Epigenetic Regulation of Oncogenes in Leukemia by the Ikaros Tumor Suppressor

The IKZF1 gene controls expression of the Ikaros protein which functions as a tumor suppressor in pediatric acute lymphoblastic leukemia (ALL). Dysfunction of Ikaros due to deletion or an inactivating mutation of a single allele is associated with high‐risk ALL, increased risk for relapse, and poor prognosis. Ikaros is a transcriptional regulator of a large set of target genes; however, the mechanism by which Ikaros regulates gene expression in leukemia and mediates its tumor‐suppressor effect has yet to be fully elucidated. In this study, chromatin immunoprecipitation with next‐generation sequencing (ChIP‐Seq) was used to identify Ikaros' target genes and their epigenetic signature. ChIP‐Seq results were confirmed using quantitative chromatin immunoprecipitation (qChIP). Ikaros gain‐ and loss‐of‐function assays were used to determine the role of Ikaros in the epigenetic regulation of gene expression which was assessed by quantitative, real‐time PCR (qRT‐PCR) and western blot. ChIP‐Seq and qChIP assays identified a large number of target genes that are regulated by Ikaros. Ikaros gain‐ and loss‐of‐function experiments in combination with qChIP “scanning” at Ikaros target gene promoters revealed that Ikaros can repress transcription by inducing the formation of heterochromatin at gene promoters. Ikaros overexpression in ALL results in an increase in H3K27me3 and H3K9me3 repressive chromatin markers at the promoters of genes that support cell cycle progression and the phosphoinositide 3‐kinase (PI3K) pathway—both pathways are frequently activated in cancer. We also demonstrate that Ikaros overexpression results in the transcriptional repression of the JARID1B/KDM5B histone demethylase. Decreased KDM5B expression is accompanied by a genome‐wide increase in H3K4me3 as evidenced by western blot. In conclusion, our results show that Ikaros' tumor suppressor activity in high‐risk ALL involves epigenetic regulation at the promoters of its target genes and regulation of H3K4me3 levels via transcriptional repression of the JARID1B histone demethylase. These data give further insight into the mechanisms underlying Ikaros' tumor suppressor function in acute lymphoblastic leukemia.Support or Funding InformationThis work was supported by National Institutes of Health (NIH) Grant R01 HL095120, a St. Baldrick's Foundation Career Development Award, a Hyundai Hope on Wheels Scholar Grant Award, the Four Diamonds Fund of the Pennsylvania State University College of Medicine, and the John Wawrynovic Leukemia Research Scholar Endowment.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.