Inactivating mutations of acetyltransferase genes in B-cell lymphoma

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Abstract

B-cell non-Hodgkin’s lymphoma comprises biologically and clinically distinct diseases the pathogenesis of which is associated with genetic lesions affecting oncogenes and tumour-suppressor genes. We report here that the two most common types—follicular lymphoma and diffuse large B-cell lymphoma—harbour frequent structural alterations inactivating CREBBP and, more rarely, EP300, two highly related histone and non-histone acetyltransferases (HATs) that act as transcriptional co-activators in multiple signalling pathways. Overall, about 39% of diffuse large B-cell lymphoma and 41% of follicular lymphoma cases display genomic deletions and/or somatic mutations that remove or inactivate the HAT coding domain of these two genes. These lesions usually affect one allele, suggesting that reduction in HAT dosage is important for lymphomagenesis. We demonstrate specific defects in acetylation-mediated inactivation of the BCL6 oncoprotein and activation of the p53 tumour suppressor. These results identify CREBBP/EP300 mutations as a major pathogenetic mechanism shared by common forms of B-cell non-Hodgkin’s lymphoma, with direct implications for the use of drugs targeting acetylation/deacetylation mechanisms.

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Figure 1: The CREBBP gene is mutated in DLBCL.
Figure 2: Mutations and deletions of CREBBP are predominantly monoallelic.
Figure 3: CREBBP and EP300 expression in normal and transformed B-cells.
Figure 4: CREBBP missense mutations impair its ability to acetylate BCL6 and p53.
Figure 5: DLBCL-associated mutations in the CREBBP HAT domain decrease its affinity for acetyl-CoA.

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Primary accessions

GenBank/EMBL/DDBJ

Gene Expression Omnibus

Data deposits

The Affymetrix expression data reported in this paper have been deposited in the NCBI Gene Expression Omnibus (GEO) database (Series Accession Number GSE12195). The SNP Array 6.0 data and the whole exome sequencing data from the seven DLBCL cases have been deposited in dbGaP under accession number phs000328.v1.p1.

References

  1. 1

    Swerdlow, S. H. et al. WHO Classification of Tumours of Haematopoietic and Lymphoid Tissues (International Agency for Research on Cancer (IARC), Lyon, 2008)

  2. 2

    Compagno, M. et al. Mutations of multiple genes cause deregulation of NF-κB in diffuse large B-cell lymphoma. Nature 459, 717–721 (2009)

  3. 3

    Davis, R. E. et al. Chronic active B-cell-receptor signalling in diffuse large B-cell lymphoma. Nature 463, 88–92 (2010)

  4. 4

    Klein, U. & Dalla-Favera, R. Germinal centres: role in B-cell physiology and malignancy. Nature Rev. Immunol. 8, 22–33 (2008)

  5. 5

    Lenz, G. et al. Oncogenic CARD11 mutations in human diffuse large B cell lymphoma. Science 319, 1676–1679 (2008)

  6. 6

    Lenz, G. & Staudt, L. M. Aggressive lymphomas. N. Engl. J. Med. 362, 1417–1429 (2010)

  7. 7

    Mandelbaum, J. BLIMP1 is a tumor suppressor gene frequently disrupted in activated B-cell like diffuse large B-cell lymphoma. Cancer Cell 18, 568–579 (2010)

  8. 8

    Morin, R. D. et al. Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin. Nature Genet. 42, 181–185 (2010)

  9. 9

    Downing, J. R. Cancer genomes—continuing progress. N. Engl. J. Med. 361, 1111–1112 (2009)

  10. 10

    Goodman, R. H. & Smolik, S. CBP/p300 in cell growth, transformation, and development. Genes Dev. 14, 1553–1577 (2000)

  11. 11

    Kalkhoven, E. CBP and p300: HATs for different occasions. Biochem. Pharmacol. 68, 1145–1155 (2004)

  12. 12

    Bannister, A. J. & Kouzarides, T. The CBP co-activator is a histone acetyltransferase. Nature 384, 641–643 (1996)

  13. 13

    Ogryzko, V. V., Schiltz, R. L., Russanova, V., Howard, B. H. & Nakatani, Y. The transcriptional coactivators p300 and CBP are histone acetyltransferases. Cell 87, 953–959 (1996)

  14. 14

    Gu, W., Shi, X. L. & Roeder, R. G. Synergistic activation of transcription by CBP and p53. Nature 387, 819–823 (1997)

  15. 15

    Lill, N. L., Grossman, S. R., Ginsberg, D., DeCaprio, J. & Livingston, D. M. Binding and modulation of p53 by p300/CBP coactivators. Nature 387, 823–827 (1997)

  16. 16

    Avantaggiati, M. L. et al. Recruitment of p300/CBP in p53-dependent signal pathways. Cell 89, 1175–1184 (1997)

  17. 17

    Blobel, G. A., Nakajima, T., Eckner, R., Montminy, M. & Orkin, S. H. CREB-binding protein cooperates with transcription factor GATA-1 and is required for erythroid differentiation. Proc. Natl Acad. Sci. USA 95, 2061–2066 (1998)

  18. 18

    Bereshchenko, O. R., Gu, W. & Dalla-Favera, R. Acetylation inactivates the transcriptional repressor BCL6. Nature Genet. 32, 606–613 (2002)

  19. 19

    Grossman, S. R. et al. Polyubiquitination of p53 by a ubiquitin ligase activity of p300. Science 300, 342–344 (2003)

  20. 20

    Shi, D. et al. CBP and p300 are cytoplasmic E4 polyubiquitin ligases for p53. Proc. Natl Acad. Sci. USA 106, 16275–16280 (2009)

  21. 21

    Oike, Y. et al. Mice homozygous for a truncated form of CREB-binding protein exhibit defects in hematopoiesis and vasculo-angiogenesis. Blood 93, 2771–2779 (1999)

  22. 22

    Yao, T. P. et al. Gene dosage-dependent embryonic development and proliferation defects in mice lacking the transcriptional integrator p300. Cell 93, 361–372 (1998)

  23. 23

    Roelfsema, J. H. & Peters, D. J. Rubinstein-Taybi syndrome: clinical and molecular overview. Expert Rev. Mol. Med. 9, 1–16 (2007)

  24. 24

    Petrif, F. et al. Rubinstein–Taybi syndrome caused by mutations in the transcriptional co-activator CBP. Nature 376, 348–351 (1995)

  25. 25

    Miller, R. W. & Rubinstein, J. H. Tumors in Rubinstein-Taybi syndrome. Am. J. Med. Genet. 56, 112–115 (1995)

  26. 26

    Iyer, N. G., Ozdag, H. & Caldas, C. p300/CBP and cancer. Oncogene 23, 4225–4231 (2004)

  27. 27

    Gayther, S. A. et al. Mutations truncating the EP300 acetylase in human cancers. Nature Genet. 24, 300–303 (2000)

  28. 28

    Ward, R., Johnson, M., Shridhar, V., van Deursen, J. & Couch, F. J. CBP truncating mutations in ovarian cancer. J. Med. Genet. 42, 514–518 (2005)

  29. 29

    Garbati, M. R., Alco, G. & Gilmore, T. D. Histone acetyltransferase p300 is a coactivator for transcription factor REL and is C-terminally truncated in the human diffuse large B-cell lymphoma cell line RC-K8. Cancer Lett. 291, 237–245 (2010)

  30. 30

    Shigeno, K. et al. Disease-related potential of mutations in transcriptional cofactors CREB-binding protein and p300 in leukemias. Cancer Lett. 213, 11–20 (2004)

  31. 31

    Borrow, J. et al. The translocation t(8;16)(p11;p13) of acute myeloid leukaemia fuses a putative acetyltransferase to the CREB-binding protein. Nature Genet. 14, 33–41 (1996)

  32. 32

    Rowley, J. D. et al. All patients with the T(11;16)(q23;p13.3) that involves MLL and CBP have treatment-related hematologic disorders. Blood 90, 535–541 (1997)

  33. 33

    Sobulo, O. M. et al. MLL is fused to CBP, a histone acetyltransferase, in therapy-related acute myeloid leukemia with a t(11;16)(q23;p13.3). Proc. Natl Acad. Sci. USA 94, 8732–8737 (1997)

  34. 34

    Mullighan, C. G. et al. CREBBP mutations in relapsed acute lymphoblastic leukaemia. Nature 10.1038/nature09727 (this issue)

  35. 35

    Liu, X. et al. The structural basis of protein acetylation by the p300/CBP transcriptional coactivator. Nature 451, 846–850 (2008)

  36. 36

    Phan, R. T. & Dalla-Favera, R. The BCL6 proto-oncogene suppresses p53 expression in germinal-centre B cells. Nature 432, 635–639 (2004)

  37. 37

    Tang, Y., Zhao, W., Chen, Y., Zhao, Y. & Gu, W. Acetylation is indispensable for p53 activation. Cell 133, 612–626 (2008)

  38. 38

    Kwok, R. P. et al. Nuclear protein CBP is a coactivator for the transcription factor CREB. Nature 370, 223–226 (1994)

  39. 39

    Kasper, L. H. et al. CBP/p300 double null cells reveal effect of coactivator level and diversity on CREB transactivation. EMBO J. 29, 3660–3672 (2010)

  40. 40

    Bordoli, L. et al. Functional analysis of the p300 acetyltransferase domain: the PHD finger of p300 but not of CBP is dispensable for enzymatic activity. Nucleic Acids Res. 29, 4462–4471 (2001)

  41. 41

    Xu, W. et al. Global transcriptional coactivators CREB-binding protein and p300 are highly essential collectively but not individually in peripheral B cells. Blood 107, 4407–4416 (2006)

  42. 42

    Kung, A. L. et al. Gene dose-dependent control of hematopoiesis and hematologic tumor suppression by CBP. Genes Dev. 14, 272–277 (2000)

  43. 43

    Legube, G. & Trouche, D. Regulating histone acetyltransferases and deacetylases. EMBO Rep. 4, 944–947 (2003)

  44. 44

    Phan, R. T., Saito, M., Basso, K., Niu, H. & Dalla-Favera, R. BCL6 interacts with the transcription factor Miz-1 to suppress the cyclin-dependent kinase inhibitor p21 and cell cycle arrest in germinal center B cells. Nature Immunol. 6, 1054–1060 (2005)

  45. 45

    Stimson, L., Wood, V., Khan, O., Fotheringham, S. & La Thangue, N. B. HDAC inhibitor-based therapies and haematological malignancy. Ann. Oncol. 20, 1293–1302 (2009)

  46. 46

    Bieber, T. & Elsasser, H. P. Preparation of a low molecular weight polyethylenimine for efficient cell transfection. Biotechniques 30, 74–77,–80–81 (2001)

  47. 47

    Huynh, K. D., Fischle, W., Verdin, E. & Bardwell, V. J. BCoR, a novel corepressor involved in BCL-6 repression. Genes Dev. 14, 1810–1823 (2000)

  48. 48

    Kuninger, D., Lundblad, J., Semirale, A. & Rotwein, P. A non-isotopic in vitro assay for histone acetylation. J. Biotechnol. 131, 253–260 (2007)

  49. 49

    Tang, Y., Luo, J., Zhang, W. & Gu, W. Tip60-dependent acetylation of p53 modulates the decision between cell-cycle arrest and apoptosis. Mol. Cell 24, 827–839 (2006)

  50. 50

    Bedford, D. C., Kasper, L. H., Fukuyama, T. & Brindle, P. K. Target gene context influences the transcriptional requirement for the KAT3 family of CBP and p300 histone acetyltransferases. Epigenetics 5, 9–15 (2010)

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Acknowledgements

We thank Q. Shen and the Molecular Pathology Shared Resource of the Herbert Irving Comprehensive Cancer Center at Columbia University for histology service; W. Gu for discussions and reagents; Y. Tang, M. Li and D. Chao for suggestions; V. Bardwell for the Bcl6 reporter construct; and R. S. K. Chaganti for sharing unpublished information. Whole-exome capture and sequencing were conducted at Roche NimbleGen and 454 Life Sciences. Automated DNA sequencing was performed at Genewiz Inc. This work was supported by NIH grants PO1-CA092625 and RO1-CA37295 (to R.D.-F.), a Specialized Center of Research grant from the Leukemia and Lymphoma Society (to R.D.-F.), NIH grant DE018183, a Cancer Center (CORE) support grant P30 CA021765, and the American Lebanese Syrian Associated Charities of St Jude Children’s Research Hospital (to P.K.B.), the Northeast Biodefence Center (U54-AI057158) and the National Library of Medicine (1R01LM010140-01) (to R.R.), and the AIRC Special Program Molecular Clinical Oncology—5 per mille (contract number 10007, Milan) (to G.G.). A. Chiarenza is on leave from the Division of Hematology, Ospedale Ferrarotto, University of Catania, Catania, Italy. L.P. is on leave from the University of Perugia Medical School, Perugia, Italy.

Author information

L.P. and R.D.-F. designed the study and wrote the manuscript, with contributions from all authors. L.P. designed and conducted experiments, analysed data and coordinated the study. D.D.-S. designed and conducted experiments, and analysed immunohistochemistry data. A. Chiarenza, G.F. and A.G. conducted CREBBP/EP300 amplification and sequencing analysis. L.H.K., S.L. and P.K.B. were responsible for the experiments in MEF cells. H.T. performed immunohistochemistry and immunofluorescence staining of human tissue biopsies. V.V.M. developed FISH assays and analysed cytogenetic data. C.G.M. and J.M. analysed microarray data. A. Chadburn, D.R. and G.G. provided well-characterized patient samples. V.T. and R.R. developed algorithms and analysed high-throughput sequencing data.

Correspondence to Laura Pasqualucci or Riccardo Dalla-Favera.

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