Whole-epigenome analysis in multiple myeloma reveals DNA hypermethylation of B cell-specific enhancers

Xabier Agirre, Giancarlo Castellano, Marien Pascual, Simon Heath, Marta Kulis, Victor Segura, Anke Bergmann, Anna Esteve, Angelika Merkel, Emanuele Raineri, Lidia Agueda, Julie Blanc, David Richardson, Laura Clarke, Avik Datta, Nuria Russiñol, Ana C. Queirós, Renée Beekman, Juan R. Rodríguez-Madoz, Edurne San José-Enériz, Fang Fang, Norma C. Gutiérrez, José M. García-Verdugo, Michael I. Robson, Eric C. Schirmer, Elisabeth Guruceaga, Joost H.A. Martens, Marta Gut, Maria J. Calasanz, Paul Flicek, Reiner Siebert, Elías Campo, Jesús F. San Miguel, Ari Melnick, Hendrik G. Stunnenberg, Ivo G. Gut, Felipe Prosper, José I. Martín-Subero

While analyzing the DNA methylome of multiple myeloma (MM), a plasma cell neoplasm, by whole-genome bisulfite sequencing and high-density arrays, we observed a highly heterogeneous pattern globally characterized by regional DNA hypermethylation embedded in extensive hypomethylation. In contrast to the widely reported DNA hypermethylation of promoter-associated CpG islands (CGIs) in cancer, hypermethylated sites in MM, as opposed to normal plasma cells, were located outside CpG islands and were unexpectedly associated with intronic enhancer regions defined in normal B cells and plasma cells. Both RNA-seq and in vitro reporter assays indicated that enhancer hypermethylation is globally associated with downregulation of its host genes. ChIP-seq and DNase-seq further revealed that DNA hypermethylation in these regions is related to enhancer decommissioning. Hypermethylated enhancer regions overlapped with binding sites of B cell-specific transcription factors (TFs) and the degree of enhancer methylation inversely correlated with expression levels of these TFs in MM. Furthermore, hypermethylated regions in MM were methylated in stem cells and gradually became demethylated during normal B-cell differentiation, suggesting that MM cells either reacquire epigenetic features of undifferentiated cells or maintain an epigenetic signature of a putative myeloma stem cell progenitor. Overall, we have identified DNA hypermethylation of developmentally-regulated enhancers as a new type of epigenetic modification associated with the pathogenesis of MM.