TAL1 activation in T-cell acute lymphoblastic leukemia: a novel oncogenic 3' neo-enhancer

Haematologica. 2023 May 1;108(5):1259-1271. doi: 10.3324/haematol.2022.281583.

Abstract

T-cell acute lymphocytic leukemia protein 1 (TAL1) is one of the most frequently deregulated oncogenes in T-cell acute lymphoblastic leukemia (T-ALL). Its deregulation can occur through diverse cis-alterations, including SIL-TAL1 microdeletions, translocations with T-cell Receptor loci, and more recently described upstream intergenic non-coding mutations. These mutations consist of recurrent focal microinsertions that create an oncogenic neo-enhancer accompanied by activating epigenetic marks. This observation laid the groundwork for an innovative paradigm concerning the activation of proto-oncogenes via genomic alterations of non-coding intergenic regions. However, for the majority of T-ALL expressing TAL1 (TAL1+), the deregulation mechanism remains 'unresolved'. We took advantage of H3K27ac and H3K4me3 chromatin immunoprecipitation sequencing data of eight cases of T-ALL, including five TAL1+ cases. We identified a putative novel oncogenic neo-enhancer downstream of TAL1 in an unresolved monoallelic TAL1+ case. A rare but recurrent somatic heterozygous microinsertion within this region creates a de novo binding site for MYB transcription factor. Here we demonstrate that this mutation leads to increased enhancer activity, gain of active epigenetic marks, and TAL1 activation via recruitment of MYB. These results highlight the diversity of non-coding mutations that can drive oncogene activation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Basic Helix-Loop-Helix Transcription Factors / metabolism
  • Enhancer Elements, Genetic*
  • Humans
  • Mutation
  • Oncogene Proteins, Fusion / genetics
  • Precursor T-Cell Lymphoblastic Leukemia-Lymphoma* / genetics
  • T-Cell Acute Lymphocytic Leukemia Protein 1* / genetics
  • T-Lymphocytes / metabolism
  • Transcription Factors / genetics

Substances

  • Basic Helix-Loop-Helix Transcription Factors
  • Oncogene Proteins, Fusion
  • SIL-TAL1 fusion protein, human
  • T-Cell Acute Lymphocytic Leukemia Protein 1
  • TAL1 protein, human
  • Transcription Factors

Grants and funding

Funding: The study was supported in part by the Helmholtz-Foundation. AT was supported by a DKFZ postdoctoral fellowship. The work in the VA lab was supported by ARC-Labellisation and the associations “Force Hémato” and “Laurette Fugain.” This study was also supported in the lab by grants from INCA PLBIO18-031, PLBIO 2018-00252, and ITMO Cancer Epig-2015 (to VA and SS). SS was supported by the Ligue Contre le Cancer (labeling 2018) and the RNA-sequencing was funded by LIGUE. This work was also supported by La Fondation pour la Recherche Médicale with grant FDT202012010638 (to CS). The ONT sequencing was also supported by ANR funding KREM-AIF (ANR-21-CE17-0014-02) (to EA).