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Disruption of KMT2D perturbs germinal center B cell development and promotes lymphomagenesis

Abstract

Mutations in the gene encoding the KMT2D (or MLL2) methyltransferase are highly recurrent and occur early during tumorigenesis in diffuse large B cell lymphoma (DLBCL) and follicular lymphoma (FL). However, the functional consequences of these mutations and their role in lymphomagenesis are unknown. Here we show that FL- and DLBCL-associated KMT2D mutations impair KMT2D enzymatic activity, leading to diminished global H3K4 methylation in germinal-center (GC) B cells and DLBCL cells. Conditional deletion of Kmt2d early during B cell development, but not after initiation of the GC reaction, results in an increase in GC B cells and enhances B cell proliferation in mice. Moreover, genetic ablation of Kmt2d in mice overexpressing Bcl2 increases the incidence of GC-derived lymphomas resembling human tumors. These findings suggest that KMT2D acts as a tumor suppressor gene whose early loss facilitates lymphomagenesis by remodeling the epigenetic landscape of the cancer precursor cells. Eradication of KMT2D-deficient cells may thus represent a rational therapeutic approach for targeting early tumorigenic events.

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Figure 1: Genetic and epigenetic inactivation of KMT2D in DLBCL.
Figure 2: KMT2D mutations are associated with defective methyltransferase activity and diminished H3K4 methylation.
Figure 3: Deletion of Kmt2d early in B cell development leads to increased GC formation.
Figure 4: Kmt2d deletion induces differentiation stage–dependent transcriptional changes in GC B cells.
Figure 5: Kmt2dfl/fl CD19-Cre B cells exhibit proliferative advantage.
Figure 6: Deletion of Kmt2d in the GC cooperates with Bcl2 deregulation to promote lymphomagenesis.

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Acknowledgements

We would like to thank U. Klein and S. Zha for discussions, S. Nataraj, L. Belver, C. Scuoppo and N. De Silva for help and suggestions on various experimental procedures, E. McIntush (Bethyl Laboratories, Inc.) for help in generating several antibodies to KMT2D, the Flow Cytometry Shared Resource of the Herbert Irving Comprehensive Cancer Center at Columbia University for assistance with cell-sorting procedures, the Molecular Pathology lab for the preparation of mouse FFPE tissue samples and the Genomic Technologies Shared Resource for sequencing the ChIP-DNA libraries. We also thank S. Cory (Walter and Eliza Hall Institute of Medical Research, Parkville, Australia) for the VavP-Bcl2 mice and K. Rajewsky (Max Delbrück Center for Molecular Medicine, Berlin, Germany) for the CD19-Cre and Cγ1-Cre mice. The indicated DLBCL cell lines in Supplementary Table 5 were a kind gift of L. Staudt, M.A. Shipp and T. Gilmore. This work was supported by US National Institutes of Health grants RO1-CA172492 (L.P.) and RO1-CA37295 (R.D.-F.), and J.Z. is supported by a Lymphoma Research Foundation postdoctoral fellowship. L.P. is on leave from the University of Perugia.

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L.P. designed and directed the study, analyzed data and wrote the manuscript, with contributions from R.D.-F. and J.Z. J.Z. performed experiments, analyzed data and prepared figures. D.D.-S. and S.H. were responsible for histopathological analysis. J.-E.L. and K.G. generated the Kmt2d conditional knockout mouse model. K.B. performed the ChIP-Seq experiment and, together with A.B.H, contributed to the implementation of tools for the analysis of ChIP-Seq data. S.V. performed mutation analysis of the rearranged immunoglobulin genes from mouse tumors and provided technical support in various experiments. M.B. conducted the analysis of gene expression data. T.M. was responsible for animal husbandry. H.T. performed mouse autopsies and processed tissues for FACS and histologic analysis. R.D.-F. contributed to the study design and data analysis. All authors reviewed the manuscript and provided final approval for submission.

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Correspondence to Laura Pasqualucci.

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Zhang, J., Dominguez-Sola, D., Hussein, S. et al. Disruption of KMT2D perturbs germinal center B cell development and promotes lymphomagenesis. Nat Med 21, 1190–1198 (2015). https://doi.org/10.1038/nm.3940

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