Abstract

Myelodysplastic syndromes and related disorders (myelodysplasia) are a heterogeneous group of myeloid neoplasms showing deregulated blood cell production with evidence of myeloid dysplasia and a predisposition to acute myeloid leukaemia, whose pathogenesis is only incompletely understood. Here we report whole-exome sequencing of 29 myelodysplasia specimens, which unexpectedly revealed novel pathway mutations involving multiple components of the RNA splicing machinery, including U2AF35, ZRSR2, SRSF2 and SF3B1. In a large series analysis, these splicing pathway mutations were frequent (45 to 85%) in, and highly specific to, myeloid neoplasms showing features of myelodysplasia. Conspicuously, most of the mutations, which occurred in a mutually exclusive manner, affected genes involved in the 3′-splice site recognition during pre-mRNA processing, inducing abnormal RNA splicing and compromised haematopoiesis. Our results provide the first evidence indicating that genetic alterations of the major splicing components could be involved in human pathogenesis, also implicating a novel therapeutic possibility for myelodysplasia.

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Accessions

Primary accessions

DDBJ/GenBank/EMBL

Gene Expression Omnibus

Data deposits

Sequence data have been deposited in the DDBJ repository under accession number DRA000433. Microarray data have been deposited in the GEO database under accession numbers GSE31174 (for SNP arrays), GSE31171 (for exon arrays) and GSE31172 (for expression arrays).

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Acknowledgements

This work was supported by Grant-in-Aids from the Ministry of Health, Labor and Welfare of Japan and from the Ministry of Education, Culture, Sports, Science and Technology, and also by the Japan Society for the Promotion of Science (JSPS) through the ‘Funding Program for World-Leading Innovative R&D on Science and Technology (FIRST Program)’, initiated by the Council for Science and Technology Policy (CSTP). pGCDNsamIRESEGFP vector was a gift from M. Onodera. We thank Y. Mori, O. Hagiwara, M. Nakamura and N. Mizota for their technical assistance. We are also grateful to K. Ikeuchi and M. Ueda for their continuous encouragement throughout the study.

Author information

Author notes

    • Kenichi Yoshida
    • , Masashi Sanada
    • , Yuichi Shiraishi
    • , Daniel Nowak
    •  & Yasunobu Nagata

    These authors contributed equally to this work.

Affiliations

  1. Cancer Genomics Project, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan

    • Kenichi Yoshida
    • , Masashi Sanada
    • , Yasunobu Nagata
    • , Yusuke Sato
    • , Aiko Sato-Otsubo
    • , Ayana Kon
    • , Masashi Shiosaka
    • , Ryoichiro Kawahata
    •  & Seishi Ogawa
  2. Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan

    • Yuichi Shiraishi
    •  & Satoru Miyano
  3. Department of Hematology and Oncology, Medical Faculty Manheim of the University of Heidelberg, 1–3 Theodor-Kutzer-Ufer, Mannheim 68167, Germany

    • Daniel Nowak
    • , Florian Nolte
    •  & Wolf-Karsten Hofmann
  4. Division of Stem Cell Therapy, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan

    • Ryo Yamamoto
    • , Makoto Otsu
    •  & Hiromitsu Nakauchi
  5. Laboratory of Functional Genomics, Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan

    • Masao Nagasaki
  6. Laboratory of Sequence Data Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan

    • George Chalkidis
    •  & Satoru Miyano
  7. Division of Systems Biomedical Technology, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan

    • Yutaka Suzuki
    •  & Sumio Sugano
  8. Nakauchi Stem Cell and Organ Regeneration Project, Exploratory Research for Advanced Technology, Japan Science and Technology Agency, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan

    • Tomoyuki Yamaguchi
    •  & Hiromitsu Nakauchi
  9. Department of Hematology, Institute of Clinical Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba-shi, Ibaraki, 305-8571, Japan

    • Naoshi Obara
    • , Mamiko Sakata-Yanagimoto
    •  & Shigeru Chiba
  10. Division of Hematology, Tokyo Metropolitan Ohtsuka Hospital, 2-8-1 Minami-Ohtsuka, Toshima-ku, Tokyo 170-0005, Japan

    • Ken Ishiyama
    •  & Shuichi Miyawaki
  11. Division of Hematology, Internal Medicine, Showa University Fujigaoka Hospital, 1-30 Fujigaoka, Aoba-ku, Yokohama, Kanagawa 227-8501, Japan

    • Hiraku Mori
  12. Munich Leukemia Laboratory, Max-Lebsche-Platz 31, Munich 81377, Germany

    • Claudia Haferlach
    •  & Torsten Haferlach
  13. Hematology/Oncology, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, California 90048, USA

    • H. Phillip Koeffler
  14. National University of Singapore, Cancer Science Institute of Singapore, 28 Medical Drive, Singapore 117456, Singapore

    • H. Phillip Koeffler
  15. Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University, 199 Tung Hwa North Rd, Taipei 105, Taiwan

    • Lee-Yung Shih

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Contributions

Y.Sh., Y.Sa., A.S.-O., Y.N., M.N., G.C., R.K. and S.Miyano were committed to bioinformatics analyses of resequencing data. M.Sa., A.S.-O. and Y.Sa. performed microarray experiments and their analyses. R.Y., T.Y., M.O., M.Sa., A.K., M.Sh. and H.N. were involved in the functional analyses of U2AF35 mutants. N.O., M.S.-Y., K.I., H.M., W.-K.H., F.N., D.N., T.H., C.H., S.Miyawaki, S.C., H.P.K. and L.-Y.S. collected specimens and were also involved in planning the project. K.Y., Y.N., Y.Su., A.S.-O. and S.S. processed and analysed genetic materials, library preparation and sequencing. K.Y., M.Sa., Y.Sh., A.S.-O., Y. Sa. and S.O. generated figures and tables. S.O. led the entire project and wrote the manuscript. All authors participated in the discussion and interpretation of the data and the results.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Seishi Ogawa.

Supplementary information

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    Supplementary Information

    This file contains Supplementary Methods 1-8 (see Contents for more details), additional references, Supplementary Figures 1-18 with legends and Supplementary Tables 1-11.

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DOI

https://doi.org/10.1038/nature10496

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