miRNA effects in gene networks
miRNA expression analyses from isolated cells, as well as in tissues from disease models, revealed simultaneously altered expression for several miRNAs. This implicates several parallel regulatory events which are not captured by traditional miRNA-single target gene identification methodologies. Recently, network methods have been utilized to assess the outcome of miRNA-regulation from a global perspective, revealing possible relationships between the miRNA-targets and the affected pathways. An example is the generation of a comprehensive regulatory miRNA-mRNA network of in vitro differentiated type 2 and Th17 cells compared to naive CD4+ T cells. It identified a strong involvement of the miR-106a~363 cluster in Th17 differentiation, with decreases particularly of miR-106a, miR-18b and miR-363 in Th17 cells153. Conversely, overexpression of the aforementioned miRNAs led to decreased expression of their confirmed target genes Nuclear Factor of Activated T cells (Nfat5 ), RAR related Orphan Receptor C (Rorc), andRora ; leading to decreased Th17 differentiation and IL-17 secretion and identifying this miRNA cluster as a potential target for Th17-mediated inflammation. Th17 cell differentiation is also controlled by the miR-17~92 cluster, in particular by miR-18a154, which targets Smad4, hypoxia-inducible factor 1a (Hif1a), and Rora. Thus, miR-18a deficiency enhances Th17 differentiation in vitro and increases Th17 cells in tissue in experimental asthma models in vivo .
Another approach identified a distinct miRNA-expression pattern in tissue resident type 2 cells in experimental allergic asthma. CD4+ type 2 cells displayed a strong downregulation of miRNAs compared to naïve CD4+ T cells155 and the expression pattern changed with the transition from acute to chronic airway inflammation. Integrating gene- and miRNA-expression using a network approach, revealed distinct disease stage specific gene-miRNA networks155. Pathogenic type 2 responses resulted from combined and cumulative activities of miRNAs, integrating the net effect of induced miR-27b and miR-23b, targeting immune regulatory Tgfb1 and Egfr pathways on the one hand. On the other side, silenced miRNA activity (miR-206, miR-106b and miR-203), allowed the expression of genes involved in immune activation. Antagonizing the ex vivo miRNA-expression levels using miRNA-inhibitors and mimics suppressed IL-13 expression in Th2 cells.