Dysregulated Mirnas after Uniform Treatment Predict Outcome of Newly-Diagnosed Multiple Myeloma

Multiple myeloma (MM) is a malignancy of the plasma cell in which clonal plasma cells infiltrate the bone marrow. Although increasingly effective treatment has significantly improved management of the disease, most MM patients ultimately relapse. Previous studies suggest that miRNA expression patterns may function as biomarkers for diagnosis, subtyping, and prognosis of the disease. However, the role of miRNAs in MM relapse and prognosis is not sufficiently understood. Therefore, in this study, we sought to understand the biological and prognostic role of dysregulated miRNAs between newly diagnosed and relapsed MM.

We performed RNA-seq as well as microarray-based miRNA profiling on 319 MM samples from newly diagnosed MM patients enrolled in the 2009 IFM/DFCI clinical trial. This included 40 samples from patients with paired samples from diagnosis and at relapse while we had additional 239 samples collected at the time of diagnosis.

Using the 40 diagnosis-relapse paired samples, we identified 48 miRNAs that are differentially expressed between diagnosis and relapse (FDR < 0.15). Of these 48 miRNAs, we found five miRNAs (miR-4484, miR-663b, miR-3687, miR-670-5p, miR-4417) whose expression level at diagnosis, expression level at relapse, and log2FC from diagnosis to relapse were significantly associated with overall survival or progression-free survival among the 40 patients with paired samples (p < 0.05). We next investigated the prognostic role of these five miRNAs through unsupervised hierarchical clustering of 239 independent, newly diagnosed MM samples. The two groups identified by the unsupervised hierarchical clustering differed significantly in both overall survival (log rank test, p = 0.009) and progression-free survival (log rank test, p = 0.012), suggesting that these five miRNAs are predictive of disease prognosis.

We then performed an integrative analysis of the miRNA and mRNA expression data in our cohort of newly diagnosed samples and identified the potential protein-coding target genes of these five miRNAs. We further filtered the target gene list using TargetScan which predicts the biological targets of miRNAs by searching for the presence of conserved 8mer, 7mer, and 6mer sites that match the seed region of each miRNA. After filtering the target genes, we found that each miRNA targets 126 mRNAs [range 26 - 258] and key MM genes, including MAF, BCL2, 14-3-3 and MYEOV, were among the top candidates. The target genes of these select miRNAs are involved in such biological pathways as NF-kB signaling, antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, and positive regulation of cell death and apoptosis.

In conclusion, this integrative analysis of miRNA and mRNA expression data from uniformly treated MM samples offers a unique perspective on the role of miRNAs in MM biology and prognosis. The study identified five miRNAs that target key MM genes, play a role in the biological processes associated with MM progression, and carry prognostic information predictive of overall and progression-free survival with prospect for future therapeutic application.