AMPK Links Metabolic Regulation to Epigenome Modification in Leukemia-Initiating-Cell

Metabolic reprogramming has been recognized as a new hallmark of cancer. Oncogenic pathways or mutations in metabolic enzymes such as isocitrate dehydrogenase are found to impinge on the epigenome through metabolites such as acetyl-CoA and alpha-ketoglutarate. Previously, we found that AMP-activated kinase (AMPK), a master regulator of energy homeostasis, is essential for the function of leukemia-initiating-cells (LICs) in MLL-AF9 driven leukemia. Deficiency of AMPK induced changes in glycolysis and impaired leukemogenic function of LICs. However, whether deficiency of AMPK results in epigenome modification through the altered metabolism in LICs is unclear.

We first analyzed some metabolites in glycolysis pathway and found that the acetylation cofactor acetyl-CoA was decreased in AMPK deficient leukemia cells. Since acetyl-CoA is the cofactor for protein acetylation, we hypothesized that AMPK deletion would lead to decreased histone acetylation. Indeed, we found that acetylated histone H3 and H4 levels were reduced in AMPK deficient LICs. Supplementation of the acetyl-CoA precursor acetate into cultured AMPK deficient LICs restored the intracellular acetyl-CoA level, histone acetylation and cell growth. Furthermore, perturbing acetyl-CoA synthesis enzymes such as Acss2 and Acly using the CRISPR-Cas9 system decreased acetyl-CoA levels and induced histone hypoacetylation. These results suggested that AMPK deficiency resulted in histone hypoacetylation through decreasing acetyl-CoA pool. Next, we profiled genes bound with acetylated histones using chromatin immunoprecipitation sequencing (ChIP-seq). The results displayed a hypoacetylation pattern across the genome in AMPK deficient LICs. Interestingly, at the MLL-AF9 bound genes such as Meis1 and Hoxa9, the acetylated histone signals were decreased in AMPK deficient LICs. Gene set enrichment analysis indicated that AMPK deficient LICs had lower expression levels of MLL-AF9 targeted genes. These results suggested that AMPK deficiency caused histone hypo-acetylation and reduced expression of MLL-AF9 targeted genes.

Our work reveals that AMPK deficiency reduces the metabolite acetyl-CoA and further reduced histone acetylation in LICs. It provides another evidence to link metabolic regulation to the epigenome. This also raises the possibility that metabolic intervention can modify the epigenome and potentially synergize with epigenetic drugs in suppressing leukemia growth.