High Resolution Epigenomic Mapping of Myelodysplastic Syndrome Reveals a High Level of Functionally Important Methylation.
Authors: Zhou Li , Opalinska Joanna , Sohal Davendra , Parmar Simrit , Pahanish Perry , Isulfi Iris , Ye Kenny , Figueroa Maria , Greally John , Melnick Ari , Verma Amit 
Published: October 2019

Abstract
The myelodysplastic syndromes (MDS) are collections of heterogeneous hematologic diseases characterized by clonal hematopoietic defects. Even though gene expression studies have tried to differentiate between prognostic subgroups, there are concerns with standardization and validity of these studies. Decitabine and 5-azacytidine have shown activity in MDS, but it is unclear if hypomethylation can explain their efficacy. To address these issues we have developed a novel platform that uses a combination of gene expression analysis, high density array based comparative genomic hybridization (aCGH) and genome wide methylation analysis to perform an integrated high throughput epigenomic analysis of MDS. Using this approach, we conducted a pilot study in 5 patients with MDS. Gene expression analysis was performed using 37K oligo maskless arrays and high density aCGH was performed at 6Kb resolution using the Nimblegen platform. Whole genome methylation was analyzed by a recently described novel method ( Khulan et al, Genome Res. 2006 Aug;16(8)) that uses differential methylation specific digestion by HpaII and MspI followed by pcr amplification, two color labeling and hybridization to quantitatively determine individual promoter CpG island methylation. aCGH revealed a very high number of deletions (range 515–2722, mean 1073±937) and amplifications (range 614–1247, mean 843±254) not visualized by conventional cytogenetic analysis. These were also seen on peripheral blood mononuclear cells and correlated with those seen in the bone marrow. 22 common regions were found to amplified and 15 regions commonly deleted in 80% of the samples and contained genes involved in transcription and signaling. A custom human oligo array was used to determine methylation by calculating HpaII/MspI cut fragment intensity ratio. MDS samples demonstrated a very high level of methylation (range 70–84%). Expression was found to be significantly decreased for the genes that were methylated (p<.0001, T test) demonstrating the functional relevance of this assay. Analysis of common differentially methylated genes (when compared to normal samples) and their validation are ongoing. Micro deletions and amplifications seen on aCGH did not correlate with changes in global expression of the involved genes. Interestingly, large deletions (-7q) and large amplifications (+1p) correlated significantly with corresponding changes in gene expression when compared to the rest of the chromosome. (p<.0001, Anova) Integration of methylation data with aCGH data increased the predictive value of corresponding changes in gene expression. This result demonstrates that loss of heterozygosity coupled with the methylation of the remaining allele may result in pathogenic gene silencing in MDS. The high rate of methylation and DNA copy number alterations demonstrated in MDS in our study suggest that this integrated approach mightl be useful to define prognostic subgroups in future studies and aid in gene discovery.