Application of microRNA and mRNA expression profiling on prognostic biomarker discovery for hepatocellular carcinoma

BMC Genomics

Volumn 15, Issue , 2014, Pages 1-13

  Wei, Lin ^a,b   Lian, Baofeng ^c,d   Zhang, Yuannv ^b   Li, Wei ^c   Gu, Jianren ^b   He, Xianghuo ^b   Xie, Lu ^c  

^a FUDAN UNIVERSITY   (China)

^b SHANGHAI JIAO TONG UNIVERSITY SCHOOL OF MEDICINE   (China)

^c SHANGHAI CENTER FOR BIOINFORMATION TECHNOLOGY   (China)

^d SHANGHAI JIAO TONG UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; MICRORNA; TUMOR MARKER;

ARTICLE; CANCER PROGNOSIS; CELL DIFFERENTIATION; CELL METABOLISM; CELL PROLIFERATION; CONTROLLED STUDY; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENOMIC INSTABILITY; HUMAN; HUMAN TISSUE; LIVER CELL CARCINOMA; MOLECULAR PATHOLOGY; SURVIVAL TIME; CHROMOSOME 1; GENE EXPRESSION REGULATION; GENETICS; LIVER; LIVER TUMOR; METABOLISM; METHODOLOGY; PROGNOSIS;

CARCINOMA, HEPATOCELLULAR; CELL DIFFERENTIATION; CHROMOSOMES, HUMAN, PAIR 1; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENOMIC INSTABILITY; HUMANS; LIVER; LIVER NEOPLASMS; METABOLISM; MICRORNAS; PROGNOSIS; RNA, MESSENGER; TUMOR MARKERS, BIOLOGICAL;

EID: 84904037894     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-S1-S13     Document Type: Article

References (69)

1. Forner A, Llovet JM, Bruix J: Hepatocellular carcinoma. Lancet 2012, 379:1245-1255.
2. El-Serag HB, Rudolph KL: Hepatocellular carcinoma: epidemiology and molecular carcinogenesis. Gastroenterology 2007, 132:2557-2576.
3. Teufel A, Staib F, Kanzler S, Weinmann A, Schulze-Bergkamen H, Galle PR: Genetics of hepatocellular carcinoma. World J Gastroenterol WJG 2007, 13:2271-2282.
4. Thorgeirsson SS, Grisham JW: Molecular pathogenesis of human hepatocellular carcinoma. Nat Genet 2002, 31:339-346.
5. Fattovich G, Stroffolini T, Zagni I, Donato F: Hepatocellular carcinoma in cirrhosis: incidence and risk factors. Gastroenterology 2004, 127(5 Suppl 1): S35-50.
6. Kumagi T, Hiasa Y, Hirschfield GM: Hepatocellular carcinoma for the nonspecialist. BMJ 2009, 339:b5039.
7. Tanaka M, Katayama F, Kato H, Tanaka H, Wang J, Qiao YL, Inoue M: Hepatitis B and C virus infection and hepatocellular carcinoma in China: a review of epidemiology and control measures. J Epidemiol Jpn Epidemiol Assoc 2011, 21:401-416.
8. Choi JK, Choi JY, Kim DG, Choi DW, Kim BY, Lee KH, Yeom YI, Yoo HS, Yoo OJ, Kim S: Integrative analysis of multiple gene expression profiles applied to liver cancer study. FEBS Lett 2004, 565:93-100.
9. Neo SY, Leow CK, Vega VB, Long PM, Islam AFM, Lai PBS, Liu ET, Ren EC: Identification of discriminators of hepatoma by gene expression profiling using a minimal dataset approach. Hepatol Baltim Md 2004, 39:944-953.
10. Tanaka S, Arii S, Yasen M, Mogushi K, Su NT, Zhao C, Imoto I, Eishi Y, Inazawa J, Miki Y, Tanaka H: Aurora kinase B is a predictive factor for the aggressive recurrence of hepatocellular carcinoma after curative hepatectomy. Br J Surg 2008, 95:611-619.
11. Wang K, Liu J, Yan ZL, Li J, Shi LH, Cong WM, Xia Y, Zou QF, Xi T, Shen F, Wang HY, Wu MC: Overexpression of aspartyl-(asparaginyl)-betahydroxylase in hepatocellular carcinoma is associated with worse surgical outcome. Hepatol Baltim Md 2010, 52:164-173.
12. Yang JD, Sun Z, Hu C, Lai J, Dove R, Nakamura I, Lee JS, Thorgeirsson SS, Kang KJ, Chu IS, Roberts LR: Sulfatase 1 and sulfatase 2 in hepatocellular carcinoma: associated signaling pathways, tumor phenotypes, and survival. Genes Chromosomes Cancer 2011, 50:122-135.
13. Ye QH, Qin LX, Forgues M, He P, Kim JW, Peng AC, Simon R, Li Y, Robles AI, Chen Y, Ma ZC, Wu ZQ, Ye SL, Liu YK, Tang ZY, Wang XW: Predicting hepatitis B virus-positive metastatic hepatocellular carcinomas using gene expression profiling and supervised machine learning. Nat Med 2003, 9:416-423.
14. Budhu A, Forgues M, Ye QH, Jia HL, He P, Zanetti KA, Kammula US, Chen Y, Qin LX, Tang ZY, Wang XW: Prediction of venous metastases, recurrence, and prognosis in hepatocellular carcinoma based on a unique immune response signature of the liver microenvironment. Cancer Cell 2006, 10:99-111.
15. Paradis V, Bièche I, Dargère D, Laurendeau I, Laurent C, Bioulac Sage P, Degott C, Belghiti J, Vidaud M, Bedossa P: Molecular profiling of hepatocellular carcinomas (HCC) using a large-scale real-time RT-PCR approach: determination of a molecular diagnostic index. Am J Pathol 2003, 163:733-741.
16. Huang T, Liu L, Liu Q, Ding G, Tan Y, Tu Z, Li Y, Dai H, Xie L: The role of Hepatitis C Virus in the dynamic protein interaction networks of hepatocellular cirrhosis and carcinoma. Int J Comput Biol Drug Des 2011, 4:5-18.
17. Li W, Xie L, He X, Li J, Tu K, Wei L, Wu J, Guo Y, Ma X, Zhang P, Pan Z, Hu X, Zhao Y, Xie H, Jiang G, Chen T, Wang J, Zheng S, Cheng J, Wan D, Yang S, Li Y, Gu J: Diagnostic and prognostic implications of microRNAs in human hepatocellular carcinoma. Int J Cancer 2008, 123:1616-1622.
18. Edgar R, Domrachev M, Lash AE: Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 2002, 30:207-210.
19. Smyth GK: Limma: linear models for microarray data. Bioinforma Comput Biol Solut Using R Bioconductor New York: Springer; 2005, 397-420.
20. Smyth GK: Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 2004, 3:Article3.
21. Bioconductor. [http://www.bioconductor.org].
22. 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, 57:289-300.
23. Wang X, Terfve C, Rose JC, Markowetz F: HTSanalyzeR: an R/Bioconductor package for integrated network analysis of high-throughput screens. Bioinforma Oxf Engl 2011, 27:879-880.
24. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP: Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 2005, 102:15545-15550.
25. BioCarta. [http://www.biocarta.com].
26. Kanehisa M, Goto S: KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 2000, 28:27-30.
27. PID. [http://pid.nci.nih.gov].
28. Reactome. [http://www.reactome.org].
29. SigmaAldrich. [http://www.sigmaaldrich.com/life-science.html].
30. Signaling Gateway. [http://www.signaling-gateway.org].
31. Signal Transduction KE. [http://stke.sciencemag.org].
32. SuperArray. [http://www.superarray.com].
33. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25:25-29.
34. Francesco F: RmiR: Package to work with miRNAs and miRNA targets with R. R package version 1.16.0.
35. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ: miRBase: tools for microRNA genomics. Nucleic Acids Res 2008, 36(Database):D154-158.
36. Garcia DM, Baek D, Shin C, Bell GW, Grimson A, Bartel DP: Weak seedpairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs. Nat Struct Mol Biol 2011, 18:1139-1146.
37. Betel D, Wilson M, Gabow A, Marks DS, Sander C: The microRNA.org resource: targets and expression. Nucleic Acids Res 2008, 36(suppl 1): D149-D153.
38. Papadopoulos GL, Reczko M, Simossis VA, Sethupathy P, Hatzigeorgiou AG: The database of experimentally supported targets: a functional update of TarBase. Nucleic Acids Res 2009, 37(Database):D155-158.
39. Wang X: miRDB: a microRNA target prediction and functional annotation database with a wiki interface. RNA N Y N 2008, 14:1012-1017.
40. PicTar. [http://pictar.mdc-berlin.de].
41. Planet E: phenoTest: Tools to test association between gene expression and phenotype in a way that is efficient, structured, fast and scalable. We also provide tools to do GSEA (Gene set enrichment analysis) and copy number variation. R package version 1.6.0. 2010.
42. Cox D: Regression models and life-tables. J R Stat Soc Ser B 1972, 34:187-220.
43. Kaplan EL, Meier P: Nonparametric Estimation from Incomplete Observations. J Am Stat Assoc 1958, 53:457.
44. Roessler S, Jia HL, Budhu A, Forgues M, Ye QH, Lee JS, Thorgeirsson SS, Sun Z, Tang ZY, Qin LX, Wang XW: A unique metastasis gene signature enables prediction of tumor relapse in early-stage hepatocellular carcinoma patients. Cancer Res 2010, 70:10202-10212.
45. Roessler S, Long EL, Budhu A, Chen Y, Zhao X, Ji J, Walker R, Jia HL, Ye QH, Qin LX, Tang ZY, He P, Hunter KW, Thorgeirsson SS, Meltzer PS, Wang XW: Integrative genomic identification of genes on 8p associated with hepatocellular carcinoma progression and patient survival. Gastroenterology 2012, 142:957-966.e12.
46. The Cancer Genome Atlas (TCGA). [http://cancergenome.nih.gov].
47. Tao YM, Liu Z, Liu HL: Dickkopf-1 (DKK1) promotes invasion and metastasis of hepatocellular carcinoma. Dig Liver Dis Off J Ital Soc Gastroenterol Ital Assoc Study Liver 2013, 45:251-257.
48. Shen Q, Fan J, Yang XR, Tan Y, Zhao W, Xu Y, Wang N, Niu Y, Wu Z, Zhou J, Qiu SJ, Shi YH, Yu B, Tang N, Chu W, Wang M, Wu J, Zhang Z, Yang S, Gu J, Wang H, Qin W: Serum DKK1 as a protein biomarker for the diagnosis of hepatocellular carcinoma: a large-scale, multicentre study. Lancet Oncol 2012, 13:817-826.
49. Fernandez F, Esposito T, Lea RA, Colson NJ, Ciccodicola A, Gianfrancesco F, Griffiths LR: Investigation of gamma-aminobutyric acid (GABA) A receptors genes and migraine susceptibility. BMC Med Genet 2008, 9:109.
50. Grupe A, Li Y, Rowland C, Nowotny P, Hinrichs AL, Smemo S, Kauwe JSK, Maxwell TJ, Cherny S, Doil L, Tacey K, van Luchene R, Myers A, Wavrant-De Vrièze F, Kaleem M, Hollingworth P, Jehu L, Foy C, Archer N, Hamilton G, Holmans P, Morris CM, Catanese J, Sninsky J, White TJ, Powell J, Hardy J, O'Donovan M, Lovestone S, Jones L, et al: A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease. Am J Hum Genet 2006, 78:78-88.
51. Svendsen JM, Smogorzewska A, Sowa ME, O'Connell BC, Gygi SP, Elledge SJ, Harper JW: Mammalian BTBD12/SLX4 assembles a Holliday junction resolvase and is required for DNA repair. Cell 2009, 138:63-77.
52. Feranchak AP, Doctor RB, Troetsch M, Brookman K, Johnson SM, Fitz JG: Calcium-dependent regulation of secretion in biliary epithelial cells: the role of apamin-sensitive SK channels. Gastroenterology 2004, 127:903-913.
53. Sukhatme VP, Cao XM, Chang LC, Tsai-Morris CH, Stamenkovich D, Ferreira PC, Cohen DR, Edwards SA, Shows TB, Curran T: A zinc fingerencoding gene coregulated with c-fos during growth and differentiation, and after cellular depolarization. Cell 1988, 53:37-43.
54. Hanahan D, Weinberg RA: Hallmarks of cancer: the next generation. Cell 2011, 144:646-674.
55. Cimprich KA, Shin TB, Keith CT, Schreiber SL: cDNA cloning and gene mapping of a candidate human cell cycle checkpoint protein. Proc Natl Acad Sci USA 1996, 93:2850-2855.
56. Holtrich U, Wolf G, Bräuninger A, Karn T, Böhme B, Rübsamen-Waigmann H, Strebhardt K: Induction and down-regulation of PLK, a human serine/ threonine kinase expressed in proliferating cells and tumors. Proc Natl Acad Sci USA 1994, 91:1736-1740.
57. Wang H, Gauthier BR, Hagenfeldt-Johansson KA, Iezzi M, Wollheim CB: Foxa2 (HNF3beta) controls multiple genes implicated in metabolismsecretion coupling of glucose-induced insulin release. J Biol Chem 2002, 277:17564-17570.
58. Mincheva A, Lichter P, Schütz G, Kaestner KH: Assignment of the human genes for hepatocyte nuclear factor 3-alpha,-beta, and-gamma (HNF3A, HNF3B, HNF3G) to 14q12-q13, 20p11, and 19q13.2-q13.4. Genomics 1997, 39:417-419.
59. Wolfrum C, Shih DQ, Kuwajima S, Norris AW, Kahn CR, Stoffel M: Role of Foxa-2 in adipocyte metabolism and differentiation. J Clin Invest 2003, 112:345-356.
60. Kim TM, Yim SH, Shin SH, Xu HD, Jung YC, Park CK, Choi JY, Park WS, Kwon MS, Fiegler H, Carter NP, Rhyu MG, Chung YJ: Clinical implication of recurrent copy number alterations in hepatocellular carcinoma and putative oncogenes in recurrent gains on 1q. Int J Cancer J Int Cancer 2008, 123:2808-2815.
61. Kauffmann A, Rosselli F, Lazar V, Winnepenninckx V, Mansuet-Lupo A, Dessen P, van den Oord JJ, Spatz A, Sarasin A: High expression of DNA repair pathways is associated with metastasis in melanoma patients. Oncogene 2008, 27:565-573.
62. McCaughan GW, Gorrell MD, Bishop GA, Abbott CA, Shackel NA, McGuinness PH, Levy MT, Sharland AF, Bowen DG, Yu D, Slaitini L, Church WB, Napoli J: Molecular pathogenesis of liver disease: an approach to hepatic inflammation, cirrhosis and liver transplant tolerance. Immunol Rev 2000, 174:172-191.
63. Enk CD, Jacob-Hirsch J, Gal H, Verbovetski I, Amariglio N, Mevorach D, Ingber A, Givol D, Rechavi G, Hochberg M: The UVB-induced gene expression profile of human epidermis in vivo is different from that of cultured keratinocytes. Oncogene 2006, 25:2601-2614.
64. Wei RR, Huang GL, Zhang MY, Li BK, Zhang HZ, Shi M, Chen XQ, Huang L, Zhou QM, Jia WHJ, Zheng XFS, Yuan YF, Wang HY: Clinical significance and prognostic value of microRNA expression signatures in hepatocellular carcinoma. Clin Cancer Res Off J Am Assoc Cancer Res 2013.
65. Smid M, Wang Y, Zhang Y, Sieuwerts AM, Yu J, Klijn JGM, Foekens JA, Martens JWM: Subtypes of breast cancer show preferential site of relapse. Cancer Res 2008, 68:3108-3114.
66. Lu M, Zhang Q, Deng M, Miao J, Guo Y, Gao W, Cui Q: An Analysis of Human MicroRNA and Disease Associations. PLoS ONE 2008, 3:e3420.
67. Zeng L, Yu J, Huang T, Jia H, Dong Q, He F, Yuan W, Qin L, Li Y, Xie L: Differential combinatorial regulatory network analysis related to venous metastasis of hepatocellular carcinoma. BMC Genomics 2012, 13 Suppl 8: S14.
68. Tu K, Yu H, Hua YJ, Li YY, Liu L, Xie L, Li YX: Combinatorial network of primary and secondary microRNA-driven regulatory mechanisms. Nucleic Acids Res 2009, 37:5969-5980.
69. Chen M, Xiao J, Zhang Z, Liu J, Wu J, Yu J: Identification of human HK genes and gene expression regulation study in cancer from transcriptomics data analysis. PloS One 2013, 8:e54082.