Abstract 1513: Epigenetic regulation of CD117 expression in B-cell acute lymphoblastic leukemia by Ikaros and histone deacetylase HDAC1

The type III receptor tyrosine kinase, CD117, functions as a receptor for stem cell factor (SCF) and is encoded by the c-kit gene. During hematopoiesis, CD117 is normally expressed in hematopoietic stem cells, multipotent progenitors, common lymphoid progenitors, and early-stage thymocytes. Overexpression and/or activating mutations of c-kit have been demonstrated in acute myeloid leukemia (AML), early T-cell precursor acute lymphoblastic leukemia (ETP-ALL), and B-cell acute lymphoblastic leukemia (B-ALL). It has been suggested that increased expression of CD117 is associated with stem-like phenotype and worse clinical outcomes in AML and T-ALL. The regulation of expression of c-kit in leukemia is still largely unknown. Here we report that transcription of c-kit in B-ALL is regulated by the Ikaros tumor suppressor protein and histone deacetylase HDAC1. Global genome-wide binding studies using ChIP-seq, demonstrate the occupancy of both Ikaros and HDAC1 at the promoter of the c-kit gene in B-ALL cells. Ikaros and HDAC1 binding to the c-kit promoter was confirmed by quantitative chromatin immunoprecipitation (qChIP). Overexpression of Ikaros via retroviral transduction results in reduced transcription of c-kit in B-ALL cells. Consistent with this, Ikaros knock-down with shRNA results in increased transcription of c-kit in B-ALL. These data suggest that Ikaros represses transcription of c-kit. Ikaros overexpression was associated with increased HDAC1 occupancy while Ikaros knock-down resulted in reduced HDAC1 binding to the promoter of the c-kit gene. We tested whether Ikaros-mediated transcriptional repression of c-kit requires HDAC1 activity. Results showed that inhibition of HDAC1 activity with a pan-histone deacetylase inhibitor, trichostatin (TSA), or a specific HDAC1 inhibitor, MS-275, abolishes Ikaros9 ability to repress c-kit transcription in luciferase reporter assays. Molecular inhibition of HDAC1 with shRNA confirmed that HDAC1 activity is essential for Ikaros-mediated transcriptional repression of c-kit. A serial qChIP assay spanning the c-kit promoter was used to analyze the epigenetic changes that are associated with Ikaros and HDAC1 binding at the c-kit promoter. Results showed that increased Ikaros and HDAC1 occupancy at the c-kit promoter in B-ALL cells results in enrichment for the markers of the repressive chromatin, H3K9me3 and H3K27me3, as well as reduced occupancy of H3K9ac, a marker of active chromatin. In conclusion, the presented results show that the expression of c-kit in B-ALL is regulated at the transcriptional level by Ikaros and HDAC1 via chromatin remodeling. These data provide a novel insight into the role of Ikaros in both tumor suppression and transcriptional regulation of gene expression in B-cell acute lymphoblastic leukemia. Citation Format: Shriya Kane, Jonathon L. Payne, Mario Soliman, Chandrika Gowda, Meixan Xiang, Chunhua Song, Kimberly J. Payne, Sinisa Dovat. Epigenetic regulation of CD117 expression in B-cell acute lymphoblastic leukemia by Ikaros and histone deacetylase HDAC1 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1513.