Highly-sensitive DNA hydroxymethylation analysis to aid clinic evaluation of myelodysplastic syndromes (MDS)

Aberrant DNA hydroxymethylation (5hmC) has been reported in patients with myelodysplastic syndromes (MDS). The dysregulation of 5hmC is not only observed in patients with TET2 mutations, but also those bearing other genetic defects, suggesting that 5hmC might act as a valuable epigenetic mark to reflect the status of MDS. To further evaluate the function of 5hmC during MDS pathogenesis, we reported herein an improved highthroughput 5hmC analysis method based on CMS-IP using low input DNA (10 ng) purified from bone marrow aspirates of MDS patients. Our analysis revealed relatively higher heterogeneity of 5hmC signals in MDS patients compared with those of healthy donors, CMML and AML patients. Our systematic bioinformatic analysis further unveiled that 5hmC signatures could be used to separate patients with good and poor clinical outcomes. At the molecular level, we observed dynamic changes of 5hmC within several key transcription factor binding motifs that are essential for hemopoiesis and myeloid lineage specification, which might result in impaired transcriptional outputs during leukemogenesis. Interestingly, we also observed massive changes in 5hmC and transcriptomes in patient showing response to hypomethylating agents (HMA) treatment, suggesting the prognostic value of 5hmC in evaluating epigenetic therapy. Overall, our high-sensitive 5hmC analysis method provides a useful means to greatly facilitate the clinic evaluation for MDS. Overall design: We collected total 82 human bone marrow samples (7 healthy; 4 AML patients; 71 MDS patients) and performed CMS-IP sequencing.