Activation of TLX3 and NKX2-5 in t(5;14)(q35;q32) T-cell acute lymphoblastic leukemia by remote 3'-BCL11B enhancers and coregulation by PU.1 and HMGA1

Cancer Res. 2007 Feb 15;67(4):1461-71. doi: 10.1158/0008-5472.CAN-06-2615.

Abstract

In T-cell acute lymphoblastic leukemia, alternative t(5;14)(q35;q32.2) forms effect dysregulation of either TLX3 or NKX2-5 homeobox genes at 5q35 by juxtaposition with 14q32.2 breakpoints dispersed across the BCL11B downstream genomic desert. Leukemic gene dysregulation by t(5;14) was investigated by DNA inhibitory treatments with 26-mer double-stranded DNA oligonucleotides directed against candidate enhancers at, or near, orphan T-cell DNase I hypersensitive sites located between 3'-BCL11B and VRK1. NKX2-5 down-regulation in t(5;14) PEER cells was almost entirely restricted to DNA inhibitory treatment targeting enhancers within the distal breakpoint cluster region and was dose and sequence dependent, whereas enhancers near 3'-BCL11B regulated that gene only. Chromatin immunoprecipitation assays showed that the four most effectual NKX2-5 ectopic enhancers were hyperacetylated. These enhancers clustered approximately 1 Mbp downstream of BCL11B, within a region displaying multiple regulatory stigmata, including a TCRA enhancer motif, deep sequence conservation, and tight nuclear matrix attachment relaxed by trichostatin A treatment. Intriguingly, although TLX3/NKX2-5 promoter/exon 1 regions were hypoacetylated, their expression was trichostatin A sensitive, implying extrinsic regulation by factor(s) under acetylation control. Knockdown of PU.1, known to be trichostatin A responsive and which potentially binds TLX3/NKX2-5 promoters, effected down-regulation of both homeobox genes. Moreover, genomic analysis showed preferential enrichment near ectopic enhancers of binding sites for the PU.1 cofactor HMGA1, the knockdown of which also inhibited NKX2-5. We suggest that HMGA1 and PU.1 coregulate ectopic homeobox gene expression in t(5;14) T-cell acute lymphoblastic leukemia by interactions mediated at the nuclear matrix. Our data document homeobox gene dysregulation by a novel regulatory region at 3'-BCL11B responsive to histone deacetylase inhibition and highlight a novel class of potential therapeutic target amid noncoding DNA.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acetylation
  • Chromosome Breakage
  • Chromosomes, Human, Pair 14
  • Chromosomes, Human, Pair 5
  • DNA-Binding Proteins / genetics*
  • Deoxyribonuclease I / metabolism
  • Enhancer Elements, Genetic
  • Gene Expression Regulation, Leukemic*
  • HMGA Proteins / genetics*
  • Histones / metabolism
  • Homeobox Protein Nkx-2.5
  • Homeodomain Proteins / genetics*
  • Humans
  • Leukemia-Lymphoma, Adult T-Cell / genetics*
  • Leukemia-Lymphoma, Adult T-Cell / metabolism
  • Multigene Family
  • Nuclear Matrix / metabolism
  • Oligonucleotides / genetics
  • Oncogene Proteins / genetics*
  • Precursor Cell Lymphoblastic Leukemia-Lymphoma / genetics*
  • Precursor Cell Lymphoblastic Leukemia-Lymphoma / metabolism
  • Proto-Oncogene Proteins / genetics*
  • RNA, Small Interfering / genetics
  • Repressor Proteins / genetics*
  • Trans-Activators / genetics*
  • Transcription Factors / genetics*
  • Translocation, Genetic
  • Tumor Suppressor Proteins / genetics*

Substances

  • BCL11B protein, human
  • DNA-Binding Proteins
  • HMGA Proteins
  • Histones
  • Homeobox Protein Nkx-2.5
  • Homeodomain Proteins
  • NKX2-5 protein, human
  • Oligonucleotides
  • Oncogene Proteins
  • Proto-Oncogene Proteins
  • RNA, Small Interfering
  • Repressor Proteins
  • TLX3 protein, human
  • Trans-Activators
  • Transcription Factors
  • Tumor Suppressor Proteins
  • proto-oncogene protein Spi-1
  • Deoxyribonuclease I