Abstract A21: Epigenetic regulation of cell cycle progression at the G2/M transition and mitosis in high-risk leukemia

High-risk acute lymphoblastic leukemia (ALL) is a clinical challenge due to drug resistance and poor prognosis. A characteristic molecular defect of most high-risk ALL is the deletion or inactivating mutation of one allele of the IKZF1 (Ikaros) tumor suppressor. Ikaros encodes a DNA-binding protein that regulates transcription of its target genes via chromatin remodeling. The mechanisms through which Ikaros regulates cellular proliferation in high-risk leukemia, are unknown. Using a systems biology approach, we determined that Ikaros regulates transcription of genes that are critical in the control of G2/M transition (CDC2) and mitotic progression (ANAPC1 and ANAPC7) in leukemia. Gain- and loss-of-function experiments demonstrate that Ikaros represses the transcription of CDC2, ANAPC1 and ANAPC7. Overexpression of Ikaros in leukemia also results in cell cycle arrest. We studied the mechanism through which Ikaros represses CDC2, ANAPC1 ad ANAPC7. The use of serial quantitative chromatin immunoprecipitation (qChIP) analyses spanning the promoters of Ikaros target genes demonstrated that Ikaros can repress transcription of its target genes by two different mechanisms: 1) via recruitment of histone deacetylase 1 (HDAC1), which is associated with the formation of repressive chromatin characterized by H3K27me3 and loss of H3K9ac (for ANAPC1 and CDC2); and 2) via an HDAC1-independent mechanism which is associated with the formation of repressive chromatin characterized by H3K9me3, along with the loss of H3K9ac (for ANAPC7). In high-risk ALL that is characterized by deletion of one Ikaros allele, the function of Ikaros as a transcriptional regulator is impaired due to reduced binding to promoters of Ikaros target genes. We showed previously that Ikaros DNA-binding affinity is regulated via direct phosphorylation by pro-oncogenic Casein Kinase II (CK2). CK2 is overexpressed in high-risk B-ALL as compared to normal B-cell precursors, which further reduces Ikaros function in this disease. In vivo CK2 inhibition with the CK2 specific inhibitor, CX-4945, results in a strong therapeutic effect in primary high-risk ALL xenografts. Analysis of primary high-risk B-ALL (that have deletion of one Ikaros allele) showed that treatment with CX-4945, restored Ikaros function as a transcriptional regulator of CDC2, ANAPC1 and ANAPC7, and was associated with cell cycle arrest. Epigenetic analysis of promoters of CDC2, ANAPC1 and ANAPC7 genes revealed that restoration of Ikaros binding to the promoters of these genes is associated with epigenetic alterations that are consistent with Ikaros overexpression and formation of repressive heterochromatin. In conclusion, our results reveal that: 1) Ikaros functions as a tumor suppressor by repressing transcription of genes that are critical for G/M transition (CDC2) and mitotic progression (ANAPC1 and ANAPC7); 2) Ikaros represses 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 of CDC2, ANAPC1 and ANAPC7 in high-risk leukemia. These results provide novel insights into the control of cell cycle progression in high-risk leukemia and the mechanisms by which CK2 inhibitors exert their therapeutic effects. Supported by the National Institutes of Health R01 HL095120, and the Four Diamonds Fund Endowment. Citation Format: Chunhua Song, Chandrika Gowda, Yali Ding, Kimberly J. Payne, Sinisa Dovat. Epigenetic regulation of cell cycle progression at the G2/M transition and mitosis in high-risk leukemia. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Cancer Cell Cycle - Tumor Progression and Therapeutic Response; Feb 28-Mar 2, 2016; Orlando, FL. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(11_Suppl):Abstract nr A21.