MDS Marrow Stroma Is Characterized by Distinct Epigenetic Alterations
Authors: Bhagat Tushar D , Spaulding Emily , Sohal Davendra , Mo Yongkai , Marcondes Mario , Zhou Li , Thompson Reid , Greally John , Deeg H. Joachim , Verma Amit 
Published: October 2019

Abstract
The bone marrow microenvironment plays an important role in the pathogenesis and perpetuation of stem cell defects in Myelodysplastic Syndrome (MDS). However, while distinct cytogenetic alterations have been described in the stem cell compartment in MDS, the bone marrow stroma has never been shown to be part of the clone. Thus, aberrant epigenetic alterations may be responsible for altered function of bone marrow stroma in MDS. DNA methyl transferase (DNMT) inhibitors, which are therapeutically effective in MDS, affect both hematopoietic cells and the stroma, providing further rationale for studying DNA methylation profiles of bone marrow stroma in this disease. To accomplish this aim, bone marrow mononuclear cells from MDS patients and controls were grown to form adherent cell layers and then depleted for hematopoietic elements by immunomagnetic CD45 negative selection. CD45 negative adherent cells were subsequently expanded and then used for whole genome methylation studies using a recently described novel method, the HELP assay (HpaII tiny fragment Enrichment by Ligation-mediated PCR; Khulan et al, Genome Res. 2006 Aug;16(8)) which uses differential methylation-specific digestion by HpaII and MspI followed by amplification, two color labeling and hybridization to quantify individual promoter CpG island methylation. A custom whole genome human promoter array (Roche-Nimblegen) was used to determine the level of methylation of 25626 gene promoters by calculating HpaII/MspI cut fragment intensity ratio. Global epigenetic profiling revealed that MDS stroma (n=6) was epigenetically distinct from normal bone marrow stroma (n=4) (ANOVA, P<0.0001). Many novel genes that were differentially methylated in MDS stroma, though majority were found to be hypomethylated when compared to normal controls. Growth regulators and transcription factors such as BMP-9, PAX-4, EIF2B1, and BATF-1, were mot significantly hypomethylated. These genes were grouped into functional pathways by Ingenuity Pathway architect and encoded for Cancer related pathways with Hepatocyte nuclear factor- alpha as their central node.
In subsequent studies, we profiled stroma from another set of MDS patients who had been treated with the DNMT inhibitor, 5-Azacytidine (n=4). In contrast to untreated MDS patients, there were no significant epigenetic differences between these 5-Azacytidine treated MDS patients and healthy controls (p = NS). These 5-Azacytidine exposed stroma cells did not demonstrate global hypomethylation (as hypothesized after DNMT inhibitor treatment) and were characterized by both hyper- and hypo-methylated loci similar to healthy controls.
Thus our results reveal that MDS is characterized by widespread aberrant epigenetic changes in the bone marrow microenvironment. Our results also demonstrate that DNMT inhibitors can alter the epigenomic profiles of stromal cells, and we hypothesize that those stroma effects contribute in part to their clinical efficacy. Overall, these studies underscore the importance of studying the entire bone marrow, including the microenvironment, if we are to improve our understanding of the pathophysiology of MDS and further improve therapy.