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Review

Liver Cancer Oncogenomics: Opportunities and Dilemmas for Clinical Applications

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Pages 79-93 | Published online: 12 Jan 2015

References

  • Vogelstein B , PapadopoulosN, VelculescuVE, ZhouS, DiazLA, Jr, KinzlerKW. Cancer genome landscapes. Science339(6127), 1546–1558 (2013).
  • Lozano R , NaghaviM, ForemanKet 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. Lancet380(9859), 2095–2128 (2012).
  • El-Serag HB . Hepatocellular carcinoma. N. Engl. J. Med.365(12), 1118–1127 (2011).
  • Marquardt JU , GallePR, TeufelA. Molecular diagnosis and therapy of hepatocellular carcinoma (HCC): an emerging field for advanced technologies. J. Hepatol.56(1), 267–275 (2012).
  • Bruix J , BoixL, SalaM, LlovetJM. Focus on hepatocellular carcinoma. Cancer Cell5(3), 215–219 (2004).
  • Thorgeirsson SS , GrishamJW. Molecular pathogenesis of human hepatocellular carcinoma. Nat. Genet.31(4), 339–346 (2002).
  • Razumilava N , GoresGJ. Classification, diagnosis, and management of cholangiocarcinoma. Clin. Gastroenterol. Hepatol.11(1), 13–21 e11; quiz e13–e14 (2013).
  • Llovet JM , RicciS, MazzaferroVet al. Sorafenib in advanced hepatocellular carcinoma. N. Engl. J. Med.359(4), 378–390 (2008).
  • Worns MA , GallePR. HCC therapies-lessons learned. Nat. Rev. Gastroenterol. Hepatol.11(7), 447–452 (2014).
  • Meyerson M , GabrielS, GetzG. Advances in understanding cancer genomes through second-generation sequencing. Nat. Rev. Genet.11(10), 685–696 (2010).
  • Krawczyk M , MullenbachR, WeberSN, ZimmerV, LammertF. Genome-wide association studies and genetic risk assessment of liver diseases. Nat. Rev. Gastroenterol. Hepatol.7(12), 669–681 (2010).
  • Kumar V , KatoN, UrabeYet al. Genome-wide association study identifies a susceptibility locus for HCV-induced hepatocellular carcinoma. Nat. Genet.43(5), 455–458 (2011).
  • Andersen JB , ThorgeirssonSS. Genetic profiling of intrahepatic cholangiocarcinoma. Curr. Opin. Gastroenterol.28(3), 266–272 (2012).
  • Andersen JB , SpeeB, BlechaczBRet al. Genomic and genetic characterization of cholangiocarcinoma identifies therapeutic targets for tyrosine kinase inhibitors. Gastroenterology142(4), 1021–1031e1015 (2012).
  • Seok JY , NaDC, WooHGet al. A fibrous stromal component in hepatocellular carcinoma reveals a cholangiocarcinoma-like gene expression trait and epithelial-mesenchymal transition. Hepatology55(6), 1776–1786 (2012).
  • Woo HG , LeeJH, YoonJHet al. Identification of a cholangiocarcinoma-like gene expression trait in hepatocellular carcinoma. Cancer Res.70(8), 3034–3041 (2010).
  • Cazals-Hatem D , RebouissouS, Bioulac-SagePet al. Clinical and molecular analysis of combined hepatocellular-cholangiocarcinomas. J. Hepatol.41(2), 292–298 (2004).
  • Fujii H , ZhuXG, MatsumotoTet al. Genetic classification of combined hepatocellular-cholangiocarcinoma. Hum. Pathol.31(9), 1011–1017 (2000).
  • Daly GM , BexfieldN, HeaneyJet al. A viral discovery methodology for clinical biopsy samples utilising massively parallel next generation sequencing. PLoS ONE6(12), e28879 (2011).
  • Bull RA , LucianiF, McelroyKet al. Sequential bottlenecks drive viral evolution in early acute hepatitis C virus infection. PLoS Pathog.7(9), e1002243 (2011).
  • Teufel A , MarquardtJU, GallePR. Next generation sequencing of HCC from European and Asian HCC cohorts. Back to p53 and Wnt/beta-catenin. J. Hepatol.58(3), 622–624 (2013).
  • Hernandez-Gea V , ToffaninS, FriedmanSL, LlovetJM. Role of the microenvironment in the pathogenesis and treatment of hepatocellular carcinoma. Gastroenterology144(3), 512–527 (2013).
  • Holczbauer A , FactorVM, AndersenJBet al. Modeling pathogenesis of primary liver cancer in lineage-specific mouse cell types. Gastroenterology145(1), 221–231 (2013).
  • International Consensus Group for Hepatocellular Neoplasia. Pathologic diagnosis of early hepatocellular carcinoma: a report of the international consensus group for hepatocellular neoplasia. Hepatology49(2), 658–664 (2009).
  • Kaposi-Novak P , LibbrechtL, WooHGet al. Central role of c-Myc during malignant conversion in human hepatocarcinogenesis. Cancer Res.69(7), 2775–2782 (2009).
  • Gomez-Quiroz LE , FactorVM, Kaposi-NovakP, CoulouarnC, ConnerEA, ThorgeirssonSS. Hepatocyte-specific c-Met deletion disrupts redox homeostasis and sensitizes to Fas-mediated apoptosis. J. Biol. Chem.283(21), 14581–14589 (2008).
  • Marquardt JU , SeoD, AndersenJBet al. Sequential transcriptome analysis of human liver cancer indicates late stage acquisition of malignant traits. J. Hepatol.60(2), 346–353 (2014).
  • Neumann O , KesselmeierM, GeffersRet al. Methylome analysis and integrative profiling of human HCCs identify novel protumorigenic factors. Hepatology56(5), 1817–1827 (2012).
  • Totoki Y , TatsunoK, YamamotoSet al. High-resolution characterization of a hepatocellular carcinoma genome. Nat. Genet.43(5), 464–469 (2011).
  • Li M , ZhaoH, ZhangXet al. Inactivating mutations of the chromatin remodeling gene ARID2 in hepatocellular carcinoma. Nat. Genet.43(9), 828–829 (2011).
  • Fujimoto A , TotokiY, AbeTet al. Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators. Nat. Genet.44(7), 760–764 (2012).
  • Farazi PA , DepinhoRA. Hepatocellular carcinoma pathogenesis: from genes to environment. Nat. Rev. Cancer6(9), 674–687 (2006).
  • Kan Z , ZhengH, LiuXet al. Whole-genome sequencing identifies recurrent mutations in hepatocellular carcinoma. Genome Res.23(9), 1422–1433 (2013).
  • Huang Q , LinB, LiuHet al. RNA-Seq analyses generate comprehensive transcriptomic landscape and reveal complex transcript patterns in hepatocellular carcinoma. PLoS ONE6(10), e26168 (2011).
  • Sung WK , ZhengH, LiSet al. Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma. Nat. Genet.44(7), 765–769 (2012).
  • Nault JC , MalletM, PilatiCet al. High frequency of telomerase reverse-transcriptase promoter somatic mutations in hepatocellular carcinoma and preneoplastic lesions. Nat. Commun.4, 2218 (2013).
  • Guichard C , AmaddeoG, ImbeaudSet al. Integrated analysis of somatic mutations and focal copy-number changes identifies key genes and pathways in hepatocellular carcinoma. Nat. Genet.44(6), 694–698 (2012).
  • Hainaut P , PfeiferGP. Patterns of p53 G‐‐>T transversions in lung cancers reflect the primary mutagenic signature of DNA-damage by tobacco smoke. Carcinogenesis22(3), 367–374 (2001).
  • Cleary SP , JeckWR, ZhaoXet al. Identification of driver genes in hepatocellular carcinoma by exome sequencing. Hepatology58(5), 1693–1702 (2013).
  • Chan TH , LinCH, QiLet al. A disrupted RNA editing balance mediated by ADARs (Adenosine DeAminases that act on RNA) in human hepatocellular carcinoma. Gut63(5), 832–843 (2014).
  • Chen L , LiY, LinCHet al. Recoding RNA editing of AZIN1 predisposes to hepatocellular carcinoma. Nat. Med.19(2), 209–216 (2013).
  • Nault JC , Bioulac-SageP, Zucman-RossiJ. Hepatocellular benign tumors-from molecular classification to personalized clinical care. Gastroenterology144(5), 888–902 (2013).
  • Pilati C , LetouzeE, NaultJCet al. Genomic Profiling of Hepatocellular Adenomas Reveals Recurrent FRK-Activating Mutations and the Mechanisms of Malignant Transformation. Cancer Cell25(4), 428–441 (2014).
  • Marquardt JU , ThorgeirssonSS. Next-generation genomic profiling of hepatocellular adenomas: a new era of individualized patient care. Cancer Cell25(4), 409–411 (2014).
  • Bridgewater J , GallePR, KhanSAet al. Guidelines for the diagnosis and management of intrahepatic cholangiocarcinoma. J. Hepatol.60(6), 1268–1289 (2014).
  • Patel T . Increasing incidence and mortality of primary intrahepatic cholangiocarcinoma in the United States. Hepatology33(6), 1353–1357 (2001).
  • Bragazzi CM , CardinaleV, CarpinoGet al. Cholangiocarcinoma: Epidemiology and risk factors. Transl. Gastrointest. Cancer1(1), 21–23 (2012).
  • Von Hahn T , CiesekS, WegenerGet al. Epidemiological trends in incidence and mortality of hepatobiliary cancers in Germany. Scand. J. Gastroenterol.46(9), 1092–1098 (2011).
  • Andersen JB , ThorgeirssonSS. A perspective on molecular therapy in cholangiocarcinoma: present status and future directions. Hepat. Oncol.1(1), 143–157 (2014).
  • Khan SA , DavidsonBR, GoldinRDet al. Guidelines for the diagnosis and treatment of cholangiocarcinoma: an update. Gut61(12), 1657–1669 (2012).
  • Everhart JE , RuhlCE. Burden of digestive diseases in the United States Part III: Liver, biliary tract, and pancreas. Gastroenterology136(4), 1134–1144 (2009).
  • Valle J , WasanH, PalmerDHet al. Cisplatin plus gemcitabine versus gemcitabine for biliary tract cancer. N. Engl. J. Med.362(14), 1273–1281 (2010).
  • Andersen JB , ThorgeirssonSS. Genomic decoding of intrahepatic cholangiocarcinoma reveals therapeutic opportunities. Gastroenterology144(4), 687–690 (2013).
  • Sia D , HoshidaY, VillanuevaAet al. Integrative molecular analysis of intrahepatic cholangiocarcinoma reveals 2 classes that have different outcomes. Gastroenterology144(4), 829–840 (2013).
  • Oishi N , KumarMR, RoesslerSet al. Transcriptomic profiling reveals hepatic stem-like gene signatures and interplay of miR-200c and epithelial-mesenchymal transition in intrahepatic cholangiocarcinoma. Hepatology56(5), 1792–1803 (2012).
  • Wang P , DongQ, ZhangCet al. Mutations in isocitrate dehydrogenase 1 and 2 occur frequently in intrahepatic cholangiocarcinomas and share hypermethylation targets with glioblastomas. Oncogene32(25), 3091–3100 (2013).
  • Ong CK , SubimerbC, PairojkulCet al. Exome sequencing of liver fluke-associated cholangiocarcinoma. Nat. Genet.44(6), 690–693 (2012).
  • Chan-On W , NairismagiML, OngCKet al. Exome sequencing identifies distinct mutational patterns in liver fluke-related and non-infection-related bile duct cancers. Nat. Genet.45(12), 1474–1478 (2013).
  • Jiao Y , PawlikTM, AndersRAet al. Exome sequencing identifies frequent inactivating mutations in BAP1, ARID1A and PBRM1 in intrahepatic cholangiocarcinomas. Nat. Genet.45(12), 1470–1473 (2013).
  • Gao Q , ZhaoYJ, WangXYet al. Activating mutations in PTPN3 promote cholangiocarcinoma cell proliferation and migration and are associated with tumor recurrence in patients. Gastroenterology146(5), 1397–1407 (2014).
  • Huang J , DengQ, WangQet al. Exome sequencing of hepatitis B virus-associated hepatocellular carcinoma. Nat. Genet.44(10), 1117–1121 (2012).
  • Morris LG , TaylorBS, BivonaTGet al. Genomic dissection of the epidermal growth factor receptor (EGFR)/PI3K pathway reveals frequent deletion of the EGFR phosphatase PTPRS in head and neck cancers. Proc. Natl Acad. Sci. USA108(47), 19024–19029 (2011).
  • Ross JS , WangK, GayLet al. New routes to targeted therapy of intrahepatic cholangiocarcinomas revealed by next-generation sequencing. Oncologist19(3), 235–242 (2014).
  • Wu YM , SuF, Kalyana-SundaramSet al. Identification of targetable FGFR gene fusions in diverse cancers. Cancer Discov.3(6), 636–647 (2013).
  • Arai Y , TotokiY, HosodaFet al. Fibroblast growth factor receptor 2 tyrosine kinase fusions define a unique molecular subtype of cholangiocarcinoma. Hepatology59(4), 1427–1434 (2014).
  • Borad MJ , ChampionMD, EganJBet al. Integrated genomic characterization reveals novel, therapeutically relevant drug targets in FGFR and EGFR pathways in sporadic intrahepatic cholangiocarcinoma. PLoS Genet.10(2), e1004135 (2014).
  • Moon RT , KohnAD, De FerrariGV, KaykasA. WNT and beta-catenin signalling: diseases and therapies. Nat. Rev. Genet.5(9), 691–701 (2004).
  • Ventura A , JacksT. MicroRNAs and cancer: short RNAs go a long way. Cell136(4), 586–591 (2009).
  • Feinberg AP . Phenotypic plasticity and the epigenetics of human disease. Nature447(7143), 433–440 (2007).
  • Feinberg AP , TyckoB. The history of cancer epigenetics. Nat. Rev. Cancer4(2), 143–153 (2004).
  • Mann DA . Epigenetics in Liver Disease. Hepatology60(4), 1418–1425 (2014).
  • Toffanin S , CornellaH, HarringtonA, LlovetJM. Next-generation sequencing: path for driver discovery in hepatocellular carcinoma. Gastroenterology143(5), 1391–1393 (2012).
  • Zhu AX . Molecularly targeted therapy for advanced hepatocellular carcinoma in 2012: current status and future perspectives. Semin. Oncol.39(4), 493–502 (2012).
  • Nault JC , Zucman-RossiJ. Genetics of hepatocellular carcinoma: the next generation. J. Hepatol.60(1), 224–226 (2014).
  • Marquardt JU , ThorgeirssonSS. Linking MLL and the HGF-MET signaling pathway in liver cancer. J. Clin. Invest.123(7), 2780–2783 (2013).
  • Wang XW , HeegaardNH, OrumH. MicroRNAs in liver disease. Gastroenterology142(7), 1431–1443 (2012).
  • Hoshida Y , ToffaninS, LachenmayerA, VillanuevaA, MinguezB, LlovetJM. Molecular classification and novel targets in hepatocellular carcinoma: recent advancements. Semin. Liver Dis.30(1), 35–51 (2010).
  • Ladeiro Y , CouchyG, BalabaudCet al. MicroRNA profiling in hepatocellular tumors is associated with clinical features and oncogene/tumor suppressor gene mutations. Hepatology47(6), 1955–1963 (2008).
  • Coulouarn C , FactorVM, AndersenJB, DurkinME, ThorgeirssonSS. Loss of miR-122 expression in liver cancer correlates with suppression of the hepatic phenotype and gain of metastatic properties. Oncogene28(40), 3526–3536 (2009).
  • Giordano S , ColumbanoA. MicroRNAs: new tools for diagnosis, prognosis, and therapy in hepatocellular carcinoma?Hepatology57(2), 840–847 (2013).
  • Hou J , LinL, ZhouWet al. Identification of miRNomes in human liver and hepatocellular carcinoma reveals miR-199a/b-3p as therapeutic target for hepatocellular carcinoma. Cancer Cell19(2), 232–243 (2011).
  • Fornari F , MilazzoM, ChiecoPet al. MiR-199a-3p regulates mTOR and c-Met to influence the doxorubicin sensitivity of human hepatocarcinoma cells. Cancer Res.70(12), 5184–5193 (2010).
  • Pineau P , VoliniaS, McjunkinKet al. miR-221 overexpression contributes to liver tumorigenesis. Proc. Natl Acad. Sci. USA107(1), 264–269 (2010).
  • Garofalo M , Di LevaG, RomanoGet al. miR-221&222 regulate TRAIL resistance and enhance tumorigenicity through PTEN and TIMP3 downregulation. Cancer Cell16(6), 498–509 (2009).
  • Budhu A , JiJ, WangXW. The clinical potential of microRNAs. J. Hematol. Oncol.3, 37 (2010).
  • Szabo G , SarnowP, BalaS. MicroRNA silencing and the development of novel therapies for liver disease. J. Hepatol.57(2), 462–466 (2012).
  • Xie HJ , BaeHJ, NohJHet al. Mutational analysis of JAK1 gene in human hepatocellular carcinoma. Neoplasma56(2), 136–140 (2009).
  • Sia D , TovarV, MoeiniA, LlovetJM. Intrahepatic cholangiocarcinoma: pathogenesis and rationale for molecular therapies. Oncogene32(41), 4861–4870 (2013).
  • Cheng AL , ShenYC, ZhuAX. Targeting fibroblast growth factor receptor signaling in hepatocellular carcinoma. Oncology81(5–6), 372–380 (2011).
  • Johnson PJ , QinS, ParkJWet al. Brivanib versus sorafenib as first-line therapy in patients with unresectable, advanced hepatocellular carcinoma: results from the randomized Phase III BRISK-FL study. J. Clin. Oncol.31(28), 3517–3524 (2013).
  • Bekaii-Saab T , PhelpsMA, LiXet al. Multi-institutional Phase II study of selumetinib in patients with metastatic biliary cancers. J. Clin. Oncol.29(17), 2357–2363 (2011).
  • Stadler ZK , SchraderKA, VijaiJ, RobsonME, OffitK. Cancer genomics and inherited risk. J. Clin. Oncol.32(7), 687–698 (2014).
  • Mccarthy JJ , McleodHL, GinsburgGS. Genomic medicine: a decade of successes, challenges, and opportunities. Sci. Transl. Med.5(189), 189sr184 (2013).
  • EASL-EORTC clinical practice guidelines: management of hepatocellular carcinoma. J. Hepatol.56(4), 908–943 (2012).
  • Santoro A , RimassaL, BorbathIet al. Tivantinib for second-line treatment of advanced hepatocellular carcinoma: a randomised, placebo-controlled Phase 2 study. Lancet Oncol.14(1), 55–63 (2013).
  • Mcdermott U , DowningJR, StrattonMR. Genomics and the continuum of cancer care. N. Engl. J. Med.364(4), 340–350 (2011).

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