Fig. 1: High-throughput stepwise DNA methylation changes in BM-derived MSCs associated with MM progression.

A Workflow depicting the methodological approach for selecting DNA methylation changes in bone marrow-derived mesenchymal stromal cells (BM-MSCs) from monoclonal gammopathy of undetermined significance (MGUS; n = 10), smoldering myeloma (SMM; n = 8), and multiple myeloma (MM; n = 9) patients versus healthy controls (HD; n = 8). An example of a CpG site experiencing increased mean (differentially methylated position, DMP) or variance (differentially variable position, DVP) in the disease versus the control condition is shown. Venn diagrams show the number of DMPs or DVPs resulting from each comparison. B Distribution of DNA methylation changes in relation to CpG islands (CGI), including shores (south, S; north, N), shelves (south, S; north, N), and open sea regions for differentially hyper- or hypomethylated CpG sites. C Enrichment analysis of differentially hyper- and hypomethylated CpG sites located in different genomic regions, annotated by 15 chromHMM states. Color scale refers to log odd ratio and circle size refers to p-value significance. D Bubble plot representation of HOMER transcription factor (TF) motif enrichment analysis of differentially hyper- and hypomethylated CpGs in MSCs during MM progression (left and right panel, respectively). Color range depicts different transcription factor families and circle size refers to p-value significance. E Box plots showing β-values from DMPs obtained from the EPIC array in MSCs from healthy donors and MGUS, SMM, and MM patients of relevant genes involved in the pathogenesis of MM and associated bone disease. HD is represented in dark blue, MGUS in light blue, SMM in orange, and MM in red. eBayes-moderated ANOVA t-test was performed to calculate statistical significance (*p < 0.05, **p < 0.01, and ***p < 0.005).