Accumulating evidence indicates that altered
miRNA expression is crucially involved in
lung cancer development, though scant information is available regarding how MYC, an archetypical oncogene, is regulated by
miRNAs, especially via a mechanism involving MYC cofactors. In this study, we attempted to identify
miRNAs involved in regulation of MYC transcriptional activity in
lung cancer. To this end, we utilized an integrative approach with combinatorial usage of
miRNA and
mRNA expression profile datasets of patient
tumor tissues, as well as those of MYC-inducible cell lines in vitro. In addition to
miRNAs previously reported to be directly regulated by MYC, including let-7 and miR-17-92, our strategy also helped to identify miR-342-3p as capable of indirectly regulating MYC activity via direct repression of E2F1, a MYC-cooperating molecule. Furthermore, miR-342-3p module activity, which we defined as a gene set reflecting the experimentally substantiated influence of miR-342-3p on
mRNA expression, was found to be inversely correlated with MYC activity reflected by MYC module activity in three independent datasets of
lung adenocarcinoma patients obtained from the Director's Challenge Consortium of the United States (P = 1.94 × 10(-73)), the National
Cancer Center of Japan (P = 9.05 × 10(-34)) and the present study (P = 1.17 × 10(-19)). Our integrative approach appears to be useful to elucidate inter-regulatory relationships between
miRNAs and
protein coding genes of interest, even those present in patient
tumor tissues, which remains a challenge to better understand the pathogenesis of this devastating disease.