Voir la notice de l'article provenant de la source Math-Net.Ru
@article{MBB_2017_12_1_a8, author = {O. F. Voropaeva and S. D. Senotrusova and Yu. I. Shokin}, title = {Deregulation of p53-dependent {microRNAs:} the results of mathematical modeling}, journal = {Matemati\v{c}eska\^a biologi\^a i bioinformatika}, pages = {151--175}, publisher = {mathdoc}, volume = {12}, number = {1}, year = {2017}, language = {ru}, url = {http://geodesic.mathdoc.fr/item/MBB_2017_12_1_a8/} }
TY - JOUR AU - O. F. Voropaeva AU - S. D. Senotrusova AU - Yu. I. Shokin TI - Deregulation of p53-dependent microRNAs: the results of mathematical modeling JO - Matematičeskaâ biologiâ i bioinformatika PY - 2017 SP - 151 EP - 175 VL - 12 IS - 1 PB - mathdoc UR - http://geodesic.mathdoc.fr/item/MBB_2017_12_1_a8/ LA - ru ID - MBB_2017_12_1_a8 ER -
%0 Journal Article %A O. F. Voropaeva %A S. D. Senotrusova %A Yu. I. Shokin %T Deregulation of p53-dependent microRNAs: the results of mathematical modeling %J Matematičeskaâ biologiâ i bioinformatika %D 2017 %P 151-175 %V 12 %N 1 %I mathdoc %U http://geodesic.mathdoc.fr/item/MBB_2017_12_1_a8/ %G ru %F MBB_2017_12_1_a8
O. F. Voropaeva; S. D. Senotrusova; Yu. I. Shokin. Deregulation of p53-dependent microRNAs: the results of mathematical modeling. Matematičeskaâ biologiâ i bioinformatika, Tome 12 (2017) no. 1, pp. 151-175. http://geodesic.mathdoc.fr/item/MBB_2017_12_1_a8/
[1] Lane D., Levine A., “p53 research: The past thirty years and the next thirty years”, Cold Spring Harb. Perspect. Biol., 2:12 (2010), a000893 | DOI
[2] Zheltukhin A. O., Chumakov P. M., “Povsednevnye i indutsiruemye funktsii gena p53”, Uspekhi biolog. khimii, 50 (2010), 447–516
[3] 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, 30:3 (2008), 277–289 | DOI
[4] 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, 447 (2007), 05939 | DOI
[5] Jansson M. D., Lund A. H., “MicroRNA and cancer”, Molecular oncology, 6 (2012), 590–610 | DOI
[6] Hermeking H., “MicroRNAs in the p53 network: micromanagement of tumor suppression”, Nature reviews cancer, 12:9 (2012), 613–626 | DOI
[7] 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), 749724 | DOI
[8] 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, 26 (2007), 745–752 | DOI
[9] 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, 26 (2007), 731–743 | DOI
[10] 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, 6:13 (2007), 1586–1593 | DOI
[11] 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, 4:8 (2009), e6816 | DOI
[12] 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, 106:9 (2009), 3207–3212 | DOI
[13] 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, 20:15 (2011), 3067–3078 | DOI
[14] 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, 13 (2013), 552 | DOI
[15] 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, 7 (2013), 178 | DOI
[16] 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, 6 (2014), 1000–1007 | DOI
[17] Kabaria S., Choi D. C., Chaudhuri A. D., Mouradian M. M., Junn E., “Inhibition of miR-34b and miR-34c enhances $\alpha$-synuclein expression in Parkinson's disease”, FEBS Lett., 589:3 (2015), 319–325 | DOI
[18] 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., 67 (2007), 8699–8707 | DOI
[19] Nikitina E. G., Urazova L. N., Stegny V. N., “MicroRNAs and human cancer”, Experimental oncology, 34:1 (2012), 2–8 | MR
[20] Kolesnikov N. N., Titov S. E., Veryaskina Yu. A., Karpinskaya E. V., Shevchenko C. P., Akhmerova L. G., Ivanov M. K., Kozlov V. V., Elisafenko E. A., Gulyaeva L. F., Zhimulev I. F., “MikroRNK, evolyutsiya i rak”, Tsitologiya, 55:3 (2013), 159–164
[21] Koshkin F. A., Chistyakov D. A., Nikitin A. G., Konovalov A. N., Potapov A. A., Usachev D. Yu., Pitskhelauri D. I., Kobyakov G. L., Shishkina L. V., Chekhonin V. P., “Izuchenie profilya ekspressii mikroRNK v opukholyakh mozga raznoi stepeni zlokachestvennosti”, Byulleten eksperimentalnoi biologii i meditsiny, 157:6 (2014), 794–797
[22] Shulenina L. V., Mikhailov V. F., Ledin E. V., Raeva N. F., Zasukhina G. D., “Otsenka effektivnosti r53-zavisimoi sistemy sokhraneniya stabilnosti genoma po soderzhaniyu mikroRNK i mRNK v krovi onkologicheskikh bolnykh”, Meditsinskaya radiologiya i radiatsionnaya bezopasnost, 60:1 (2015), 5–14
[23] 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, 9:5 (2014), e94839 | DOI
[24] Lukiw W. J., Andreeva T. V., Grigorenko A. P., Rogaev E. I., “Studying microRNA function and dysfunction in Alzheimer's disease”, Frontiers in Genetics, 3 (2013), 327 | DOI
[25] Mihalas G. I., Simon Z., Balea G., Popa E., “Possible oscillatory behavior in p53-Mdm2 interaction computer simulation”, J. Biol. Syst., 8:1 (2000), 21–29 | DOI
[26] 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, 97:21 (2000), 11250–11255 | DOI
[27] Tiana G., Jensen M. H., Sneppen K., “Time delay as a key to apoptosis induction in the p53 network”, Eur. Phys. J. B, 29 (2002), 135–140 | DOI
[28] Ciliberto A., Novak B., Tyson J. J., “Steady states and oscillations in the p53-Mdm2 network”, Cell Cycle, 4:3 (2005), 488–493 | DOI
[29] 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, 102:4 (2005), 014266–14271 | DOI
[30] 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, 2:1 (2006), 2006.0033 | DOI
[31] Chickarmane V., Ray A., Sauro H. M., Nadim A., “A Model for p53 Dynamics Triggered by Damage”, SIAM J. Applied Dynamical Systems, 6:1 (2007), 61–78 | DOI | MR
[32] Qi J. P., Shao S. H., Zhu Y., “A mathematical model of P53 gene regulatory networks under radiotherapy”, Biosystems, 90:3 (2007), 698–706 | DOI
[33] 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, 30 (2008), 277–289 | DOI
[34] Horhat R. F., Neamtu M., Mircea G., “Mathematical models and numerical simulations for the P53-Mdm2 network”, Applied Sciences, 10 (2008), 94–106 | MR
[35] Likhoshvai V. A., Golubyatnikov V. P., Demidenko G. V., Fadeev S. I., Evdokimov A. A., “Teoriya gennykh setei”, Sistemnaya kompyuternaya biologiya, SO RAN, Novosibirsk, 2008, 395–480
[36] Golubyatnikov V. P., Mjolsness E., Gaidov Yu. A., “Topological index of the p53-Mdm2 circuit”, Vestnik VOGiS, 13:1 (2009), 160–162
[37] 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, 4:3 (2009), e4795 | DOI
[38] Sun T., Chen C., Shen P., “Modeling the role of p53 pulses in DNA damage-induced cell death decision”, BMC Bioinformatics, 10 (2009), 190 | DOI
[39] Zhang T., Brazhnik P., Tyson J., “Exploring mechanisms of the DNA-damage response: p53 pulses and their possible relevance to apoptosis”, Cell Cycle, 6 (2007), 85–94 | DOI
[40] Cai X., Yuan Z. M., “Stochastic modeling and simulation of the p53-MDM2/MDMX loop”, J. Comput. Biol., 16 (2009), 917–933 | DOI | MR
[41] Jolma I. W., Ni X. Y., Rensing L., Ruoff P., “Harmonic Oscillations in Homeostatic Controllers: Dynamics of the p53 Regulatory System”, Biophysical Journal, 98 (2010), 743–752 | DOI
[42] Lai X., Wolkenhauer O., Vera Ju., “Understanding microRNA-mediated gene regulatory networks through mathematical modelling”, Nucleic Acids Research, 44:13 (2016), 6019–6035 | DOI
[43] 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. Methods in Molecular Biology, 880 (2012), 87–108 | DOI
[44] 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, 11:12 (2015), e1004653 | DOI
[45] Jonak K., Kurpas M., Szoltysek K., Janus P., Abramowicz A., Puszynski K., “A novel mathematical model of ATM/p53/NF-$\kappa$B pathways points to the importance of the DDR switch-off mechanisms”, BMC Systems Biology, 10 (2016), 75 | DOI
[46] Luo Z., Azencott R., Zhao Y., “Modeling miRNA-mRNA interactions: fitting chemical kinetics equations to microarray data”, BMC Systems Biology, 8 (2014), 19 | DOI
[47] Schon O., Friedler A., Bycroft M., Freund S., Fersht A., “Molecular mechanism of the interaction between MDM2 and p53”, Molecular Biology, 323:3 (2002), 491–501 | DOI
[48] Voropaeva O. F., Shokin Yu. I., Senotrusova S. D., “Matematicheskoe modelirovanie funktsionirovaniya seti onkomarkerov”, Doklady VI Mezhdunarodnoi konferentsii «Matematicheskaya biologiya i bioinformatika» (Puschino, 16–21 oktyabrya 2016 g.), Maks-Press, M., 2016, 102–103
[49] Voropaeva O. F., Kozlova A. O., Senotrusova S. D., “Chislennyi analiz perekhoda ot uravneniya s zapazdyvaniem k sisteme ODU v matematicheskoi modeli seti onkomarkerov”, Vychislitelnye tekhnologii, 21:2 (2016), 12–25
[50] Voropaeva O. F., Shokin Yu. I., Nepomnyaschikh L. M., Senchukova S. R., Matematicheskoe modelirovanie funktsionirovaniya i regulyatsii biologicheskoi sistemy p53-Mdm2, Izd-vo RAMN, M., 2014, 176 pp.
[51] Voropaeva O. F., Senchukova S. R., Brodt K. V., Garbuzov K. E., Melnichenko A. V., Starikova A. A., “Chislennoe modelirovanie ultradiannykh kolebanii v biologicheskoi sisteme p53-Mdm2 v usloviyakh stressa”, Matematicheskoe modelirovanie, 26:11 (2014), 105–122
[52] Voropaeva O. F., Shokin Yu. I., Nepomnyaschikh L. M., Senchukova S. R., “Matematicheskoe modelirovanie funktsionirovaniya sistemy belkov p53-Mdm2”, Byulleten eksperimentalnoi biologii i meditsiny, 157:2 (2014), 261–264
[53] Voropaeva O. F., Shokin Yu. I., Nepomnyaschikh L. M., Senchukova S. R., “Matematicheskoe modelirovanie regulyatsii biologicheskoi sistemy p53-Mdm2”, Byulleten eksperimentalnoi biologii i meditsiny, 157:4 (2014), 539–542