Abstract PR09: CK2 inhibition exerts a therapeutic effect in high-risk ALL by restoring IKZF1-mediated repression of cell cycle progression and the PI3K pathway

The IKZF1 (Ikaros) gene encodes a DNA-binding protein that acts as a tumor suppressor in leukemia. Deletion of one Ikaros allele results in B-cell acute lymphoblastic leukemia (B-ALL) with a high rate of relapse and poor outcome. The mechanisms through which Ikaros suppresses leukemogenesis and that regulate Ikaros activity as a tumor suppressor in leukemia are unknown. Using a systems biology approach, we determined that Ikaros regulates transcription of genes that control two pathways crucial for proliferation of leukemia cells: 1) cell cycle progression and 2) the phosphatidylinositol 3-kinase (PI3K) pathway. Using gain-of-function and loss-of-function experiments we demonstrate that Ikaros transcriptionally represses genes that promote cell cycle progression and the PI3K pathway and activates transcription of a gene that suppresses the PI3K pathway. In high-risk B-ALL with deletion of one Ikaros allele, we show that the function of Ikaros as a transcriptional regulator is impaired due to reduced binding at promoters of its target genes. Previous work shows that Ikaros DNA-binding affinity is regulated via direct phosphorylation by the pro-oncogenic kinase, CK2 (Casein Kinase II). We show that CK2 is overexpressed in high-risk B-ALL as compared to normal B-cell precursors, further reducing Ikaros function. Treatment of primary high-risk B-ALL (with deletion of one IKZF1allele) using the CK2 specific inhibitor, CX-4945, restored Ikaros function as a transcriptional regulator of genes that control cell cycle progression and the PI3K pathway. Treatment with CK2 inhibitor was also associated with cell cycle arrest and reduced phosphorylation of the AKT kinase, a downstream PI3K pathway target. Using serial quantitative chromatin immunoprecipitation (qChIP) analyses spanning the promoters of Ikaros target genes, we demonstrated that Ikaros can repress transcription of its target genes through two distinct mechanisms: 1) via recruitment of histone deacetylase 1 (HDAC1), which is associated with the formation of repressive chromatin characterized by H3K27me3 and the loss of H3K9ac; and 2) by an HDAC1-independent mechanism that is associated with the formation of repressive chromatin characterized by H3K9me3, along with the loss of H3K9ac. The therapeutic efficacy of CK2 inhibition using CX-4945 against high-risk B-ALL was demonstrated in vivo using 4 different xenografts: 3 different high-risk primary pre-B-ALL patient-derived xenografts and Nalm6 xenografts. CX-4945 showed strong therapeutic effects in all 4 xenografts, as evidence by reduced leukemia cell numbers in bone marrow and in spleen, together with prolonged survival of treated xenograft animals. Expression analysis of Ikaros target genes in leukemia cells treated in vivo with CX-4945 revealed an expression pattern cell cycle regulatory and PI3K pathway genes that was highly similar to that observed with Ikaros overexpression. These data suggest that CK2 inhibition in vivo exerts its therapeutic effect on high-risk B-ALL by restoring Ikaros function as a transcriptional regulator of genes that promote cell cycle progression and the PI3K pathway. In summary, our results reveal that: 1) Ikaros functions as a tumor suppressor by suppressing cell cycle progression and the PI3K pathway; 2) Ikaros regulates transcription by inducing two distinct epigenetic alterations at promoters of its target genes and 3) CK2 inhibition with CX-4945 restores Ikaros function as a transcriptional regulator in vivo, and has a strong therapeutic effect in primary xenografts of high-risk B-ALL. These results provide support for the use of CK2 inhibitors in clinical trials for high-risk B-ALL. Supported by the National Institutes of Health R01 HL095120, and the Four Diamonds Fund Endowment. This abstract is also presented as Poster B10. Citation Format: Chunhua Song, Chandrika Gowda, XiaoKang Pan, Kimberly J. Payne, Sinisa Dovat. CK2 inhibition exerts a therapeutic effect in high-risk ALL by restoring IKZF1-mediated repression of cell cycle progression and the PI3K pathway. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Pediatric Cancer Research: From Mechanisms and Models to Treatment and Survivorship; 2015 Nov 9-12; Fort Lauderdale, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(5 Suppl):Abstract nr PR09.