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.
This is a preview of subscription content
Subscribe to Journal
Get full journal access for 1 year
only $4.92 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Tax calculation will be finalised during checkout.
Get time limited or full article access on ReadCube.
All prices are NET prices.
Van Vlierberghe, P. & Ferrando, A. The molecular basis of T cell acute lymphoblastic leukemia. J. Clin. Invest. 122, 3398–3406 (2012).
Ferrando, A.A. et al. Gene expression signatures define novel oncogenic pathways in T cell acute lymphoblastic leukemia. Cancer Cell 1, 75–87 (2002).
De Keersmaecker, K. et al. The TLX1 oncogene drives aneuploidy in T cell transformation. Nat. Med. 16, 1321–1327 (2010).
Della Gatta, G. et al. Reverse engineering of TLX oncogenic transcriptional networks identifies RUNX1 as tumor suppressor in T-ALL. Nat. Med. 18, 436–440 (2012).
Sanda, T. et al. Core transcriptional regulatory circuit controlled by the TAL1 complex in human T cell acute lymphoblastic leukemia. Cancer Cell 22, 209–221 (2012).
Weng, A.P. et al. Activating mutations of NOTCH1 in human T cell acute lymphoblastic leukemia. Science 306, 269–271 (2004).
Tzoneva, G. & Ferrando, A.A. Recent advances on NOTCH signaling in T-ALL. Curr. Top. Microbiol. Immunol. 360, 163–182 (2012).
Koch, U. & Radtke, F. Mechanisms of T cell development and transformation. Annu. Rev. Cell Dev. Biol. 27, 539–562 (2011).
Radtke, F. et al. Deficient T cell fate specification in mice with an induced inactivation of Notch1. Immunity 10, 547–558 (1999).
Schroeter, E.H., Kisslinger, J.A. & Kopan, R. Notch-1 signalling requires ligand-induced proteolytic release of intracellular domain. Nature 393, 382–386 (1998).
Jarriault, S. et al. Signalling downstream of activated mammalian Notch. Nature 377, 355–358 (1995).
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).
Zhang, J. et al. The genetic basis of early T-cell precursor acute lymphoblastic leukaemia. Nature 481, 157–163 (2012).
Watson, I.R., Takahashi, K., Futreal, P.A. & Chin, L. Emerging patterns of somatic mutations in cancer. Nat. Rev. Genet. 14, 703–718 (2013).
Weng, A.P. et al. c-Myc is an important direct target of Notch1 in T-cell acute lymphoblastic leukemia/lymphoma. Genes Dev. 20, 2096–2109 (2006).
Sharma, V.M. et al. Notch1 contributes to mouse T-cell leukemia by directly inducing the expression of c-myc. Mol. Cell. Biol. 26, 8022–8031 (2006).
Palomero, T. et al. CUTLL1, a novel human T-cell lymphoma cell line with t(7;9) rearrangement, aberrant NOTCH1 activation and high sensitivity to γ-secretase inhibitors. Leukemia 20, 1279–1287 (2006).
Wang, H. et al. Genome-wide analysis reveals conserved and divergent features of Notch1/RBPJ binding in human and murine T-lymphoblastic leukemia cells. Proc. Natl. Acad. Sci. USA 108, 14908–14913 (2011).
Ashworth, T.D. et al. Deletion-based mechanisms of Notch1 activation in T-ALL: key roles for RAG recombinase and a conserved internal translational start site in Notch1. Blood 116, 5455–5464 (2010).
Lovén, J. et al. Selective inhibition of tumor oncogenes by disruption of super-enhancers. Cell 153, 320–334 (2013).
He, T.C. et al. Identification of c-MYC as a target of the APC pathway. Science 281, 1509–1512 (1998).
Sulis, M.L. et al. NOTCH1 extracellular juxtamembrane expansion mutations in T-ALL. Blood 112, 733–740 (2008).
Pear, W.S. et al. Exclusive development of T cell neoplasms in mice transplanted with bone marrow expressing activated Notch alleles. J. Exp. Med. 183, 2283–2291 (1996).
Ferrando, A.A. The role of NOTCH1 signaling in T-ALL. Hematology Am. Soc. Hematol. Educ. Program 353–361 (2009).
Hnisz, D. et al. Super-enhancers in the control of cell identity and disease. Cell 155, 934–947 (2013).
Amundadottir, L.T. et al. A common variant associated with prostate cancer in European and African populations. Nat. Genet. 38, 652–658 (2006).
Easton, D.F. et al. Genome-wide association study identifies novel breast cancer susceptibility loci. Nature 447, 1087–1093 (2007).
Haiman, C.A. et al. Multiple regions within 8q24 independently affect risk for prostate cancer. Nat. Genet. 39, 638–644 (2007).
Haiman, C.A. et al. A common genetic risk factor for colorectal and prostate cancer. Nat. Genet. 39, 954–956 (2007).
Kiemeney, L.A. et al. Sequence variant on 8q24 confers susceptibility to urinary bladder cancer. Nat. Genet. 40, 1307–1312 (2008).
Jia, L. et al. Functional enhancers at the gene-poor 8q24 cancer-linked locus. PLoS Genet. 5, e1000597 (2009).
Pomerantz, M.M. et al. The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer. Nat. Genet. 41, 882–884 (2009).
Wright, J.B., Brown, S.J. & Cole, M.D. Upregulation of c-MYC in cis through a large chromatin loop linked to a cancer risk–associated single-nucleotide polymorphism in colorectal cancer cells. Mol. Cell. Biol. 30, 1411–1420 (2010).
Sur, I.K. et al. Mice lacking a Myc enhancer that includes human SNP rs6983267 are resistant to intestinal tumors. Science 338, 1360–1363 (2012).
Shi, J. et al. Role of SWI/SNF in acute leukemia maintenance and enhancer-mediated Myc regulation. Genes Dev. 27, 2648–2662 (2013).
Dose, M. et al. c-Myc mediates pre-TCR–induced proliferation but not developmental progression. Blood 108, 2669–2677 (2006).
Athineos, D. & Sansom, O.J. Myc heterozygosity attenuates the phenotypes of APC deficiency in the small intestine. Oncogene 29, 2585–2590 (2010).
Sansom, O.J. et al. Myc deletion rescues Apc deficiency in the small intestine. Nature 446, 676–679 (2007).
Nie, Z. et al. c-Myc is a universal amplifier of expressed genes in lymphocytes and embryonic stem cells. Cell 151, 68–79 (2012).
Lin, C.Y. et al. Transcriptional amplification in tumor cells with elevated c-Myc. Cell 151, 56–67 (2012).
Lovén, J. et al. Revisiting global gene expression analysis. Cell 151, 476–482 (2012).
Zippo, A. et al. Histone crosstalk between H3S10ph and H4K16ac generates a histone code that mediates transcription elongation. Cell 138, 1122–1136 (2009).
Real, P.J. et al. γ-secretase inhibitors reverse glucocorticoid resistance in T cell acute lymphoblastic leukemia. Nat. Med. 15, 50–58 (2009).
Clappier, E. et al. Clonal selection in xenografted human T cell acute lymphoblastic leukemia recapitulates gain of malignancy at relapse. J. Exp. Med. 208, 653–661 (2011).
Soulier, J. et al. HOXA genes are included in genetic and biologic networks defining human acute T-cell leukemia (T-ALL). Blood 106, 274–286 (2005).
Clappier, E. et al. NOTCH1 and FBXW7 mutations have a favorable impact on early response to treatment, but not on outcome, in children with T-cell acute lymphoblastic leukemia (T-ALL) treated on EORTC trials 58881 and 58951. Leukemia 24, 2023–2031 (2010).
Palomero, T. et al. Mutational loss of PTEN induces resistance to NOTCH1 inhibition in T-cell leukemia. Nat. Med. 13, 1203–1210 (2007).
Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576–589 (2010).
Encode Project Consortium. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 9, e1001046 (2011).
Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).
Blanchette, M. et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 14, 708–715 (2004).
Simonis, M. et al. High-resolution identification of balanced and complex chromosomal rearrangements by 4C technology. Nat. Methods 6, 837–842 (2009).
Guo, K. et al. Disruption of peripheral leptin signaling in mice results in hyperleptinemia without associated metabolic abnormalities. Endocrinology 148, 3987–3997 (2007).
Byers, S.L., Wiles, M.V., Dunn, S.L. & Taft, R.A. Mouse estrous cycle identification tool and images. PLoS ONE 7, e35538 (2012).
Chiang, M.Y. et al. Leukemia-associated NOTCH1 alleles are weak tumor initiators but accelerate K-ras–initiated leukemia. J. Clin. Invest. 118, 3181–3194 (2008).
Kim, Y.H. et al. Combined microarray analysis of small cell lung cancer reveals altered apoptotic balance and distinct expression signatures of MYC family gene amplification. Oncogene 25, 130–138 (2006).
Zeller, K.I., Jegga, A.G., Aronow, B.J., O'Donnell, K.A. & Dang, C.V. An integrated database of genes responsive to the Myc oncogenic transcription factor: identification of direct genomic targets. Genome Biol. 4, R69 (2003).
Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 102, 15545–15550 (2005).
Huang da, W., Sherman, B.T. & Lempicki, R.A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44–57 (2009).
Hu, Y. & Smyth, G.K. ELDA: extreme limiting dilution analysis for comparing depleted and enriched populations in stem cell and other assays. J. Immunol. Methods 347, 70–78 (2009).
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.
The authors declare no competing financial interests.
About this article
Cite this article
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
Nature Reviews Cancer (2022)
Nature Reviews Cancer (2022)
Nature Reviews Genetics (2022)