DNA methylation-based prognosis and epidrivers in hepatocellular carcinoma

Hepatology

Volumn 61, Issue 6, 2015, Pages 1945-1956

  Villanueva, Augusto ^a,b   Portela, Anna ^c   Sayols, Sergi ^c,d   Battiston, Carlo ^e   Hoshida, Yujin ^a   Méndez González, Jesús ^c   Imbeaud, Sandrine ^f,g   Letouzé, Eric ^h   Hernandez Gea, Virginia ^b   Cornella, Helena ^b   Pinyol, Roser ^b   Solé, Manel ^b   Fuster, Josep ^b   Zucman Rossi, Jessica ^f,g   Mazzaferro, Vincenzo ^e   Esteller, Manel ^b,c,i   Llovet, Josep M ^a,b,i  

^a MOUNT SINAI SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF BARCELONA   (Spain)

^c BELLVITGE BIOMEDICAL RESEARCH INSTITUTE IDIBELL   (Spain)

^d INSTITUTE OF MOLECULAR BIOLOGY   (Germany)

^e NATIONAL CANCER INSTITUTE   (Italy)

^f INSERM   (France)

^g UNIVERSITÉ PARIS DESCARTES   (France)

^h Programme Cartes d'Identite des Tumeurs   (France)

ⁱ INSTITUCIÓ CATALANA DE RECERCA I ESTUDIS AVANÇATS ICREA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ALBUMIN; APC PROTEIN; BILIRUBIN; CADHERIN; CYCLIN DEPENDENT KINASE 2; DOPAMINE 4 RECEPTOR; EPHRIN B2; FORKHEAD BOX PROTEIN E3; FORKHEAD TRANSCRIPTION FACTOR; MESSENGER RNA; MICRORNA; NOTCH3 RECEPTOR; PHOSPHATIDYLINOSITOL 3 KINASE; RAS ASSOCIATION DOMAIN FAMILY PROTEIN 1A; SEPTIN; SEPTIN 9; SOMATOMEDIN B; TRANSCRIPTION FACTOR TBX15; TRANSFORMING GROWTH FACTOR BETA; UNCLASSIFIED DRUG;

AGED; ALBUMIN BLOOD LEVEL; ARTICLE; BILIRUBIN BLOOD LEVEL; CANCER MORTALITY; CANCER PROGNOSIS; CANCER SURVIVAL; CELL PROLIFERATION; CONTROLLED STUDY; CPG ISLAND; DNA METHYLATION; EPIGENETICS; FEMALE; GENETIC ASSOCIATION; HEPATITIS B; HEPATITIS C; HUMAN; HUMAN TISSUE; LIVER CELL CARCINOMA; MAJOR CLINICAL STUDY; MALE; OUTCOME ASSESSMENT; PRIORITY JOURNAL; PYROSEQUENCING; SINGLE NUCLEOTIDE POLYMORPHISM; STEM CELL; SURVIVAL PREDICTION; THROMBOCYTE COUNT; TUMOR RECURRENCE; TUMOR VOLUME; CARCINOMA, HEPATOCELLULAR; CASE CONTROL STUDY; CLINICAL TRIAL; EPIDEMIOLOGY; GENETICS; HUMAN GENOME; ITALY; LIVER NEOPLASMS; METABOLISM; MORTALITY; MULTICENTER STUDY; PROGNOSIS; SPAIN;

AGED; CARCINOMA, HEPATOCELLULAR; CASE-CONTROL STUDIES; DNA METHYLATION; FEMALE; GENOME, HUMAN; HUMANS; ITALY; LIVER NEOPLASMS; MALE; PROGNOSIS; SPAIN;

EID: 84929606441     PISSN: 02709139     EISSN: 15273350     Source Type: Journal    
DOI: 10.1002/hep.27732     Document Type: Article

References (39)

1. Lozano R, Naghavi M, Foreman K, Lim S, Shibuya K, Aboyans V, et al. Global and regional mortality from 235 causes of death for 20 age groups in 1990 and 2010: a systematic analysis for the Global Burden of Disease Study 2010. Lancet 2012;380:2095-2128.
2. Murray CJL, Vos T, Lozano R, Naghavi M, Flaxman AD, Michaud C, et al. Disability-adjusted life years (DALYs) for 291 diseases and injuries in 21 regions, 1990-2010: a systematic analysis for the Global Burden of Disease Study 2010. Lancet 2013;380:2197-2223.
3. European Association for the Study Of The Liver, European Organisation for Research and Treatment of Cancer. EASL-EORTC Clinical Practice Guidelines: management of hepatocellular carcinoma. J Hepatol 2012;56:908-943.
4. Bruix J, Sherman M; American Association for the Study of Liver Diseases. Management of hepatocellular carcinoma: an update. Hepatology 2011;53:1020-1022.
5. Villanueva A, Hoshida Y, Battiston C, Tovar V, Sia D, Alsinet C, et al. Combining clinical, pathology, and gene expression data to predict recurrence of hepatocellular carcinoma. Gastroenterology 2011;140:1501-1502.e2.
6. Hoshida Y, Villanueva A, Kobayashi M, Peix J, Chiang DY, Camargo A, et al. Gene expression in fixed tissues and outcome in hepatocellular carcinoma. N Engl J Med 2008;359:1995-2004.
7. Hoshida Y, Villanueva A, Sangiovanni A, Sole M, Hur C, Andersson KL, et al. Prognostic gene expression signature for patients with hepatitis C-related early-stage cirrhosis. Gastroenterology 2013;144:1024-1030.
8. Portela A, Esteller M. Epigenetic modifications and human disease. Nat Biotechnol 2010;28:1057-1068.
9. Heyn H, Esteller M. DNA methylation profiling in the clinic: applications and challenges. Nat Rev Genet 2012;13:679-692.
10. Hinoue T, Weisenberger DJ, Lange CPE, Shen H, Byun HM, Van Den Berg D, et al. Genome-scale analysis of aberrant DNA methylation in colorectal cancer. Genome Res 2012;22:271-282.
11. Villanueva A, Hoshida Y, Toffanin S, Lachenmayer A, Alsinet C, Savic R, et al. New strategies in hepatocellular carcinoma: genomic prognostic markers. Clin Cancer Res 2010;16:4688-4694.
12. Sandoval J, Heyn HA, Moran S, Serra-Musach J, Pujana MA, Bibikova M, Esteller M. Validation of a DNA methylation microarray for 450, 000 CpG sites in the human genome. Epigenetics 2011;6:692-702.
13. Ishwaran H, Kogalur UB. Consistency of random survival forests. Stat Probab Lett 2010;80:1056-1064.
14. Hoshida Y. Nearest template prediction: a single-sample-based flexible class prediction with confidence assessment. PLoS One 2010;5:e15543.
15. Riley RD, Hayden JA, Steyerberg EW, Moons KG, Abrams K, Kyzas PA, et al.; PROGRESS Group. Prognosis Research Strategy (PROGRESS) 2: prognostic factor research. PLoS Med 2013;10:e1001380.
16. Nault JC, de Reyniès A, Villanueva A, Calderaro J, Rebouissou S, Couchy G, et al. A hepatocellular carcinoma 5-gene score associated with survival of patients following liver resection. Gastroenterology 2013;145:176-187.
17. Forner A, Llovet JM, Bruix J. Hepatocellular carcinoma. Lancet 2012;379:1245-1255.
18. Yamashita T, Ji J, Budhu A, Forgues M, Yang W, Wang HY, et al. EpCAM-positive hepatocellular carcinoma cells are tumor-initiating cells with stem/progenitor cell features. Gastroenterology 2009;136:1012-1024.
19. Hoshida Y, Nijman SMB, Kobayashi M, Chan JA, Brunet JP, Chiang DY, et al. Integrative transcriptome analysis reveals common molecular subclasses of human hepatocellular carcinoma. Cancer Res 2009;69:7385-7392.
20. Song MA, Tiirikainen M, Kwee S, Okimoto G, Yu H, Wong LL. Elucidating the landscape of aberrant DNA methylation in hepatocellular carcinoma. PLoS One 2013;8:e55761.
21. Revill K, Wang T, Lachenmayer A, Kojima K, Harrington A, Li J, et al. Genome-wide methylation analysis and epigenetic unmasking identify tumor suppressor genes in hepatocellular carcinoma. Gastroenterology 2013;145:1424-1435.e1-25.
22. Garraway LA, Lander ES. Lessons from the cancer genome. Cell 2013;153:17-37.
23. Gyparaki MT, Basdra EK, Papavassiliou AG. DNA methylation biomarkers as diagnostic and prognostic tools in colorectal cancer. J Mol Med 2013;91:1249-1256.
24. Kuang SQ, Bai H, Fang ZH, Lopez G, Yang H, Tong W, et al. Aberrant DNA methylation and epigenetic inactivation of Eph receptor tyrosine kinases and ephrin ligands in acute lymphoblastic leukemia. Blood 2010;115:2412-2419.
25. Toffanin S, Hoshida Y, Lachenmayer A, Villanueva A, Cabellos L, Minguez B, et al. MicroRNA-based classification of hepatocellular carcinoma and oncogenic role of miR-517a. Gastroenterology 2011;140:1618-1628.e16.
26. Mah WC, Thurnherr T, Chow PKH, Chung AY, Ooi LL, Toh HC, et al. Methylation profiles reveal distinct subgroup of hepatocellular carcinoma patients with poor prognosis. PLoS One 2014;9:e104158.
27. Shen J, Wang S, Zhang YJ, Wu HC, Kibriya MG, Jasmine F, et al. Exploring genome-wide DNA methylation profiles altered in hepatocellular carcinoma using Infinium HumanMethylation 450 BeadChips. Epigenetics 2013;8:34-43.
28. Hemingway H, Croft P, Perel P, Hayden JA, Abrams K, Timmis A, et al.; PROGRESS Group. Prognosis research strategy (PROGRESS) 1: a framework for researching clinical outcomes. BMJ 2013;346:e5595.
29. McShane LM, Altman DG, Sauerbrei W, Taube SE, Gion M, Clark GM; Statistics Subcommittee of the NCI-EORTC Working Group on Cancer Diagnostics. Reporting recommendations for tumor marker prognostic studies (REMARK). J Natl Cancer Inst 2005;97:1180-1184.
30. Li X, Zhou F, Jiang C, Wang Y, Lu Y, Yang F, et al. Identification of a DNA methylome profile of esophageal squamous cell carcinoma and potential plasma epigenetic biomarkers for early diagnosis. PLoS One 2014;9:e103162.
31. Esteller M. Cancer epigenomics: DNA methylomes and histone-modification maps. Nat Rev Genet 2007;8:286-298.
32. Vickers KC, Shoucri BM, Levin MG, Wu H, Pearson DS, Osei-Hwedieh D, et al. MicroRNA-27b is a regulatory hub in lipid metabolism and is altered in dyslipidemia. Hepatology 2013;57:533-542.
33. Lee JJ, Drakaki A, Iliopoulos D, Struhl K. MiR-27b targets PPARγ to inhibit growth, tumor progression and the inflammatory response in neuroblastoma cells. Oncogene 2012;31:3818-3825.
34. Tanaka N, Moriya K, Kiyosawa K, Koike K, Gonzalez FJ, Aoyama T. PPARalpha activation is essential for HCV core protein-induced hepatic steatosis and hepatocellular carcinoma in mice. J Clin Invest 2008;118:683-694.
35. Chang CH, Lin JW, Wu LC, Lai MS, Chuang LM, Chan KA. Association of thiazolidinediones with liver cancer and colorectal cancer in type 2 diabetes mellitus. Hepatology 2012;55:1462-1472.
36. Vogelstein B, Papadopoulos N, Velculescu VE, Zhou S, Diaz LA, Kinzler KW. Cancer genome landscapes. Science 2013;339:1546-1558.
37. Cui H, Kong Y, Xu M, Zhang H. Notch3 functions as a tumor suppressor by controlling cellular senescence. Cancer Res 2013;73:3451-3459.
38. Berdasco M, Ropero S, Setien F, Fraga MF, Lapunzina P, Losson R, et al. Epigenetic inactivation of the Sotos overgrowth syndrome gene histone methyltransferase NSD1 in human neuroblastoma and glioma. Proc Natl Acad Sci U S A 2009; 106: 21830-21835.
39. Gan L, Chen S, Zhong J, Wang X, Lam EK, Liu X, et al. ZIC1 is downregulated through promoter hypermethylation, and functions as a tumor suppressor gene in colorectal cancer. PLoS One 2011;6:e16916.