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.
Highlights
BCL11B is a Kruppel family zinc finger gene located at 14q32, which is expressed during thymocyte maturation from CD4À/CD8À to CD4+/CD8+ stages [1]
This insertion is presumably responsible for activating TLX3 in DND-41 cells [33] by introducing ectopic (3¶-BCL11B) regulatory enhancers and resembles that reported in a T-cell ALL patient [34]
We investigated leukemic activation of Nirenberg-Kim family homeobox genes NKX2-5 and TLX3 involved in alternative t(5;14) translocations by carrying out DNA inhibitory treatments directed against candidate enhancers within the 3¶-BCL11B breakpoint cluster region, initially focusing on T-cell single DNaseI hypersensitive sites identified therein by global screening [17]
Summary
BCL11B ( known as CTIP2/Rit1) is a Kruppel family zinc finger gene located at 14q32, which is expressed during thymocyte maturation from CD4À/CD8À to CD4+/CD8+ stages [1]. 3); or, as an oncogenic activator, first detected by its juxtaposition with the TLX3 ( known as HOX11L2) homeobox gene at 5q35 via the recurrent t(5;14) (q35;q32) rearrangement in T-cell ALL [4,5,6]. A neighboring related homeobox gene, NKX2-5 ( known as CSX), is activated in T-cell ALL by a variant t(5;14)(q35;q32) or by t(5;14)(q35;q11.2) involving the T-cell receptor D locus at 14q11.2 [7, 8]. The ectopic expression of Nirenberg-Kim family homeobox genes (e.g., TLX3) has been recently shown to drive proliferation of myeloid progenitor cells in a mouse model [10]. Analogies with T-cell receptor loci and the nature of the ‘‘genomic desert’’ covering 3¶-BCL11B support the existence of underlying interactions between TLX3 /NKX2-5 and remote transcriptional enhancers
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
