The common oncogenomic program of NOTCH1 and NOTCH3 signaling in T-cell acute lymphoblastic leukemia

PLoS One. 2017 Oct 12;12(10):e0185762. doi: 10.1371/journal.pone.0185762. eCollection 2017.

Abstract

Notch is a major oncogenic driver in T cell acute lymphoblastic leukemia (T-ALL), in part because it binds to an enhancer that increases expression of MYC. Here, we exploit the capacity of activated NOTCH1 and NOTCH3 to induce T-ALL, despite substantial divergence in their intracellular regions, as a means to elucidate a broad, common Notch-dependent oncogenomic program through systematic comparison of the transcriptomes and Notch-bound genomic regulatory elements of NOTCH1- and NOTCH3-dependent T-ALL cells. ChIP-seq studies show a high concordance of functional NOTCH1 and NOTCH3 genomic binding sites that are enriched in binding motifs for RBPJ, the transcription factor that recruits activated Notch to DNA. The interchangeability of NOTCH1 and NOTCH3 was confirmed by rescue of NOTCH1-dependent T-ALL cells with activated NOTCH3 and vice versa. Despite remarkable overall similarity, there are nuanced differences in chromatin landscapes near critical common Notch target genes, most notably at a Notch-dependent enhancer that regulates MYC, which correlates with responsiveness to Notch pathway inhibitors. Overall, a common oncogenomic program driven by binding of either Notch is sufficient to maintain T-ALL cell growth, whereas cell-context specific differences appear to influence the response of T-ALL cells to Notch inhibition.

MeSH terms

  • Cell Line, Tumor
  • Gene Expression Regulation, Leukemic
  • Humans
  • Immunoglobulin J Recombination Signal Sequence-Binding Protein / biosynthesis
  • Immunoglobulin J Recombination Signal Sequence-Binding Protein / genetics
  • Precursor T-Cell Lymphoblastic Leukemia-Lymphoma / genetics
  • Precursor T-Cell Lymphoblastic Leukemia-Lymphoma / metabolism*
  • Proto-Oncogene Proteins c-myc / biosynthesis
  • Proto-Oncogene Proteins c-myc / genetics
  • Receptor, Notch1 / genetics
  • Receptor, Notch1 / metabolism*
  • Receptor, Notch3 / genetics
  • Receptor, Notch3 / metabolism*
  • Response Elements
  • Signal Transduction*

Substances

  • Immunoglobulin J Recombination Signal Sequence-Binding Protein
  • MYC protein, human
  • NOTCH1 protein, human
  • NOTCH3 protein, human
  • Proto-Oncogene Proteins c-myc
  • RBPJ protein, human
  • Receptor, Notch1
  • Receptor, Notch3