Diverse modes of genomic alteration in hepatocellular carcinoma
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- 作者：Suchit Jhunjhunwala (1)
Zhaoshi Jiang (1)
Eric W Stawiski (1) (2)
Florian Gnad (1)
Jinfeng Liu (1)
Oleg Mayba (1)
Pan Du (1)
Jingyu Diao (3)
Stephanie Johnson (4)
Kwong-Fai Wong (5)
Zhibo Gao (6)
Yingrui Li (6)
Thomas D Wu (1)
Sharookh B Kapadia (3)
Zora Modrusan (2)
Dorothy M French (4)
John M Luk (5) (7) (8)
Somasekar Seshagiri (2)
Zemin Zhang (1)
1. Department of Bioinformatics and Computational Biology ; Genentech Inc. ; South San Francisco ; CA ; 94080 ; USA
2. Department of Molecular Biology ; Genentech Inc. ; South San Francisco ; CA ; 94080 ; USA
3. Department of Infectious diseases ; Genentech Inc. ; South San Francisco ; CA ; 94080 ; USA
4. Department of Pathology ; Genentech Inc. ; South San Francisco ; CA ; 94080 ; USA
5. Department of Surgery ; University of Hong Kong ; Pokfulam ; Hong Kong
6. BGI-Shenzhen ; Shenzhen ; 518083 ; China
7. Department of Pharmacology ; National University of Singapore ; Singapore ; 117597 ; Singapore
8. Institute of Molecular and Cell Biology ; A*STAR ; 61 Biopolis Drive ; Singapore ; 138673 ; Singapore - 刊名：Genome Biology
- 出版年：2014
- 出版时间：August 2014
- 年：2014
- 卷：15
- 期：8
- 全文大小：2,070 KB
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- 出版者：BioMed Central
- ISSN：1465-6906
文摘
Background Hepatocellular carcinoma (HCC) is a heterogeneous disease with high mortality rate. Recent genomic studies have identified TP53, AXIN1, and CTNNB1 as the most frequently mutated genes. Lower frequency mutations have been reported in ARID1A, ARID2 and JAK1. In addition, hepatitis B virus (HBV) integrations into the human genome have been associated with HCC. Results Here, we deep-sequence 42 HCC patients with a combination of whole genome, exome and transcriptome sequencing to identify the mutational landscape of HCC using a reasonably large discovery cohort. We find frequent mutations in TP53, CTNNB1 and AXIN1, and rare but likely functional mutations in BAP1 and IDH1. Besides frequent hepatitis B virus integrations at TERT, we identify translocations at the boundaries of TERT. A novel deletion is identified in CTNNB1 in a region that is heavily mutated in multiple cancers. We also find multiple high-allelic frequency mutations in the extracellular matrix protein LAMA2. Lower expression levels of LAMA2 correlate with a proliferative signature, and predict poor survival and higher chance of cancer recurrence in HCC patients, suggesting an important role of the extracellular matrix and cell adhesion in tumor progression of a subgroup of HCC patients. Conclusions The heterogeneous disease of HCC features diverse modes of genomic alteration. In addition to common point mutations, structural variations and methylation changes, there are several virus-associated changes, including gene disruption or activation, formation of chimeric viral-human transcripts, and DNA copy number changes. Such a multitude of genomic events likely contributes to the heterogeneous nature of HCC.