Abstract B05: Transcriptional antagonism between the cooperative oncogenes TLX1 and NOTCH1 in T-cell acute lymphoblastic leukemia

• Published in: Clinical cancer research 2015-09, Vol.21 (17_Supplement), p.B05-B05
• Main Authors: Durinck, Kaat, Loocke, Wouter Van, Meulen, Joni Van der, Walle, Inge Van de, Rondou, Pieter, Bock, Charles E. De, Poppe, Bruce, Cools, Jan, Soulier, Jean, Taghon, Tom, Speleman, Frank, Vlierberghe, Pieter Van
• Format: Article
• Language: English
• ISSN: 1078-0432; 1557-3265
• DOI: 10.1158/1557-3265.HEMMAL14-B05

Introduction: Combined activation of specific oncogenes is a general feature of human cancer and suggests that co-occurrence of particular oncogenic factors provides a selective advantage during cellular transformation. However, the exact molecular mechanisms by which oncoproteins cooperate during malignant transformation often remains elusive. Here, we study the functional relationship between the cooperative oncogenes NOTCH1 and TLX1 in the context of T-cell acute lymphoblastic leukemia to better understand their cooperative mechanism of action during T cell transformation. Methods: In this study, we performed chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) for the TLX1 homeobox oncoprotein in the T-ALL cell line ALL-SIL and analyzed the transcriptional response before and after TLX1 modulation using microarray based methods. We performed integration of TLX1 ChIPseq data with publically available transcription factor binding profiles in T-ALL and evaluated the immunophenotypic and transcriptional effects of ectopic TLX1 expression in thymus-derived CD34+ T-cell progenitors. Results: Integration of TLX1 ChIPseq data with gene expression profiles after TLX1 knockdown in the TLX1 positive T-ALL cell line ALL-SIL, confirmed the previously established role for TLX1 as transcriptional repressor in T-ALL biology. In line with previous reports (Della-Gatta et al., Nature Medicine, 2012), de novo TLX1 motif discovery identified RUNX1 and ETS1 as important mediators of the global TLX1 transcriptional network. Next, we used TLX1 ChIPseq data to define TLX1 bound super-enhancer including several loci critically involved in T-cell biology (e.g. T-cell receptor loci, RAG2, MYB). Furthermore, Gene set Enrichment Analysis (GSEA) showed that TLX1-defined super-enhancers were significantly affected by JQ1 treatment in ALL-SIL. Integration of our TLX1 ChIP-seq data with publically available ChIP-seq data for ICN1, RUNX1 and ETS1 in T-ALL cells (Wang et al., PNAS, 2013) showed a remarkable genome-wide overlap between the binding sites of these four transcription factors. Integration of these binding patterns with transcriptional read-out revealed an unprecedented transcriptional antagonism between TLX1 and NOTCH1, in which TLX1 suppresses the oncogenic NOTCH1 transcriptional program including IL7R, NOTCH3 and c-MYC. In line with this observation, ectopic TLX1 expression in CD34+ human thymic precursor T-cells broadly interfered with the normal T-cell di