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Frequent pathway mutations of splicing machinery in myelodysplasia

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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Figure 1: Components of the splicing E/A complex mutated in myelodysplasia.
Figure 2: Mutations of multiple components of the splicing machinery.
Figure 3: Frequencies and distribution of spliceosome pathway gene mutations in myeloid neoplasms.
Figure 4: Altered RNA splicing caused by a U2AF35 mutant.
Figure 5: Functional analysis of mutant U2AF35.

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Accession codes

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.

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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.

Corresponding author

Correspondence to Seishi Ogawa.

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The authors declare no competing financial interests.

Supplementary information

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. (PDF 7293 kb)

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Yoshida, K., Sanada, M., Shiraishi, Y. et al. Frequent pathway mutations of splicing machinery in myelodysplasia. Nature 478, 64–69 (2011). https://doi.org/10.1038/nature10496

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