Loss of SETD8 remodels enhancer chromatin accessibility to eliminate t(8;21) leukemia stem cells by mitochondrial homeostasis reprogramming [ATAC-seq]

Leukemic stem cells (LSCs) are at least partially responsible for relapse and resistance in patients with t(8;21) acute myeloid leukemia (AML), while the intricate regulatory network governing LSC stemness is yet to be fully elucidated. Chromatin accessibility remodeled by epigenetic alterations represents a defining hallmark of LSCs, endowing them with enhanced survival and self-renewal capacities, which may offer potential therapeutic opportunities for intervention. Here, we show that SETD8, a lysine methyltransferase that monomethylates lysine 20 of histone H4 (H4K20me1), is essential for the maintenance of stemness in t(8;21) AML LSCs. Genetic deletion or pharmacological inhibition of SETD8 impairs the survival and self-renewal of LSCs in retroviral AML1-ETO9a-driven t(8;21) AML mice and primary t(8;21) AML CD34+ cells. Mechanistically, SETD8 promotes the expression of Ras homolog family member T1 (RHOT1), a mitochondrial outer membrane protein, by increasing chromatin accessibility at the enhancer region, thereby reprogramming mitochondrial homeostasis. These findings improve our understanding of the gene regulation through chromatin accessibility remodeling and establish a link between histone lysine methylation and mitochondrial homeostasis, suggesting a potential strategy for eliminating LSCs in t(8;21) AML. Overall design: ATAC-seq in Kasumi-1 cells after SETD8 knockout by CRISPR/Cas9.