Exploring microRNA-mediated alteration of EGFR signaling pathway in non-small cell lung cancer using an mRNA: MiRNA regression model supported by target prediction databases

Genomics

Volumn 104, Issue 6, 2014, Pages 504-511

  Wang, Fengfeng ^a   Chan, Lawrence W C ^a   Law, Helen K W ^a   Cho, William C S ^b   Tang, Petrus ^c   Yu, Jun ^d   Shyu, Chi Ren ^e   Wong, S C Cesar ^a   Yip, S P ^a   Yung, Benjamin Y M ^a  

^a HONG KONG POLYTECHNIC UNIVERSITY   (Hong Kong)

^b QUEEN ELIZABETH HOSPITAL   (Hong Kong)

^c CHANG GUNG UNIVERSITY   (Taiwan)

^d Chinese Academy of Sciences   (China)

^e University of Missouri   (United States)

Author keywords

EGFR signaling pathway; Microarray analysis; MiRNA; Non small cell lung cancer; Regression model

Indexed keywords

EPIDERMAL GROWTH FACTOR; FOCAL ADHESION KINASE 1; MICRORNA; MICRORNA 145; MICRORNA 199A; UNCLASSIFIED DRUG; VASCULOTROPIN RECEPTOR; EPIDERMAL GROWTH FACTOR RECEPTOR; MESSENGER RNA; PTK2 PROTEIN, HUMAN;

APOPTOSIS; ARTICLE; CANCER GROWTH; DATA BASE; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORK; GENETIC ASSOCIATION; HUMAN; HUMAN GENOME; MICROARRAY ANALYSIS; NON SMALL CELL LUNG CANCER; PREDICTION; BIOLOGICAL MODEL; GENE EXPRESSION REGULATION; GENETICS; LUNG TUMOR; METABOLISM; REGRESSION ANALYSIS; SIGNAL TRANSDUCTION;

CARCINOMA, NON-SMALL-CELL LUNG; FOCAL ADHESION KINASE 1; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; LUNG NEOPLASMS; MICRORNAS; MODELS, GENETIC; RECEPTOR, EPIDERMAL GROWTH FACTOR; REGRESSION ANALYSIS; RNA, MESSENGER; SIGNAL TRANSDUCTION;

EID: 84918786483     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2014.09.004     Document Type: Article

References (50)

1. Nacht M., Dracheva T., Gao Y., Fujii T., Chen Y., Player A., Akmaev V., Cook B., Dufault M., Zhang M., Zhang W., Guo M., Curran J., Han S., Sidransky D., Buetow K., Madden S.L., Jen J. Molecular characteristics of non-small cell lung cancer. Proc. Natl. Acad. Sci. U. S. A. 2001, 98(26):15203-15208.
2. Breuer R.H.J., Postmus P.E., Smit E.F. Molecular pathology of non-small-cell lung cancer. Respiration 2005, 72(3):313-330.
3. Ma L., Huang Y., Zhu W., Zhou S., Zhou J., Zeng F., Liu X., Zhang Y., Yu J. An integrated analysis of miRNA and mRNA expressions in non-small cell lung cancers. PLoS ONE 2011, 6(10):e26502.
4. Normanno N., Luca A.D., Bianco C., Strizzib L., Mancinoa M., Maielloa M.R., Carotenutoa A., De Feoa G., Caponigroc F., Salomonb D.S. Epidermal growth factor receptor (EGFR) signaling in cancer. Gene 2006, 366(1):2-16.
5. Lynch T.J., Bell D.W., Sordella R., Gurubhagavatula S., Okimoto R.A., Brannigan B.W., Harris P.L., Haserlat S.M., Supko J.G., Haluska F.G., Louis D.N., Christiani D.C., Settleman J., Haber D.A. Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib. N. Engl. J. Med. 2004, 350(21):2129-2139.
6. Scagliotti G.V., Selvaggi G., Novello S., Hirsch F.R. The biology of epidermal growth factor receptor in lung cancer. Clin. Cancer Res. 2004, 10(12):4227s-4232s.
7. Webster R.J., Giles K.M., Price K.J., Zhang P.M., Mattick J.S., Leedman P.J. Regulation of epidermal growth factor receptor signaling in human cancer cells by microRNA-7. J. Biol. Chem. 2009, 284(9):5731-5741.
8. Kumar M.S., Lu J., Mercer K.L., Golub T.R., Jacks T. Impaired microRNA processing enhances cellular transformation and tumorigenesis. Nat. Genet. 2007, 39(5):673-677.
9. Seggerson K., Tang L., Moss E.G. Two genetic circuits repress the Caenorhabditis elegans heterochronic gene lin-28 after translation initiation. Dev. Biol. 2002, 243(2):215-225.
10. Wu L., Belasco J.G. Micro-RNA regulation of the mammalian lin-28 gene during neuronal differentiation of embryonal carcinoma cells. Mol. Cell. Biol. 2005, 25(21):9198-9208.
11. Bagga S., Bracht J., Hunter S., Massirer K., Holtz J., Eachus R., Pasquinelli A.E. Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation. Cell 2005, 122(4):553-563.
12. Cho W.C. MicroRNAs in cancer - from research to therapy. Biochim. Biophys. Acta 2010, 1805(2):209-217.
13. Bartel D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004, 116(2):281-297.
14. Ambros V. The functions of animal microRNAs. Nature 2004, 431(7006):350-355.
15. Hammond S.M. MicroRNAs as oncogenes. Curr. Opin. Genet. Dev. 2006, 16(1):4-9.
16. Bueno M.J., Pérez de Castro I., Malumbres M. Control of cell proliferation pathways by microRNAs. Cell Cycle 2008, 7(20):3143-3148.
17. Chen C.Y., Chen S.T., Fuh C.S., Juan H.F., Huang H.C. Coregulation of transcription factors and microRNAs in human transcriptional regulatory network. BMC Bioinforma. 2011, 12:S41.
18. Cui Q., Yu Z., Pan Y., Purisima E.O., Wang E. MicroRNAs preferentially target the genes with high transcriptional regulation complexity. Biochem. Biophys. Res. Commun. 2007, 352(3):733-738.
19. Chou Y.T., Lin H.H., Lien Y.C., Wang Y.H., Hong C.F., Kao Y.R., Lin S.C., Chang Y.C., Lin S.Y., Chen S.J., Chen H.C., Yeh S.D., Wu C.W. EGFR promotes lung tumorigenesis by activating miR-7 through a Ras/ERK/Myc pathway that targets the Ets2 transcriptional repressor ERF. Cancer Res. 2010, 70(21):8822-8831.
20. Li J., Pandey V., Kessler T., Lehrach H., Wierling C. Modeling of miRNA and drug action in the EGFR signaling pathway. PLoS ONE 2012, 7(1):e30140.
21. Baskerville S., Bartel D.P. Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA 2005, 11(3):241-247.
22. Wang Y.P., Li K.B. Correlation of expression profiles between microRNAs and mRNA targets using NCI-60 data. BMC Genomics 2009, 10:218.
23. Androsavich J.R., Chau B.N., Bhat B., Linsley P.S., Walter N.G. Disease-linked microRNA-21 exhibits drastically reduced mRNA binding and silencing activity in healthy mouse liver. RNA 2012, 18(8):1510-1526.
24. Franco-Zorrilla J.M., Valli A., Todesco M., Mateos I., Puga M.I., Rubio-Somoza I., Leyva A., Weigel D., García J.A., Paz-Ares J. Target mimicry provides a new mechanism for regulation of microRNA activity. Nat. Genet. 2007, 39(8):1033-1037.
25. Ambs S., Prueitt R.L., Yi M., Hudson R.S., Howe T.M., Petrocca F., Wallace T.A., Liu C.G., Volinia S., Calin G.A., Yfantis H.G., Stephens R.M., Croce C.M. Genomic profiling of microRNA and messenger RNA reveals deregulated microRNA expression in prostate cancer. Cancer Res. 2008, 68(15):6162-6170.
26. Axtell M.J., Jan C., Rajagopalan R., Bartel D.P. A two-hit trigger for siRNA biogenesis in plants. Cell 2006, 127(3):565-577.
27. van Kouwenhove M., Kedde M., Agami R. MicroRNA regulation by RNA-binding proteins and its implications for cancer. Nat. Rev. Cancer 2011, 11(9):644-656.
28. Yang S., Raymond-Stintz M.A., Ying W., Zhang J., Lidke D.S., Steinberg S.L., Williams L., Oliver J.M., Wilson B.S. Mapping ErbB receptors on breast cancer cell membranes during signal transduction. J. Cell Sci. 2007, 120(16):2763-2773.
29. Thelemann A., Petti F., Griffin G., Iwata K., Hunt T., Settinari T., Fenyo D., Gibson N., Haley J.D. Phosphotyrosine signaling networks in epidermal growth factor receptor overexpressing squamous carcinoma cells. Mol. Cell. Proteomics 2005, 4(4):356-376.
30. Zhu H., Dougherty U., Robinson V., Mustafi R., Pekow J., Kupfer S., Li Y.C., Hart J., Goss K., Fichera A., Joseph L., Bissonnette M. EGFR signals downregulate tumor suppressors miR-143 and miR-145 in Western diet-promoted murine colon cancer: role of G1 regulators. Mol. Cancer Res. 2011, 9(7):960-975.
31. Cho W.C., Chow A.S., Au J.S. Restoration of tumour suppressor has-miR-145 inhibits cancer cell growth in lung adenocarcinoma patients with epidermal growth factor receptor mutation. Eur. J. Cancer 2009, 45(12):2197-2206.
32. Li Z., Cao Y., Jie Z., Liu Y., Li Y., Li J., Zhu G., Liu Z., Tu Y., Peng G., Lee D.W., Park S.S. miR-495 and miR-551a inhibit the migration and invasion of human gastric cancer cells by directly interacting with PRL-3. Cancer Lett. 2012, 323(1):41-47.
33. Hwang-Verslues W.W., Chang P.H., Wei P.C., Yang C.Y., Huang C.K., Kuo W.H., Shew J.Y., Chang K.J., Lee E.Y., Lee W.H. miR-495 is upregulated by E12/E47 in breast cancer stem cells, and promotes oncogenesis and hypoxia resistance via downregulation of E-cadherin and REDD1. Oncogene 2011, 30(21):2463-2474.
34. Jiang X., Huang H., Li Z., He C., Li Y., Chen P., Gurbuxani S., Arnovitz S., Hong G.M., Price C., Ren H., Kunjamma R.B., Neilly M.B., Salat J., Wunderlich M., Slany R.K., Zhang Y., Larson R.A., Le Beau M.M., Mulloy J.C., Rowley J.D., Chen J. miR-495 is a tumor-suppressor microRNA down-regulated in MLL-rearranged leukemia. Proc. Natl. Acad. Sci. U. S. A. 2012, 109(47):19397-19402.
35. Dudoit S., Yang Y.H., Callow M.J., Speed T.P. Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Stat. Sin. 2002, 12:111-139.
36. Showe M.K., Vachani A., Kossenkov A.V., Yousef M., Nichols C., Nikonova E.V., Chang C., Kucharczuk J., Tran B., Wakeam E., Yie T.A., Speicher D., Rom W.N., Albelda S., Showe L.C. Gene expression profiles in peripheral blood mononuclear cells can distinguish patients with non-small cell lung cancer from patients with nonmalignant lung disease. Cancer Res. 2009, 69(24):9202-9210.
37. Kossenkov A.V., Vachani A., Chang C., Nichols C., Billouin S., Horng W., Rom W.N., Albelda S.M., Showe M.K., Showe L.C. Resection of non-small cell lung cancers reverses tumor-induced gene expression changes in the peripheral immune system. Clin. Cancer Res. 2011, 17(18):5867-5877.
38. Barrett T., Edgar R. Gene Expression Omnibus (GEO): microarray data storage, submission, retrieval, and analysis. Methods Enzymol. 2006, 411:352-369.
39. Breslin T., Krogh M., Peterson C., Troein C. Signal transduction pathway profiling of individual tumor samples. BMC Bioinforma. 2005, 6:163.
40. Kapp A.V., Jeffrey S.S., Langerød A., Børresen-Dale A.L., Han W., Noh D.Y., Bukholm I.R., Nicolau M., Brown P.O., Tibshirani R. Discovery and validation of breast cancer subtypes. BMC Genomics 2006, 7:231.
41. Chan L.W., Wang F.F., Cho W.C. Genomic sequence analysis of EGFR regulation by microRNAs in lung cancer. Curr. Top. Med. Chem. 2012, 12(8):920-926.
42. Wang F., Wong S.C.C., Chan L.W.C., Cho W.C.S., Yip S.P., Yung B.Y.M. Multiple regression analysis of mRNA-miRNA associations in colorectal cancer pathway. BioMed. Res. Int. 2014, 676724. (Special Issue).
43. Li L., Xu J., Yang D., Tan X., Wang H. Computational approaches for microRNA studies: a review. Mamm. Genome 2010, 21(1-2):1-12.
44. Betel D., Koppal A., Agius P., Sander C., Leslie C. Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biol. 2010, 11(8):R90.
45. Portney L.G., Watkins M.P. Foundations of Clinical Research: Applications and Practice 2009, Upper Saddle River, NJ, Prentice Hall. 3rd edition.
46. Benjamini Y., Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B Methodol. 1995, 57(1):289-300.
47. Kohavi R. A study of cross-validation and bootstrap for accuracy estimation and model selection. 14th I.J.C.A.I. 1995, 2:1137-1143. (12).
48. Chen K. Forecasting systems reliability based on support vector regression with genetic algorithms. Reliab. Eng. Syst. Saf. 2007, 92(4):423-432.
49. Kiran N.R., Ravi V. Software reliability prediction by soft computing techniques. J. Syst. Softw. 2008, 81(4):576-583.
50. Appeltant L., Soriano M.C., Van der Sande G., Danckaert J., Massar S., Dambre J., Schrauwen B., Mirasso C.R., Fischer I. Information processing using a single dynamical node as complex system. Nat. Commun. 2011, 2(468):1-6.