Genetic inactivation of the polycomb repressive complex 2 in T cell acute lymphoblastic leukemia (original) (raw)

T cell acute lymphoblastic leukemia (T-ALL) is an immature hematopoietic malignancy driven mainly by oncogenic activation of NOTCH1 signaling1. In this study we report the presence of loss-of-function mutations and deletions of the EZH2 and SUZ12 genes, which encode crucial components of the Polycomb repressive complex 2 (PRC2)2,3, in 25% of T-ALLs. To further study the role of PRC2 in T-ALL, we used NOTCH1-dependent mouse models of the disease, as well as human T-ALL samples, and combined locus-specific and global analysis of NOTCH1-driven epigenetic changes. These studies demonstrated that activation of NOTCH1 specifically induces loss of the repressive mark Lys27 trimethylation of histone 3 (H3K27me3)4 by antagonizing the activity of PRC2. These studies suggest a tumor suppressor role for PRC2 in human leukemia and suggest a hitherto unrecognized dynamic interplay between oncogenic NOTCH1 and PRC2 function for the regulation of gene expression and cell transformation.

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References

1. Aster, J.C., Blacklow, S.C. & Pear, W.S. Notch signalling in T-cell lymphoblastic leukaemia/lymphoma and other haematological malignancies. J. Pathol. 223, 262–273 (2011).
   Article CAS Google Scholar
2. Margueron, R. & Reinberg, D. The Polycomb complex PRC2 and its mark in life. Nature 469, 343–349 (2011).
   Article CAS Google Scholar
3. Orlando, V. Polycomb, epigenomes and control of cell identity. Cell 112, 599–606 (2003).
   Article CAS Google Scholar
4. Barski, A. et al. High-resolution profiling of histone methylations in the human genome. Cell 129, 823–837 (2007).
   Article CAS Google Scholar
5. Aifantis, I., Raetz, E. & Buonamici, S. Molecular pathogenesis of T-cell leukaemia and lymphoma. Nat. Rev. Immunol. 8, 380–390 (2008).
   Article CAS Google Scholar
6. Paganin, M. & Ferrando, A. Molecular pathogenesis and targeted therapies for NOTCH1-induced T-cell acute lymphoblastic leukemia. Blood Rev. 25, 83–90 (2010).
   Article Google Scholar
7. Carpenter, A.C. & Bosselut, R. Decision checkpoints in the thymus. Nat. Immunol. 11, 666–673 (2010).
   Article CAS Google Scholar
8. Weng, A.P. et al. Activating mutations of NOTCH1 in human T cell acute lymphoblastic leukemia. Science 306, 269–271 (2004).
   Article CAS Google Scholar
9. Thompson, B.J. et al. The SCFFBW7 ubiquitin ligase complex as a tumor suppressor in T cell leukemia. J. Exp. Med. 204, 1825–1835 (2007).
   Article CAS Google Scholar
10. Chase, A. & Cross, N.C. Aberrations of EZH2 in cancer. Clin. Cancer Res. 17, 2613–2618 (2011).
    Article CAS Google Scholar
11. Ernst, T. et al. Inactivating mutations of the histone methyltransferase gene EZH2 in myeloid disorders. Nat. Genet. 42, 722–726 (2010).
    Article CAS Google Scholar
12. Nikoloski, G. et al. Somatic mutations of the histone methyltransferase gene EZH2 in myelodysplastic syndromes. Nat. Genet. 42, 665–667 (2010).
    Article CAS Google Scholar
13. Bracken, A.P., Dietrich, N., Pasini, D., Hansen, K.H. & Helin, K. Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitions. Genes Dev. 20, 1123–1136 (2006).
    Article CAS Google Scholar
14. Cao, R. & Zhang, Y. SUZ12 is required for both the histone methyltransferase activity and the silencing function of the EED-EZH2 complex. Mol. Cell 15, 57–67 (2004).
    Article CAS Google Scholar
15. Chase, A. & Cross, N.C. Aberrations of EZH2 in cancer. Clin. Cancer Res. 17, 2613–2618 (2011).
    Article CAS Google Scholar
16. Yap, D.B. et al. Somatic mutations at EZH2 Y641 act dominantly through a mechanism of selectively altered PRC2 catalytic activity, to increase H3K27 trimethylation. Blood 117, 2451–2459 (2011).
    Article CAS Google Scholar
17. Morin, R.D. et al. Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin. Nat. Genet. 42, 181–185 (2010).
    Article CAS Google Scholar
18. Berger, A.H., Knudson, A.G. & Pandolfi, P.P. A continuum model for tumour suppression. Nature 476, 163–169 (2011).
    Article CAS Google Scholar
19. Sulis, M.L. et al. NOTCH1 extracellular juxtamembrane expansion mutations in T-ALL. Blood 112, 733–740 (2008).
    Article CAS Google Scholar
20. Palomero, T. et al. NOTCH1 directly regulates c-MYC and activates a feed-forward-loop transcriptional network promoting leukemic cell growth. Proc. Natl. Acad. Sci. USA 103, 18261–18266 (2006).
    Article CAS Google Scholar
21. Wendorff, A.A. et al. Hes1 is a critical but context-dependent mediator of canonical Notch signaling in lymphocyte development and transformation. Immunity 33, 671–684 (2010).
    Article CAS Google Scholar
22. Buonamici, S. et al. CCR7 signalling as an essential regulator of CNS infiltration in T-cell leukaemia. Nature 459, 1000–1004 (2009).
    Article CAS Google Scholar
23. Kuo, M.H. et al. Transcription-linked acetylation by Gcn5p of histones H3 and H4 at specific lysines. Nature 383, 269–272 (1996).
    Article CAS Google Scholar
24. Santos-Rosa, H. et al. Active genes are tri-methylated at K4 of histone H3. Nature 419, 407–411 (2002).
    Article CAS Google Scholar
25. Rada-Iglesias, A., et al. A unique chromatin signature uncovers early developmental enhancers in humans. Nature 470, 279–283 (2010).
    Article Google Scholar
26. Peng, J.C. et al. Jarid2/Jumonji coordinates control of PRC2 enzymatic activity and target gene occupancy in pluripotent cells. Cell 139, 1290–1302 (2009).
    Article Google Scholar
27. Landeira, D. et al. Jarid2 is a PRC2 component in embryonic stem cells required for multi-lineage differentiation and recruitment of PRC1 and RNA Polymerase II to developmental regulators. Nat. Cell Biol. 12, 618–624 (2010).
    Article CAS Google Scholar
28. Ferres-Marco, D. et al. Epigenetic silencers and Notch collaborate to promote malignant tumours by Rb silencing. Nature 439, 430–436 (2006).
    Article CAS Google Scholar
29. Palomero, T. et al. Mutational loss of PTEN induces resistance to NOTCH1 inhibition in T-cell leukemia. Nat. Med. 13, 1203–1210 (2007).
    Article CAS Google Scholar
30. Dietzl, G. et al. A genome-wide transgenic RNAi library for conditional gene inactivation in Drosophila. Nature 448, 151–156 (2007).
    Article CAS Google Scholar
31. Lopez, J., Percharde, M., Coley, H.M., Webb, A. & Crook, T. The context and potential of epigenetics in oncology. Br. J. Cancer 100, 571–577 (2009).
    Article CAS Google Scholar
32. Rodríguez-Paredes, M. & Esteller, M. Cancer epigenetics reaches mainstream oncology. Nat. Med. 17, 330–339 (2011).
    Article Google Scholar
33. Natoli, G., Testa, G. & De Santa, F. The future therapeutic potential of histone demethylases: A critical analysis. Curr. Opin. Drug Discov. Devel. 12, 607–615 (2009).
    CAS PubMed Google Scholar
34. Rahl, P.B. et al. c-Myc regulates transcriptional pause release. Cell 141, 432–445 (2010).
    Article CAS Google Scholar
35. Klinakis, A. et al. Myc is a Notch1 transcriptional target and a requisite for Notch1-induced mammary tumorigenesis in mice. Proc. Natl. Acad. Sci. USA 103, 9262–9267 (2006).
    Article CAS Google Scholar
36. Tu, Y., Stolovitzky, G. & Klein, U. Quantitative noise analysis for gene expression microarray experiments. Proc. Natl. Acad. Sci. USA 99, 14031–14036 (2002).
    Article CAS Google Scholar
37. Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26, 589–595 (2010).
    Article Google Scholar
38. Tsirigos, A., Haiminen, N., Bilal, E. & Utro, F. GenomicTools: a computational platform for developing high-throughput analytics in genomics. Bioinformatics published online, doi: 10.1093/bioinformatics/btr646 (22 November 2011).
39. Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).
    Article Google Scholar
40. Gerby, B. et al. Expression of CD34 and CD7 on human T-cell acute lymphoblastic leukemia discriminates functionally heterogeneous cell populations. Leukemia 25, 1249–1258 (2011).
    Article CAS Google Scholar

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Acknowledgements

We would like to thank R. Bonasio and D. Reinberg (Howard Hughes Medical Institute and NYU School of Medicine) for critical reading of the manuscript and Ezh2-specific antibody; C. Siebel (Genentech) for technical advice; and P. Ballerini, C. Deswartes, T. Leblanc and A. Baruchel (Services d'Hématologie Pédiatrique, Hôpital Trousseau and Hôpital Robert Debré Saint-Louis, respectively) for providing primary human T-ALL samples. We thank M. Gialitakis, L. Parida and G. Stolovitzky for comments on the manuscript and J. Zavadil, B. Berrin and the NYU Genome Technology Center (supported in part by US National Institutes of Health National Cancer Institute P30 CA016087-30 grant) for expert genomic assistance. The NYU Flow Cytometry facility (supported in part by US National Institutes of Health National Cancer Institute grant 5 P30CA16087-31) for expert cell sorting. We also thank the NYU Histology Core (5P30CA16087-31) and the Transgenic Mouse Core (NYU Cancer Institute Center Grant (5P30CA16087-31). J.N. was supported by the Damon Runyon Cancer Research Foundation. I.A. was supported by the US National Institutes of Health (RO1CA133379, RO1CA105129, R21CA141399, RO1CA149655 and RO1GM088847), The Leukemia & Lymphoma Society, The V Foundation, the American Cancer Society (RSG0806801) and the Dana Foundation. The Aifantis laboratory is also supported by a Feinberg Lymphoma Pilot grant. This study was also supported by the Fund for Scientific Research of Flanders (P.V.V. and K.D.K.); the US National Library of Medicine (1R01LM010140-01 to R.R.); the Eastern Cooperative Oncology Group tumor bank; a Northeast Biodefense Center American Recovery and Reinvestment Act award (U54-AI057158 to R.R.); the US National Institutes of Health (R01CA120196 and R01CA155743 to A.F.); the Stand Up To Cancer Innovative Research Award (A.F.), the Chemotherapy Foundation (I.A. and A.F.); the Rally Across America Foundation (A.F.) and the Swim Across America Foundation (A.F.). P.V.V. is an American Society of Hematology Scholar, and I.A. and A.F. are Leukemia & Lymphoma Society Scholars. M.D. is supported by grants from Spanish Ministerio de Ciencia e Innovación (BFU2009-09074 and MEC-CONSOLIDER CSD2007-00023), Generalitat Valenciana (PROMETEO2006/134) and an EU Research Grant (UE-HEALH-F2-2008-201666). F.P. is supported by the Institut du Cancer, the Association Laurette Fugain, the Ligue National Contre le Cancer and also by INSERM, CEA and StemPole. S.P. is supported by a fellowship by the Institut du Cancer. I.A. is a Howard Hughes Medical Institute Early Career Scientist.

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1. Panagiotis Ntziachristos, Aristotelis Tsirigos, Pieter Van Vlierberghe, Adolfo Ferrando and Iannis Aifantis: These authors contributed equally to this work.

Authors and Affiliations

1. Howard Hughes Medical Institute and Department of Pathology, New York University (NYU) School of Medicine, New York, New York, USA
   Panagiotis Ntziachristos, Jelena Nedjic, Thomas Trimarchi, Jasmin Siegle & Iannis Aifantis
2. NYU Cancer Institute and Helen L. and Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, New York, USA
   Panagiotis Ntziachristos, Jelena Nedjic, Thomas Trimarchi, Jasmin Siegle, Patrik Asp & Iannis Aifantis
3. Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York, USA
   Aristotelis Tsirigos, Tien Huynh & Filippo Utro
4. Institute for Cancer Genetics, Columbia University Medical Center, New York, New York, USA
   Pieter Van Vlierberghe, Maria Sol Flaherty, Michael Hadler, Isaura Rigo, Jeremy B Samon & Adolfo Ferrando
5. Department of Pathology, Columbia University Medical Center, New York, New York, USA
   Pieter Van Vlierberghe, Jeremy B Samon & Adolfo Ferrando
6. Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
   Pieter Van Vlierberghe, Jeremy B Samon & Adolfo Ferrando
7. Instituto de Neurociencias de Alicante,Consejo Superior de Investigaciones Cientificas-Universidad Miguel Hernandez, Alicante, Spain
   Dolors Ferres-Marco, Vanina da Ros & Maria Dominguez
8. Department of Cell Biology, NYU School of Medicine, New York, New York, USA
   Zuojian Tang & Stuart Brown
9. Center for Health Informatics and Bioinformatics, NYU School of Medicine, New York, New York, USA
   Zuojian Tang & Stuart Brown
10. Department of Molecular and Developmental Genetics, Flanders Institute for Biotechnology, Leuven, Belgium
    Kim De Keersmaecker
11. Center for Human Genetics, Catholic University Leuven, Leuven, Belgium
    Kim De Keersmaecker
12. Department of Medicine, Human Oncology and Pathogenesis Program and Leukemia Service, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
    Jay Patel & Ross L Levine
13. Commissariat à l'Energie Atomique (CEA), Institut de Radiobiologie Cellulaire et Moléculaire, Unité mixte de Recherche 967, Fontenay-aux-Roses, France
    Sandrine Poglio & Francoise Pflumio
14. Institut National de la Santé et de la Recherche Médicale (INSERM), U967, Fontenay-aux-Roses, France
    Sandrine Poglio & Francoise Pflumio
15. Université Paris Diderot, Sorbonne Paris Cité, UMR 967, Fontenay-aux-Roses, France
    Sandrine Poglio & Francoise Pflumio
16. Université Paris-Sud, UMR 967, Fontenay-aux-Roses, France
    Sandrine Poglio & Francoise Pflumio
17. Montefiore Medical Center North, Bronx, New York, USA
    Elisabeth Paietta & Janis Racevskis
18. Rambam Medical Center, Haifa, Israel
    Jacob M Rowe
19. Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, USA
    Raul Rabadan

Authors

1. Panagiotis Ntziachristos
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2. Aristotelis Tsirigos
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3. Pieter Van Vlierberghe
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4. Jelena Nedjic
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5. Thomas Trimarchi
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6. Maria Sol Flaherty
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7. Dolors Ferres-Marco
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8. Vanina da Ros
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9. Zuojian Tang
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10. Jasmin Siegle
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11. Patrik Asp
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12. Michael Hadler
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13. Isaura Rigo
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14. Kim De Keersmaecker
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15. Jay Patel
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16. Tien Huynh
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17. Filippo Utro
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18. Sandrine Poglio
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19. Jeremy B Samon
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20. Elisabeth Paietta
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21. Janis Racevskis
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22. Jacob M Rowe
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23. Raul Rabadan
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24. Ross L Levine
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25. Stuart Brown
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26. Francoise Pflumio
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27. Maria Dominguez
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28. Adolfo Ferrando
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29. Iannis Aifantis
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Contributions

I.A. and P.N. conceived of the studies, directed research, analyzed the results and wrote the manuscript. P.N. performed xenograft experiments, isolated and characterized mouse samples and performed and analyzed the biochemical experiments, helped by T.T. and J.S. A.T. directed research, analyzed data, developed computational methods and wrote the manuscript. J.N. isolated and characterized mouse samples, helped to project design and wrote the manuscript. S.B., Z.T. and T.H. helped with the analysis of the genome-wide data. P.A. helped with the design and execution of the biochemical experiments. F.U. created the resource website. P.V.V., M.H., I.R., J.B.S. and J.P. performed mutation analysis of SUZ12, EZH2 and EED. R.L.L. designed and supervised sequence analysis. P.V.V. performed xenograft experiments. P.V.V. and K.D.K. performed aCGH analysis. R.R. analyzed aCGH data. M.S.F. performed the genetic silencing studies of PRC2. E.P., J.R. and J.M.R. provided samples and correlative clinical data from the Eastern Cooperative Oncology Group. S.P. and F.P. performed and supervised experiments related to NOTCH activation into primary T-ALL samples and provided crucial materials. A.F. designed the studies, directed research and wrote the manuscript. D.F.-M., V.d.R. and M.D. designed and performed the Drosophila tumor experiments.

Corresponding authors

Correspondence toAristotelis Tsirigos, Adolfo Ferrando or Iannis Aifantis.

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The authors declare no competing financial interests.

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Ntziachristos, P., Tsirigos, A., Vlierberghe, P. et al. Genetic inactivation of the polycomb repressive complex 2 in T cell acute lymphoblastic leukemia.Nat Med 18, 298–302 (2012). https://doi.org/10.1038/nm.2651

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• Received: 23 August 2011
• Accepted: 21 December 2011
• Published: 06 February 2012
• Issue Date: February 2012
• DOI: https://doi.org/10.1038/nm.2651