Abstract

Cohesin is a multimeric protein complex that is involved in the cohesion of sister chromatids, post-replicative DNA repair and transcriptional regulation. Here we report recurrent mutations and deletions involving multiple components of the cohesin complex, including STAG2, RAD21, SMC1A and SMC3, in different myeloid neoplasms. These mutations and deletions were mostly mutually exclusive and occurred in 12.1% (19/157) of acute myeloid leukemia, 8.0% (18/224) of myelodysplastic syndromes, 10.2% (9/88) of chronic myelomonocytic leukemia, 6.3% (4/64) of chronic myelogenous leukemia and 1.3% (1/77) of classical myeloproliferative neoplasms. Cohesin-mutated leukemic cells showed reduced amounts of chromatin-bound cohesin components, suggesting a substantial loss of cohesin binding sites on chromatin. The growth of leukemic cell lines harboring a mutation in RAD21 (Kasumi-1 cells) or having severely reduced expression of RAD21 and STAG2 (MOLM-13 cells) was suppressed by forced expression of wild-type RAD21 and wild-type RAD21 and STAG2, respectively. These findings suggest a role for compromised cohesin functions in myeloid leukemogenesis.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Accessions

Primary accessions

Gene Expression Omnibus

References

  1. 1.

    , & Unraveling the molecular pathophysiology of myelodysplastic syndromes. J. Clin. Oncol. 29, 504–515 (2011).

  2. 2.

    , & Molecular genetics of adult acute myeloid leukemia: prognostic and therapeutic implications. J. Clin. Oncol. 29, 475–486 (2011).

  3. 3.

    et al. Frequent pathway mutations of splicing machinery in myelodysplasia. Nature 478, 64–69 (2011).

  4. 4.

    , & Chromosomal cohesin forms a ring. Cell 112, 765–777 (2003).

  5. 5.

    & Cohesin: its roles and mechanisms. Annu. Rev. Genet. 43, 525–558 (2009).

  6. 6.

    et al. Postreplicative formation of cohesion is required for repair and induced by a single DNA break. Science 317, 242–245 (2007).

  7. 7.

    & The cohesin complex is required for the DNA damage-induced G2/M checkpoint in mammalian cells. EMBO J. 28, 2625–2635 (2009).

  8. 8.

    Cohesin, gene expression and development: lessons from Drosophila. Chromosome Res. 17, 185–200 (2009).

  9. 9.

    et al. Effects of sister chromatid cohesion proteins on cut gene expression during wing development in Drosophila. Development 132, 4743–4753 (2005).

  10. 10.

    et al. Cohesin-dependent regulation of Runx genes. Development 134, 2639–2649 (2007).

  11. 11.

    et al. Cohesins functionally associate with CTCF on mammalian chromosome arms. Cell 132, 422–433 (2008).

  12. 12.

    et al. Cohesin mediates transcriptional insulation by CCCTC-binding factor. Nature 451, 796–801 (2008).

  13. 13.

    & Cohesinopathies, gene expression, and chromatin organization. J. Cell Biol. 189, 201–210 (2010).

  14. 14.

    et al. HDAC8 mutations in Cornelia de Lange syndrome affect the cohesin acetylation cycle. Nature 489, 313–317 (2012).

  15. 15.

    et al. RAD21 mutations cause a human cohesinopathy. Am. J. Hum. Genet. 90, 1014–1027 (2012).

  16. 16.

    et al. Mutational inactivation of STAG2 causes aneuploidy in human cancer. Science 333, 1039–1043 (2011).

  17. 17.

    et al. An Smc3 acetylation cycle is essential for establishment of sister chromatid cohesion. Mol. Cell 39, 689–699 (2010).

  18. 18.

    et al. Transcriptional dysregulation in NIPBL and cohesin mutant human cells. PLoS Biol. 7, e1000119 (2009).

  19. 19.

    et al. Genome-wide DNA methylation analysis in cohesin mutant human cell lines. Nucleic Acids Res. 38, 5657–5671 (2010).

  20. 20.

    et al. Regulation of the Drosophila enhancer of split and invected-engrailed gene complexes by sister chromatid cohesion proteins. PLoS ONE 4, e6202 (2009).

  21. 21.

    et al. Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. Nature 481, 506–510 (2012).

  22. 22.

    et al. Clonal architecture of secondary acute myeloid leukemia. N. Engl. J. Med. 366, 1090–1098 (2012).

  23. 23.

    et al. The origin and evolution of mutations in acute myeloid leukemia. Cell 150, 264–278 (2012).

  24. 24.

    The Cancer Genome Atlas Research Network. Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N. Engl. J. Med. 368, 2059–2074 (2013).

  25. 25.

    et al. Clonal diversity of recurrently mutated genes in myelodysplastic syndromes. Leukemia 27, 12785–1282 (2013).

  26. 26.

    et al. Chromatid cohesion defects may underlie chromosome instability in human colorectal cancers. Proc. Natl. Acad. Sci. USA 105, 3443–3448 (2008).

  27. 27.

    , , , & Systematic reduction of cohesin differentially affects chromosome segregation, condensation, and DNA repair. Curr. Biol. 20, 957–963 (2010).

  28. 28.

    et al. Cohesins form chromosomal cis-interactions at the developmentally regulated IFNG locus. Nature 460, 410–413 (2009).

  29. 29.

    & Harnessing synthetic lethal interactions in anticancer drug discovery. Nat. Rev. Drug Discov. 10, 351–364 (2011).

  30. 30.

    et al. Integrated molecular analysis of clear-cell renal cell carcinoma. Nat. Genet. doi:10.1038/ng.2699 (24 June 2013).

  31. 31.

    BLAT—the BLAST-like alignment tool. Genome Res. 12, 656–664 (2002).

  32. 32.

    et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

  33. 33.

    , & Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat. Protoc. 4, 1073–1081 (2009).

  34. 34.

    et al. A method and server for predicting damaging missense mutations. Nat. Methods 7, 248–249 (2010).

  35. 35.

    , , & MutationTaster evaluates disease-causing potential of sequence alterations. Nat. Methods 7, 575–576 (2010).

  36. 36.

    Pyrosequencing sheds light on DNA sequencing. Genome Res. 11, 3–11 (2001).

  37. 37.

    et al. Emerging kinetics of BCR-ABL1 mutations and their effect on disease outcomes in chronic myeloid leukemia patients with imatinib failure. Leuk. Res. 37, 43–49 (2013).

  38. 38.

    , & Studying copy number variations using a nanofluidic platform. Nucleic Acids Res. 36, e116 (2008).

  39. 39.

    , & Mathematical analysis of copy number variation in a DNA sample using digital PCR on a nanofluidic device. PLoS ONE 3, e2876 (2008).

  40. 40.

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

  41. 41.

    et al. A robust algorithm for copy number detection using high-density oligonucleotide single nucleotide polymorphism genotyping arrays. Cancer Res. 65, 6071–6079 (2005).

  42. 42.

    et al. Highly sensitive method for genomewide detection of allelic composition in nonpaired, primary tumor specimens by use of affymetrix single-nucleotide-polymorphism genotyping microarrays. Am. J. Hum. Genet. 81, 114–126 (2007).

  43. 43.

    et al. Genomewide screening of DNA copy number changes in chronic myelogenous leukemia with the use of high-resolution array-based comparative genomic hybridization. Genes Chromosom. Cancer 45, 482–494 (2006).

  44. 44.

    et al. Gain-of-function of mutated C-CBL tumour suppressor in myeloid neoplasms. Nature 460, 904–908 (2009).

  45. 45.

    et al. Tissue-specific demethylation in CpG-poor promoters during cellular differentiation. Hum. Mol. Genet. 20, 2710–2721 (2011).

  46. 46.

    , , , & Potent vaccine therapy with dendritic cells genetically modified by the gene-silencing–resistant retroviral vector GCDNsap. Mol. Ther. 13, 301–309 (2006).

  47. 47.

    et al. Isolation, characterization, and genetic complementation of a cellular mutant resistant to retroviral infection. Proc. Natl. Acad. Sci. USA 103, 15933–15938 (2006).

  48. 48.

    & Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc. Natl. Acad. Sci. USA 98, 31–36 (2001).

  49. 49.

    , , , & Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5, 621–628 (2008).

  50. 50.

    , , & NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res. 40, D130–D135 (2012).

Download references

Acknowledgements

This work was supported by Grants-in-Aid from the Ministry of Health, Labor and Welfare of Japan and KAKENHI (23249052, 22134006 and 21790907; S.O.), the Industrial Technology Research Grant Program from the New Energy and Industrial Technology Development Organization (NEDO; S.O.) (08C46598a), NHRI-EX100-10003NI Taiwan (L.-Y.S.), the project for development of innovative research on cancer therapies (p-direct; S.O.) and the Japan Society for the Promotion of Science through the Funding Program for World-Leading Innovative R&D on Science and Technology, initiated by the Council for Science and Technology Policy (CSTP; S.O.). We thank Y. Hayashi (Gunma Children's Medical Centre), R.C. Mulligan (Harvard Medical School), S. Sugano (The University of Tokyo), M. Onodera (National Center for Child Health and Development, Japan) and L. Ström (Karolinska Institute) for providing materials. We thank Y. Yamazaki for cell sorting. We also thank Y. Mori, M. Nakamura, N. Mizota and S. Ichimura for their technical assistance and M. Ueda for encouragement.

Author information

Affiliations

  1. Cancer Genomics Project, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.

    • Ayana Kon
    • , Masashi Sanada
    • , Yasunobu Nagata
    • , Kenichi Yoshida
    • , Yusuke Okuno
    • , Aiko Sato-Otsubo
    • , Yusuke Sato
    •  & Seishi Ogawa
  2. Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University, Taipei, Taiwan.

    • Lee-Yung Shih
  3. Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.

    • Masashi Minamino
    • , Masashige Bando
    • , Ryuichiro Nakato
    •  & Katsuhiko Shirahige
  4. Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Kyoto-shi Sakyo-ku, Kyoto, Japan.

    • Masashi Sanada
    •  & Seishi Ogawa
  5. Laboratory of DNA Information Analysis, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan.

    • Yuichi Shiraishi
    • , Teppei Shimamura
    • , Kenichi Chiba
    •  & Satoru Miyano
  6. Department of Pathology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.

    • Shumpei Ishikawa
    •  & Aiko Nishimoto
  7. Department of Genomic Pathology, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan.

    • Shumpei Ishikawa
  8. Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Meguro-ku, Tokyo, Japan.

    • Genta Nagae
    •  & Hiroyuki Aburatani
  9. Munich Leukemia Laboratory, Munich, Germany.

    • Claudia Haferlach
    • , Tamara Alpermann
    •  & Torsten Haferlach
  10. Department of Hematology and Oncology, University Hospital Mannheim, Mannheim, Germany.

    • Daniel Nowak
    • , Florian Nolte
    •  & Wolf-Karsten Hofmann
  11. Division of Biomedical Information Analysis, Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Aoba-ku, Sendai, Japan.

    • Masao Nagasaki
  12. Laboratory of Sequence Data Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan.

    • Hiroko Tanaka
    •  & Satoru Miyano
  13. Division of Stem Cell Therapy, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan.

    • Ryo Yamamoto
    • , Tomoyuki Yamaguchi
    •  & Hiromitsu Nakauchi
  14. Stem Cell and Organ Regeneration Project, Exploratory Research for Advanced Technology (ERATO), Japan Science and Technology Agency (JST), Chiyoda-ku, Tokyo, Japan.

    • Tomoyuki Yamaguchi
    •  & Hiromitsu Nakauchi
  15. Stem Cell Bank, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan.

    • Makoto Otsu
  16. Department of Hematology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan.

    • Naoshi Obara
    • , Mamiko Sakata-Yanagimoto
    •  & Shigeru Chiba
  17. Division of Hematology, Department of Medicine, Showa University School of Medicine, Shinagawa-ku, Tokyo, Japan.

    • Tsuyoshi Nakamaki
    •  & Hiraku Mori
  18. Division of Hematology, Tokyo Metropolitan Ohtsuka Hospital, Toshima-ku, Tokyo, Japan.

    • Ken Ishiyama
    •  & Shuichi Miyawaki
  19. Hematology/Oncology, Cedars-Sinai Medical Center, Los Angeles, California, USA.

    • H Phillip Koeffler
  20. National University of Singapore, Cancer Science Institute of Singapore, Singapore.

    • H Phillip Koeffler

Authors

  1. Search for Ayana Kon in:

  2. Search for Lee-Yung Shih in:

  3. Search for Masashi Minamino in:

  4. Search for Masashi Sanada in:

  5. Search for Yuichi Shiraishi in:

  6. Search for Yasunobu Nagata in:

  7. Search for Kenichi Yoshida in:

  8. Search for Yusuke Okuno in:

  9. Search for Masashige Bando in:

  10. Search for Ryuichiro Nakato in:

  11. Search for Shumpei Ishikawa in:

  12. Search for Aiko Sato-Otsubo in:

  13. Search for Genta Nagae in:

  14. Search for Aiko Nishimoto in:

  15. Search for Claudia Haferlach in:

  16. Search for Daniel Nowak in:

  17. Search for Yusuke Sato in:

  18. Search for Tamara Alpermann in:

  19. Search for Masao Nagasaki in:

  20. Search for Teppei Shimamura in:

  21. Search for Hiroko Tanaka in:

  22. Search for Kenichi Chiba in:

  23. Search for Ryo Yamamoto in:

  24. Search for Tomoyuki Yamaguchi in:

  25. Search for Makoto Otsu in:

  26. Search for Naoshi Obara in:

  27. Search for Mamiko Sakata-Yanagimoto in:

  28. Search for Tsuyoshi Nakamaki in:

  29. Search for Ken Ishiyama in:

  30. Search for Florian Nolte in:

  31. Search for Wolf-Karsten Hofmann in:

  32. Search for Shuichi Miyawaki in:

  33. Search for Shigeru Chiba in:

  34. Search for Hiraku Mori in:

  35. Search for Hiromitsu Nakauchi in:

  36. Search for H Phillip Koeffler in:

  37. Search for Hiroyuki Aburatani in:

  38. Search for Torsten Haferlach in:

  39. Search for Katsuhiko Shirahige in:

  40. Search for Satoru Miyano in:

  41. Search for Seishi Ogawa in:

Contributions

A.K., Y.N., K.Y., A.S.-O., Y. Sato and M.S. processed and analyzed genetic materials and performed sequencing and SNP array analysis. Y. Shiraishi, Y.O., R.N., A.S.-O., H.T., T.S., K.C., M.N. and S. Miyano performed bioinformatics analyses of the sequencing data. L.-Y.S. performed pyrosequencing analysis, and A.N. and S.I. performed digital PCR. G.N. and H.A. performed methylation analysis. M.M., M.B. and K.S. performed studies on protein expression of cohesin components. A.K., M.S., T.Y., R.Y., M.O. and H.N. were involved in the functional studies. A.K. and A.S.-O. performed expression microarray experiments and their analyses. L.-Y.S., D.N., T.A., C.H., F.N., W.-K.H., T.H., H.P.K., T.N., H.M., S. Miyawaki, M.S.-Y., K.I., N.O. and S.C. collected specimens and were involved in project planning. A.K., L.-Y.S., M.M., A.S.-O. and S.O. generated figures and tables. S.O. led the entire project, and A.K. and S.O. wrote the manuscript. All authors participated in the discussion and interpretation of the data.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Seishi Ogawa.

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–13 and Supplementary Tables 1–18

About this article

Publication history

Received

Accepted

Published

DOI

https://doi.org/10.1038/ng.2731

Further reading

Newsletter Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing