly induced by p53‐activating agents and inhibited by MDM2 , 2001, The EMBO journal.

[14]  Guy Karlebach,et al.  Modelling and analysis of gene regulatory networks , 2008, Nature Reviews Molecular Cell Biology.

[15]  Charles J. Sherr,et al.  Nucleolar Arf sequesters Mdm2 and activates p53 , 1999, Nature Cell Biology.

[16]  Ronen Marmorstein,et al.  Acetylation of the p53 DNA-binding domain regulates apoptosis induction. , 2006, Molecular cell.

[17]  W. El-Deiry,et al.  Regulation of p53 downstream genes. , 1998, Seminars in cancer biology.

[18]  Rebecca W Doerge,et al.  An Empirical Bayesian Method for Estimating Biological Networks from Temporal Microarray Data , 2010, Statistical applications in genetics and molecular biology.

[19]  Hisham Bahmad,et al.  Genomic alterations during p53-dependent apoptosis induced by γ-irradiation of Molt-4 leukemia cells , 2017, PloS one.

[20]  Robert J. Gelinas,et al.  Sensitivity analysis of ordinary differential equation systems—A direct method , 1976 .

[21]  D. Faller,et al.  DNA-damaging Aryl Hydrocarbons Induce Mdm2 Expression via p53-independent Post-transcriptional Mechanisms* , 2000, The Journal of Biological Chemistry.

[22]  A. Levine,et al.  p53-Mdm2 loop controlled by a balance of its feedback strength and effective dampening using ATM and delayed feedback. , 2005, Systems biology.

[23]  Andreas Villunger,et al.  p53- and Drug-Induced Apoptotic Responses Mediated by BH3-Only Proteins Puma and Noxa , 2003, Science.

[24]  Tamer Başar,et al.  Controllability of Conjunctive Boolean Networks With Application to Gene Regulation , 2017, IEEE Transactions on Control of Network Systems.

[25]  Fangfei Li,et al.  Single-Input Pinning Controller Design for Reachability of Boolean Networks , 2018, IEEE Transactions on Neural Networks and Learning Systems.

[26]  Guanrong Chen,et al.  Pinning control of scale-free dynamical networks , 2002 .

[27]  George J. Pappas,et al.  Analysis and Control of Epidemics: A Survey of Spreading Processes on Complex Networks , 2015, IEEE Control Systems.

[28]  Mario di Bernardo,et al.  Pinning Controllability of Complex Network Systems With Noise , 2019, IEEE Transactions on Control of Network Systems.

[29]  Sonia Lain,et al.  Differences in the ubiquitination of p53 by Mdm2 and the HPV protein E6 , 2003, FEBS letters.

[30]  Paul R. Selvin,et al.  Single-molecule techniques , 2008 .

[31]  Junwu Zhu,et al.  Robust Gene Circuit Control Design for Time-Delayed Genetic Regulatory Networks Without SUM Regulatory Logic , 2018, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[32]  F. Zindy,et al.  Functional and physical interactions of the ARF tumor suppressor with p53 and Mdm2. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[33]  H. Erickson,et al.  Kinetics of protein-protein association explained by Brownian dynamics computer simulation. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[34]  N. Friedman,et al.  Stochastic protein expression in individual cells at the single molecule level , 2006, Nature.

[35]  Uttam Surana,et al.  Oscillations of the p53-Akt Network: Implications on Cell Survival and Death , 2009, PloS one.

[36]  P. Meltzer,et al.  Amplification of a gene encoding a p53-associated protein in human sarcomas , 1992, Nature.

[37]  Albert-László Barabási,et al.  Control Principles of Complex Networks , 2015, ArXiv.

[38]  Bert Vogelstein,et al.  Oncoprotein MDM2 conceals the activation domain of tumour suppressor p53 , 1993, Nature.

[39]  Vipul Periwal,et al.  System Modeling in Cellular Biology: From Concepts to Nuts and Bolts , 2006 .

[40]  R. Milo,et al.  Oscillations and variability in the p53 system , 2006, Molecular systems biology.

[41]  Masaru Tomita,et al.  Dynamic modeling of genetic networks using genetic algorithm and S-system , 2003, Bioinform..

[42]  Rui-Sheng Wang,et al.  Boolean modeling in systems biology: an overview of methodology and applications , 2012, Physical biology.

[43]  J. Roth,et al.  Induction of apoptosis in human esophageal cancer cells by sequential transfer of the wild-type p53 and E2F-1 genes: involvement of p53 accumulation via ARF-mediated MDM2 down-regulation. , 2000, Clinical cancer research : an official journal of the American Association for Cancer Research.

[44]  Daniel J Brat,et al.  P14ARF suppresses tumor-induced thrombosis by regulating the tissue factor pathway. , 2014, Cancer research.

[45]  K. Chiam,et al.  Transcription factor oscillations induce differential gene expressions. , 2012, Biophysical journal.

[46]  Eduardo Sontag,et al.  Transcriptional control of human p53-regulated genes , 2008, Nature Reviews Molecular Cell Biology.

[47]  Edward R. Dougherty,et al.  Inference of Gene Regulatory Networks using S-System: A Unified Approach , 2007, 2007 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology.

[48]  Xiaodong Cai,et al.  Stochastic Modeling and Simulation of the p53-MDM2/MDMX Loop , 2009, J. Comput. Biol..

[49]  Olivier F. Roux,et al.  Hybrid modeling of biological networks: mixing temporal and qualitative biological properties , 2009, BMC Systems Biology.

[50]  D. Hamby A review of techniques for parameter sensitivity analysis of environmental models , 1994, Environmental monitoring and assessment.

[51]  Hidde de Jong,et al.  Modeling and Simulation of Genetic Regulatory Systems: A Literature Review , 2002, J. Comput. Biol..

[52]  Michal Linial,et al.  Using Bayesian Networks to Analyze Expression Data , 2000, J. Comput. Biol..

[53]  A. Di Cristofano,et al.  Transcriptional regulation of the human tumor suppressor p14(ARF) by E2F1, E2F2, E2F3, and Sp1-like factors. , 2002, Biochemical and biophysical research communications.

[54]  Ronit Vogt Sionov,et al.  The cellular response to p53: the decision between life and death , 1999, Oncogene.

[55]  Jiguo Cao,et al.  Modeling gene regulation networks using ordinary differential equations. , 2012, Methods in molecular biology.

[56]  A. Levine,et al.  A Single Nucleotide Polymorphism in the MDM2 Promoter Attenuates the p53 Tumor Suppressor Pathway and Accelerates Tumor Formation in Humans , 2004, Cell.

[57]  Daniel J Brat,et al.  P14ARF inhibits human glioblastoma-induced angiogenesis by upregulating the expression of TIMP3. , 2012, The Journal of clinical investigation.

[58]  Uri Alon,et al.  Dynamics of the p53-Mdm2 feedback loop in individual cells , 2004, Nature Genetics.

[59]  Edward R. Dougherty,et al.  Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks , 2002, Bioinform..

[60]  Satoru Miyano,et al.  Identification of Genetic Networks from a Small Number of Gene Expression Patterns Under the Boolean Network Model , 1998, Pacific Symposium on Biocomputing.

[61]  Brian J. Smith,et al.  Differential targeting of prosurvival Bcl-2 proteins by their BH3-only ligands allows complementary apoptotic function. , 2005, Molecular cell.

[62]  Hui Wang,et al.  MDM2 and human malignancies: expression, clinical pathology, prognostic markers, and implications for chemotherapy. , 2005, Current cancer drug targets.

[63]  Zachary A. Szpiech,et al.  Statistical Applications in Genetics and Molecular Biology Comparing Spatial Maps of Human Population-Genetic Variation Using Procrustes Analysis , 2011 .

[64]  Zhi-Hong Guan,et al.  Event-based cluster synchronization of coupled genetic regulatory networks ☆ , 2017 .

[65]  Liqing Wang,et al.  Stabilization and Finite-Time Stabilization of Probabilistic Boolean Control Networks , 2019, IEEE Transactions on Systems, Man, and Cybernetics: Systems.

[66]  A. Levine,et al.  The mdm-2 oncogene product forms a complex with the p53 protein and inhibits p53-mediated transactivation , 1992, Cell.

[67]  Edward R. Dougherty,et al.  From Boolean to probabilistic Boolean networks as models of genetic regulatory networks , 2002, Proc. IEEE.

[68]  Jeremy E Purvis,et al.  p53 pulses lead to distinct patterns of gene expression albeit similar DNA-binding dynamics , 2017, Nature Structural &Molecular Biology.

[69]  Zidong Wang,et al.  Pinning controllability of autonomous Boolean control networks , 2016, Science China Information Sciences.

[70]  David Parry,et al.  p14ARF is a component of the p53 response following ionizing irradiation of normal human fibroblasts , 2004, Oncogene.

[71]  Guanrong Chen,et al.  Pinning a complex dynamical network to its equilibrium , 2004, IEEE Transactions on Circuits and Systems I: Regular Papers.

[72]  A L Jackman,et al.  Balb/c mice as a preclinical model for raltitrexed-induced gastrointestinal toxicity. , 2000, Clinical cancer research : an official journal of the American Association for Cancer Research.

[73]  Masaaki Matsuoka,et al.  p19ARF-induced p53-independent apoptosis largely occurs through BAX. , 2003, Biochemical and biophysical research communications.

[74]  P. D. Dal Cin,et al.  Coordinated expression and amplification of the MDM2, CDK4, and HMGI‐C genes in atypical lipomatous tumours , 2000, The Journal of pathology.

[75]  Guanrong Chen,et al.  Pinning control and controllability of complex dynamical networks , 2017, Int. J. Autom. Comput..

[76]  D. Lane,et al.  p53, guardian of the genome , 1992, Nature.

[77]  S. Kauffman Metabolic stability and epigenesis in randomly constructed genetic nets. , 1969, Journal of theoretical biology.

[78]  D. Green,et al.  The Pathophysiology of Mitochondrial Cell Death , 2004, Science.

[79]  A. Fersht,et al.  Comparative binding of p53 to its promoter and DNA recognition elements. , 2005, Journal of molecular biology.

[80]  X. Chen,et al.  p53 levels, functional domains, and DNA damage determine the extent of the apoptotic response of tumor cells. , 1996, Genes & development.

[81]  Mei-Ling Kuo,et al.  N-terminal polyubiquitination and degradation of the Arf tumor suppressor. , 2004, Genes & development.

[82]  M. Oren,et al.  Mdm2 promotes the rapid degradation of p53 , 1997, Nature.

[83]  A. Barabasi,et al.  Controllability analysis of the directed human protein interaction network identifies disease genes and drug targets , 2015, Proceedings of the National Academy of Sciences.

[84]  F. Garofalo,et al.  Controllability of complex networks via pinning. , 2007, Physical review. E, Statistical, nonlinear, and soft matter physics.

[85]  Jack A. Tuszynski,et al.  Stochastic and Deterministic Models of Cellular p53 Regulation , 2013, Front. Oncol..

[86]  Randal W. Beard,et al.  Distributed Consensus in Multi-vehicle Cooperative Control - Theory and Applications , 2007, Communications and Control Engineering.

[87]  E. Davidson,et al.  Modeling transcriptional regulatory networks. , 2002, BioEssays : news and reviews in molecular, cellular and developmental biology.

[88]  Mef Nilbert,et al.  MDM2 gene amplification correlates with ring chromosomes in soft tissue tumors , 1994 .

[89]  Yue Xiong,et al.  ARF Promotes MDM2 Degradation and Stabilizes p53: ARF-INK4a Locus Deletion Impairs Both the Rb and p53 Tumor Suppression Pathways , 1998, Cell.

[90]  C. Rubbi,et al.  Nutlin-3, the small-molecule inhibitor of MDM2, promotes senescence and radiosensitises laryngeal carcinoma cells harbouring wild-type p53 , 2010, British Journal of Cancer.

[91]  Weiping Li,et al.  Applied Nonlinear Control , 1991 .

[92]  Arnold J. Levine,et al.  The E6 oncoprotein encoded by human papillomavirus types 16 and 18 promotes the degradation of p53 , 1990, Cell.

[93]  Dmitri Papatsenko,et al.  Feedback control of pluripotency in embryonic stem cells: Signaling, transcription and epigenetics. , 2018, Stem cell research.

[94]  Claudine Chaouiya,et al.  Petri net modelling of biological networks , 2007, Briefings Bioinform..

[95]  Jeremy E. Purvis,et al.  p53 Dynamics Control Cell Fate , 2012, Science.

[96]  M. Kastan,et al.  DNA damage activates ATM through intermolecular autophosphorylation and dimer dissociation , 2003, Nature.