Identifying hub genes and dysregulated pathways in hepatocellular carcinoma

European Review for Medical and Pharmacological Sciences

Volumn 19, Issue 4, 2015, Pages 592-601

  Jin, B ^a   Wang, W ^b   Du, G ^a   Huang, G Z ^a   Han, L T ^a   Tang, Z Y ^a   Fan, D G ^c   Li, J ^a   Zhang, S Z ^a  

^a SHANDONG UNIVERSITY   (China)

^b SHANDONG UNIVERSITY   (China)

^c Caoxian People's Hospital   (China)

Author keywords

Bioprocess; Hepatocellular carcinoma; Hub genes; Signaling pathway

Indexed keywords

AKR1B10 PROTEIN; ANLN PROTEIN; ASPM PROTEIN; AURKA PROTEIN; BIRC5 PROTEIN; BUB1B PROTEIN; CCNB1 PROTEIN; CCNB2 PROTEIN; CDK1 PROTEIN; CDKN3 PROTEIN; CELL CYCLE PROTEIN 20; CENPF PROTEIN; CRNDE PROTEIN; ECT2 PROTEIN; FLVCR1 PROTEIN; GPC3 PROTEIN; HMMR PROTEIN; IGF2BP3 PROTEIN; MAD2L1 PROTEIN; NEK2 PROTEIN; NUSAP1 PROTEIN; PEG10 PROTEIN; PROGESTERONE; PROTEIN P53; RRM2 PROTEIN; SPINK1 PROTEIN; SULT1C2 PROTEIN; TOP2A PROTEIN; TUMOR MARKER; UNCLASSIFIED DRUG; ZIC2 PROTEIN; TRANSCRIPTOME;

ARTICLE; CELL CYCLE; CELL CYCLE M PHASE; CONTROLLED STUDY; DOWN REGULATION; DRUG METABOLISM; GENE EXPRESSION; GENE IDENTIFICATION; GENE ONTOLOGY; GENETIC ASSOCIATION; HUMAN; LIVER CELL CARCINOMA; MEIOSIS; MITOSIS; NUCLEAR DIVISION; OOCYTE; OOCYTE MATURATION; PROTEIN PROTEIN INTERACTION; SIGNAL TRANSDUCTION; UPREGULATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETICS; LIVER TUMOR; META ANALYSIS; MICROARRAY ANALYSIS; PATHOLOGY; TUMOR GENE;

CARCINOMA, HEPATOCELLULAR; CELL CYCLE; DOWN-REGULATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE REGULATORY NETWORKS; GENES, NEOPLASM; HUMANS; LIVER NEOPLASMS; MICROARRAY ANALYSIS; SIGNAL TRANSDUCTION; TRANSCRIPTOME; UP-REGULATION;

EID: 84942256203     PISSN: 11283602     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (50)

1. BOSCH FX, RIBES J, DÍ AZ M, CLÉRIES R. Primary liver cancer: worldwide incidence and trends. Gastroenterology 2004; 127: S5-S16.
2. STEFAN IUK P, CIANCIARA J, WIERCINSKA-DRAPALO A. Present and future possibilities for early diagnosis of hepatocellular carcinoma. World J Gastroenterol 2010; 16: 418.
3. STARLEY BQ, CALCAGNO CJ, H ARRISON SA. Nonalcoholic fatty liver disease and hepatocellular carcinoma: a weighty connection. Hepatology 2010; 51: 1820-1832.
4. IIZUKA N,OKA M,YAMADA-OKABE H,NISHIDA M,MAEDA Y,MORI N,TAKAO T,TAMESA T,TANGOKU A,TABUCHI H. Oligonucleotide microarray for prediction of early intrahepatic recurrence of hepatocellular carcinoma after curative resection Lancet 2003, 361, 923-929.
5. ANTHONY P. Primary carcinoma of the liver: a study of 282 cases inugandan africans. J Pathol 1973; 110: 37-48.
6. WANG Y, LI J, CHEN J, LIU L, PENG Z, DING J, DING K. From cirrhosis to hepatocellular carcinoma in HCV-infected patients: genes involved in tumor progression. Eur Rev Med Pharmacol Sci 2012; 16 : 995-1000.
7. LLOVET JM, BRUIX J. Molecular targeted therapies in hepatocellular carcinoma. Hepatology 2008; 48: 1312-1327.
8. WHITTAKER S, MARAIS R, ZHU A. The role of signaling pathways in the development and treatment of hepatocellular carcinoma. Oncogene 2010; 29: 4989-5005.
9. THORGEIRSSON SS, GRISHAM JW. Molecular pathogenesis of human hepatocellular carcinoma. Nat Genet 2002; 31: 339-346.
10. RINNINELLA E, ZOCCO MA, DE GAETANO A, IEZZI R, CAMPANALE M, CESARIO V, BARBARO F, PONZIANI FR, CARACCIOLO G, TRIARICO S. From sma ll nodule to overt HCC: a multistep process of carcinogenesis as seen during surveillance. Eur Rev Med Pharmacol Sci 2012; 16: 1292-1294.
11. BRAZMA A, PARKINSON H, SARKANS U, SHOJATALAB M, VILO J, ABEYGUNAWARDENA N, HOLLOWAY E, KAPUSHESKY M, KEMMEREN P, LARA GG. ArrayExpress-A public repository for microarray gene expression data at the EBI. Nucleic Acids Res 2003; 31: 68-71.
12. BARRETT T, EDGAR R. Gene expression omnibus: microarray data storage, submission, retrieval, and analysis. Method Enzymol 2006; 411: 352-369.
13. LIAO YL, SUN YM, CHAU GY, CHAU YP, LAI TC, WANG JL, HORNG JT, HSIAO M, TSOU AP. Identification of SOX4 target genes using phylogenetic footprinting-based prediction from expression microarrays suggests that overexpression of SOX4 potentiates metastasis in hepatocellular ca rcinoma. Oncogene 2008; 27: 5578-5589.
14. HODO Y, HONDA M, TANAKA A, NOMURA Y, ARAI K, YAMASHITA T, SAKAI Y, MIZUKOSHI E, SAKAI A, SASAKI M, NAKANUMA Y, MORIYAMA M, KANEKO S. Association of interleukin-28B genotype and hepatocellular carcinoma recurrence in patients with chronic hepatitis C. Clin Cancer Res 2013; 19: 1827-1837.
15. BUDHU A, ROESSLER S, ZHA O X, YU Z, FORGUES M, JI J, KAROLY E, QIN LX, YE QH, JIA HL. Integrated metabolite and gene expression profiles identify lipid biomarkers associated with progression of hepatocellular carcinoma and patient outcomes. G astroenterology 2013; 144: 1066-1075.
16. CHANG W, MA L, LIN L, GU L, LIU X, CAI H, YU Y, TAN X, ZHAI Y, XU X. Identification of novel hub genes associated with liver metastasi s of gastric cancer. Int J Cancer 2009; 125: 2844-2853.
17. WRAY CJ, KO TC, TAN FK. Secondary use of existing public microarray data to predict outcome for hepatocellular carcinoma. J Surg Res 2014; 188: 137-142.
18. WANG HB, JIANG ZB, LI M. Research on the typical miRNA and target genes in squamous cell carcinoma and adenocarcinoma of esophagus cancer with DNA microarray. Pathol Oncol Res 2014; 20: 245-252.
19. LIANG D, HAN G, FENG X, SUN J, DUAN Y, LEI H. Concerted perturbation observed in a hub network in Alzheimer's disease. PLoS One 2012; 7: e40498.
20. CHO JH, GE LINAS R, WANG K, ETHERIDGE A, PIPER MG, BATTE K, DAKHALLAH D, PRICE J, BORNMAN D, ZHANG S, MARSH C, GALAS D. Systems biology of interstitial lung diseases: integration of mRNA and microRNA expression changes. BMC Med Genomics 2011; 4: 8.
21. LIAO Y, SUN Y, CHAU G, CHAU Y, LAI T, WANG J, HORNG J, HSIAO M, TSOU A. Identification of SOX4 target genes using phylogenetic footprinting-bas ed prediction from expression microarrays suggests that overexpression of SOX4 potentiates metastasis in hepatocellular carcinoma. Oncogene 2008; 27: 5578-5589.
22. SUN H, WANG X. Expression data from tumor-Associated endothelial cells of hepatocellular carcinoma. Gene Expression Omnibus 2013.
23. LIU W, PENG Y, TOBIN DJ. A new 12-gene diagnostic biomarker signature of melanoma revealed by integrated microarray analysis. PeerJ 2013; 1: e49.
24. DA WEI HUANG BTS, LEMPICKI RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2008; 4: 44-57.
25. SRIHARI S,LEONG HW. Temporal dynamics of protein complexes in PPI networks: a case study using yeast cell cycle dynamics BMC Bioinformatics 2012, 13, S16.
26. LIU G, W ONG L, CHUA HN. Complex discovery from weighted PPI networks. Bioinformatics 2009; 25: 1891-1897.
27. SCARDONI G, LAUDANNA C. Centralities based analysis of complex networks. New Frontiers in Graph Theory. InTech Open 2012.
28. VASSILEV LT, VU BT, GRAVES B, CARVAJAL D, PODLASKI F, FILIPOVIC Z, KONG N, KAMMLOTT U, LUKACS C, KLEIN C. In vivo activation of the p53 pathway by smallmolec ule antagonists of MDM2. Science 2004; 303: 844-848.
29. PRIVES C, HALL PA. The p53 pathway. J Pathol 1999; 187: 112-126.
30. BOND GL, HU W, BOND EE, RO BINS H, LUTZKER SG, ARVA NC, BARGONETTI J, BARTEL F, TAUBERT H, WUERL P. A single nucleotide polymorphism in the MDM2 promoter attenuates the p53 tumor suppressor pathway and accelerates tumor formation in humans. Cell 2004; 119: 591-602.
31. EL-SERAG HB, RUDOLPH KL. Hepatocellular carcinoma: epidemiology and molecular carcinogenesis. Gastroenterology 2007; 132: 2557-2576.
32. JABBOUR AM, GORDON L, DAUNT CP, GREEN BD, KOK CH, D'ANDREA R, EKERT PG. p53-dependent transcriptional responses to interleukin-3 signaling. PloS One 2012; 7: e31428.
33. EDAMOTO Y, HARA A, BIERNAT W, TERRACCIANO L, CATHOMAS G, RIEHLE HM, MATSUDA M, FUJII H, SCOAZEC JY, OHGAKI H. Alterations of RB1, p53 and Wnt pathways in hepatocellular carcinomas associated with hepatitis C, h epatitis B and alcoholic liver cirrhosis. Int J Cancer 2003; 106:334-341.
34. KREIS N, SANHAJI M, KRÄMER A, SOMMER K, RÖ DEL F, STREBHARDT K, YUAN J. Restoration of the tumor suppressor p53 by downregulating cyclin B1 in human papillomavirus 16/18-infected cancer cells. Oncogene 2010; 29: 5591-5603.
35. DAMERON KM, VOLPERT OV, TAINSKY MA, BOUCK N. Control of angiogenesis in fibroblasts by p53 regulation of thrombospondin-1. Science 1994; 265: 1582-1584.
36. MUKHOPADHYAY D, TSIOKAS L, SUKHATME VP. Wild-type p53 and v-Src exert opposing influences on human vascular endothelial growth factor gene expression. Cancer Res 1995; 55: 6161-6165.
37. MIAO W-M, SENG WL, DUQUETTE M, LAWLER P, LAUS C, LAWLER J. Thrombospondin-1 type 1 repeat recombinant proteins inhibit tumor growth through transforming growth factor-dependent and-independent mechanisms. Cancer Res 2001; 61: 7830-7839.
38. MOUILLESS EAUX K, CHEN J-N. Mutation in utp15 disrupts vascular patterning in a p53-dependent manner in zebrafish embryos. PloS One 2011; 6: e25013.
39. FUKUMOTO S-I, YAMAUCHI N, MORIGUCHI H, HIPPO Y, WATANABE A, SHIBAHARA J, TANIGUCHI H, ISHIKAWA S, ITO H, YAMAMOTO S. Overexpression of the aldo-keto reductase family protein AKR1B10 Is highly correlated with smokers' non-small cell lung carcinomas. Clin Cancer Res 2005; 11: 1776-1785.
40. PENNING TM. AKR1B10: a new diagnostic marker of non-small cell lung carcinoma in smokers. Clin Cancer Res 2005; 11: 1687-1690.
41. SCHMITZ KJ, SOTIROPOULOS GC, BABA HA, SCHMID KW, MÜLLER D, PAUL A, AUER T, GAMERITH G, LOEFFLER-RAGG J. AKR1B10 expression is associated with less aggressive hepatocellular carcinoma: a clinicopathological study of 168 cases. Live r Int 2011; 31: 810-816.
42. LAMERS F, SCHILD L, KOSTER J, VERSTEEG R, CARON HN, MOLENAAR JJ. Targeted BIRC5 silencing using YM155 causes cell death in neuroblastoma cells with low ABCB1 expr ession. Eur J Cancer 2012; 48: 763-771.
43. HINGORANI P, DICKMAN P, GARCIA-FILION P, WHITECOLLINS A, KOLB EA, AZORSA DO. BIRC5 expression is a poor prognostic marker in ewing sarcoma. Pediatr Blood Cancer 2013; 60: 35-40.
44. BOIDOT R, VEGRAN F, JACOB D, CHEVRIER S, GANGNEUX N, TABOUREAU J, OUDIN C, RAINVILLE V, MERCIER L, LIZARD-NACOL S. The expression of BIRC5 is correlated with loss of specific chromosomal regions in breast carcinomas. Genes Chromosomes Cancer 2008; 47: 299-308.
45. GLIENKE W, MAUTE L, WICHT J, BERGMANN L. Curcumin inhibits c onstitutive STAT3 phosphorylation in human pancreatic cancer cell lines and downregulation of survivin/BIRC5 gene expression. Cancer Invest 2009; 28: 166-171.
46. NILSSON J, YEKEZARE M, MINSHULL J, PINES J. The APC/C maintains the spindle assembly checkpoint by targeting Cdc20 for destruction. Nat Cell Biol 2008; 10: 1411-1420.
47. SKOUFIAS DA,ANDREASSEN PR,LACROIX FB,WILSON L,MARGOLI S RL. Mammalian mad2 and bub1/bubR1 recognize distinct spindle-Attachment and kinetochore-tension checkpoints Proc Natl Acad Sci USA 2001 98 4492-4497.
48. WANG Z, XU W, SAN LUCAS FA, LIU Y. Incorporating prior knowledge into gene network study. Bioinformatics 2013; 29: 2633-2640.
49. WANG G, HU N, YANG HH, WANG L, SU H, WANG C, CLIFFORD R, DAWSEY EM, LI JM, DING T. Comparison of global gene expression of gastric cardia and noncardia cancers from a high-risk population in china. PloS One 2013; 8: e63826.
50. SANTAMARÍ A D, BARRIÉRE C, CERQUEIRA A, HUNT S, TARDY C, NEWTON K, CÁ CERES JF, DUBUS P, MALUMBRES M, BARBACID M. Cdk1 is sufficient to drive the mammalian cell cycle. Nature 2007; 448: 811-815.