Acute lymphoblastic leukemia displays a distinct highly methylated genome

Using genome-wide bisulfite sequencing of acute lymphoblastic leukemia subtypes, cell lines and healthy cells, Hetzel et. al. find that unlike most cancers, ALL has a highly methylated genome, which points to a distinct mode of epigenome regulation in this cancer type. DNA methylation is tightly regulated during development and is stably maintained in healthy cells. In contrast, cancer cells are commonly characterized by a global loss of DNA methylation co-occurring with CpG island hypermethylation. In acute lymphoblastic leukemia (ALL), the commonest childhood cancer, perturbations of CpG methylation have been reported to be associated with genetic disease subtype and outcome, but data from large cohorts at a genome-wide scale are lacking. Here, we performed whole-genome bisulfite sequencing across ALL subtypes, leukemia cell lines and healthy hematopoietic cells, and show that unlike most cancers, ALL samples exhibit CpG island hypermethylation but minimal global loss of methylation. This was most pronounced in T cell ALL and accompanied by an exceptionally broad range of hypermethylation of CpG islands between patients, which is influenced by TET2 and DNMT3B. These findings demonstrate that ALL is characterized by an unusually highly methylated genome and provide further insights into the non-canonical regulation of methylation in cancer.

Automated summary

In acute lymphoblastic leukemia (ALL), unlike most cancers, there is a highly methylated genome with CpG island hypermethylation, particularly pronounced in T cell ALL. This hypermethylation is influenced by TET2 and DNMT3B, suggesting a non-canonical regulation of methylation in ALL.