Integrative analysis of gene and miRNA expression profiles with transcription factor-miRNA feed-forward loops identifies regulators in human cancers

Nucleic Acids Research

Volumn 40, Issue 17, 2012, Pages

  Yan, Zhenyu ^a   Shah, Parantu K ^a   Amin, Samir B ^a   Samur, Mehmet K ^a,b   Huang, Norman ^a   Wang, Xujun ^c   Misra, Vikas ^d   Ji, Hongbin ^e   Gabuzda, Dana ^d   Li, Cheng ^a,b  

^a HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^b AKDENIZ UNIVERSITY   (Turkey)

^c TONGJI UNIVERSITY   (China)

^d DANA FARBER CANCER INSTITUTE   (United States)

^e INSTITUTE OF BIOCHEMISTRY AND CELL BIOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIC AMP RESPONSIVE ELEMENT BINDING PROTEIN; HYPOXIA INDUCIBLE FACTOR 1BETA; MICRORNA; MYC PROTEIN; RNA; TRANSCRIPTION FACTOR; TRANSCRIPTOME;

ARTICLE; CHROMATIN IMMUNOPRECIPITATION GENE AND MIRNA NETWORK BASED INTEGRATION; CLIENT SERVER APPLICATION; GENE EXPRESSION; GENE EXPRESSION PROFILING; GERM CELL TUMOR; INTERMETHOD COMPARISON; KIDNEY CANCER; LIVER CANCER; LUNG CANCER; MOLECULAR INTERACTION; POSITIVE FEEDBACK; PRIORITY JOURNAL; PROSTATE CANCER; SOLID TUMOR; STATISTICAL ANALYSIS;

FEEDBACK, PHYSIOLOGICAL; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE REGULATORY NETWORKS; HUMANS; MICRORNAS; NEOPLASMS; TRANSCRIPTION FACTORS; TRANSCRIPTOME;

EID: 84866929613     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks395     Document Type: Article

References (49)

1. Barabasi, A.L. and Oltvai, Z.N. (2004) Network biology: understanding the cell's functional organization. Nat. Rev. Genet., 5, 101-113. (Pubitemid 38160277)
2. Croce, C.M. (2009) Causes and consequences of microRNA dysregulation in cancer. Nat. Rev. Genet., 10, 704-714.
3. Esquela-Kerscher, A. and Slack, F.J. (2006) Oncomirs-microRNAs with a role in cancer. Nat. Rev. Cancer, 6, 259-269.
4. Calin, G.A., Sevignani, C., Dumitru, C.D., Hyslop, T., Noch, E., Yendamuri, S., Shimizu, M., Rattan, S., Bullrich, F., Negrini, M. et al. (2004) Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers. Proc. Natl Acad. Sci. USA., 101, 2999-3004. (Pubitemid 38327724)
5. Guo, H., Ingolia, N.T., Weissman, J.S. and Bartel, D.P. Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature, 466, 835-840.
6. Mangan, S. and Alon, U. (2003) Structure and function of the feed-forward loop network motif. Proc. Natl Acad. Sci. USA., 100, 11980-11985. (Pubitemid 37271501)
7. Tsang, J., Zhu, J. and van Oudenaarden, A. (2007) MicroRNA-mediated feedback and feedforward loops are recurrent network motifs in mammals. Mol. Cell, 26, 753-767. (Pubitemid 46856248)
8. O'Donnell, K.A., Wentzel, E.A., Zeller, K.I., Dang, C.V. and Mendell, J.T. (2005) c-Myc-regulated microRNAs modulate E2F1 expression. Nature, 435, 839-843. (Pubitemid 40839736)
9. He, L., He, X., Lim, L.P., de Stanchina, E., Xuan, Z., Liang, Y., Xue, W., Zender, L., Magnus, J., Ridzon, D. et al. (2007) A microRNA component of the p53 tumour suppressor network. Nature, 447, 1130-1134. (Pubitemid 47014436)
10. Li, X., Cassidy, J.J., Reinke, C.A., Fischboeck, S. and Carthew, R.W. (2009) A microRNA imparts robustness against environmental fluctuation during development. Cell, 137, 273-282.
11. Shalgi, R., Brosh, R., Oren, M., Pilpel, Y. and Rotter, V. (2009) Coupling transcriptional and post-transcriptional miRNA regulation in the control of cell fate. Aging, 1, 762-770.
12. El Baroudi, M., Cora, D., Bosia, C., Osella, M. and Caselle, M. (2011) A curated database of miRNA mediated feedforward loops involving MYC as master regulator. PLoS One, 6, e14742.
13. Friard, O., Re, A., Taverna, D., De Bortoli, M. and Cora, D. (2010) CircuitsDB: a database of mixed microRNA/transcription factor feed-forward regulatory circuits in human and mouse. BMC Bioinformatics, 11, 435.
14. McLendon, R., Friedman, A., Bigner, D., Van Meir, E.G., Brat, D.J., Mastrogianakis, G.M., Olson, J.J., Mikkelsen, T., Lehman, N., Aldape, K. et al. (2008) Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature, 455, 1061-1068.
15. Hudson, T.J., Anderson, W., Artez, A., Barker, A.D., Bell, C., Bernabe, R.R., Bhan, M.K., Calvo, F., Eerola, I., Gerhard, D.S. et al. (2010) International network of cancer genome projects. Nature, 464, 993-998.
16. Fulci, V., Colombo, T., Chiaretti, S., Messina, M., Citarella, F., Tavolaro, S., Guarini, A., Foa, R. and Macino, G. (2009) Characterization of B-and T-lineage acute lymphoblastic leukemia by integrated analysis of MicroRNA and mRNA expression profiles. Genes Chromosomes Cancer, 48, 1069-1082.
17. Qin, L.X. (2008) An integrative analysis of microRNA and mRNA expression-a case study. Cancer Inform., 6, 369-379.
18. Guo, A.Y., Sun, J., Jia, P. and Zhao, Z. A novel microRNA and transcription factor mediated regulatory network in schizophrenia. BMC Syst. Biol., 4, 10.
19. Shalgi, R., Lieber, D., Oren, M. and Pilpel, Y. (2007) Global and local architecture of the mammalian microRNA-transcription factor regulatory network. PLoS Comput. Biol., 3, e131.
20. Re, A., Cora, D., Taverna, D. and Caselle, M. (2009) Genome-wide survey of microRNA-transcription factor feed-forward regulatory circuits in human. Mol. Biosyst., 5, 854-867.
21. Lenhard, B. and Wasserman, W.W. (2002) TFBS: computational framework for transcription factor binding site analysis. Bioinformatics, 18, 1135-1136. (Pubitemid 34919236)
22. Kozomara, A. and Griffiths-Jones, S. (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res., 39, D152-D157.
23. Kim, Y.K. and Kim, V.N. (2007) Processing of intronic microRNAs. EMBO J., 26, 775-783.
24. Lagos-Quintana, M., Rauhut, R., Lendeckel, W. and Tuschl, T. (2001) Identification of novel genes coding for small expressed RNAs. Science, 294, 853-858. (Pubitemid 33032103)
25. Rajewsky, N. (2006) microRNA target predictions in animals. Nat. Genet., 38(Suppl.), S8-S13.
26. Kertesz, M., Iovino, N., Unnerstall, U., Gaul, U. and Segal, E. (2007) The role of site accessibility in microRNA target recognition. Nat. Genet., 39, 1278-1284. (Pubitemid 47482690)
27. Sethupathy, P., Megraw, M. and Hatzigeorgiou, A.G. (2006) A guide through present computational approaches for the identification of mammalian microRNA targets. Nat. Methods, 3, 881-886. (Pubitemid 44614721)
28. Selbach, M., Schwanhausser, B., Thierfelder, N., Fang, Z., Khanin, R. and Rajewsky, N. (2008) Widespread changes in protein synthesis induced by microRNAs. Nature, 455, 58-63.
29. Baek, D., Villen, J., Shin, C., Camargo, F.D., Gygi, S.P. and Bartel, D.P. (2008) The impact of microRNAs on protein output. Nature, 455, 64-71.
30. Barrett, T., Troup, D.B., Wilhite, S.E., Ledoux, P., Evangelista, C., Kim, I.F., Tomashevsky, M., Marshall, K.A., Phillippy, K.H., Sherman, P.M. et al. (2011) NCBI GEO: archive for functional genomics data sets-10 years on. Nucleic Acids Res., 39, D1005-D1010.
31. Parkinson, H., Sarkans, U., Kolesnikov, N., Abeygunawardena, N., Burdett, T., Dylag, M., Emam, I., Farne, A., Hastings, E., Holloway, E. et al. (2011) ArrayExpress update-an archive of microarray and high-throughput sequencing-based functional genomics experiments. Nucleic Acids Res., 39, D1002-D1004.
32. Burchard, J., Zhang, C., Liu, A.M., Poon, R.T., Lee, N.P., Wong, K.F., Sham, P.C., Lam, B.Y., Ferguson, M.D., Tokiwa, G. et al. (2010) microRNA-122 as a regulator of mitochondrial metabolic gene network in hepatocellular carcinoma. Mol. Syst. Biol., 6, 402.
33. Liu, H., Brannon, A.R., Reddy, A.R., Alexe, G., Seiler, M.W., Arreola, A., Oza, J.H., Yao, M., Juan, D., Liou, L.S. et al. (2010) Identifying mRNA targets of microRNA dysregulated in cancer: with application to clear cell Renal Cell Carcinoma. BMC Syst. Biol., 4, 51.
34. Taylor, B.S., Schultz, N., Hieronymus, H., Gopalan, A., Xiao, Y., Carver, B.S., Arora, V.K., Kaushik, P., Cerami, E., Reva, B. et al. (2010) Integrative genomic profiling of human prostate cancer. Cancer Cell, 18, 11-22.
35. Palmer, R.D., Murray, M.J., Saini, H.K., van Dongen, S., Abreu-Goodger, C., Muralidhar, B., Pett, M.R., Thornton, C.M., Nicholson, J.C., Enright, A.J. et al. (2010) Malignant germ cell tumors display common microRNA profiles resulting in global changes in expression of messenger RNA targets. Cancer Res., 70, 2911-2923.
36. Puissegur, M.P., Mazure, N.M., Bertero, T., Pradelli, L., Grosso, S., Robbe-Sermesant, K., Maurin, T., Lebrigand, K., Cardinaud, B., Hofman, V. et al. (2011) miR-210 is overexpressed in late stages of lung cancer and mediates mitochondrial alterations associated with modulation of HIF-1 activity. Cell Death Differ., 18, 465-478.
37. Yanaihara, N., Caplen, N., Bowman, E., Seike, M., Kumamoto, K., Yi, M., Stephens, R.M., Okamoto, A., Yokota, J., Tanaka, T. et al. (2006) Unique microRNA molecular profiles in lung cancer diagnosis and prognosis. Cancer Cell, 9, 189-198. (Pubitemid 43357945)
38. Fujiwara, T., Hiramatsu, M., Isagawa, T., Ninomiya, H., Inamura, K., Ishikawa, S., Ushijima, M., Matsuura, M., Jones, M.H., Shimane, M. et al. (2012) ASCL1-coexpression profiling but not single gene expression profiling defines lung adenocarcinomas of neuroendocrine nature with poor prognosis. Lung Cancer, 75, 119-125.
39. Wang, J., Lu, M., Qiu, C. and Cui, Q. (2010) TransmiR: a transcription factor-microRNA regulation database. Nucleic Acids Res., 38, D119-D122.
40. Cho, W.C. (2007) OncomiRs: the discovery and progress of microRNAs in cancers. Mol. Cancer, 6, 60.
41. Garzon, R., Marcucci, G. and Croce, C.M. Targeting microRNAs in cancer: rationale, strategies and challenges. Nat. Rev. Drug Discov., 9, 775-789.
42. Hanahan, D. and Weinberg, R.A. Hallmarks of cancer: the next generation. Cell, 144, 646-674.
43. Meyer, N. and Penn, L.Z. (2008) Reflecting on 25 years with MYC. Nat. Rev. Cancer, 8, 976-990.
44. Dews, M., Homayouni, A., Yu, D., Murphy, D., Sevignani, C., Wentzel, E., Furth, E.E., Lee, W.M., Enders, G.H., Mendell, J.T. et al. (2006) Augmentation of tumor angiogenesis by a Myc-activated microRNA cluster. Nat. Genet., 38, 1060-1065. (Pubitemid 44325933)
45. Mestdagh, P., Fredlund, E., Pattyn, F., Schulte, J.H., Muth, D., Vermeulen, J., Kumps, C., Schlierf, S., De Preter, K., Van Roy, N. et al. MYCN/c-MYC-induced microRNAs repress coding gene networks associated with poor outcome in MYCN/c-MYC-activated tumors. Oncogene, 29, 1394-1404.
46. Liang, Y., Li, W.W., Yang, B.W., Tao, Z.H., Sun, H.C., Wang, L., Xia, J.L., Qin, L.X., Tang, Z.Y., Fan, J. et al. (2012) Aryl hydrocarbon receptor nuclear translocator is associated with tumor growth and progression of hepatocellular carcinoma. Int. J. Cancer, 130, 1745-1754.
47. Xiao, X., Li, B.X., Mitton, B., Ikeda, A. and Sakamoto, K.M. Targeting CREB for cancer therapy: friend or foe. Curr. Cancer Drug Targets, 10, 384-391.
48. Aggarwal, S., Kim, S.W., Ryu, S.H., Chung, W.C. and Koo, J.S. (2008) Growth suppression of lung cancer cells by targeting cyclic AMP response element-binding protein. Cancer Res., 68, 981-988. (Pubitemid 351272215)
49. Kumar, A.P., Bhaskaran, S., Ganapathy, M., Crosby, K., Davis, M.D., Kochunov, P., Schoolfield, J., Yeh, I.T., Troyer, D.A. and Ghosh, R. (2007) Akt/cAMP-responsive element binding protein/cyclin D1 network: a novel target for prostate cancer inhibition in transgenic adenocarcinoma of mouse prostate model mediated by Nexrutine, a Phellodendron amurense bark extract. Clin. Cancer Res., 13, 2784-2794. (Pubitemid 46788048)