A systematic analysis of miRNA-mRNA paired variations reveals widespread miRNA misregulation in breast cancer

BioMed Research International

Volumn 2014, Issue , 2014, Pages

  Zhong, Lei ^a   Zhu, Kuixi ^b   Jin, Nana ^b   Wu, Deng ^b   Zhang, Jianguo ^a   Guo, Baoliang ^a   Yan, Zhaoqi ^a   Zhang, Qingyuan ^b  

^a THE SECOND AFFILIATED HOSPITAL OF HARBIN MEDICAL UNIVERSITY   (China)

^b HARBIN MEDICAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

EPIDERMAL GROWTH FACTOR RECEPTOR 2; ESTROGEN RECEPTOR; MESSENGER RNA; MICRORNA; ERBB2 PROTEIN, HUMAN; ESTROGEN RECEPTOR ALPHA; ESTROGEN RECEPTOR ALPHA, HUMAN; PROTEIN P53; TP53 PROTEIN, HUMAN;

ARTICLE; BREAST CANCER; CANCER SURVIVAL; GENE EXPRESSION; HUMAN; HUMAN CELL; MOUSE; NONHUMAN; RNA DEGRADATION; SURVIVAL TIME; BIOSYNTHESIS; BREAST TUMOR; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; PATHOLOGY; SURVIVAL;

BREAST NEOPLASMS; ESTROGEN RECEPTOR ALPHA; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; MICRORNAS; RECEPTOR, ERBB-2; RNA, MESSENGER; SURVIVAL ANALYSIS; TUMOR SUPPRESSOR PROTEIN P53;

EID: 84902190191     PISSN: 23146133     EISSN: 23146141     Source Type: Journal    
DOI: 10.1155/2014/291280     Document Type: Article

References (48)

1. Iorio M. V., Ferracin M., Liu C. G., Veronese A., Spizzo R., Sabbioni S., Magri E., Pedriali M., Fabbri M., Campiglio M., Ménard S., Palazzo J. P., Rosenberg A., Musiani P., Volinia S., Nenci I., Calin G. A., Querzoli P., Negrini M., Croce C. M., MicroRNA gene expression deregulation in human breast cancer. Cancer Research 2005 65 16 7065 7070 2-s2.0-23844555119 10.1158/0008-5472.CAN-05-1783 (Pubitemid 41161233)
2. Bartel D. P., MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004 116 2 281 297 2-s2.0-0347444723 10.1016/S0092-8674(04)00045-5 (Pubitemid 38167318)
3. Bueno M. J., de Castro I. P., Malumbres M., Control of cell proliferation pathways by microRNAs. Cell Cycle 2008 7 20 3143 3148 2-s2.0-54049156472
4. Bartel D. P., MicroRNAs: target recognition and regulatory functions. Cell 2009 136 2 215 233 2-s2.0-58249088751 10.1016/j.cell.2009.01.002
5. Kusenda B., Mraz M., Mayer J., Pospisilova S., MicroRNA biogenesis, functionality and cancer relevance. Biomedical Papers of the Medical Faculty of the University Palacký 2006 150 2 205 215 10.5507/bp.2006.029
6. Zhang R., Su B., Small but influential: the role of microRNAs on gene regulatory network and 3′UTR evolution. Journal of Genetics and Genomics 2009 36 1 1 6 2-s2.0-58249084043 10.1016/S1673-8527(09)60001-1
7. Vasudevan S., Tong Y., Steitz J. A., Switching from repression to activation: microRNAs can up-regulate translation. Science 2007 318 5858 1931 1934 2-s2.0-36749026906 10.1126/science.1149460
8. Lai E. C., Wiel C., Rubin G. M., Complementary miRNA pairs suggest a regulatory role for miRNA:miRNA duplexes. RNA 2004 10 2 171 175 2-s2.0-1642540283 10.1261/rna.5191904 (Pubitemid 38129821)
9. Yu J., Liu F., Yin P., Zhu X., Cheng G., Wang N., Lu A., Luan W., Zhang N., Li J., Guo K., Yin Y., Wang H., Xu J., Integrating miRNA and mRNA expression profiles in response to heat stress-induced injury in rat small intestine. Functional & Integrative Genomics 2011 11 2 203 213 10.1007/s10142-010-0198- 8
10. Liu B., Liu L., Tsykin A., Goodall G. J., Green J. E., Zhu M., Kim C. H., Li J., Identifying functional miRNA-mRNA regulatory modules with correspondence latent dirichlet allocation. Bioinformatics 2010 26 24 3105 3111 2-s2.0-79951751828 10.1093/bioinformatics/btq576
11. Nielsen J. A., Lau P., Maric D., Barker J. L., Hudson L. D., Integrating microRNA and mRNA expression profiles of neuronal progenitors to identify regulatory networks underlying the onset of cortical neurogenesis. BMC Neuroscience 2009 10 article 98 2-s2.0-69849087551 10.1186/1471-2202-10-98
12. Maire G., Martin J. W., Yoshimoto M., Chilton-MacNeill S., Zielenska M., Squire J. A., Analysis of miRNA-gene expression-genomic profiles reveals complex mechanisms of microRNA deregulation in osteosarcoma. Cancer Genetics 2011 204 3 138 146 2-s2.0-79960673180 10.1016/j.cancergen.2010.12.012
13. Wang C., Su Z., Sanai N., Xue X., Lu L., Chen Y., Wu J., Zheng W., Zhuge Q., Wu Z. B., microRNA expression profile and differentially-expressed genes in prolactinomas following bromocriptine treatment. Oncology Reports 2012 27 5 1312 1320 0.3892/or.2012.1690
14. Tsai K. W., Liao Y. L., Wu C. W., Hu L. Y., Li S. C., Chan W. C., Ho M. R., Lai C. H., Kao H. W., Fang W. L., Huang K. H., Lin W. C., Aberrant hypermethylation of miR-9 genes in gastric cancer. Epigenetics 2011 6 10 1189 1197 2-s2.0-80053450990 10.4161/epi.6.10.16535
15. Dudziec E., Gogol-Döring A., Cookson V., Chen W., Catto J., Integrated epigenome profiling of repressive histone modifications, DNA methylation and gene expression in normal and malignant urothelial cells. PLoS ONE 2012 7 3 e32750 10.1371/journal.pone.0032750
16. Enerly E., Steinfeld I., Kleivi K., Leivonen S. K., Aure M. R., Russnes H. G., Rønneberg J. A., Johnsen H., Navon R., Rødland E., Mäkelä R., Naume B., Perälä M., Kallioniemi O., Kristensen V. N., Yakhini Z., Børresen-Dale A. L., miRNA-mRNA integrated analysis reveals roles for miRNAs in primary breast tumors. PLoS ONE 2011 6 2 e16915 10.1371/journal.pone.0016915
17. Vergoulis T., Vlachos I. S., Panagiotis Alexiou, TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support. Nucleic Acids Research 2012 40 database issue D222 D229 10.1093/nar/gkr1161
18. Eden E., Navon R., Steinfeld I., Lipson D., Yakhini Z., GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinformatics 2009 10 article 48 2-s2.0-60849139395 10.1186/1471-2105-10-48
19. Menard S., Tagliabue E., Campiglio M., Pupa S. M., Role of HER2 gene overexpression in breast carcinoma. Journal of Cellular Physiology 2000 182 2 150 162 (Pubitemid 30022667)
20. Cheng C., Fu X., Alves P., Gerstein M., MRNA expression profiles show differential regulatory effects of microRNAs between estrogen receptor-positive and estrogen receptor-negative breast cancer. Genome Biology 2009 10 9, article R90 2-s2.0-76249103552 10.1186/gb-2009-10-9-r90
21. Suzuki H. I., Yamagata K., Sugimoto K., Iwamoto T., Kato S., Miyazono K., Modulation of microRNA processing by p53. Nature 2009 460 7254 529 533 2-s2.0-67749143728 10.1038/nature08199
22. Calin G. A., Sevignani C., Dumitru C. D., Hyslop T., Noch E., Yendamuri S., Shimizu M., Rattan S., Bullrich F., Negrini M., Croce C. M., Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers. Proceedings of the National Academy of Sciences of the United States of America 2004 101 9 2999 3004 2-s2.0-12144290519 10.1073/pnas.0307323101 (Pubitemid 38327724)
23. Rakha E. A., Reis-Filho J. S., Ellis I. O., Basal-like breast cancer: a critical review. Journal of Clinical Oncology 2008 26 15 2568 2581 2-s2.0-45149094267 10.1200/JCO.2007.13.1748
24. Blenkiron C., Goldstein L. D., Thorne N. P., Spiteri I., Chin S. F., Dunning M. J., Barbosa-Morais N. L., Teschendorff A. E., Green A. R., Ellis I. O., Tavaré S., Caldas C., Miska E. A., MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype. Genome Biology 2007 8 10, article R214 2-s2.0-37549024511 10.1186/gb-2007-8-10-r214 (Pubitemid 351917463)
25. Clark G. M., McGuire W. L., Prognostic factors in primary breast cancer. Breast Cancer Research and Treatment 1983 3 supplement 1 S69 S72 10.1007/BF01855130 2-s2.0-0020958764
26. Early Breast Cancer Trialists' Collaborative Group, Effects of chemotherapy and hormonal therapy for early breast cancer on recurrence and 15-year survival: an overview of the randomised trials. The Lancet 2005 365 9472 1687 1717 10.1016/S0140-6736(05)66544-0 (Pubitemid 40719106)
27. Thorpe S. M., Estrogen and progesterone receptor determinations in breast cancer: technology, biology and clinical significance. Acta Oncologica 1988 27 1 1 19 2-s2.0-0023897749
28. Rocha Simonini P. D. S., Breiling A., Gupta N., Malekpour M., Youns M., Omranipour R., Malekpour F., Volinia S., Croce C. M., Najmabadi H., Diederichs S., Sahin Ö., Mayer D., Lyko F., Hoheisel J. D., Riazalhosseini Y., Epigenetically deregulated microRNA-375 is involved in a positive feedback loop with estrogen receptor α in breast cancer cells. Cancer Research 2010 70 22 9175 9184 2-s2.0-78549249846 10.1158/0008-5472.CAN-10-1318
29. Kelley K. M. M., Rowan B. G., Ratnam M., Modulation of the folate receptor α gene by the estrogen receptor: mechanism and implications in tumor targeting. Cancer Research 2003 63 11 2820 2828 2-s2.0-0038615895 (Pubitemid 36667153)
30. Mitchell P. J., Sara E. A., Crompton M. R., A novel adaptor-like protein which is a substrate for the non-receptor tyrosine kinase, BRK. Oncogene 2000 19 37 4273 4282 2-s2.0-0034738966
31. Ikeda O., Sekine Y., Yasui T., Oritani K., Sugiyma K., Muromoto R., Ohbayashi N., Yoshimura A., Matsuda T., STAP-2 negatively regulates both canonical and noncanonical NF- B activation induced by Epstein-Barr virus-derived latent membrane protein. Molecular and Cellular Biology 2008 28 16 5027 5042 2-s2.0-49449084104 10.1128/MCB.00194-08
32. Ikeda O., Sekine Y., Mizushima A., Nakasuji M., Miyasaka Y., Yamamoto C., Muromoto R., Nanbo A., Oritani K., Yoshimura A., Matsuda T., Interactions of STAP-2 with Brk and STAT3 participate in cell growth of human breast cancer cells. Journal of Biological Chemistry 2010 285 49 38093 38103 2-s2.0-78649671506 10.1074/jbc.M110.162388
33. Ikeda O., Mizushima A., Sekine Y., Yamamoto C., Muromoto R., Nanbo A., Oritani K., Yoshimura A., Matsuda T., Involvement of STAP-2 in Brk-mediated phosphorylation and activation of STAT5 in breast cancer cells. Cancer Science 2011 102 4 756 761 2-s2.0-79952774372 10.1111/j.1349-7006.2010.01842.x
34. Biswas D. K., Cruz A. P., Gansberger E., Pardee A. B., Epidermal growth factor-induced nuclear factor B activation: a major pathway of cell-cycle progression in estrogen-receptor negative breast cancer cells. Proceedings of the National Academy of Sciences of the United States of America 2000 97 15 8542 8547 2-s2.0-0034682527 10.1073/pnas.97.15.8542 (Pubitemid 30639709)
35. Valladares A., Hernández N. G., Gómez F. S., Curiel-Quezada E., Madrigal-Bujaidar E., Vergara M. D., Martínez M. S., Arenas Aranda D. J., Genetic expression profiles and chromosomal alterations in sporadic breast cancer in Mexican women. Cancer Genetics and Cytogenetics 2006 170 2 147 151 2-s2.0-33749182371 10.1016/j.cancergencyto.2006.06.002 (Pubitemid 44472569)
36. Wei X., Xu H., Kufe D., Human mucin 1 oncoprotein represses transcription of the p53 tumor suppressor gene. Cancer Research 2007 67 4 1853 1858 2-s2.0-33847752147 10.1158/0008-5472.CAN-06-3063 (Pubitemid 46383412)
37. Nguyen T., Kuo C., Nicholl M. B., Sim M. S., Turner R. R., Morton D. L., Hoon D. S. B., Downregulation of microRNA-29c is associated with hypermethylation of tumor-related genes and disease outcome in cutaneous melanoma. Epigenetics 2011 6 3 388 394 2-s2.0-79952421239 10.4161/epi.6.3.14056
38. Toledo F., Bardot B., Cancer: three birds with one stone. Nature 2009 460 7254 466 467 2-s2.0-67749116091 10.1038/460466a
39. Charafe-Jauffret E., Ginestier C., Monville F., Finetti P., Adélaïde J., Cervera N., Fekairi S., Xerri L., Jacquemier J., Birnbaum D., Bertucci F., Gene expression profiling of breast cell lines identifies potential new basal markers. Oncogene 2006 25 15 2273 2284 2-s2.0-31044441241 10.1038/sj.onc.1209254
40. Kluger H. M., Dolled-Filhart M., Rodov S., Kacinski B. M., Camp R. L., Rimm D. L., Macrophage colony-stimulating factor-1 receptor expression is associated with poor outcome in breast cancer by large cohort tissue microarray analysis. Clinical Cancer Research 2004 10 1 173 177 2-s2.0-1642576136 10.1158/1078-0432.CCR-0699-3 (Pubitemid 38114176)
41. Pinhel I., Hills M., Drury S., Salter J., Sumo G., A'Hern R., Bliss J. M., Sestak I., Cuzick J., Barrett-Lee P., Harris A., Dowsett M., Bliss M., Johnson L., Lawrence D., Price D., Peto J., Yarnold J., Barrett-Lee P., Brunt A. M., Dodwell D., Earl H., Fernando I., Foster L., George W. D., Harnett A. M., Perren T., Poole C., Raina V., Robinson A., ER and HER2 expression are positively correlated in HER2 non-overexpressing breast cancer. Breast Cancer Research 2012 14 2, article R46 2-s2.0-84858052884 10.1186/bcr3145
42. Wilson C. A., Cajulis E. E., Green J. L., Olsen T. M., Chung Y. A., Damore M. A., Dering J., Calzone F. J., Slamon D. J., HER-2 overexpression differentially alters transforming growth factor-beta responses in luminal versus mesenchymal human breast cancer cells. Breast Cancer Research 2005 7 6 R1058 R1079 10.1186/bcr1343
43. Ramsay R. G., Gonda T. J., MYB function in normal and cancer cells. Nature Reviews Cancer 2008 8 7 523 534 2-s2.0-45849137069 10.1038/nrc2439 (Pubitemid 351881853)
44. Mucenski M. L., McLain K., Kier A. B., Swerdlow S. H., Schreiner C. M., Miller T. A., Pietryga D. W., Scott W. J. Jr., Potter S. S., A functional c-myb gene is required for normal murine fetal hepatic hematopoiesis. Cell 1991 65 4 677 689 2-s2.0-0025821494 10.1016/0092-8674(91)90099-K
45. Li Y. M., Pan Y., Wei Y., Cheng X., Zhou B. P., Tan M., Zhou X., Xia W., Hortobagyi G. N., Yu D., Hung M. C., Upregulation of CXCR4 is essential for HER2-mediated tumor metastasis. Cancer Cell 2004 6 5 459 469 2-s2.0-7944223780 10.1016/j.ccr.2004.09.027 (Pubitemid 39469982)
46. Abramson V. G., Troxel A. B., Feldman M., Mies C., Wang Y., Sherman L., Mcnally S., Diehl A., Demichele A., Cyclin D1b in human breast carcinoma and coexpression with cyclin D1a is associated with poor outcome. Anticancer Research 2010 30 4 1279 1285 2-s2.0-77953732182
47. Anaganti S., Fernández-Cuesta L., Langerød A., Hainaut P., Olivier M., p53-dependent repression of focal adhesion kinase in response to estradiol in breast cancer cell-lines. Cancer Letters 2011 300 2 215 224 2-s2.0-78649633119 10.1016/j.canlet.2010.10.008
48. Yang Y., Han L., Yuan Y., Li J., Hei N., Liang H., Gene co-expression network analysis reveals common system-level properties of prognostic genes across cancer types. Nature Communications 2014 5 article 3231 10.1038/ncomms4231