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Oncogene-tumor suppressor gene feedback interactions and their control
1. | DiseasePathways LLC, Bethesda, Maryland, 20814, United States |
2. | Computational and Systems Biology, Genome Institute of Singapore, 60 Biopolis St., #02-01 Genome, 138672, Singapore |
3. | Department of Life Science & Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, China-Yi, Taiwan |
References:
[1] |
B. D. Aguda, Network pharmacology of glioblastoma, Curr Drug Discov Technol., 10 (2013), 125-138. |
[2] |
B. D. Aguda, The significance of the feedback loops between KRas and Ink4a in pancreatic cancer, in Molecular Diagnostics and Therapy of Pancreatic Cancer (ed. A. Azmi), Elsevier Academic Press, (2014), 281-296.
doi: 10.1016/B978-0-12-408103-1.00012-1. |
[3] |
B. D. Aguda and A. B. Goryachev, From pathways databases to network models of switching behavior, PLoS Comput Biol., 3 (2007), 1674-1678.
doi: 10.1371/journal.pcbi.0030152. |
[4] |
B. D. Aguda, Y. Kim, H. S. Kim, A. Friedman and H. A. Fine, Qualitative network modeling of the Myc-p53 control system of cell proliferation and differentiation, Biophys J., 101 (2011), 2082-2091.
doi: 10.1016/j.bpj.2011.09.052. |
[5] |
B. D. Aguda, Y. Kim, M. G. Piper-Hunter, A. Friedman and C. B. Marsh, MicroRNA regulation of a cancer network: Consequences of the feedback loops involving miR-17-92, E2F and Myc, Proc Natl Acad Sci USA, 105 (2008), 19678-19683.
doi: 10.1073/pnas.0811166106. |
[6] |
R. C. Bast, B. Henessy and G. B. Mills, Jr., The biology of ovarian cancer: New opportunities for translation, Nat Rev Cancer, 9 (2009), 415-428. |
[7] |
Cancer Genome Atlas Research Network, Comprehensive genomic characterization defines human glioblastoma genes and core pathways, Nature, 494 (2013), p506.
doi: 10.1038/nature11903. |
[8] |
Cancer Genome Atlas Research Network, Comprehensive molecular profiling of lung adenocarcinoma, Nature, 511 (2014), 543-550. |
[9] |
W. A. Cooper, D. C. Lam, S. A. O'Toole and J. D. Minna, Molecular biology of lung cancer, J Thorac Dis., 5 (2013), S479-S490. |
[10] |
J. Daniluk, Y. Liu, D. Deng, J. Chu, H. Huang, S. Gaiser, Z. Cruz-Monserrate, H. Wang, B. Ji and C. D. Logsdon, An NF-$\kappa$B pathway-mediated positive feedback loop amplifies Ras activity to pathological levels in mice, J Clin Invest., 122 (2012), 1519-1528. |
[11] |
A. Dhooge, W. Govaerts and Y. A. Kuznetsov, MATCONT: A Matlab package for numerical bifurcation analysis of ODEs, ACM Trans Math Softw (TOMS), 29 (2003), 141-164.
doi: 10.1145/779359.779362. |
[12] |
J. Drost and R. Agami, Transformation locked in a loop, Cell, 139 (2009), 654-656.
doi: 10.1016/j.cell.2009.10.035. |
[13] |
P. A. Futreal, L. Coin, M. Marshall, T. Down, T. Hubbard, R. Wooster, N. Rahman and M. R. Stratton, A census of human cancer genes, Nat Rev Cancer, 4 (2004), 177-183.
doi: 10.1038/nrc1299. |
[14] |
P. K. Ha, S. S. Chang, C. A. Glazer, J. A. Califano and D. Sidransky, Molecular techniques and genetic alterations in head and neck cancer, Oral Oncol, 45 (2009), 335-339.
doi: 10.1016/j.oraloncology.2008.05.015. |
[15] | |
[16] |
http://ncg.kcl.ac.uk (network of cancer genes). |
[17] |
C. Kandoth, M. D. McLellan, F. Vandin, K. Ye, B. Niu, C. Lu, M. Xie, Q. Zhang, J. F. McMichael, M. A. Wyczalkowski, M. D. Leiserson, C. A. Miller, J. S. Welch, M. J. Walter, M. C. Wendl, T. J. Ley, R. K. Wilson, B. J. Raphael and L. Ding, Mutational landscape and significance across 12 major cancer types, Nature, 502 (2013), 333-339. |
[18] |
J. E. Larsen and J. D. Minna, Molecular biology of lung cancer: Clinical applications, Clin Chest Med., 32 (2011), 703-740.
doi: 10.1016/j.ccm.2011.08.003. |
[19] |
E. Y. Lee and W. J. Muller, Oncogenes and tumor suppressor genes, Cold Spring Harb Perpect Biol., 2 (2010), a003236.
doi: 10.1101/cshperspect.a003236. |
[20] |
Y. Li, Y. Li, H. Zhang and Y. Chen, MicroRNA-mediated positive feedback loop and optimized bistable switch in a cancer network involving miR-17-92, PLoS One, 6 (2011), e26302.
doi: 10.1371/journal.pone.0026302. |
[21] |
P. Liao, W. Wang, M. Shen, W. Pan, K. Zhang, R. Wang, T. Chen, Y. Chen, H. Chen and P. Wang, A positive feedback loop between EBP2 and c-Myc regulates rDNA transcription, cell proliferation, and tumorigenesis, Cell Death Dis., 5 (2014), e1032.
doi: 10.1038/cddis.2013.536. |
[22] |
L. Mao, W. K. Hong and V. A. Papadimitrakopoulou, Focus on head and neck cancer, Cancer Cell, 5 (2004), 311-316.
doi: 10.1016/S1535-6108(04)00090-X. |
[23] |
G. M. Marshall, P. Y. Liu, S. Gherardi, C. J. Scarlett, A. Bedalov, N. Xu, N. Iraci, E. Valli, D. Ling, W. Thomas, M. van Bekkum, E. Sekyere, K. Jankowski, T. Trahair, K. L. Mackenzie, M. Haber, M. D. Norris, A. V. Biankin, G. Perini and T. Liu, SIRT1 promotes N-Myc oncogenesis through a positive feedback loop involving the effects of MKP3 and ERK on N-Myc protein stability, PLoS Genet., 7 (2011), e1002135.
doi: 10.1371/journal.pgen.1002135. |
[24] |
K. Nowak, K. Kerl, D. Fehr, C. Kramps, C. Gessner, K. Killmer, B. Samans, B. Berwanger, H. Christiansen and W. Lutz, BMI1 is a target gene of E2F-1 and is strongly expressed in primary neuroblastomas, Nucleic Acids Res., 34 (2006), 1745-1754.
doi: 10.1093/nar/gkl119. |
[25] |
B. Perez-Ordoñez, M. Beauchemin and R. C. Jordan, Molecular biology of squamous cell carcinoma of the head and neck, J Clin Pathol., 59 (2006), 445-4453. |
[26] |
C. C. Pritchard and W. M. Grady, Colorectal cancer molecular biology moves into clinical practice, Gut., 60 (2011), 116-129.
doi: 10.1136/gut.2009.206250. |
[27] |
T. Santarius, J. Shipley, D. Brewer, M. R. Stratton and C. S. Cooper, A census of amplified and overexpressed human cancer genes, Nat Rev Cancer, 10 (2010), 59-64.
doi: 10.1038/nrc2771. |
[28] |
K. Tago, M. Funakoshi-Tago, H. Itoh, Y. Furukawa, J. Kikuchi, T. Kato, K. Suzuki and K. Yanagisawa, Arf tumor suppressor disrupts the oncogenic positive feedback loop including c-Myc and DDX5, Oncogene, 34 (2015), 314-322.
doi: 10.1038/onc.2013.561. |
[29] |
P. Takahashi, A. Polson and D. Reisman, Elevated transcription of the p53 gene in early S-phase leads to a rapid DNA-damage response during S-phase of the cell cycle, Apoptosis, 16 (2011), 950-958.
doi: 10.1007/s10495-011-0623-z. |
[30] |
D. Tamborero, A. Gonzalez-Perez, C. Perez-Llamas, J. Deu-Pons, C. Kandoth, J. Reimand, M. S. Lawrence, G. Getz, G. D. Bader, L. Ding and N. Lopez-Bigas, Comprehensive identification of mutational cancer driver genes across 12 tumor types, Sci Rep., 3 (2013), p2650.
doi: 10.1038/srep02650. |
[31] |
M. Vauhkonen, H. Vauhkonen and P. Sipponen, Pathology and molecular biology of gastric cancer, Best Pract Res Clin Gastroenterol, 20 (2006), 651-674.
doi: 10.1016/j.bpg.2006.03.016. |
show all references
References:
[1] |
B. D. Aguda, Network pharmacology of glioblastoma, Curr Drug Discov Technol., 10 (2013), 125-138. |
[2] |
B. D. Aguda, The significance of the feedback loops between KRas and Ink4a in pancreatic cancer, in Molecular Diagnostics and Therapy of Pancreatic Cancer (ed. A. Azmi), Elsevier Academic Press, (2014), 281-296.
doi: 10.1016/B978-0-12-408103-1.00012-1. |
[3] |
B. D. Aguda and A. B. Goryachev, From pathways databases to network models of switching behavior, PLoS Comput Biol., 3 (2007), 1674-1678.
doi: 10.1371/journal.pcbi.0030152. |
[4] |
B. D. Aguda, Y. Kim, H. S. Kim, A. Friedman and H. A. Fine, Qualitative network modeling of the Myc-p53 control system of cell proliferation and differentiation, Biophys J., 101 (2011), 2082-2091.
doi: 10.1016/j.bpj.2011.09.052. |
[5] |
B. D. Aguda, Y. Kim, M. G. Piper-Hunter, A. Friedman and C. B. Marsh, MicroRNA regulation of a cancer network: Consequences of the feedback loops involving miR-17-92, E2F and Myc, Proc Natl Acad Sci USA, 105 (2008), 19678-19683.
doi: 10.1073/pnas.0811166106. |
[6] |
R. C. Bast, B. Henessy and G. B. Mills, Jr., The biology of ovarian cancer: New opportunities for translation, Nat Rev Cancer, 9 (2009), 415-428. |
[7] |
Cancer Genome Atlas Research Network, Comprehensive genomic characterization defines human glioblastoma genes and core pathways, Nature, 494 (2013), p506.
doi: 10.1038/nature11903. |
[8] |
Cancer Genome Atlas Research Network, Comprehensive molecular profiling of lung adenocarcinoma, Nature, 511 (2014), 543-550. |
[9] |
W. A. Cooper, D. C. Lam, S. A. O'Toole and J. D. Minna, Molecular biology of lung cancer, J Thorac Dis., 5 (2013), S479-S490. |
[10] |
J. Daniluk, Y. Liu, D. Deng, J. Chu, H. Huang, S. Gaiser, Z. Cruz-Monserrate, H. Wang, B. Ji and C. D. Logsdon, An NF-$\kappa$B pathway-mediated positive feedback loop amplifies Ras activity to pathological levels in mice, J Clin Invest., 122 (2012), 1519-1528. |
[11] |
A. Dhooge, W. Govaerts and Y. A. Kuznetsov, MATCONT: A Matlab package for numerical bifurcation analysis of ODEs, ACM Trans Math Softw (TOMS), 29 (2003), 141-164.
doi: 10.1145/779359.779362. |
[12] |
J. Drost and R. Agami, Transformation locked in a loop, Cell, 139 (2009), 654-656.
doi: 10.1016/j.cell.2009.10.035. |
[13] |
P. A. Futreal, L. Coin, M. Marshall, T. Down, T. Hubbard, R. Wooster, N. Rahman and M. R. Stratton, A census of human cancer genes, Nat Rev Cancer, 4 (2004), 177-183.
doi: 10.1038/nrc1299. |
[14] |
P. K. Ha, S. S. Chang, C. A. Glazer, J. A. Califano and D. Sidransky, Molecular techniques and genetic alterations in head and neck cancer, Oral Oncol, 45 (2009), 335-339.
doi: 10.1016/j.oraloncology.2008.05.015. |
[15] | |
[16] |
http://ncg.kcl.ac.uk (network of cancer genes). |
[17] |
C. Kandoth, M. D. McLellan, F. Vandin, K. Ye, B. Niu, C. Lu, M. Xie, Q. Zhang, J. F. McMichael, M. A. Wyczalkowski, M. D. Leiserson, C. A. Miller, J. S. Welch, M. J. Walter, M. C. Wendl, T. J. Ley, R. K. Wilson, B. J. Raphael and L. Ding, Mutational landscape and significance across 12 major cancer types, Nature, 502 (2013), 333-339. |
[18] |
J. E. Larsen and J. D. Minna, Molecular biology of lung cancer: Clinical applications, Clin Chest Med., 32 (2011), 703-740.
doi: 10.1016/j.ccm.2011.08.003. |
[19] |
E. Y. Lee and W. J. Muller, Oncogenes and tumor suppressor genes, Cold Spring Harb Perpect Biol., 2 (2010), a003236.
doi: 10.1101/cshperspect.a003236. |
[20] |
Y. Li, Y. Li, H. Zhang and Y. Chen, MicroRNA-mediated positive feedback loop and optimized bistable switch in a cancer network involving miR-17-92, PLoS One, 6 (2011), e26302.
doi: 10.1371/journal.pone.0026302. |
[21] |
P. Liao, W. Wang, M. Shen, W. Pan, K. Zhang, R. Wang, T. Chen, Y. Chen, H. Chen and P. Wang, A positive feedback loop between EBP2 and c-Myc regulates rDNA transcription, cell proliferation, and tumorigenesis, Cell Death Dis., 5 (2014), e1032.
doi: 10.1038/cddis.2013.536. |
[22] |
L. Mao, W. K. Hong and V. A. Papadimitrakopoulou, Focus on head and neck cancer, Cancer Cell, 5 (2004), 311-316.
doi: 10.1016/S1535-6108(04)00090-X. |
[23] |
G. M. Marshall, P. Y. Liu, S. Gherardi, C. J. Scarlett, A. Bedalov, N. Xu, N. Iraci, E. Valli, D. Ling, W. Thomas, M. van Bekkum, E. Sekyere, K. Jankowski, T. Trahair, K. L. Mackenzie, M. Haber, M. D. Norris, A. V. Biankin, G. Perini and T. Liu, SIRT1 promotes N-Myc oncogenesis through a positive feedback loop involving the effects of MKP3 and ERK on N-Myc protein stability, PLoS Genet., 7 (2011), e1002135.
doi: 10.1371/journal.pgen.1002135. |
[24] |
K. Nowak, K. Kerl, D. Fehr, C. Kramps, C. Gessner, K. Killmer, B. Samans, B. Berwanger, H. Christiansen and W. Lutz, BMI1 is a target gene of E2F-1 and is strongly expressed in primary neuroblastomas, Nucleic Acids Res., 34 (2006), 1745-1754.
doi: 10.1093/nar/gkl119. |
[25] |
B. Perez-Ordoñez, M. Beauchemin and R. C. Jordan, Molecular biology of squamous cell carcinoma of the head and neck, J Clin Pathol., 59 (2006), 445-4453. |
[26] |
C. C. Pritchard and W. M. Grady, Colorectal cancer molecular biology moves into clinical practice, Gut., 60 (2011), 116-129.
doi: 10.1136/gut.2009.206250. |
[27] |
T. Santarius, J. Shipley, D. Brewer, M. R. Stratton and C. S. Cooper, A census of amplified and overexpressed human cancer genes, Nat Rev Cancer, 10 (2010), 59-64.
doi: 10.1038/nrc2771. |
[28] |
K. Tago, M. Funakoshi-Tago, H. Itoh, Y. Furukawa, J. Kikuchi, T. Kato, K. Suzuki and K. Yanagisawa, Arf tumor suppressor disrupts the oncogenic positive feedback loop including c-Myc and DDX5, Oncogene, 34 (2015), 314-322.
doi: 10.1038/onc.2013.561. |
[29] |
P. Takahashi, A. Polson and D. Reisman, Elevated transcription of the p53 gene in early S-phase leads to a rapid DNA-damage response during S-phase of the cell cycle, Apoptosis, 16 (2011), 950-958.
doi: 10.1007/s10495-011-0623-z. |
[30] |
D. Tamborero, A. Gonzalez-Perez, C. Perez-Llamas, J. Deu-Pons, C. Kandoth, J. Reimand, M. S. Lawrence, G. Getz, G. D. Bader, L. Ding and N. Lopez-Bigas, Comprehensive identification of mutational cancer driver genes across 12 tumor types, Sci Rep., 3 (2013), p2650.
doi: 10.1038/srep02650. |
[31] |
M. Vauhkonen, H. Vauhkonen and P. Sipponen, Pathology and molecular biology of gastric cancer, Best Pract Res Clin Gastroenterol, 20 (2006), 651-674.
doi: 10.1016/j.bpg.2006.03.016. |
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