DNA methylation is important during development of vertebrate organisms as well as for sustaining genome integrity and gene expression. Alterations of DNA methylation patterns are often associated with different diseases, for instance myelodysplastic syndromes (MDS) or acute myeloid leukemia (AML). Consequences of aberrant DNA methylation are the silencing of tumor suppressor genes due to hypermethylation as well as the hypomethylation‐mediated weakening of transcriptional repression, reactivation of retrotransposons and genomic instability.
The major aim of this thesis was the integrated analysis of epigenetic and genetic changes during disease progression to identify target genes that could be involved in development or progression of myelodysplastic syndromes. To address this issue, DNA methylation analysis was performed in pediatric and adult MDS patients using the methyl-CpG-immunoprecipitation sequencing approach (MCIp-seq) and the targeted bisulfite sequencing of the myeloid regulome, respectively.
It could be demonstrated that adult MDS patients show largely private DNA methylation changes and almost no common differentially methylated regions. Identified DMRs include RUNX1, FOXO3 and ZFPM1, which show methylation sensitivity in in vitro reporter gene assays. Another observation was made in this patient cohort in which DNA methylation changes only occur with alterations in clonal architecture. In cases of a genetically stable disease, no differences in DNA methylation patterns were observed over time.
In pediatric MDS patients global DNA methylation analysis revealed a correlation of DNA methylation changes with germline GATA2 mutations and refractory cytopenia (RC). In detail, a patient cluster with lower DNA methylation degree exhibited the mentioned two features, while the other cluster of patients was associated with more advanced subtypes and higher DNA methylation. DMRs identified between these two patient groups are ZIC5, VILL and TRIM45, possibly playing a role in cancer. Methylation sensitivity of these regions has to be tested with in vitro reporter gene assays and will give information about a possible role for the development or progress of MDS.
Regarding longitudinal studies in pediatric MDS patients, we could show the same result like in adult patients where DNA methylation changes correlate with alterations in genetic landscape. One potential epigenetic target gene found to be methylation sensitive and already described to play an important role in AML is the VENTX promoter region.
In summary, our data suggest a tight correlation of epigenetic changes with clonal architecture of the diseased hematopoiesis, but the chronological order of appearance is still an open issue
