Global miRNA expression analysis identifies novel key regulators of plasma cell differentiation and malignant plasma cell

Background: MicroRNAs (miRNAs) are small noncoding RNAs that attenuate expression of their mRNA targets. miRNAs have been involved in fine-tuning critical biological processes, but the potential contribution of miRNAs to human plasma cell differentiation (PCD) has remained largely unknown. Methods: We analyzed the expression profile of miRNAs and mRNAs during PCD. We developed a method and R package, to infer candidate miRNA-mRNA target interactions that could be active and functional in PCD. Finally, we experimentally validated biologically relevant miRNA – mRNA networks. Results: Our results reveal 63 miRNAs with significant temporal changes in their expression during normal PCD. We derived a high-confidence network of 295 target relationships comprising 47 miRNAs and 141 targets. These relationships include new examples of miRNAs (miR-30, miR-106b and miR-16) that appear to coordinately regulate multiple members of critical pathways associated with PCD, including IRF4/PRDM1 axis, TGF-b pathway, autophagy, ZBTB4/EZH2 axis and cell cycle. Consistent with this, we have experimentally validated a role for the miRNA-30b/c/d-mediated regulation of key PCD factors (IRF4, PRDM1, ELL2 and ARID3A), which expression was altered significantly upon transfection of pre-miRNA-30 or anti-miR-30 oligunucleotides. Furthermore, we found that 24 PCD stage-specific miRNAs are aberrantly overexpressed in multiple myeloma (MM) tumor cells compared to their normal counterpart and/or are associated with high risk myeloma, suggesting that MM cells frequently acquired expression changes in miRNAs already undergoing dynamic expression modulation during normal PCD. Conclusions: Our comprehensive analysis of normal PCD miRNome identifies candidate novel key miRNAs regulating networks of significance for normal PCD and malignant plasma cell biology. Global miRNA expression profiling was carried out for in vitro human plasma cell differentiation cell subpopulations, including memory B cells, preplasmablasts, plasmablasts and plasma cells.