Epigenomic repression by APL oncoprotein

In acute promyelocytic leukemia (APL), a t(15;17) translocation leads to the production of PML-RARα, the fusion oncoprotein responsible for the vast majority of APL cases. Expression of PML-RARα leads to transcriptional repression of RARα target genes and a differentiation block at the promyelocytic stage, but also to a unique responsiveness to treatment with all-trans retinoic acid (ATRA).

In this issue of Blood, Hoemme and colleagues present a comprehensive study using chromatin precipitation (ChIP)–chip as well as microarrays to analyze changes that occur with induced expression of PML-RARα in a promonocytic cell line. The authors used different antibodies to correlate PML-RARα binding to gene promoters with epigenetic modifications, including histone acetylation and methylation. Their data show a strong trend for promoters bound by PML-RARα to display lower levels of histone H3 acetylation, confirming that PML-RARα acts as a global repressor of gene transcription. Interestingly, a significant correlation between PML-RARα binding and increased levels of tri-methylated H3 lysine-9 is also evident, suggesting that a major effect of PML-RARα binding may be recruitment of the histone methyltransferase SUV39H1 to target promoters.¹ 

The study identified binding of PML-RARα to 372 genomic locations. Most were found close to the transcriptional start site of genes, but only about 40% of the targets contained bona fide retinoic acid receptor response elements, a finding that is in line with previous studies showing much more “relaxed” DNA binding requirements for PML-RARα compared with wildtype RARα.²  Microarray analyses were performed to assess global changes in gene expression associated with induced PML-RARα, and the resulting data show quite convincingly that PML-RARα binding, and the resulting chromatin changes, correlate with a global repression of transcription.

Pathway analysis of genes repressed by PML-RARα identified genes regulating many important cellular functions. Further analysis of these genes and their de-repression by ATRA in APL may shed important light on the molecular mechanisms of APL pathogenesis. In fact, 2 of the 3 most strongly repressed genes identified in the study, RGS2 and S100P, are previously identified regulators of myeloid differentiation, and RGS2 has been shown by the authors to be induced during ATRA treatment of the APL cell line NB4.³  Additional information about ATRA regulation of the identified epigenetic and genetic targets will be valuable, especially in light of other studies that have shown reversal of epigenetic silencing by ATRA⁴  and our recent data showing that ATRA can induce chromatin changes associated with transcriptional activation via binding to either PML-RARα or wild-type RARα.⁵ 

Understanding the mechanisms of deregulated transcription by leukemia fusion onco-proteins is critical for the design of tailored antileukemic strategies aimed at re-establishing the differentiation program. The use of global epigenetic and genetic analysis tools to identify targets of different leukemia-associated oncoproteins will likely prove increasingly important in this quest.