The genome wide mapping of H3K4kme3, H3K27ac and H3K27me3 in Ctcf f/f and Ctcf Δ/Δ CALM-AF10 AML cells [ChiP-seq]

CALM (Clathrin Assembly Lymphoid Myeloid Leukemia)-AF10, a fusion gene frequently observed in acute myeloid leukemia (AML), is caused by the t(10;11)(q13;q14) translocation, and is associated with poor prognosis. In this study, we demonstrate that the CCCTC-binding factor (CTCF) is crucial for both the initiation and maintenance of CALM-AF10-induced AML (CALM-AF10 AML). To investigate the role of CTCF in CALM-AF10 AML, we used hematopoietic stem and progenitor cells (HSPCs) from conditional knockout (KO) mice and immortalized them by introducing the CALM-AF10 fusion gene to generate CALM-AF10 AML models. Our in vivo experiments revealed that CTCF deficiency significantly prolonged the survival of CALM-AF10 AML mice. Similarly, in vitro analyses showed that CTCF KO inhibited the colony-forming ability of CALM-AF10 AML cells and induced differentiation into macrophage-like cells. RNA sequencing (RNA-seq) of CTCF KO cells identified that the most downregulated gene was Transglutaminase 2 (TGM2). Chromatin immunoprecipitation followed by sequencing (ChIP-seq) showed that increase in levels of trimethylation of histone H3K27 as well as decrease in levels of trimethylation of histone H3K4 and acetylation of histone H3K27 were observed at the transcription start site (TSS) of the Tgm2 gene after CTCF KO. Knocking down (KD) TGM2 using small hairpin RNA (shRNA) in both CALM-AF10 AML cells and the human leukemic cell line U937, which expresses the CALM-AF10 fusion gene, resulted in reduced colony-forming ability and cell proliferation, alongside differentiation into macrophage-like cells. These results mirrored those observed with CTCF KO. Furthermore, treatment with GK921, a TGM2 inhibitor, yielded similar effects. Taken together, our findings suggest that CTCF regulates the expression of TGM2 by altering histone modifications at its TSS, thereby contributing to the maintenance of the undifferentiated state in CALM-AF10 AML. Given the efficacy of TGM2 inhibitors, such as GK921, against CALM-AF10 AML, TGM2 represents a promising therapeutic target for this leukemia subtype.