A functional genomics screen for microRNA regulators of NF-kappaB signaling

Background: The nuclear factor-KappaB (NF-kappa B) pathway is conserved from fruit flies to humans and is a key mediator of inflammatory signaling. Aberrant regulation of NF-kappa B is associated with several disorders including autoimmune disease, chronic inflammation, and cancer, making the NF-kappa B pathway an attractive therapeutic target. Many regulatory components of the NF-kappa B pathway have been identified, including microRNAs (miRNAs). miRNAs are small non-coding RNAs and are common components of signal transduction pathways. Here we present a cell-based functional genomics screen to systematically identify miRNAs that regulate NF-kappa B signaling. Results: We screened a library of miRNA mimics using a NF-kappa B reporter cell line in the presence and absence of tumor necrosis factor (+/-TNF). There were 9 and 15 hits in the -TNF and +TNF screens, respectively. We identified putative functional targets of these hits by integrating computational predictions with NF-kappa B modulators identified in a previous genome-wide cDNA screen. miR-517a and miR-517c were the top hits, activating the reporter 86- and 126-fold, respectively. Consistent with these results, miR-517a/c induced the expression of endogenous NF-kappa B targets and promoted the nuclear localization of p65 and the degradation of I kappa B. We identified TNFAIP3 interacting protein1 (TNIP1) as a target and characterized a functional SNP in the miR-517a/c binding site. Lastly, miR-517a/c induced apoptosis in vitro, which was phenocopied by knockdown of TNIP1. Conclusions: Our study suggests that miRNAs are common components of NF-kappa B signaling and miR-517a/c may play an important role in linking NF-kappa B signaling with cell survival through TNIP1.