NEW YORK – New research has highlighted enhanced DNA methylation levels in acute lymphoblastic leukemia (ALL) genomes, particularly in cases arising from T lymphocytes, known as T-cell ALL or T-ALL.
"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," co-senior and co-corresponding authors Alexander Meissner and Charles Mullighan and their colleagues wrote in Nature Cancer on Thursday.
Meissner is a researcher affiliated with the Max Planck Institute for Molecular Genetics, Harvard University, Broad Institute, and Freie Universität Berlin, while Mullighan is an investigator at St. Jude Children's Research Hospital as well as the deputy director and co-leader of the St. Jude Comprehensive Cancer Center's Hematological Malignancies Program.
For their analyses, the researchers turned to whole-genome bisulfite sequencing to profile cytosine methylation patterns in tumors from 82 children with ALL. The cases included tumors spanning T-ALL, along with two B-cell ALL (B-ALL) subtypes affecting B lymphocytes. They noted that while past studies of pediatric ALL have identified informative methylation subtypes, most prior work has relied on array-based methylation profiling or targeted enrichment rather than more comprehensive bisulfite sequencing across the genome.
"In this study, using integrated genomic analysis of a large cohort of B-progenitor and T-lineage ALL, corresponding cell lines, and healthy samples, we describe the distinct methylome of ALL and provide insights into the epigenomic alterations in leukemogenesis," the authors explained.
When the team compared methylation profiles in the ALL samples with those in five B-ALL cell lines, nine T-ALL cell lines, and healthy B- or T-cell progenitor cells, it uncovered hypermethylation at cytosine-guanine nucleotides in ALL. In contrast, methylation declines were rare in the ALL samples relative to the unaffected cell types, in contrast to other cancer types such as colorectal cancer or chronic lymphocytic leukemia (CLL) that have been profiled epigenetically in the past.
"Global loss of methylation has long been viewed as a characteristic feature accompanying tumorigenesis," the authors explained, noting that "[i]n contrast, T-ALL exhibited a global DNA methylation landscape comparable to precursor T cells derived from healthy infant [thymus samples], whereas B-ALL samples showed mild loss of methylation at varying degrees."
The team expanded those findings by comparing DNA methylation profiles across ALL, in other hematopoietic tumor types such as CLL or acute myeloid leukemia (AML), and in eight solid tumor types. Again, the results pointed to higher-than-usual methylation levels in both T-ALL and AML. In B-ALL, meanwhile, samples from the Ph-like subtype and pediatric samples of unknown subtype were marked by genome-wide sites with increased methylation and modest methylation losses.
Along with more detailed analyses of the differentially methylated regions found in each ALL subtypes and potential methylation ties to gene or chromatin features, the investigators went on to consider genes linked to epigenetic regulation in ALL.
In particular, they flagged hypermethylation in the promoter of the Tet methylcytosine dioxygenase 2 gene (TET2) in more than a quarter of the T-ALL samples. Those promoter changes coincided with lower-than-usual TET2 expression levels — findings the team explored further with bisulfite sequencing, RNA sequencing, and other experiments on cell lines missing the TET2 gene.
Similarly, the team saw ties between increased DNA methylation and enhanced expression of DNMT3B, a DNA methyltransferase enzyme-coding gene known for its role in epigenetic regulation, in T-ALL tumor samples, and in at least one of the T-ALL cell lines. Even so, the authors cautioned that such methylation patterns were not consistent across all the cell assessed.
"[A]lthough our selection of T-ALL cell lines seemed to resemble parts of the DNA methylation dynamics in patients with T-ALL," they explained, "their respective methylome still deviates from primary T-ALL cases, most notably by lower genome-wide methylation levels, likely reflecting culture-induced changes."
Based on these and other results, the authors suggested that the study offers "important data and insights into the non-canonical epigenetic regulation of ALL as well as cancer more generally that, combined with recent studies, helps to focus our attention on particular aspects of the cancer methylome and will help us move toward an improved mechanistic understanding of the common epigenetic changes in cancer."