We carried out several studies with the aim of deepening global understanding of the pathogenesis of Hepatocellular carcinoma (HCC), a cancer with an incidence of 750,000 new cases yearly that ranks as the 3rd cause of global cancer-related death. Sorafenib is the sole systemic therapy for this disease, and thus, identifying novel drivers and targets for therapies remains a relevant unmet medical need. In parallel, we studied rare liver tumors that lack clear molecular understanding and effective targeted therapies such as intrahepatic cholangiocarcinoma (iCCA) and fibrolamellar (FLC).

Genomic studies and molecular classification of HCC

Establishment of a molecular diagnosis of HCC: Gene-set (3 genes) based diagnosis of HCC included in EASL-EORTC guidelines and reported in:

A molecular signature to discriminate dysplastic nodules from early hepatocellular carcinoma in HCV cirrhosis
Llovet JM, Chen Y, Wurmbach E, Roayaie S, Fiel MI, Schwartz M, Thung SN, Khitrov G, Zhang W, Villanueva A, Battiston C, Mazzaferro V, Bruix J, Waxman S, Friedman SL.
Gastroenterology. 2006 Dec;131(6):1758-67. Epub 2006 Sep 19.

Proposal of molecular classifications: A final proposal of a molecular classification of HCC is based on the results reported in the following publications:

Genome-wide molecular profiles of HCV-induced dysplasia and hepatocellular carcinoma
Wurmbach E, Chen YB, Khitrov G, Zhang W, Roayaie S, Schwartz M, Fiel I, Thung S, Mazzaferro V, Bruix J, Bottinger E, Friedman S, Waxman S, Llovet JM.
Hepatology. 2007 Apr;45(4):938-47.

Gene expression in fixed tissues and outcome in hepatocellular carcinoma
Hoshida Y, Villanueva A, Kobayashi M, Peix J, Chiang DY, Camargo A, Gupta S, Moore J, Wrobel MJ, Lerner J, Reich M, Chan JA, Glickman JN, Ikeda K, Hashimoto M, Watanabe G, Daidone MG, Roayaie S, Schwartz M, Thung S, Salvesen HB, Gabriel S, Mazzaferro V, Bruix J, Friedman SL, Kumada H, Llovet JM, Golub TR.
N Engl J Med. 2008 Nov 6;359(19):1995-2004. doi: 10.1056/NEJMoa0804525. Epub 2008 Oct 15.

Focal gains of VEGFA and molecular classification of hepatocellular carcinoma
Chiang DY, Villanueva A, Hoshida Y, Peix J, Newell P, Minguez B, LeBlanc AC, Donovan DJ, Thung SN, Solé M, Tovar V, Alsinet C, Ramos AH, Barretina J, Roayaie S, Schwartz M, Waxman S, Bruix J, Mazzaferro V, Ligon AH, Najfeld V, Friedman SL, Sellers WR, Meyerson M, Llovet JM.
Cancer Res. 2008 Aug 15;68(16):6779-88. doi: 10.1158/0008-5472.CAN-08-0742.

Integrative transcriptome analysis reveals common molecular subclasses of human hepatocellular carcinoma
Hoshida Y, Nijman SM, Kobayashi M, Chan JA, Brunet JP, Chiang DY, Villanueva A, Newell P, Ikeda K, Hashimoto M, Watanabe G, Gabriel S, Friedman SL, Kumada H, Llovet JM, Golub TR.
Cancer Res. 2009 Sep 15;69(18):7385-92. doi: 10.1158/0008-5472.CAN-09-1089. Epub 2009 Sep 1.

Combining clinical, pathology, and gene expression data to predict recurrence of hepatocellular carcinoma
Villanueva A, Hoshida Y, Battiston C, Tovar V, Sia D, Alsinet C, Cornella H, Liberzon A, Kobayashi M, Kumada H, Thung SN, Bruix J, Newell P, April C, Fan JB, Roayaie S, Mazzaferro V, Schwartz ME, Llovet JM.
Gastroenterology. 2011 May;140(5):1501-12.e2. doi: 10.1053/j.gastro.2011.02.006. Epub 2011 Feb 12.

Following our previous research on molecular classification of HCC, we generated

1) A 186-gene signature from adjacent tissue able to identify a subgroup of hepatitis C-related early-stage cirrhotic patients at high-risk of HCC development. This gene signature might be used for selection in chemo preventive studies.

Prognostic gene expression signature for patients with hepatitis C-related early-stage cirrhosis
Hoshida Y, Villanueva A, Sangiovanni A, Sole M, Hur C, Andersson KL, Chung RT, Gould J, Kojima K, Gupta S, Taylor B, Crenshaw A, Gabriel S, Minguez B, Iavarone M, Friedman SL, Colombo M, Llovet JM, Golub TR.
Gastroenterology. 2013 May;144(5):1024-30. doi: 10.1053/j.gastro.2013.01.021. Epub 2013 Jan 17.

2) A refined prognostic signature from tumoral tissue. After providing an integrative analysis of clinical, pathological and genomic signatures to predict outcome in HCC patients (Villanueva et al., Gastroenterology 2011), a 5-gene signature associated with disease-specific survival was generated and validated in four different Eastern and Western cohorts.

A hepatocellular carcinoma 5-gene score associated with survival of patients after liver resection.

Nault JC, De Reyniès A, Villanueva A, Calderaro J, Rebouissou S, Couchy G, Decaens T, Franco D, Imbeaud S, Rousseau F, Azoulay D, Saric J, Blanc JF, Balabaud C, Bioulac-Sage P, Laurent A, Laurent-Puig P, Llovet JM, Zucman-Rossi J.

Gastroenterology. 2013 Jul;145(1):176-87. doi: 10.1053/j.gastro.2013.03.051. Epub 2013 Apr 6.


Oncogenic drivers and signaling pathways in HCC

The European project HEPTROMIC ( based on cancer genomics was awarded with a European Commission grant (FP-7 Health grant No. 259744-2). The project was coordinated by Dr. Llovet and includes the participation of 6 research centers [M. Esteller (Spain), J. Zucman-Rossi (France), V. Mazzaferro (Italy), L. Zender (Germany), T. Golub (Harvard, USA)] and 2 small-medium enterprises that are involved in the transfer of knowledge to industry (Diagenode, Belgium and TCLand, France). Several articles were published as a result of this project. Among those, though, the most relevant define novel mutations identified by whole exome sequencing associated with epidemiological events such as HCV, alcohol and HBV infection:


Exome sequencing of hepatocellular carcinomas identifies new mutational signatures and potential therapeutic targets.

Schulze K, Imbeaud S, Letouzé E, Alexandrov LB, Calderaro J, Rebouissou S, Couchy G, Meiller C, Shinde J, Soysouvanh F, Calatayud AL, Pinyol R, Pelletier L, Balabaud C, Laurent A, Blanc JF, Mazzaferro V, Calvo F, Villanueva A, Nault JC, Bioulac-Sage P, Stratton MR, Llovet JM, Zucman-Rossi J. Nat Genet. 2015 May;47(5):505-11. doi: 10.1038/ng.3252. Epub 2015 Mar 30.


In addition by exploring the whole methylome we identified a methylome-based 35 gene signature with prognostic implications:


DNA methylation-based prognosis and epidrivers in hepatocellular carcinoma.

Villanueva A, Portela A, Sayols S, Battiston C, Hoshida Y, Méndez-González J, Imbeaud S, Letouzé E, Hernandez-Gea V, Cornella H, Pinyol R, Solé M, Fuster J, Zucman-Rossi J, Mazzaferro V, Esteller M, Llovet JM; HEPTROMIC Consortium.  Hepatology. 2015 Jun;61(6):1945-56. doi: 10.1002/hep.27732. Epub 2015 Mar 18.



Following our previous publications aiming to dissect the role of signaling cascades in the pathogenesis of HCC (mTOR, Ras signaling), we have been exploring additional pathways such as:

1) IGF signaling:

IGF activation in a molecular subclass of hepatocellular carcinoma and pre-clinical efficacy of IGF-1R blockage
Tovar V, Alsinet C, Villanueva A, Hoshida Y, Chiang DY, Solé M, Thung S, Moyano S, Toffanin S, Mínguez B, Cabellos L, Peix J, Schwartz M, Mazzaferro V, Bruix J, Llovet JM.
J Hepatol. 2010 Apr;52(4):550-9. doi: 10.1016/j.jhep.2010.01.015. Epub 2010 Feb 13.


2) The role of IGF signaling in mediating resistance to sorafenib:

Tumour initiating cells and IGF/FGF signalling contribute to sorafenib resistance in hepatocellular carcinoma.

Tovar V, Cornella H, Moeini A, Vidal S, Hoshida Y, Sia D, Peix J, Cabellos L, Alsinet C, Torrecilla S, Martinez-Quetglas I, Lozano JJ, Desbois-Mouthon C, Solé M, Domingo-Domenech J, Villanueva A, Llovet JM. Gut. 2015 Dec 11. pii: gutjnl-2015-309501. doi: 10.1136/gutjnl-2015-309501. [Epub ahead of print]


3) Wnt signaling:

Wnt-pathway activation in two molecular classes of hepatocellular carcinoma and experimental modulation by sorafenib
Lachenmayer A, Alsinet C, Savic R, Cabellos L, Toffanin S, Hoshida Y, Villanueva A, Minguez B, Newell P, Tsai HW, Barretina J, Thung S, Ward SC, Bruix J, Mazzaferro V, Schwartz M, Friedman SL, Llovet JM.
Clin Cancer Res. 2012 Sep 15;18(18):4997-5007. Epub 2012 Jul 18.


4) Notch signaling:

Notch signaling is activated in human hepatocellular carcinoma and induces tumor formation in mice
Villanueva A, Alsinet C, Yanger K, Hoshida Y, Zong Y, Toffanin S, Rodriguez-Carunchio L, Solé M, Thung S, Stanger BZ, Llovet JM.
Gastroenterology. 2012 Dec;143(6):1660-1669.e7. doi: 10.1053/j.gastro.2012.09.002. Epub 2012 Sep 11.

Astrocyte elevated gene-1 regulates hepatocellular carcinoma development and progression
Yoo BK, Emdad L, Su ZZ, Villanueva A, Chiang DY, Mukhopadhyay ND, Mills AS, Waxman S, Fisher RA, Llovet JM, Fisher PB, Sarkar D.
J Clin Invest. 2009 Mar;119(3):465-77. doi: 10.1172/JCI36460. Epub 2009 Feb 16.


5) Tumor suppressors and HDAC inhibitors:

Combination therapy for hepatocellular carcinoma: additive preclinical efficacy of the HDAC inhibitor panobinostat with sorafenib.

Lachenmayer A, Toffanin S, Cabellos L, Alsinet C, Hoshida Y, Villanueva A, Minguez B, Tsai HW, Ward SC, Thung S, Friedman SL, Llovet JM. J Hepatol. 2012 Jun;56(6):1343-50. doi: 10.1016/j.jhep.2012.01.009. Epub 2012 Feb 6.

Genome-wide methylation analysis and epigenetic unmasking identify tumor suppressor genes in hepatocellular carcinoma.

Revill K, Wang T, Lachenmayer A, Kojima K, Harrington A, Li J, Hoshida Y, Llovet JM, Powers S. Gastroenterology. 2013 Dec;145(6):1424-35.e1-25. doi: 10.1053/j.gastro.2013.08.055. Epub 2013 Sep 5.


6) UHRF1:


UHRF1 overexpression drives DNA hypomethylation and hepatocellular carcinoma
Mudbhary R, Hoshida Y, Chernyavskaya Y, Jacob V, Villanueva A, Fiel MI, Chen X, Kojima K, Thung S, Bronson RT, Lachenmayer A, Revill K, Alsinet C, Sachidanandam R, Desai A, SenBanerjee S, Ukomadu C, Llovet JM, Sadler KC.
Cancer Cell. 2014 Feb 10;25(2):196-209. doi: 10.1016/j.ccr.2014.01.003. Epub 2014 Jan 30.


7) miRNAs:

MicroRNA-based classification of hepatocellular carcinoma and oncogenic role of miR-517a.

Toffanin S, Hoshida Y, Lachenmayer A, Villanueva A, Cabellos L, Minguez B, Savic R, Ward SC, Thung S, Chiang DY, Alsinet C, Tovar V, Roayaie S, Schwartz M, Bruix J, Waxman S, Friedman SL, Golub T, Mazzaferro V, Llovet JM.

Gastroenterology. 2011 May;140(5):1618-28.e16. doi: 10.1053/j.gastro.2011.02.009. Epub 2011 Feb 13.

Lin28 promotes transformation and is associated with advanced human malignancies
Viswanathan SR, Powers JT, Einhorn W, Hoshida Y, Ng TL, Toffanin S, O’Sullivan M, Lu J, Phillips LA, Lockhart VL, Shah SP, Tanwar PS, Mermel CH, Beroukhim R, Azam M, Teixeira J, Meyerson M, Hughes TP, Llovet JM, Radich J, Mullighan CG, Golub TR, Sorensen PH, Daley GQ.
Nat Genet. 2009 Jul;41(7):843-8. doi: 10.1038/ng.392. Epub 2009 May 31.


Genomic studies and molecular classification of intrahepatic cholangiocarcinoma

Only 30% of iCCAs are amenable for curative resection, while there is no standard of care for systemic treatment. We performed an integrative genomic analysis (transcriptome, SNP array and mutations) in 149 iCCA samples and used next-generation sequencing for discovery of novel oncogenic drivers. The study supported by a grant from AECC (2011-2016) led to three main publications:


1) Molecular classification of iCCA

Integrative molecular analysis of intrahepatic cholangiocarcinoma reveals 2 classes that have different outcomes
Sia D, Hoshida Y, Villanueva A, Roayaie S, Ferrer J, Tabak B, Peix J, Sole M, Tovar V, Alsinet C, Cornella H, Klotzle B, Fan JB, Cotsoglou C, Thung SN, Fuster J, Waxman S, Garcia-Valdecasas JC, Bruix J, Schwartz ME, Beroukhim R, Mazzaferro V, Llovet JM.
Gastroenterology. 2013 Apr;144(4):829-40. doi: 10.1053/j.gastro.2013.01.001. Epub 2013 Jan 4.


2) Role of IDH mutations in iCCA development and progression.

Mutant IDH inhibits HNF-4α to block hepatocyte differentiation and promote biliary cancer
Saha SK, Parachoniak CA, Ghanta KS, Fitamant J, Ross KN, Najem MS, Gurumurthy S, Akbay EA, Sia D, Cornella H, Miltiadous O, Walesky C, Deshpande V, Zhu AX, Hezel AF, Yen KE, Straley KS, Travins J, Popovici-Muller J, Gliser C, Ferrone CR, Apte U, Llovet JM, Wong KK, Ramaswamy S, Bardeesy N.
Nature. 2014 Sep 4;513(7516):110-4. doi: 10.1038/nature13441. Epub 2014 Jul 2.


3) Identification of a novel oncogenic fusion FGFR2-PPHLN1 as targetable drivers. By applying RNA-seq and exome sequencing, we discovered a gene translocation leading to an oncogenic fusion including FGFR2 with intact kinase domain. This fusion is present in 16% of cases and has transforming properties and responds to specific inhibitors.


Massive parallel sequencing uncovers actionable FGFR2-PPHLN1 fusion and ARAF mutations in intrahepatic cholangiocarcinoma
Sia D, Losic B, Moeini A, Cabellos L, Hao K, Revill K, Bonal D, Miltiadous O, Zhang Z, Hoshida Y, Cornella H, Castillo-Martin M, Pinyol R, Kasai Yumi, Roayaie S, Thung S, Fuster J, Schwartz M, Waxman S, Cordon-Cardo C, Schadt E, Mazzaferro V, Llovet J.


Molecular classification of fibrolamellar hepatocellular carcinoma

FLC accounts for less than 1% of liver cancers, and it develops in non-cirrhotic livers of children/young adults with unknown etiologic factors. Treatment options are limited to surgical intervention. We have provided an integrative genomic analysis from a large series of FLC patients revealing a molecular classification (3 subclasses), description of mutational landscape (DNAJB1-PRKACA fusion 79%, BRAC2) and proposing a prognostic signature.


Unique genomic profile of fibrolamellar hepatocellular carcinoma.

Cornella H, Alsinet C, Sayols S, Zhang Z, Hao K, Cabellos L, Hoshida Y, Villanueva A, Thung S, Ward SC, Rodriguez-Carunchio L, Vila-Casadesús M, Imbeaud S, Lachenmayer A, Quaglia A, Nagorney DM, Minguez B, Carrilho F, Roberts LR, Waxman S, Mazzaferro V, Schwartz M, Esteller M, Heaton ND, Zucman-Rossi J, Llovet JM.

Gastroenterology. 2015 Apr;148(4):806-18.e10. doi: 10.1053/j.gastro.2014.12.028. Epub 2014 Dec 31.