A distal single nucleotide polymorphism alters long-range regulation of the PU.1 gene in acute myeloid leukemia
Ulrich Steidl, … , Frank Griesinger, Daniel G. Tenen
Ulrich Steidl, … , Frank Griesinger, Daniel G. Tenen
Published September 4, 2007
Citation Information: J Clin Invest. 2007;117(9):2611-2620. https://doi.org/10.1172/JCI30525.
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Research Article Oncology

A distal single nucleotide polymorphism alters long-range regulation of the PU.1 gene in acute myeloid leukemia

Abstract

Targeted disruption of a highly conserved distal enhancer reduces expression of the PU.1 transcription factor by 80% and leads to acute myeloid leukemia (AML) with frequent cytogenetic aberrations in mice. Here we identify a SNP within this element in humans that is more frequent in AML with a complex karyotype, leads to decreased enhancer activity, and reduces PU.1 expression in myeloid progenitors in a development-dependent manner. This SNP inhibits binding of the chromatin-remodeling transcriptional regulator special AT-rich sequence binding protein 1 (SATB1). Overexpression of SATB1 increased PU.1 expression, and siRNA inhibition of SATB1 downregulated PU.1 expression. Targeted disruption of the distal enhancer led to a loss of regulation of PU.1 by SATB1. Interestingly, disruption of SATB1 in mice led to a selective decrease of PU.1 RNA in specific progenitor types (granulocyte-macrophage and megakaryocyte-erythrocyte progenitors) and a similar effect was observed in AML samples harboring this SNP. Thus we have identified a SNP within a distal enhancer that is associated with a subtype of leukemia and exerts a deleterious effect through remote transcriptional dysregulation in specific progenitor subtypes.

Authors

Ulrich Steidl, Christian Steidl, Alexander Ebralidze, Björn Chapuy, Hye-Jung Han, Britta Will, Frank Rosenbauer, Annegret Becker, Katharina Wagner, Steffen Koschmieder, Susumu Kobayashi, Daniel B. Costa, Thomas Schulz, Karen B. O’Brien, Roel G.W. Verhaak, Ruud Delwel, Detlef Haase, Lorenz Trümper, Jürgen Krauter, Terumi Kohwi-Shigematsu, Frank Griesinger, Daniel G. Tenen

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Figure 1

Genomic analysis of distal URE of PU.1.

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Genomic analysis of distal URE of PU.1. (A) Schematics of genomic locus...
(A) Schematics of genomic locus of human PU.1 gene including its 5 exons (white box) and –16-kb URE consisting of 2 highly conserved homology regions (gray boxes). Localization of the probes for fluorescence in situ hybridization (RP11-17G12 and RP11-379M04) is indicated by lines with filled circles at the ends. The long (q) and short (p) arms of chromosome 11 and the band 11.2 are indicated. (B) Fluorescence in situ hybridization with probe RP11-379M04 covering the URE locus. Left: Metaphase FISH showing 2 signals on each chromosome 11 (arrows). Right: Interphase FISH of 1 representative of 80 patients with 2 signals per cell. (C) Direct sequencing identifies SNP in the first homology region of PU.1 URE. Representative sequencing traces of patients with wild-type site (WT hom), heterozygous site (het), and homozygous SNP (SNP hom) shown. (D) Identification of a SNP in the second homology region of URE. Representative sequencing graphs of patients with wild-type site, heterozygous site, and homozygous SNP shown. (E) Higher abundance of the homozygous SNP in first homology region in patients with AML with complex karyotypes. Bar diagram shows SNP status of normal controls and AML with normal karyotype, with aberrant noncomplex karyotype, and with complex karyotype. *P = 0.027 (χ2) and P = 0.018 (Fisher’s exact); odds ratio, 2.9; odds ratio 95% confidence interval, 1.22–6.83. (F) Frequency of SNP in the second homology region of URE is not different between normal controls or AML.