Targeting the epigenetic state of refractory and relapsing acute myeloid leukaemia

Abstract: Acute myeloid leukaemia (AML) is a heterogeneous group of myeloid lineage malignancies arising from a spectrum of mutations. AML is characterized by the uncontrolled proliferation of clonal cells, which are unable to properly differentiate into mature myeloid cells. The present day standard treatment of care for AML patients under 60 years of age is the “7+3” induction chemotherapy. The survival rate beyond 5 years has been maintained at 40%. Most AML patients older than 60 years are unable to tolerate this intensive cytotoxic induction regimen and are treated with hypomethylating drugs. The two-year relapse-free survival rate of these patients remains at 40% (exceptionally low) with a median survival of 6.5 months. Thus, novel therapeutic strategies are urgently needed to improve the overall survival of both young and elderly AML patients. Therefore, elucidating the molecular mechanisms underlying AML has been of prime importance in the development of efficacious targeted therapeutics to treat subtypes of this heterogeneous haematological malignancy. Next-generation sequencing has uncovered that the most frequently mutated class of genes in AML encode epigenetic modifiers, suggesting that alterations in the epigenetic landscape contribute to the development of AML. H3K27me3 is an epigenetic alteration of the Histone H3, one of the five principal histones involved in chromatin construction in eukaryotic cells. In refractory acute myeloid leukaemia, a study found an epigenetic relationship between the decreased abundance of the Polycomb related protein MTF2 and chemotherapy resistance. MTF2 loss hampered PRC2 complex expression and H3K27me3 deposition at numerous genes, including the major target gene MDM2, resulting in enhanced MDM2 expression, which depleted p53 and conferred chemoresistance. This study aimed to elucidate the epigenetic dysregulation in chemorefractory and chemoresponsive AML.     A systems biology methodology was utilized here. Two AML sample types were collected from the bone marrow of AML patients. The first sample (AML_4) had basal levels of the epigenetic modification H3K27me3 and basal levels of MTF2. The second sample (AML_1) had low levels of H3K27me3 and basal levels of MTF2. ATAC-seq (Assay for Transposase Accessible Chromatin with High-Throughput Sequencing) is a powerful tool for revealing chromatin accessibility across the genome. By probing hyperactive Tn5 transposase to a DNA sequence, ATAC-seq generates reads from cells representing accessible regions that correspond to nucleosome positioning and transcription factor binding sites. ATAC-seq was performed on AML_4 and AML_1. Bioinformatics analysis was conducted on the two ATAC-seq data to identify transcription factors with differential activity in each of the AML types. 36 transcription factors with significant differential activity were identified in AML_1 while 4 transcription factors were identified in AML_4. These results reveal higher epigenetic dysregulation in AML_1. These results reveal higher epigenetic dysregulation in AML_1 compared to AML_4. These transcription factors with significant activity in the different AML types would be combined with CHIP-seq and RNA-seq data thereafter used for gene regulatory network analysis of key AML genes to uncover the underlying mechanisms of the regulation of these genes.