Differentiation block in acute myeloid leukemia regulated by intronic sequences of FTO
Francesco Camera, Isabel Romero-Camarero, Bradley Revell, Fabio M. R. Amaral, Oliver Sinclair, Fabrizio Simeoni, Daniel H. Wiseman, Lovorka Stojic, Tim C. P. Somervaille
Abstract
Iroquois transcription factor gene IRX3 is highly expressed in 20–30% of acute myeloid leukemia (AML) and contributes to the pathognomonic differentiation block. Intron 8 FTO sequences ∼220kB downstream of IRX3 exhibit histone acetylation, DNA methylation, and contacts with the IRX3 promoter, which correlate with IRX3 expression. Deletion of these intronic elements confirms a role in positively regulating IRX3 . RNAseq revealed long non-coding (lnc) transcripts arising from this locus. FTO -lncAML knockdown (KD) induced differentiation of AML cells, loss of clonogenic activity, and reduced FTO intron 8: IRX3 promoter contacts. While both FTO -lncAML KD and IRX3 KD induced differentiation, FTO -lncAML but not IRX3 KD led to HOXA downregulation suggesting transcript activity in trans . FTO -lncAML high AML samples expressed higher levels of HOXA and lower levels of differentiation genes. Thus, a regulatory module in FTO intron 8 consisting of clustered enhancer elements and a long non-coding RNA is active in human AML, impeding myeloid differentiation.