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Exome sequencing of hepatitis B virus–associated hepatocellular carcinoma

Nature Genetics volume 44, pages 1117–1121 (2012)Cite this article

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Abstract

Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide and shows a propensity to metastasize and infiltrate adjacent and more distant tissues1. HCC is associated with multiple risk factors, including hepatitis B virus (HBV) infection, which is especially prevalent in China. Here, we used exome sequencing to identify somatic mutations in ten HBV-positive individuals with HCC with portal vein tumor thromboses (PVTTs), intrahepatic metastases. Both C:G>A:T and T:A>A:T transversions were frequently found among the 331 non-silent mutations. Notably, ARID1A, which encodes a component of the SWI/SNF chromatin remodeling complex, was mutated in 14 of 110 (13%) HBV-associated HCC specimens. We used RNA interference to assess the roles of 91 of the confirmed mutated genes in cellular survival. The results suggest that seven of these genes, including VCAM1 and CDK14, may confer growth and infiltration capacity to HCC cells. This study provides a view of the landscape of somatic mutations that may be implicated in advanced HCC.

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Figure 1: The mutation spectra of somatic variation in ten individuals with advanced HCC.
Figure 2: Correlation of somatic mutations in matched primary tumors and PVTTs.
Figure 3: ARID1A mutations in HCC samples and cell lines have roles in cell proliferation and metastasis.
Figure 4: Effects of mutated genes on cell behaviors as determined using cell-based RNAi.

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References

  1. Bosch, F.X., Ribes, J., Diaz, M. & Cleries, R. Primary liver cancer: worldwide incidence and trends. Gastroenterology 127, S5–S16 (2004).

    Article  Google Scholar 

  2. Liver Cancer Study Group of Japan. Primary liver cancer in Japan. Clinicopathologic features and results of surgical treatment. Ann. Surg. 211, 277–287 (1990).

  3. Llovet, J.M. et al. Natural history of untreated nonsurgical hepatocellular carcinoma: rationale for the design and evaluation of therapeutic trials. Hepatology 29, 62–67 (1999).

    Article  CAS  Google Scholar 

  4. Totoki, Y. et al. High-resolution characterization of a hepatocellular carcinoma genome. Nat. Genet. 43, 464–469 (2011).

    Article  CAS  Google Scholar 

  5. Sjöblom, T. et al. The consensus coding sequences of human breast and colorectal cancers. Science 314, 268–274 (2006).

    Article  Google Scholar 

  6. Wood, L.D. et al. The genomic landscapes of human breast and colorectal cancers. Science 318, 1108–1113 (2007).

    Article  CAS  Google Scholar 

  7. Parsons, D.W. et al. An integrated genomic analysis of human glioblastoma multiforme. Science 321, 1807–1812 (2008).

    Article  CAS  Google Scholar 

  8. Jones, S. et al. Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science 321, 1801–1806 (2008).

    Article  CAS  Google Scholar 

  9. Hussain, S.P., Schwank, J., Staib, F., Wang, X.W. & Harris, C.C. TP53 mutations and hepatocellular carcinoma: insights into the etiology and pathogenesis of liver cancer. Oncogene 26, 2166–2176 (2007).

    Article  CAS  Google Scholar 

  10. Aguilar, F., Hussain, S.P. & Cerutti, P. Aflatoxin B1 induces the transversion of G––>T in codon 249 of the p53 tumor suppressor gene in human hepatocytes. Proc. Natl. Acad. Sci. USA 90, 8586–8590 (1993).

    Article  CAS  Google Scholar 

  11. Hsu, I.C. et al. Mutational hotspot in the p53 gene in human hepatocellular carcinomas. Nature 350, 427–428 (1991).

    Article  CAS  Google Scholar 

  12. Besaratinia, A., Kim, S.I., Hainaut, P. & Pfeifer, G.P. In vitro recapitulating of TP53 mutagenesis in hepatocellular carcinoma associated with dietary aflatoxin B1 exposure. Gastroenterology 137, 1127–1137 (2009).

    Article  CAS  Google Scholar 

  13. Arlt, V.M., Stiborova, M. & Schmeiser, H.H. Aristolochic acid as a probable human cancer hazard in herbal remedies: a review. Mutagenesis 17, 265–277 (2002).

    Article  CAS  Google Scholar 

  14. Moriya, M. et al. TP53 mutational signature for aristolochic acid: an environmental carcinogen. Int. J. Cancer 129, 1532–1536 (2011).

    Article  CAS  Google Scholar 

  15. Wang, Y. et al. Aristolochic acid–induced carcinogenesis examined by ACB-PCR quantification of H–Ras and K–Ras mutant fraction. Mutagenesis 26, 619–628 (2011).

    Article  Google Scholar 

  16. Barbin, A. Etheno-adduct-forming chemicals: from mutagenicity testing to tumor mutation spectra. Mutat. Res. 462, 55–69 (2000).

    Article  CAS  Google Scholar 

  17. Staib, F., Hussain, S.P., Hofseth, L.J., Wang, X.W. & Harris, C.C. TP53 and liver carcinogenesis. Hum. Mutat. 21, 201–216 (2003).

    Article  CAS  Google Scholar 

  18. Imbeaud, S., Ladeiro, Y. & Zucman–Rossi, J. Identification of novel oncogenes and tumor suppressors in hepatocellular carcinoma. Semin. Liver Dis. 30, 75–86 (2010).

    Article  CAS  Google Scholar 

  19. Li, M. et al. Inactivating mutations of the chromatin remodeling gene ARID2 in hepatocellular carcinoma. Nat. Genet. 43, 828–829 (2011).

    Article  CAS  Google Scholar 

  20. Jones, S. et al. Frequent mutations of chromatin remodeling gene ARID1A in ovarian clear cell carcinoma. Science 330, 228–231 (2010).

    Article  CAS  Google Scholar 

  21. Wiegand, K.C. et al. ARID1A mutations in endometriosis-associated ovarian carcinomas. N. Engl. J. Med. 363, 1532–1543 (2010).

    Article  CAS  Google Scholar 

  22. Gui, Y. et al. Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder. Nat. Genet. 43, 875–878 (2011).

    Article  CAS  Google Scholar 

  23. Wang, K. et al. Exome sequencing identifies frequent mutation of ARID1A in molecular subtypes of gastric cancer. Nat. Genet. 43, 1219–1223 (2011).

    Article  CAS  Google Scholar 

  24. Topaz, O. et al. A deleterious mutation in SAMD9 causes normophosphatemic familial tumoral calcinosis. Am. J. Hum. Genet. 79, 759–764 (2006).

    Article  CAS  Google Scholar 

  25. Li, Y. et al. Stepwise metastatic human hepatocellular carcinoma cell model system with multiple metastatic potentials established through consecutive in vivo selection and studies on metastatic characteristics. J. Cancer Res. Clin. Oncol. 130, 460–468 (2004).

    Article  CAS  Google Scholar 

  26. Tang, Z.Y. et al. A decade's studies on metastasis of hepatocellular carcinoma. J. Cancer Res. Clin. Oncol. 130, 187–196 (2004).

    Article  Google Scholar 

  27. Stratton, M.R., Campbell, P.J. & Futreal, P.A. The cancer genome. Nature 458, 719–724 (2009).

    Article  CAS  Google Scholar 

  28. Wong, K.M., Hudson, T.J. & McPherson, J.D. Unraveling the genetics of cancer: genome sequencing and beyond. Annu. Rev. Genomics Hum. Genet. 12, 407–430 (2011).

    Article  CAS  Google Scholar 

  29. Shu, F. et al. Functional characterization of human PFTK1 as a cyclin-dependent kinase. Proc. Natl. Acad. Sci. USA 104, 9248–9253 (2007).

    Article  CAS  Google Scholar 

  30. Leung, W.K. et al. A novel interplay between oncogenic PFTK1 protein kinase and tumor suppressor TAGLN2 in the control of liver cancer cell motility. Oncogene 30, 4464–4475 (2011).

    Article  CAS  Google Scholar 

  31. Li, H., Ruan, J. & Durbin, R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18, 1851–1858 (2008).

    Article  CAS  Google Scholar 

  32. McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).

    Article  CAS  Google Scholar 

  33. Koboldt, D.C. et al. VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics 25, 2283–2285 (2009).

    Article  CAS  Google Scholar 

  34. Robinson, J.T. et al. Integrative Genomics Viewer. Nat. Biotechnol. 29, 24–26 (2011).

    Article  CAS  Google Scholar 

  35. Huang, W., Sherman, B.T. & Lempicki, R.A. Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources. Nat. Protoc. 4, 44–57 (2009).

    Article  CAS  Google Scholar 

  36. Huang, W., Sherman, B.T. & Lempicki, R.A. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 37, 1–13 (2009).

    Article  Google Scholar 

  37. Boutros, M., Brás, L.P. & Huber, W. Analysis of cell-based RNAi screens. Genome Biol. 7, R66 (2006).

    Article  Google Scholar 

Download references

Acknowledgements

We gratefully acknowledge support from the Chinese National Key Program on Basic Research (2010CB529204 and 2010CB529206), the China National Key Projects for Infectious Disease (2012ZX10002012-008), the National Natural Science Foundation of China (81071722 and 81101875), the Shanghai Commission for Science and Technology (11ZR1425300), the International Scientific Collaborative Project (2011ZR0001) and the National High Technology Research and Development Program of China (863 Program, 2012AA02A205 and SS2012AA020103).

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Author notes

  1. Jian Huang, Qing Deng and Qun Wang: These authors contributed equally to this work.

Authors and Affiliations

  1. Human Genome Center of Rui-Jin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China

    Jian Huang, Qing Deng, Qun Wang, Niu Li, Bo Zhou, Xiao-Yan Liu, Rui-Fang Liu & Ze-Guang Han

  2. Shanghai Ministry of Science and Technology (MOST) Key Laboratory for Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China

    Jian Huang, Qing Deng, Qun Wang, Kun-Yu Li, Ji-Hong Dai, Niu Li, Bo Zhou, Xiao-Yan Liu, Rui-Fang Liu, Qian-Lan Fei, Hui Chen & Ze-Guang Han

  3. National Engineering Center for Biochip at Shanghai, Shanghai, China

    Jian Huang, Zhi-Dong Zhu & Hua-Sheng Xiao

  4. Shenzhen Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Shenzhen Third People's Hospital, Guangdong Medical College, Shenzhen, China

    Jian Huang & Boping Zhou

  5. Department of Hepatobiliary Surgery, Wuxi People's Hospital of Nanjing Medical University, Wuxi, China

    Bing Cai

  6. Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China

    Lun-Xiu Qin

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  1. Jian Huang
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Contributions

Z.-G.H. conceived and designed the study. Q.D., J.H., Z.-D.Z. and H.-S.X. performed exome sequencing and analyzed the sequence data set. Q.D., Q.W., K.-Y.L., J.-H.D., R.-F.L. and H.C. evaluated mutations in HCC samples. Q.D. and N.L. performed large-scale RNA interference against mutated genes. Q.D., Q.W., K.-Y.L., N.L., Bo Zhou, X.-Y.L. and Q.-L.F. performed in vitro experiments on individual genes. B.C., Boping Zhou and L.-X.Q. contributed HCC samples. Z.-G.H. and Q.D. integrated, analyzed and interpreted all data. Z.-G.H. contributed to the supervision of the work. Z.-G.H. and Q.D. wrote the manuscript. All authors read and approved the final version of the manuscript.

Corresponding author

Correspondence to Ze-Guang Han.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Note, Supplementary Figures 1–17 and Supplementary Tables 1, 2, 6 and 8–14 (PDF 3710 kb)

Supplementary Table 3

Potential somatic base substitution mutations were identified using massively parallel sequencings (XLSX 110 kb)

Supplementary Table 4

The 682 potential non-silent somatic mutations identified using massively parallel sequencings (XLSX 93 kb)

Supplementary Table 5

The 347 genes harboring non-silent SNVs and indel mutations (XLSX 66 kb)

Supplementary Table 7

The mutation patterns between the primary tumors and the matched PVTTs (XLSX 67 kb)

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Huang, J., Deng, Q., Wang, Q. et al. Exome sequencing of hepatitis B virus–associated hepatocellular carcinoma. Nat Genet 44, 1117–1121 (2012). https://doi.org/10.1038/ng.2391

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