Hepatocellular Carcinoma Clinical and Genomic Features

Transcription

1 Hepatocellular Carcinoma Clinical and Genomic Features

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3 Regional varia,ons in the mortality rates of HCC

4 Liver cancer has the fastest growing death rate in USA

5 A shi6 toward younger ages is observed concomitant with the recent increase in the overall incidence of this malignancy EL SERAG et al, GASTROENTEROLOGY 2007

6 Malignant TransformaIon MulIstep HCC [2] Liver cirrhosis Epigene,c altera,ons Gene,c altera,ons Dysplas,c nodules [1] Normal liver Hepa,,s C Hepa,,s B Ethanol NASH Oxidative stress and inflammation Growth factors Loss of cell cycle checkpoints 1. Tornillo L, et al. Lab Invest. 2002;82: Verslype C, et al. AASLD Potential Targets Viral oncogenes Telomere shortening Antiapoptosis Carcinogens Cancer stem cells Angiogenesis

7 Mortality from cancer in obese US men NEJM 2003

8 Racial Differences in Survival of Pa,ents 100 with HCC Survival (%) Caucasian Hispanic Black Asian Years Davila J, El- Serag HB. Clin Gastro Hepatol; 2006

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10 Ref. Study design Summary of results High-resolution characterization of a hepatocellular carcinoma genome Nat Genet (2011) WGS and WES of a 1 HCV positive HCC Identified and validated 63 non-synonymous somatic substitutions including mutations of TP53 and AXIN1. Identified and validated 22 chromosome rearrangements generating four fusion transcripts Rapid growth of a hepatocellular carcinoma and the driving mutations revealed by cell-population genetic analysis of whole-genome data PNAS USA (2011) Inactivating mutations of the chromatin remodeling gene ARID2 in hepatocellular carcinoma Nat Genet (2011) The effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patients Genome Res (2012) Integrated analysis of somatic mutations and focal copynumber changes identifies key genes and pathways in hepatocellular carcinoma Nat Genet (2012) Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators Nat Genet (2012) Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma Nat Genet (2012) Exome sequencing of hepatitis B virus-associated hepatocellular carcinoma Nat Genet (2012) Exome sequencing of liver fluke-associated cholangiocarcinoma Nat Genet (2012) Endogenous retrotransposition activates oncogenic pathways in HCC Cell (2013) Highly eecurrent TERT promoter mutations in human melanoma Science (2013) Genetic variants in STAT4 and HLA-DQ genes confer risk of HBV related HCC Nat Genet (2013) WGS or WES of nine tumor samples and seven adjacent normal liver samples from a HBV positive HCC WES of 10 HCV positive HCCs. Screening of five recurrently mutated genes in an additional cohort of 129 HCCs associated various disease etiologies Identified and validated 24 somatic mutations that alter amino acid sequences. Evolution of tumors was inferred from mutations derived from multiple primary and recurrent tumor samples Identified frequent mutations in CTNNB1 and TP53. Identified novel and frequent inactivating mutations in ARID2 gene. Mutation frequencies of CTNNB1, TP53 and ARID2 are associated with disease etiology WGS of four HCCs (3 HBV positive and 1 HBV negative) Identified 255 HBV integration sites. HBV integration into MLL4, ANGPT1, and a novel transcript resulted in elevated gene expression WES of 24 HCCs, among them one is HBV positive, four are HCV positive, 12 are alcohol related. Screening of 14 genes in an additional cohort of 125 HCCs WGS of 27 HCCs (11 HBV positive, 15 HCV positive, two non-viral). Screening of significantly mutated genes in an additional cohort of 120 HCCs WGS of 88 HCCs (81 HBV positive, 7 HBV negative) WES of 10 HBV positive HCCs. Screening 10 significantly mutated genes in an additional cohort of 100 HCCs WES of eight cholangiocarcinomas (CCAs). Screening of 15 significantly mutated in 46 additional CCAs retrotransposon capture sequencing (RC-seq) of 19 HCCs systematic query for noncoding somatic mutations using published WGS data GWAS 2,514 chronic HBV carriers (1,161 HCC cases and 1,353 controls) followed by a 2-stage validation (4,319 cases and 4,966 controls) Identified frequent mutations in CTNNB1 and TP53. Identified novel and frequent inactivating mutations in ARID1A, ARID2 and other genes involved in chromatin remodeling. Mutation frequencies of these genes are associated with disease etiology Identified frequent and novel mutations in genes involved in chromatin remodeling, e.g. ARID1A, ARID1B, ARID2, MLL and MLL3. HBV integration in TERT gene in 4 of the 11 HBV positive HCCs Recurrent HBV integration in TERT, MLL4 and CCNE1. HBV integrations led to elevated gene expression. HBV integration associated with chromosome instability, early onset and poor outcome ARID1A mutations in 13% of HBV associated HCCs. Functional study suggested ARID1A mutation may be crucial in HCC invasion and metastasis Identified frequent mutations in TP53, KRAS, SMAD4 and MLL3 Recurrent somatic integrations in 2 genes (MCC, ST18) Recurrent mutations in TERT promoter in multiple tumor types including HCC HCC risk was significantly associated with two independent loci: STAT4 and HLA-DQ

11 Key Genes and Pathways in HCC (Jessica Zucman- Rossi, Nature GeneIcs 2012) new recurrent alterations in 4 genes: ARID1A, RPS6KA3, NFE2L2 & IRF2. IRF2, in HBV-related tumors (impairs P53 function); inactivation of chromatin remodelers in alcohol-related tumors. over-representation of G:C>T:A nucleotide transversion (usually C:G>T:A) G>T transversions were significantly enriched in the non-transcribed DNA strand

12 Retrotransposons cause mutaions in HCC (Geoffrey J. Faulkner, Cell 2013) LINE- 1 (L1) retrotransposons are mobile gene,c elements comprising 17% of the human genome. New L1 inser,ons can profoundly alter gene func,on and cause disease, though their significance in cancer was unclear. retrotransposon capture sequencing (RC- seq) to 19 HCCs two L1- mediated muta,ons enabling tumorigenesis: Mutated in Colorectal Cancers (MCC) LOF resul,ng in wnt ac,va,on (4/19). Suppression of Tumorigenicity 18 (ST18) GOF (1/19).

13 Recurrent TERT mutaions in cancer (Levi Garraway, Science 2013) Recurrent muta,ons within the core promoter of telomerase reverse transcriptase (TERT) Melanoma 71%, Liver 67%, Bladder 100%. Generate de novo consensus binding mo,fs for ETS transcrip,on factors Increased transcrip,onal ac,vity from the TERT promoter Another study showed HBV inser,on into TERT (Sung, Nat Genet, 2012)

14 Frequency of TERT promoter mutations; 15 or more tumors were analyzed in 26 tumor types. Killela P J et al. PNAS 2013;110: by National Academy of Sciences

15 STAT4 and HLA- DQ in HBV induced HCC (Long Yu, Nature GeneIcs 2013) GWAS: 2,514 chronic HBV carriers (1,161 HCC cases and 1,353 controls) followed by a 2- stage valida,on (4,319 cases and 4,966 controls) Other studies showed that MICA and DEPDC are associated with HCV

16 Han Z- G, Annu. Rev. Genomics Hum. Genet

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18 Sorafenib in Advanced HCC Llovet et al, NEJM 2008

19 unbiased surveys of cancer genomes afford an unprecedented opportunity to generate new ideas.

20 Cancer mutaions SomaIc mutaion frequencies differ between different cancer types. New geneic mechanisms for mutaions have been discovered: Specific carcinogenes can be inferred Viral inserion TranslocaIons Kataegis (muliple base mutaions that occur in cis near rearrangement breakpoints (AID, APOBEC)) chromothripsis Chromoplexy

21 Chromothripsis & Chromoplexy Non- coninuous model of tumor evoluion chromothripsis correlates with poor prognosis (plasma cell myeloma, meduloblastoma) Similar chromosome- rearrangement pagerns have recently been reported in the germ- line DNA of paients with de novo congenital anomalies now also in benign tumors. Shen, Cancer Cell 2013

22 Surprising New Oncogenes and Tumor Suppressors DNA methylation DNA hydroxymethylation histone methyltransferases histone demethylases histone acetyltransferases SWI/SNF complex Lineage Transcription factors RNA Splicing Metabolism Axon Guidance DNMT3A TET2 MLLs, EZH2, histone methyltransferases JARID, UTX CREBP SMARCAs, ARIDs MITF, TTF1, OCT4 SF3B1, U2AF1, SFRS1, SFRS7, SF3A1, ZRSR2, SRSF2, U2AF2, IDH1 and IDH2 SLIT/ROBO But also more classical ones: BRAF, GNAS QuesIon: Is deranged regulaion a hallmark of cancer?

23 More issues Tumor heterogeneity Same pathway in different clones Studies of genome mutaions in relapsed cancers Relapsed AML can be associated with the predominant clone at diagnosis gaining addiional mutaions,or it can represent expansion and further mutaion of minor subclones present in the iniial diagnosic specimen. New viral pathogens a new polyoma virus integrated into the genomes of approximately 80% of cases of Merkel cell carcinoma.

24 Genomics- Driven Oncology: Framework for an Emerging Paradigm Levi A. Garraway, JCO

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