Genome-wide pharmacologic unmasking identifies tumor suppressive microRNAs in multiple myeloma

// Chonglei Bi 1,2 , Tae-Hoon Chung 1 , Gaofeng Huang 1 , Jianbiao Zhou 1 , Junli Yan 1 , Gregory J. Ahmann 3 , Rafael Fonseca 3 and Wee Joo Chng 1,2,4 1 Experimental Therapeutics, Cancer Science Institute of Singapore, Singapore 2 Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 3 Mayo Clinic, Scottsdale, Arizona, USA 4 Department of Hematology-Oncology, National University Cancer Institute, National University Health System, Singapore Correspondence to: Wee Joo Chng, email: // Keywords : tumor suppressor, epigenetics, microRNA, myeloma Received : April 16, 2015 Accepted : June 25, 2015 Published : July 03, 2015 Abstract Epigenetic alterations have emerged as an important cause of microRNA (miRNA) deregulation. In Multiple Myeloma (MM), a few tumor suppressive miRNAs silenced by DNA hypermethylation have been reported, but so far there are few systemic investigations on epigenetically silenced miRNAs. We conducted genome-wide screening for tumor suppressive miRNAs epigenetically silenced in MM. Four Human MM Cell lines were treated with demethylating agent 5’azacytidine (5’aza). Consistently upregulated miRNAs include miR-155, miR-198, miR-135a*, miR-200c, miR-125a-3p, miR-188-5p, miR-483-5p, miR-663, and miR-630. Methylation array analysis revealed increased methylation at or near miRNA-associated CpG islands in MM patients. Ectopic restoration of miR-155, miR-198, miR-135a*, miR-200c, miR-663 and miR-483-5p significantly repressed MM cell proliferation, migration and colony formation. Furthermore, we derived a 33-gene signature from predicted miRNA target genes that were also upregulated in MM patients and associated with patient survival in three independent myeloma datasets. In summary, we have revealed important, epigenetically silenced tumor suppressive miRNAs by pharmacologic reversal of epigenetic silencing.