Abstract 2727: Histone deacetylase (HDAC1) and IKAROS are critical regulators of histone methylation and epigenomic landscape in T-cell acute lymphoblastic leukemia

Abstract Objective: To dissect the role of IKAROS-HDAC1 complexes in global regulation of gene expression and chromatin landscape in T-ALL. Methods: We studied IKAROS and HDAC1 role in epigenomic regulation of gene expression in primary human T-ALL, IKZF1-null human T-ALL, Ikzf1-null mouse T-ALL cells and following IKZF1-re-introduction into IKZF1-null human and mouse T-ALL cells. We used ATAC-seq and ChIP-seq of IKAROS, HDAC1, Enhancer of zeste homolog 2 (EZH2), along with CUT&Tag of histone modification markers, coupled with RNA-seq to study dynamic effect of IKAROS in IKZF1- null T-ALL and at several time points following IKZF1 re-introduction. Results: Deletion of IKZF1 results in severely reduced HDAC1 DNA occupancy and reduced H3K27me3 enrichment. Re-introduction of IKZF1 results in the increased HDAC1 recruitment to promoters, EZH2 re-distribution, and de novo formation of H3K27me3 facultative heterochromatin. This was associated with cessation of cellular proliferation and induction of T- cell differentiation. The newly-formed heterochromatin was often located at promoters of known oncogenes and the genes that promote cell cycle progression. In contrast, IKAROS binding to DNA, without concomitant HDAC1 recruitment results in increased H3K27 histone acetylation with de novo formation of active enhancers, characterized with H3K4me1+/H3K27ac+ and super- enhancers, with a broad enrichment of histone H3K27 acetylation across the large genomic areas. Pathway enrichment analysis showed that newly-formed active enhancers positively regulate genes that are involved in cell cycle suppression and T cell differentiation. Conclusion: Our results demonstrated that IKAROS and HDAC1 are the key regulators of histone acetylation and epigenomic landscape in T-ALL. HDAC1 recruitment by IKAROS is critical for formation of facultative heterochromatin, while IKAROS DNA binding without HDAC1 promotes of histone H3K27 acetylation. Results provide novel insight into mechanisms of regulation of histone acetylation, gene expression and tumor suppression in T-ALL. Citation Format: Jiaxing Tan, Yali Ding, Bing He, Daniel Bogush, Joseph Schramm, Chingakham Singh, Diwakar Tukaramrao, Charyguly Annageldiyev, Avinash Kudva, Dhimant Desai, Arati Sharma, Sinisa Dovat. Histone deacetylase (HDAC1) and IKAROS are critical regulators of histone methylation and epigenomic landscape in T-cell acute lymphoblastic leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 2727.