An intronic region within FTO confers differentiation block in acute myeloid leukaemia through regulation of IRX3 and HOX [ChIP-seq re-analysis]

Transcription factors are key determinants in myeloid identity and differentiation fates and when mis- expressed or mutated, they cause a differentiation block, the cardinal feature of acute myeloid leukaemia (AML). The Forkhead family transcription factor FOXC1, is de-repressed in a lineage- inappropriate manner in approximately 30% of cases of HOXAhigh AML with functional consequences and prognostic significance. The mechanisms by which FOXC1 is mis-expressed remain to be determined and they presumably belong to a network of transcription factors and chromatin proteins that represent attractive therapeutic targets in AML. We performed an integrative omics analysis using AML primary samples and discovered an active distal enhancer at the FOXC1 topologically associated domain (TAD) that is more acetylated, accessible and differentially interacts with FOXC1, positively regulating its expression in FOXC1high AML. Moreover, through integrated next generation sequencing and functional analysis, we identified SOX4 as one of the upstream regulators of FOXC1 in leukaemia, where it is broadly expressed and associated with a high level of differentiation block. SOX4 binds at multiple sites across the FOXC1 TAD and directly controls its expression. Genome wide, SOX4 is preferentially bound at sites of accessible and acetylated chromatin at both promoter regions and active enhancers of transcription factors genes that include FOXC1, where it acts as a transcription activator. Our studies reveal a set of regulatory elements that control FOXC1 expression and highlight the role of SOX4 as a transcriptional activator that promotes differentiation block in AML. Primary human AML cells were obtained from the Manchester Cancer Research Centre Tissue Biobank (approved by the South Manchester Research Ethics Committee). The Biobank archive was searched for samples from patients with different levels of FOXC1 expression. Please note that GSM5292586-GSM5292594 (in GSE174352) samples have been re-analyzed for the current study.