miR-106b-responsive gene landscape identifies regulation of Kruppel-like factor family

Abstract

List of abbreviations:3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide, MTT; 4′,6-diamidine-2′phenylindole dihydrochloride, DAPI; Crosslinking, ligation, and sequencing of hybrids, CLASH;Death receptor-5, DR5; Dulbecco's Modified Eagle's Medium, DMEM; False discovery rate, FDR; Fetal bovine serum, FBS; Kruppel-like factor, KLF; Locked-nucleic acid, LNA;Quantitative reverse-transcription PCR, qRT-PCR; Sodium dodecylsulfate-polyacrylamide gel electrophoresis, SDS-PAGE; Untranslated region, UTR; miR-106b-responsive gene landscape identifies regulation of Kruppel-like factor familyAbstract: MicroRNA dysregulation is a common feature of cancer and due to the promiscuity of microRNA binding this can result in a wide array of genes whose expression is altered. miR-106b is an oncomiR overexpressed in cholangiocarcinoma and its upregulation in this and other cancers often leads to repression of anti-tumorigenic targets. The goal of this study was to identify the miR-106b-regulated gene landscape in cholangiocarcinoma cells using a genomewide, unbiased mRNA analysis. Through RNA-Seq we found 112 mRNAs significantly repressed by miR-106b. The majority of these genes contain the specific miR-106b seedbinding site. We have validated 11 genes from this set at the mRNA level and demonstrated regulation by miR-106b of five proteins. Combined analysis of our miR-106b-regulated mRNA data set plus published reports indicate that miR-106b binding is anchored by G:C pairing in and near the seed. Novel targets Kruppel-like factor 2 (KLF2) and KLF6 were verified both at the mRNA and at the protein level. Further investigation showed regulation of four other KLF family members by miR-106b. We have discovered coordinated repression of several members of the KLF family by miR-106b that may play a role in cholangiocarcinoma tumor biology.