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A NOTCH1-driven MYC enhancer promotes T cell development, transformation and acute lymphoblastic leukemia

Abstract

Efforts to identify and annotate cancer driver genetic lesions have been focused primarily on the analysis of protein-coding genes; however, most genetic abnormalities found in human cancer are located in intergenic regions. Here we identify a new long range–acting MYC enhancer controlled by NOTCH1 that is targeted by recurrent chromosomal duplications in human T cell acute lymphoblastic leukemia (T-ALL). This highly conserved regulatory element, hereby named N-Me for NOTCH MYC enhancer, is located within a broad super-enhancer region +1.47 Mb from the MYC transcription initiating site, interacts with the MYC proximal promoter and induces orientation-independent MYC expression in reporter assays. Moreover, analysis of N-Me knockout mice demonstrates a selective and essential role of this regulatory element during thymocyte development and in NOTCH1-induced T-ALL. Together these results identify N-Me as a long-range oncogenic enhancer implicated directly in the pathogenesis of human leukemia and highlight the importance of the NOTCH1-MYC regulatory axis in T cell transformation and as a therapeutic target in T-ALL.

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Figure 1: Identification of N-Me, a NOTCH-bound MYC enhancer recurrently amplified in T-ALL.
Figure 2: Functional characterization of the N-Me enhancer.
Figure 3: Histological analysis of the thymus in N-Me knockout mice.
Figure 4: Characterization of T cell development in N-Me knockout mice.
Figure 5: Analysis of T-ALL tumor initiation in N-Me knockout mice.
Figure 6: Analysis of leukemia maintenance in N-Me knockout cells.

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Acknowledgements

This work was supported by the US National Institutes of Health (grant CA120196 to A.A.F.), the Stand Up To Cancer Innovative Research Award (A.A.F.), The Pershing Square Sohn Foundation Award (A.A.F.), the Swim Across America Foundation (A.A.F.), the Canceropole Ile de France (J.S.), the program Cartes d'Identité des Tumeurs from the Ligue Contre le Cancer (J.S.), the European Research Council St. Grant Consolidator 311660 (J.S.) and the Saint-Louis Institute program ANR-10-IBHU-0002 (J.S.). D.H. is a Leukemia and Lymphoma Society postdoctoral fellow. L.B. is a postdoctoral researcher supported by the Lymphoma Research Foundation. We are grateful to P. Sumazin for assistance on the analysis of ChIP-seq data, T. Ludwig (Ohio State University) for the ROSA26cre-ERT2/+ mouse, R. Kopan (Cincinnati Children's Hospital Medical Center, University of Cincinnati) for the ΔE-NOTCH1 construct and R. Baer for helpful discussions and revision of the manuscript.

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Contributions

D.H. performed most of the experiments and wrote the manuscript. A.A.-I. performed bioinfomatic analyses. T.P. performed the ChIP-seq and 3C studies. S.A.S. performed in vitro studies. L.B. and A.A.W. analyzed hematopoietic phenotypes. L.X. performed some animal studies with D.H. M.C.-M. and D.L.-N. performed histological analyses. C.C.-C. supervised histological analyses. J.S. and E.C. performed genomic analyses of human leukemias. A.A.F. designed the study, supervised research and wrote the manuscript.

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Correspondence to Adolfo A Ferrando.

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Herranz, D., Ambesi-Impiombato, A., Palomero, T. et al. A NOTCH1-driven MYC enhancer promotes T cell development, transformation and acute lymphoblastic leukemia. Nat Med 20, 1130–1137 (2014). https://doi.org/10.1038/nm.3665

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