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Nature Genetics | Letter

日本語要約

Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators

Journal name:
Nature Genetics
Volume:
44,
Pages:
760–764
Year published:
DOI:
doi:10.1038/ng.2291
Received
Accepted
Published online

Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related death worldwide. We sequenced and analyzed the whole genomes of 27 HCCs, 25 of which were associated with hepatitis B or C virus infections, including two sets of multicentric tumors. Although no common somatic mutations were identified in the multicentric tumor pairs, their whole-genome substitution patterns were similar, suggesting that these tumors developed from independent mutations, although their shared etiological backgrounds may have strongly influenced their somatic mutation patterns. Statistical and functional analyses yielded a list of recurrently mutated genes. Multiple chromatin regulators, including ARID1A, ARID1B, ARID2, MLL and MLL3, were mutated in ~50% of the tumors. Hepatitis B virus genome integration in the TERT locus was frequently observed in a high clonal proportion. Our whole-genome sequencing analysis of HCCs identified the influence of etiological background on somatic mutation patterns and subsequent carcinogenesis, as well as recurrent mutations in chromatin regulators in HCCs.

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  1. Somatic substitution patterns of HCCs.
    Figure 1: Somatic substitution patterns of HCCs.

    (a) The number of somatic substitutions and indels (top) and somatic substitution patterns (bottom) of the 27 HCC genomes. (b) Repair on the transcribed strand. Fitted curves show the effect of gene expression and strand bias on substitution prevalence. We used Agilent microarray expression data (Whole Human Genome 8 × 60K Oligonucleotide Microarray) in this transcription-coupled repair (TCR) analysis, and expression level indicates Agilent microarray intensity level units with a log2 scale. UT, untranscribed strands; T, transcribed strands.

  2. Mutation patterns of MCTs.
    Figure 2: Mutation patterns of MCTs.

    (a) Circos plots20 of the MCTs from two subjects (HC3 and HC7). Each circle plot represents validated rearrangements (inner arcs) and copy-number alternations (inner rings). In rearrangements, lines show translocations (green), deletions (blue), inversions (orange) and tandem duplications (red). Copy-number gain and loss regions are shown in green and red. (b) PCA of the somatic substitution patterns of 25 HCC genomes. Two sets of MCT pairs (HC3 and HC7) are shown by green and blue, respectively, and are circled in red. (c) Three-dimensional plot of principal components (PCs) for 25 HCCs on somatic substitution pattern. Two sets of MCT pairs (HC3 and HC7) are shown in green and blue, respectively.

  3. Mutant allele proportions of point mutations.
    Figure 3: Mutant allele proportions of point mutations.

    HMG, highly mutated genes, genes whose mutation frequency was greater than 3% in the validation set (ARID1A, IGSF10, ATM, ZNF226, ZIC3, WWP1 and ERRFI1); TSG, known tumor suppressor genes annotated by MutationAssessor21; NS, nonsynonymous; S, synonymous. Non-coding includes point mutations in non-coding regions except for in splice sites. The edges of the boxes represent the 25th and 75th percentile values. The whiskers represent the most extreme data points, which are no more than 1.5 times the interquartile range from the boxes. *P < 0.05; **P < 0.01; ***P < 0.001.

  4. Mutations in chromatin regulators and functional analysis of potential driver genes.
    Figure 4: Mutations in chromatin regulators and functional analysis of potential driver genes.

    (a) Mutations in chromatin regulators in 27 HCC genomes. Mutations in chromatin-regulator genes are summarized. In addition to point mutations, 55.6-kb genomic deletion of ARID2 in NBNC2, which was identified by the read-pair method, and several copy-number alternations of chromatin-regulator genes are included. HC6 had both 1-bp deletion and low-level loss in ARID1A. (b) Functional assays of potential driver genes in HCC cell lines. Changes in cell proliferation in five HCCs compared to proliferation with control siRNA treatment are presented. Magenta and blue boxes represent more than 2-fold and less than 0.5-fold changes in the cell number, respectively. Genes involved in chromatin modification are indicated by the line.

  5. Clonal proportion of HBV integration sites in cancer cell populations of four HBV-integrated HCCs.
    Figure 5: Clonal proportion of HBV integration sites in cancer cell populations of four HBV-integrated HCCs.

    Integration sites (ISs) in the TERT locus are indicated by red. Digital PCR analysis indicates 4.0–57.8% clonal population of HBV integration at each locus. The average proportion of the TERT integration sites (41%) was higher than that of other integration sites (32%). Error bars, s.e.m. from four replicate measures.

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Gene Expression Omnibus

Referenced accessions

NCBI Reference Sequence

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Author information

  1. These authors contributed equally to this work.

    • Akihiro Fujimoto &
    • Yasushi Totoki

Affiliations

  1. Center for Genomic Medicine, RIKEN, Yokohama, Japan.

    • Akihiro Fujimoto,
    • Tetsuo Abe,
    • Keith A Boroevich,
    • Ha Hai Nguyen,
    • Masayuki Aoki,
    • Naoya Hosono,
    • Michiaki Kubo,
    • Fuyuki Miya,
    • Kaoru Nakano,
    • Kumiko Watanabe-Makino,
    • Kazuaki Chayama,
    • Naoyuki Kamatani,
    • Yusuke Nakamura,
    • Tatsuhiko Tsunoda &
    • Hidewaki Nakagawa

  2. Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan.

    • Yasushi Totoki,
    • Fumie Hosoda,
    • Yasuhito Arai,
    • Hiroyuki Takahashi,
    • Takuya Shirakihara,
    • Hiromi Nakamura &
    • Tatsuhiro Shibata

  3. Laboratory of DNA Informatics Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan.

    • Masao Nagasaki,
    • Tetsuo Shibuya,
    • Hiroko Tanaka &
    • Satoru Miyano

  4. National Institute of Biomedical Innovation, Ibaraki, Osaka, Japan.

    • Jun Kusuda

  5. Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo, Japan.

    • Hidenori Ojima &
    • Hitoshi Nakagama

  6. Hepatobiliary and Pancreatic Surgery Division, National Cancer Center Hospital, Tokyo, Japan.

    • Kazuaki Shimada &
    • Tomoo Kosuge

  7. Hepatobiliary and Pancreatic Oncology Division, National Cancer Center Hospital, Tokyo, Japan.

    • Takuji Okusaka

  8. Department of Gastroenterological Surgery, Wakayama Medical University, Wakayama, Japan.

    • Masaki Ueno,
    • Yoshinobu Shigekawa &
    • Hiroki Yamaue

  9. Department of Medicine & Molecular Science, Hiroshima University School of Medicine, Hiroshima, Japan.

    • Yoshiiku Kawakami &
    • Kazuaki Chayama

  10. Department of Gastroenterological Surgery, Hiroshima University School of Medicine, Hiroshima, Japan.

    • Koji Arihiro

  11. Department of Anatomical Pathology, Hiroshima University School of Medicine, Hiroshima, Japan.

    • Hideki Ohdan

  12. Department of Surgery, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan.

    • Kunihito Gotoh,
    • Osamu Ishikawa &
    • Terumasa Yamada

  13. Department of Gastroenterological Surgery, Tokyo Women's Medical University, Tokyo, Japan.

    • Shun-ichi Ariizumi &
    • Masakazu Yamamoto

  14. Division of Cancer Development System, National Cancer Center Research Institute, Tokyo, Japan.

    • Hitoshi Nakagama

  15. Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan.

    • Yusuke Nakamura

Contributions

A.F., Y.T., T.A., K.A.B., F.M., H. Nakamura, T.T., T. Shibata and H. Nakagawa performed data analyses. F.H., Y.A., H. Takahashi, T. Shirakihara, K.N., K.W.-M., T. Shibata and H. Nakagawa performed whole-genome sequencing. F.H., H.H.N., K.N. and K.W.-M. performed the validation sequencing study. F.H., Y.A., H. Takahashi, T. Shirakihara and T. Shibata performed siRNA experiments. A.F., M.A., N.H. and M.K. performed digital PCR and SNP microarray experiments. M.N., T. Shibuya, H. Tanaka and S.M. operated the supercomputer system. H. Ojima, K.S., T.O., M.U., Y.S., Y.K., K.A., H. Ohdan, K.G., O.I., S.A., M.Y., T.Y., K.C., T.K. and H.Y. collected clinical samples. A.F., Y.T., T.T., T. Shibata and H. Nakagawa wrote the manuscript. Y.N., T.T., T. Shibata and H. Nakagawa conceived the study and led the design of the experiments. J.K., N.K., H. Nakagama, Y.N., T. Shibata and H. Nakagawa contributed to the findings for this study.

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The authors declare no competing financial interests.

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