Identifying MicroRNA-mRNA regulatory network in colorectal cancer by a combination of expression profile and bioinformatics analysis

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• 作者：Jihong Fu (1)
  Wentao Tang (2)
  Peng Du (1)
  Guanghui Wang (1)
  Wei Chen (1)
  Jingming Li (1)
  Yunxiang Zhu (1) (2)
  Jun Gao (3)
  Long Cui (1)
  
• 关键词：MicroRNAs ; Target mRNAs ; Colorectal cancer ; Microarray
• 刊名：BMC Systems Biology
• 出版年：2012
• 出版时间：December 2012
• 年：2012
• 卷：6
• 期：1
• 全文大小：478KB
• 参考文献：1. Gregory RI, Shiekhattar R: MicroRNA biogenesis and cancer. / Cancer Res 2005,65(9):3509鈥?512. CrossRef
  2. Esquela-Kerscher A, Slack FJ: Oncomirs - microRNAs with a role in cancer. / Nat Rev Cancer 2006,6(4):259鈥?69. CrossRef
  3. Schee K, Fodstad O, Flatmark K: MicroRNAs as biomarkers in colorectal cancer. / Am J Pathol 2010,177(4):1592鈥?599. CrossRef
  4. Xi Y, Formentini A, Chien M, Weir DB, Russo JJ, Ju J, Kornmann M: Prognostic Values of microRNAs in Colorectal Cancer. / Biomark Insights 2006, 2:113鈥?21.
  5. Slaby O, Svoboda M, Michalek J, Vyzula R: MicroRNAs in colorectal cancer: translation of molecular biology into clinical application. / Mol Cancer 2009, 8:102. CrossRef
  6. Ahmed FE, Jeffries CD, Vos PW, Flake G, Nuovo GJ, Sinar DR, Naziri W, Marcuard SP: Diagnostic microRNA markers for screening sporadic human colon cancer and active ulcerative colitis in stool and tissue. / Cancer Genomics Proteomics 2009,6(5):281鈥?95.
  7. Faber C, Kirchner T, Hlubek F: The impact of microRNAs on colorectal cancer. / Virchows Arch 2009,454(4):359鈥?67. CrossRef
  8. Huang Z, Huang D, Ni S, Peng Z, Sheng W, Du X: Plasma microRNAs are promising novel biomarkers for early detection of colorectal cancer. / Int J Cancer 2010,127(1):118鈥?26. CrossRef
  9. Li JM, Zhao RH, Li ST, Xie CX, Jiang HH, Ding WJ, Du P, Chen W, Yang M, Cui L: Down-regulation of fecal miR-143 and miR-145 as potential markers for colorectal cancer. / Saudi Med J 2012,33(1):24鈥?9.
  10. Motoyama K, Inoue H, Takatsuno Y, Tanaka F, Mimori K, Uetake H, Sugihara K, Mori M: Over- and under-expressed microRNAs in human colorectal cancer. / Int J Oncol 2009,34(4):1069鈥?075.
  11. Wang YX, Zhang XY, Zhang BF, Yang CQ, Chen XM, Gao HJ: Initial study of microRNA expression profiles of colonic cancer without lymph node metastasis. / J Dig Dis 2010,11(1):50鈥?4. CrossRef
  12. Mosakhani N, Sarhadi VK, Borze I, Karjalainen-Lindsberg ML, Sundstrom J, Ristamaki R, Osterlund P, Knuutila S: MicroRNA profiling differentiates colorectal cancer according to KRAS status. / Genes Chromosomes Cancer 2012,51(1):1鈥?. CrossRef
  13. Chen X, Guo X, Zhang H, Xiang Y, Chen J, Yin Y, Cai X, Wang K, Wang G, Ba Y, / et al.: Role of miR-143 targeting KRAS in colorectal tumorigenesis. / Oncogene 2009,28(10):1385鈥?392. CrossRef
  14. Monzo M, Navarro A, Bandres E, Artells R, Moreno I, Gel B, Ibeas R, Moreno J, Martinez F, Diaz T, / et al.: Overlapping expression of microRNAs in human embryonic colon and colorectal cancer. / Cell Res 2008,18(8):823鈥?33. CrossRef
  15. Ng EK, Chong WW, Jin H, Lam EK, Shin VY, Yu J, Poon TC, Ng SS, Sung JJ: Differential expression of microRNAs in plasma of patients with colorectal cancer: a potential marker for colorectal cancer screening. / Gut 2009,58(10):1375鈥?381. CrossRef
  16. Huang Z, Huang S, Wang Q, Liang L, Ni S, Wang L, Sheng W, He X, Du X: MicroRNA-95 promotes cell proliferation and targets sorting Nexin 1 in human colorectal carcinoma. / Cancer Res 2011,71(7):2582鈥?589. CrossRef
  17. Chang KH, Miller N, Kheirelseid EA, Ingoldsby H, Hennessy E, Curran CE, Curran S, Smith MJ, Regan M, McAnena OJ, / et al.: MicroRNA-21 and PDCD4 expression in colorectal cancer. / Eur J Surg Oncol 2011,37(7):597鈥?03. CrossRef
  18. Sun K, Wang W, Zeng JJ, Wu CT, Lei ST, Li GX: MicroRNA-221 inhibits CDKN1C/p57 expression in human colorectal carcinoma. / Acta Pharmacol Sin 2011,32(3):375鈥?84. CrossRef
  19. Wang H, Wu J, Meng X, Ying X, Zuo Y, Liu R, Kang T, Huang W: MicroRNA-342 Inhibits Colorectal Cancer Cell Proliferation and Invasion by Directly Targeting DNA Methyltransferase 1. / Carcinogenesis 2011, 7:1033鈥?2. CrossRef
  20. Lewis BP, Burge CB, Bartel DP: Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. / Cell 2005,120(1):15鈥?0. CrossRef
  21. Maziere P, Enright AJ: Prediction of microRNA targets. / Drug Discov Today 2007,12(11鈥?2):452鈥?58. CrossRef
  22. John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS: Human MicroRNA targets. / PLoS Biol 2004,2(11):e363. CrossRef
  23. Betel D, Wilson M, Gabow A, Marks DS, Sander C: The microRNA.org resource: targets and expression. / Nucleic Acids 2008, 36:149鈥?53. CrossRef
  24. Bartel DP: MicroRNAs: genomics, biogenesis, mechanism, and function. / Cell 2004,116(2):281鈥?97. CrossRef
  25. Cannell IG, Kong YW, Bushell M: How do microRNAs regulate gene expression? / Biochem Soc Trans 2008,36(Pt 6):1224鈥?231. CrossRef
  26. Peng X, Li Y, Walters KA, Rosenzweig ER, Lederer SL, Aicher LD, Proll S, Katze MG: Computational identification of hepatitis C virus associated microRNA-mRNA regulatory modules in human livers. / BMC Genomics 2009, 10:373. CrossRef
  27. Liu H, Brannon AR, Reddy AR, Alexe G, Seiler MW, Arreola A, Oza JH, Yao M, Juan D, Liou LS, / et al.: Identifying mRNA targets of microRNA dysregulated in cancer: with application to clear cell Renal Cell Carcinoma. / BMC Syst Biol 2010, 4:51. CrossRef
  28. Lopez-Romero P, Gonzalez MA, Callejas S, Dopazo A, Irizarry RA: Processing of Agilent microRNA array data. / BMC Res Notes 2010, 3:18. CrossRef
  29. Tusher VG, Tibshirani R, Chu G: Significance analysis of microarrays applied to the ionizing radiation response. / Proc Natl Acad Sci U S A 2001,98(9):5116鈥?121. CrossRef
  30. Smyth GK, Speed TP: Normalization of cDNA microarray data. / Methods 2003, 31:265鈥?73. CrossRef
  31. Ghaleb AM, Yang VW: The Pathobiology of Kruppel-like Factors in Colorectal Cancer. / Curr Colorectal Cancer Rep 2008,4(2):59鈥?4. CrossRef
  32. Caldwell GM, Jones C, Gensberg K, Jan S, Hardy RG, Byrd P, Chughtai S, Wallis Y, Matthews GM, Morton DG: The Wnt antagonist sFRP1 in colorectal tumorigenesis. / Cancer Res 2004,64(3):883鈥?88. CrossRef
  33. Qi J, Zhu YQ, Luo J, Tao WH: Hypermethylation and expression regulation of secreted frizzled-related protein genes in colorectal tumor. / World J Gastroenterol 2006,12(44):7113鈥?117.
  34. Yamada M, Ohnishi J, Ohkawara B, Iemura S, Satoh K, Hyodo-Miura J, Kawachi K, Natsume T, Shibuya H: NARF, an nemo-like kinase (NLK)-associated ring finger protein regulates the ubiquitylation and degradation of T cell factor/lymphoid enhancer factor (TCF/LEF). / J Biol Chem 2006,281(30):20749鈥?0760. CrossRef
  35. da Huang W, Sherman BT, Lempicki RA: Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. / Nat Protoc 2009,4(1):44鈥?7. CrossRef
  36. Caldwell GM, Jones CE, Taniere P, Warrack R, Soon Y, Matthews GM, Morton DG: The Wnt antagonist sFRP1 is downregulated in premalignant large bowel adenomas. / Br J Cancer 2006,94(6):922鈥?27. CrossRef
  37. Huang D, Yu B, Deng Y, Sheng W, Peng Z, Qin W, Du X: SFRP4 was overexpressed in colorectal carcinoma. / J Cancer Res Clin Oncol 2010,136(3):395鈥?01. CrossRef
  38. MacDonald BT, Tamai K, He X: Wnt/beta-catenin signaling: components, mechanisms, and diseases. / Dev Cell 2009,17(1):9鈥?6. CrossRef
  39. Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA: Sjoblom T, Barad O, Bentwich Z, Szafranska AE, Labourier E et al: The colorectal microRNAome. / Proc Natl Acad Sci U S A 2006,103(10):3687鈥?692. CrossRef
  40. Wang X, Wang J, Ma H, Zhang J, Zhou X: Downregulation of miR-195 correlates with lymph node metastasis and poor prognosis in colorectal cancer. / Med Oncol 2011,29(2):919鈥?7. CrossRef
  41. Chou YT, Lin HH, Lien YC, Wang YH, Hong CF, Kao YR, Lin SC, Chang YC, Lin SY, Chen SJ, / et al.: 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鈥?831. CrossRef
  42. Foekens JA, Sieuwerts AM, Smid M, Look MP, de Weerd V, Boersma AW, Klijn JG, Wiemer EA, Martens JW: Four miRNAs associated with aggressiveness of lymph node-negative, estrogen receptor-positive human breast cancer. / Proc Natl Acad Sci U S A 2008,105(35):13021鈥?3026. CrossRef
  43. Kefas B, Godlewski J, Comeau L, Li Y, Abounader R, Hawkinson M, Lee J, Fine H, Chiocca EA, Lawler S, / et al.: microRNA-7 inhibits the epidermal growth factor receptor and the Akt pathway and is down-regulated in glioblastoma. / Cancer Res 2008,68(10):3566鈥?572. CrossRef
  44. Webster RJ, Giles KM, Price KJ, Zhang PM, Mattick JS, Leedman PJ: Regulation of epidermal growth factor receptor signaling in human cancer cells by microRNA-7. / J Biol Chem 2009,284(9):5731鈥?741. CrossRef
  45. Sugimura R, Li L: Noncanonical Wnt signaling in vertebrate development, stem cells, and diseases. / Birth Defects Res C Embryo Today 2010,90(4):243鈥?56. CrossRef
  46. Polakis P: Wnt signaling and cancer. / Genes Dev 2000,14(15):1837鈥?851.
  
• 作者单位：Jihong Fu (1)
  Wentao Tang (2)
  Peng Du (1)
  Guanghui Wang (1)
  Wei Chen (1)
  Jingming Li (1)
  Yunxiang Zhu (1) (2)
  Jun Gao (3)
  Long Cui (1)
  
  1. Colorectal Surgery Department, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Kongjiang Road 1665, Shanghai, 200092, China
  2. Second Affiliated Hospital, Yangzhou University, Jiangsu, 225001, China
  3. Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Changhai Road 168, Shanghai, 200433, China
  

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