Global chromatin profiling reveals NSD2 mutations in pediatric acute lymphoblastic leukemia

Abstract

Epigenetic dysregulation is an emerging hallmark of cancers. We developed a high-information-content mass spectrometry approach to profile global histone modifications in human cancers. When applied to 115 lines from the Cancer Cell Line Encyclopedia1, this approach identified distinct molecular chromatin signatures. One signature was characterized by increased histone 3 lysine 36 (H3K36) dimethylation, exhibited by several lines harboring translocations in NSD2, which encodes a methyltransferase. A previously unknown NSD2 p.Glu1099Lys (p.E1099K) variant was identified in nontranslocated acute lymphoblastic leukemia (ALL) cell lines sharing this signature. Ectopic expression of the variant induced a chromatin signature characteristic of NSD2 hyperactivation and promoted transformation. NSD2 knockdown selectively inhibited the proliferation of NSD2-mutant lines and impaired the in vivo growth of an NSD2-mutant ALL xenograft. Sequencing analysis of >1,000 pediatric cancer genomes identified the NSD2 p.E1099K alteration in 14% of t(12;21) ETV6-RUNX1–containing ALLs. These findings identify NSD2 as a potential therapeutic target for pediatric ALL and provide a general framework for the functional annotation of cancer epigenomes.

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Figure 1: Global chromatin profiling identifies distinct molecular chromatin-signature profiles in the CCLE collection.
Figure 2: H3K27 and H3K36 methylation alterations drive the identification of unique molecular chromatin signatures.
Figure 3: Identification of recurrent NSD2 alterations in ALL.
Figure 4: NSD2 p.E1099K alteration leads to increased enzymatic activity and promotes transformation.
Figure 5: NSD2 is required for the growth and proliferation of ALL cells carrying the p.E1099K alteration.

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Acknowledgements

We thank R. Pagliarini and R. Tiedt for their critical comments on the manuscript, and the NIBR-BROAD CCLE team for their guidance and contributions to the CCLE project. KMS11-TKO cells were generously provided by Horizon Discovery Ltd., UK. We are grateful for the technical assistance of X. Liu. We thank the members of the St. Jude Children's Research Hospital Washington University Pediatric Cancer Genome Project and the American Lebanese Syrian Associated Charities (ALSAC) of St. Jude Children's Research Hospital for funding. The global chromatin profiling project was enabled by a grant from the Novartis Institutes for Biomedical Research. Additional funding support was provided by the National Cancer Institute and the U.S. Department of Defense (L.A.G.), the Pew Scholars Program in the Biomedical Sciences (C.M.) and the St. Baldrick's Foundation Scholar Award (C.M.).

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Y.W., N.P.E., F.Y., H.M.C. and J.L. performed or directed cellular assays data generation. M.H. and Z.W. performed or directed biochemical experiments. E.R.M. III, R.deB., N.P.E. and Y.W. performed or directed nucleic acid extraction and targeted sequencing of NSD2. J.Z., L.W., J.M., J.E. and C.M. identified the NSD2 somatic mutations in tumor samples. J.Z., L.W., J.M., G.V.K. and K.V. performed bioinformatic analysis. J.E.T. performed MS experiments. Z.Y. and R.H. performed structural modeling. J.D.J., Y.W., H.M.C., M.H., R.M., R.deB., J.L., S.A.C. and F.S. designed experiments and analyzed biological data. Y.W., V.G.C., H.C.B. and V.G. performed or directed tumor xenograft studies. J.D.J., Y.W., H.M.C., M.H., E.R.M. III., K.V., J.Z., L.W. and R.H. prepared figures and tables. J.D.J., H.M.C., J.Z., J.R.D., W.R.S., L.A.G. and F.S. wrote and edited the main text and Supplementary Information. R.S., J.B., G.C., W.R.S. and N.K. contributed to overall project oversight and advising; F.S., J.R.D. and L.A.G. provided overall project leadership.

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Correspondence to Levi A Garraway or Frank Stegmeier.

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Competing interests

Y.W., H.M.C., H.C.B., M.H., N.P.E., F.Y., Z.W., E.R.M. III, Z.Y., R.deB., V.G., K.V., R.S., W.R.S., N.K., J.L., G.C., J.B., V.G.C. and F.S. are employees of Novartis, Inc., as noted in the affiliations. L.A.G. consults for and holds equity in Foundation Medicine and consults for and receives research sponsorship from Novartis, Inc.

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Supplementary Figures 1–9 and Supplementary Tables 1–7 (PDF 1697 kb)

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Jaffe, J., Wang, Y., Chan, H. et al. Global chromatin profiling reveals NSD2 mutations in pediatric acute lymphoblastic leukemia. Nat Genet 45, 1386–1391 (2013). https://doi.org/10.1038/ng.2777

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