Olga F. Voropaeva, Sofia D. Senotrusova, Yurii I. Shokin
Deregulation of p53-dependent microRNAs: the results of mathematical modeling
Mathematical Biology & Bioinformatics. 2017;12(1):151-175.
doi: 10.17537/2017.12.151.
References
- Lane D., Levine A. p53 research: The past thirty years and the next thirty years. Cold Spring Harb. Perspect. Biol. 2010;2(12). Article No. a000893. doi: 10.1101/cshperspect.a000893
- Zheltukhin A.O., Chumakov P.M. Constitutive and Induced Functions of the p53 Gene. Biochemistry (Moscow). 2010;75(13):1692-1721. doi: 10.1134/S0006297910130110
- Batchelor E., Mock C.S., Bhan I., Loewer A., Lahav G. Recurrent initiation: A mechanism for triggering p53 pulses in response to DNA damage. Molecular Cell. 2008;30(3):277-289. doi: 10.1016/j.molcel.2008.03.016
- He L., He X., Lim L.P., Stanchina E., Xuan Z., Liang Y., Xue W., Zender L., Magnus J., Ridzon D., Jackson A.L., Linsley P.S., Chen C., Lowe S.W., Cleary M.A., Hannon G.J. A microRNA component of the p53 tumour suppressor network. Nature. 2007;447:05939. doi: 10.1038/nature05939
- Jansson M.D., Lund A.H. MicroRNA and cancer. Molecular oncology. 2012;6:590-610. doi: 10.1016/j.molonc.2012.09.006
- Hermeking H. MicroRNAs in the p53 network: micromanagement of tumor suppression. Nature reviews cancer. 2012;12(9):613-626. doi: 10.1038/nrc3318
- Otsuka K., Ochiya T. Genetic networks lead and follow tumor development: microRNA regulation of cell cycle and apoptosis in the p53 pathways. BioMed Research International. 2014;2014. Article No. 749724.
- Chang T.-C., Wentzel E.A., Kent O.A., Ramachandran K., Mullendore M., Lee K.H., Feldmann G., Yamakuchi M., Ferlito M., Lowenstein C.J., Arking D.E., Beer M.A., Maitra A., Mendell J.T. Transactivation of miR-34a by p53 broadly influences gene expression and promotes apoptosis. Molecular Cell. 2007;26:745-752. doi: 10.1016/j.molcel.2007.05.010
- Raver-Shapira N., Marciano E., Meiri E., Spector Ya., Rosenfeld N., Moskovits N., Bentwich Z., Oren M. Transcriptional activation of miR-34a contributes to p53-mediated apoptosis. Molecular Cell. 2007;26:731-743. doi: 10.1016/j.molcel.2007.05.017
- Tarasov V., Jung P., Verdoodt B., Lodygin D., Epanchintsev A., Menssen A., Maister G., Hermeking H. Differential Regulation of microRNAs by p53 Revealed by Massively Parallel Sequencing. Cell Cycle. 2007;6(13):1586-1593. doi: 10.4161/cc.6.13.4436
- Ji Q., Hao X., Zhang M., Tang W., Meng Ya., Li L., Xiang D., DeSano J.T., Bommer G.T., Fan D., Fearon E.R., Lawrence T.S., Xu L. MicroRNA miR-34 inhibits human pancreatic cancer tumor-initiating cells. PLoS ONE. 2009;4(8). Article No. e6816. doi: 10.1371/journal.pone.0006816
- Sachdeva M., Zhu S., Wu F., Wu H., Walia V., Kumar S., Elble R., Watabe K., Mo Y.-Y. P53 represses c-Myc through induction of the tumor suppressor miR-145. PNAS. 2009;106(9):3207-3212. doi: 10.1073/pnas.0808042106
- Minones-Moyano E., Porta S., Escaram’s G., Rabionet R., Iraola S., Kagerbauer B., Espinosa-Parrilla Yo., Ferrer I., Estivill X., Marti E. MicroRNA profiling of Parkinson’s disease brains identifies early downregulation of miR-34b/c which modulate mitochondrial function. Human Molecular Genetics. 2011;20(15):3067-3078. doi: 10.1093/hmg/ddr210
- Bisio A., Sanctis V., Vescovo V., Denti M., Jegga A., Inga A., Ciribilli Ya. Identification of new p53 target microRNAs by bioinformatics and functional analysis. BMC Cancer. 2013;13. Article No. 552. doi: 10.1186/1471-2407-13-552
- Goodall E., Heath P.R., Bandmann O., Kirby J., Shaw P.J. Neuronal dark matter: the emerging role of microRNAs in neurodegeneration. Frontiers in Cellular Neuroscience. 2013;7. Article No. 178. doi: 10.3389/fncel.2013.00178
- Cheng C.-Y, Hwang C.-I., Corney D.C., Flesken-Nikitin A., Long-Chang J., Oner G.M., Munroe R.J., Schimenti J.C., Hermeking H., Nikitin A.Yu. MiR-34 Cooperates with p53 in Suppression of Prostate Cancer by Joint Regulation of Stem Cell Compartment. Cell Reports. 2014;6:1000-1007. doi: 10.1016/j.celrep.2014.02.023
- Kabaria S., Choi D.C., Chaudhuri A.D., Mouradian M.M., Junn E. Inhibition of miR-34b and miR-34c enhances α-synuclein expression in Parkinson’s disease. FEBS Lett. 2015;589(3):319-325. doi: 10.1016/j.febslet.2014.12.014
- Iorio M.V., Visone R., Leva G., Donati V., Petrocca F., Casalini P., Taccioli C., Volinia S., Liu C.G., Alder H., Calin G.A., Menard S., Croce C.M. MicroRNA signatures in human ovarian cancer. Cancer Res. 2007;67:8699-8707. doi: 10.1158/0008-5472.CAN-07-1936
- Nikitina E.G., Urazova L.N., Stegny V.N. MicroRNAs and human cancer. Experimental oncology. 2012;34(1):2-8.
- Kolesnikov N.N., Titov S.E., Veryaskina Yu.A., Karpinskaya E.V., Schevschenko S.P., Akhmerova L.G., Ivanov M.K., Kozlov V.V., Elisaphenko E.A., Gulyaeva L.F., Zhimulev I.F. Tsitologiia (Tsitologia). 2013;55(3):159-164 (in Russ.).
- Koshkin F.A., Chistyakov D.A., Nikitin A.G., Konovalov A.N., Potapov A.A., Usachyov D.Yu., Pitskhelauri D.I., Kobyakov G.L., Shishkina L.V., Chekhonin V.P. Profile of MicroRNA Expression in Brain Tumors of Different Malignancy. Bulletin of Experimental Biology and Medicine. 2014;157(6):794-797. doi: 10.1007/s10517-014-2669-8
- Shulenina L.V., Mikhailov V.F., Ledin E.V., Raeva N.F., Zasukhina G.D. Evaluation of P53-Dependent System of Maintaining the Genome Stability by Content of MicroRNA and MRNA in Blood of Cancer Patients. Ìedical Radiology and Radiation Safety. 2015;60(1):5-14 (in Russ.).
- Burgos K., Malenica I., Metpally R., Courtright A., Rakela B., Beach T., Shill H., Adler C., Sabbagh M., Villa W., Tembe S., Craig D., Van Keuren-Jensen K. Profiles of Extracellular miRNA in cerebrospinal fluid and serum from patients with Alzheimer’s and Parkinson’s diseases correlate with disease status and features of Pathology. PLoS ONE. 2014;9(5). Article No. e94839. doi: 10.1371/journal.pone.0094839
- Lukiw W.J., Andreeva T.V., Grigorenko A.P., Rogaev E.I. Studying microRNA function and dysfunction in Alzheimer’s disease. Frontiers in Genetics. 2013;3. Article No. 327. doi: 10.3389/fgene.2012.00327
- Mihalas G.I., Simon Z., Balea G., Popa E. Possible oscillatory behavior in p53-Mdm2 interaction computer simulation. J. Biol. Syst. 2000;8(1):21-29. doi: 10.1142/S0218339000000031
- Bar-Or R.L., Maya R., Segel L.A., Alon U., Levine A.J., Oren M. Generation of oscillations by the p53-Mdm2 feedback loop: A theoretical and experimental study. PNAS. 2000;97(21):11250-11255. doi: 10.1073/pnas.210171597
- Tiana G., Jensen M.H., Sneppen K. Time delay as a key to apoptosis induction in the p53 network. Eur. Phys. J. B. 2002;29:135-140. doi: 10.1140/epjb/e2002-00271-1
- Ciliberto A., Novak B., Tyson J.J. Steady states and oscillations in the p53-Mdm2 network. Cell Cycle. 2005;4(3):488-493. doi: 10.4161/cc.4.3.1548
- Ma L., Wagner J., Rice J., Hu W., Levine A.J., Stolovitzky G.A. A plausible model for the digital response of p53 to DNA damage. PNAS. 2005;102(4):014266-14271. doi: 10.1073/pnas.0501352102
- Geva-Zatorsky N., Rosenfeld N., Itzkovitz Sh., Milo R., Sigal A., Dekel E., Yarnitzky T., Liron Y., Polak P., Lahav G., Alon U. Oscillations and variability in the p53 system. Molecular Systems Biology. 2006;2(1). Article No. 2006.0033.
- Chickarmane V., Ray A., Sauro H.M., Nadim A.A Model for p53 Dynamics Triggered by Damage. SIAM J. Applied Dynamical Systems. 2007;6(1):61-78. doi: 10.1137/060653925
- Qi J.P., Shao S.H., Zhu Y. A mathematical model of P53 gene regulatory networks under radiotherapy. Biosystems. 2007;90(3):698-706. doi: 10.1016/j.biosystems.2007.02.007
- Batchelor E., Mock C.S., Bhan I., Loewer A., Lahav G. Recurrent Initiation: A Mechanism for Triggering p53 Pulses in Response to DNA Damage. Molecular Cell. 2008;30:277-289. doi: 10.1016/j.molcel.2008.03.016
- Horhat R.F., Neamtu M., Mircea G. Mathematical models and numerical simulations for the P53-Mdm2 network. Applied Sciences. 2008;10:94-106.
- Theory of Gene Networks. In: Computational systems biology: Chapter 5. Eds. Kolchanov N.A., Goncharov S.S., Likhoshvai V.A., Ivanisenko V.A. Novosibirsk; 2008. P. 395-480. (Integration Projects of SB RAS, Issue 14) (in Russ.).
- Golubyatnikov V.P., Mjolsness E., Gaidov Yu.A. Topological index of the p53-Mdm2 circuit. VOGiS Herald. 2009;13(1):160-162.
- Hamada H., Tashima Y., Kisaka Y., Iwamoto K., Hanai T., Eguchi Y., Okamoto M. Sophisticated Framework between Cell Cycle Arrest and Apoptosis Induction Based on p53 Dynamics. PLoS ONE. 2009;4(3). Article No. e4795. doi: 10.1371/journal.pone.0004795
- Sun T., Chen C., Shen P. Modeling the role of p53 pulses in DNA damage- induced cell death decision. BMC Bioinformatics. 2009;10. Article No. 190. doi: 10.1186/1471-2105-10-190
- Zhang T., Brazhnik P., Tyson J. Exploring mechanisms of the DNA-damage response: p53 pulses and their possible relevance to apoptosis. Cell Cycle. 2007;6:85-94. doi: 10.4161/cc.6.1.3705
- Cai X., Yuan Z.M. Stochastic modeling and simulation of the p53-MDM2/MDMX loop. J. Comput. Biol. 2009;16:917-933. doi: 10.1089/cmb.2008.0231
- Jolma I.W., Ni X.Y., Rensing L., Ruoff P. Harmonic Oscillations in Homeostatic Controllers: Dynamics of the p53 Regulatory System. Biophysical Journal. 2010;98:743-752. doi: 10.1016/j.bpj.2009.11.013
- Lai X., Wolkenhauer O., Vera Ju. Understanding microRNA-mediated gene regulatory networks through mathematical modelling. Nucleic Acids Research. 2016;44(13):6019-6035. doi: 10.1093/nar/gkw550
- Lai X., Wolkenhauer O., Vera Ju. Modeling miRNA Regulation in Cancer Signaling Systems: miR-34a Regulation of the p53/Sirt1 Signaling Module. Computational Modeling of Signaling Networks. 2012;880:87-108. (Methods in Molecular Biology). doi: 10.1007/978-1-61779-833-7_6
- Moore R., Ooi H.K., Kang T., Bleris L., Ma L. MiR-192-Mediated Positive Feedback Loop Controls the Robustness of Stress-Induced p53 Oscillations in Breast Cancer Cells. PLoS Computational Biology. 2015;11(12). Article No. e1004653. doi: 10.1371/journal.pcbi.1004653
- Jonak K., Kurpas M., Szoltysek K., Janus P., Abramowicz A., Puszynski K. A novel mathematical model of ATM/p53/NF-κB pathways points to the importance of the DDR switch-off mechanisms. BMC Systems Biology. 2016;10. Article No. 75.
- Luo Z., Azencott R., Zhao Y. Modeling miRNA-mRNA interactions: fitting chemical kinetics equations to microarray data. BMC Systems Biology. 2014;8. Article No. 19. doi: 10.1186/1752-0509-8-19
- Schon O., Friedler A., Bycroft M., Freund S., Fersht A. Molecular mechanism of the interaction between MDM2 and p53. Molecular Biology. 2002;323(3):491-501. doi: 10.1016/S0022-2836(02)00852-5
- Voropaeva O.F., Shokin Yu.I., Senotrusova S.D. Mathematical modelling of the tumor markers network. In: Mathematical Biology and Bioinformatics: Proceedings of the 6th International Conference (Pushchino, 16-21 October 2016). Eds. V.D. Lakhno. M.: MAKS Press; 2016. P. 102-103 (in Russ.).
- Voropaeva O.F., Kozlova A.O., Senotrusova S.D. Numerical analysis of the transition from the equation with retarded argument to the ODE system in a mathematical model of the tumor markers network. Computational Technologies. 2016;21(2):12-25 (in Russ.).
- Voropaeva O.F., Shokin Yu.I., Nepomnyashchikh L.M., Senchukova S.R. Matematicheskoe modelirovanie funktsionirovaniia i reguliatsii biologicheskoi sistemy p53-Mdm2 (Mathematical modeling of functioning and regulation of biological system p53-Mdm2). Moscow; 2014. 176 p. (in Russ.).
- Voropaeva O.F., Senchukova S.R., Brodt K.V., Garbuzov K.E., Melnitchenko A.V., Starikova A.A. Numerical simulation of ultradian oscillations in p53-Mdm2-network under stress conditions. Mathematical Models and Computer Simulations. 2015;7(3):281-293. doi: 10.1134/S2070048215030102
- Voropaeva O.F., Shokin Yu.I., Nepomnyashchikh L.M., Senchukova S.R. Mathematical Modeling of Functioning of the p53-Mdm2 Protein System. Bulletin of Experimental Biology and Medicine. 2014;157(2):291-294. doi: 10.1007/s10517-014-2548-3
- Voropaeva O.F., Shokin Yu.I., Nepomnyashchikh L.M., Senchukova S.R. Mathematical Simulation of p53-Mdm2 Protein Biological System Regulation. Bulletin of Experimental Biology and Medicine. 2014;157(4):535-538. doi: 10.1007/s10517-014-2608-8
|
|
|