Whole-genome mutational landscape of liver cancers displaying biliary phenotype reveals hepatitis impact and molecular diversity

Nature Communications

Volumn 6, Issue , 2015, Pages

  Fujimoto, Akihiro ^a   Furuta, Mayuko ^a   Shiraishi, Yuichi ^b   Gotoh, Kunihito ^c   Kawakami, Yoshiiku ^d   Arihiro, Koji ^d   Nakamura, Toru ^e   Ueno, Masaki ^f   Ariizumi, Shun Ichi ^g   Nguyen, Ha Hai ^a,h   Shigemizu, Daichi ^a   Abe, Tetsuo ^a   Boroevich, Keith A ^a   Nakano, Kaoru ^a   Sasaki, Aya ^a   Kitada, Rina ^a   Maejima, Kazihiro ^a   Yamamoto, Yujiro ^a   Tanaka, Hiroko ^b   Shibuya, Tetsuo ^b   Shibata, Tatsuhiro ⁱ   Ojima, Hidenori ⁱ   Shimada, Kazuaki ⁱ   Hayami, Shinya ^f   Shigekawa, Yoshinobu ^f   Aikata, Hiroshi ^d   Ohdan, Hideki ^d   Marubashi, Shigeru ^c   Yamada, Terumasa ^c   Kubo, Michiaki ^a   Hirano, Satoshi ^e   Ishikawa, Osamu ^c   Yamamoto, Masakazu ^g   Yamaue, Hiroki ^f   Chayama, Kazuaki ^a,d   Miyano, Satoru ^b   Tsunoda, Tatsuhiko ^a   Nakagawa, Hidewaki ^a   more..

^a RIKEN Center for Integrative Medical Sciences   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

^c OSAKA MEDICAL CENTER FOR CANCER AND CARDIOVASCULAR DISEASES   (Japan)

^d HIROSHIMA UNIV SCHOOL OF MEDICINE   (Japan)

^e HOKKAIDO UNIVERSITY GRADUATE SCHOOL OF MEDICINE   (Japan)

^f WAKAYAMA MEDICAL UNIVERSITY   (Japan)

^g TOKYO WOMEN'S MEDICAL UNIVERSITY   (Japan)

^h GRADUATE UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Viet Nam)

ⁱ NATIONAL CANCER CENTER   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CELL ADHESION MOLECULE; ISOCITRATE DEHYDROGENASE; PHOSPHATIDYLINOSITOL 3,4,5 TRISPHOSPHATE 3 PHOSPHATASE; PHOSPHATIDYLINOSITOL KINASE; PROTEIN P53; REGULATOR PROTEIN; TELOMERASE REVERSE TRANSCRIPTASE; TRANSCRIPTOME; ARID2 PROTEIN, HUMAN; BAP1 PROTEIN, HUMAN; CYTOSKELETON PROTEIN; KRAS PROTEIN, HUMAN; NEUROPEPTIDE; NUCLEAR PROTEIN; ONCOPROTEIN; PBRM1 PROTEIN, HUMAN; PCLO PROTEIN, HUMAN; RAS PROTEIN; TELOMERASE; TERT PROTEIN, HUMAN; TRANSCRIPTION FACTOR; TUMOR SUPPRESSOR PROTEIN; UBIQUITIN THIOLESTERASE;

CANCER; CHROMOSOME; GENE EXPRESSION; GENETIC ANALYSIS; GENOME; HEPATITIS; MOLECULAR ANALYSIS; MUTATION;

ARID2; ARTICLE; BAP1 GENE; CANCER INCIDENCE; CHROMATIN; CHRONIC HEPATITIS; CONTROLLED STUDY; CYTOSKELETON; DISEASE FREE SURVIVAL; FEMALE; GENE; GENE EXPRESSION; GENE MUTATION; GENE SEQUENCE; GENETIC HETEROGENEITY; GENETIC VARIABILITY; HUMAN; HUMAN TISSUE; LIVER CANCER DISPLAYING BILIARY PHENOTYPE; LIVER CELL CARCINOMA; MALE; MOLECULAR DYNAMICS; ODZ1 GENE; ONCOGENE K RAS; PBRM1 GENE; PCLO GENE; PHENOTYPE; SEQUENCE ANALYSIS; SOMATIC MUTATION; SUBSTITUTION REACTION; TUMOR SUPPRESSOR GENE; XIRP2 GENE; AGED; BILE DUCT CARCINOMA; BILE DUCT TUMOR; GENETICS; HEPATITIS; INTRAHEPATIC BILE DUCT; LIVER TUMOR; MIDDLE AGED; MUTATION; PATHOPHYSIOLOGY; PROMOTER REGION; VERY ELDERLY;

AGED; AGED, 80 AND OVER; BILE DUCT NEOPLASMS; BILE DUCTS, INTRAHEPATIC; CARCINOMA, HEPATOCELLULAR; CHOLANGIOCARCINOMA; CYTOSKELETAL PROTEINS; FEMALE; HEPATITIS; HUMANS; LIVER NEOPLASMS; MALE; MIDDLE AGED; MUTATION; NEUROPEPTIDES; NUCLEAR PROTEINS; PROMOTER REGIONS, GENETIC; PROTO-ONCOGENE PROTEINS; RAS PROTEINS; TELOMERASE; TRANSCRIPTION FACTORS; TUMOR SUPPRESSOR PROTEINS; UBIQUITIN THIOLESTERASE;

EID: 84943272498     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms7120     Document Type: Article

References (48)

1. Blechacz, B. & Gores, G. J. Cholangiocarcinoma: advances in pathogenesis, diagnosis, and treatment. Hepatology 48, 308-321 (2008).
2. Shin, H. R. et al. Epidemiology of cholangiocarcinoma: an update focusing on risk factors. Cancer Sci. 101, 579-585 (2010).
3. Sia, D., Tovar, V., Moeini, A. & Llovet, J. M. Intrahepatic cholangiocarcinoma: pathogenesis and rationale for molecular therapies. Oncogene 32, 4861-4870 (2013).
4. Sripa, B. et al. Liver fluke induces cholangiocarcinoma. PLoS Med. 4, e201 (2007).
5. Lee, C. H. et al. Viral hepatitis-associated intrahepatic cholangiocarcinoma shares common disease processes with hepatocellular carcinoma. Br. J. Cancer 100, 1765-1770 (2009).
6. Sekiya, S. & Suzuki, A. Intrahepatic cholangiocarcinoma can arise from Notchmediated conversion of hepatocytes. J. Clin. Invest. 122, 3914-3918 (2012).
7. Xu, J. et al. Intrahepatic cholangiocarcinoma arising in chronic advanced liver disease and the cholangiocarcinomatous component of hepatocellular cholangiocarcinoma share common phenotypes and cholangiocarcinogenesis. Histopathology 59, 1090-1099 (2011).
8. Coulouarn, C. et al. Combined hepatocellular-cholangiocarcinomas exhibit progenitor features and activation of Wnt and TGFbeta signaling pathways. Carcinogenesis 33, 1791-1796 (2012).
9. Guest, R. V. et al. Cell lineage tracing reveals a biliary origin of intrahepatic cholangiocarcinoma. Cancer Res. 74, 1005-1010 (2013).
10. Li, M. et al. Inactivating mutations of the chromatin remodeling gene ARID2 in hepatocellular carcinoma. Nat. Genet. 43, 828-829 (2011).
11. Totoki, Y. et al. High-resolution characterization of a hepatocellular carcinoma genome. Nat. Genet. 43, 464-469 (2011).
12. Fujimoto, A. et al. Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators. Nat. Genet. 44, 760-764 (2012).
13. Guichard, C. et al. Integrated analysis of somatic mutations and focal copynumber changes identifies key genes and pathways in hepatocellular carcinoma. Nat. Genet. 44, 694-698 (2012).
14. Jiang, Z. et al. The effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patients. Genome Res. 22, 593-601 (2012).
15. Sung, W. K. et al. Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma. Nat. Genet. 44, 765-769 (2012).
16. Huang, J. et al. Exome sequencing of hepatitis B virus-associated hepatocellular carcinoma. Nat. Genet. 44, 1117-1121 (2012).
17. Kan, Z. et al. Whole-genome sequencing identifies recurrent mutations in hepatocellular carcinoma. Genome Res. 23, 1422-1433 (2013).
18. Ong, C. K. et al. Exome sequencing of liver fluke-associated cholangiocarcinoma. Nat. Genet. 44, 690-693 (2012).
19. Chan-On, W. et al. Exome sequencing identifies distinct mutational patterns in liver fluke-related and non-infection-related bile duct cancers. Nat. Genet. 45, 1474-1478 (2013).
20. Jiao, Y. et al. Exome sequencing identifies frequent inactivating mutations in BAP1, ARID1A and PBRM1 in intrahepatic cholangiocarcinomas. Nat. Genet. 45, 1470-1473 (2013).
21. Alexandrov, L. B. et al. Signatures of mutational processes in human cancer. Nature 500, 415-421 (2013).
22. Gammie, A. E. et al. Functional characterization of pathogenic human MSH2 missense mutations in Saccharomyces cerevisiae. Genetics 177, 707-721 (2007).
23. Vogelstein, B. et al. Cancer genome landscapes. Science 339, 1546-1558 (2013).
24. Raimondo, G., Pollicino, T., Cacciola, I. & Squadrito, G. Occult hepatitis B virus infection. J. Hepatol. 46, 160-170 (2007).
25. Tsai, W. L. & Chung, R. T. Viral hepatocarcinogenesis. Oncogene 29, 2309-2324 (2010).
26. Komuta, M. et al. Clinicopathological study on cholagiolocellular carcinoma suggesting hepatic progenitor cell origin. Hepatology 47, 1544-1566 (2008).
27. Fischer, A., Illingworth, C. J., Campbell, P. J. & Mustonen, V. EMu: probabilistic inference of mutational processes and their localization in the cancer genome. Genome Biol. 14, R39 (2013).
28. Borger, D. R. et al. Frequent mutation of isocitrate dehydrogenase (IDH) 1 and IDH2 in cholangiocarcinoma identified through broad-based tumor genotyping. Oncologist 17, 72-79 (2011).
29. Nault, J. C. et al. High frequency of telomerase reverse-transcriptase promoter somatic mutations in hepatocellular carcinoma and preneoplastic lesions. Nat. Commun. 4, 2218 (2013).
30. Romero, O. A. & Sanchez-Cespedes, M. The SWI/SNF genetic blockade: effects in cell differentiation, cancer and developmental diseases. Oncogene 33, 2681-2689 (2014).
31. Huang da, 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).
32. Biankin, A. V. et al. Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes. Nature 491, 399-405 (2012).
33. Shah, S. P. et al. The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature 486, 395-399 (2012).
34. Nik-Zainal, S. et al. The life history of 21 breast cancers. Cell 149, 994-1007 (2012).
35. Ding, L. et al. Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. Nature 481, 506-510 (2012).
36. Landau, D. A. et al. Evolution and impact of subclonal mutations in chronic lymphocytic leukemia. Cell 152, 714-726 (2013).
37. Lim, E. et al. Aberrant luminal progenitors as the candidate target population for basal tumor development in BRCA1 mutation carriers. Nat. Med. 15, 907-913 (2009).
38. Gidekel Friedlander, S. Y. et al. Context-dependent transformation of adult pancreatic cells by oncogenic K-Ras. Cancer Cell 16, 379-389 (2009).
39. Goldstein, A. S., Huang, J., Guo, C., Garraway, I. P. & Witte, O. N. Identification of a cell of origin for human prostate cancer. Science 329, 568-571 (2010).
40. Komuta, M. et al. Histological diversity in cholangiocellular carcinoma reflects the different cholangiocyte phenotypes. Hepatology 55, 1876-1888 (2012).
41. Bosman, F. T. et al. WHO Classification of Tumors of the Digestive System 4th edn, 225-227 (IARC, 2010).
42. Hudson, T. J. et al. International network of cancer genome projects. Nature 464, 993-998 (2010).
43. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009).
44. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
45. Abecasis, G. R. et al. A map of human genome variation from population-scale sequencing. Nature 467, 1061-1073 (2010).
46. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memoryefficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
47. Kent, W. J. BLAT - the BLAST-like alignment tool. Genome Res. 12, 656-664 (2002).
48. Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5, 621-628 (2008).