title: An arrayed RNA interference genome-wide screen identifies candidate genes involved in the MicroRNA 21 biogenesis pathway.
abstract: MicroRNAs (miRNAs) are evolutionary conserved noncoding molecules that regulate gene expression. They influence a number of diverse biological functions, such as development and differentiation. However, their dysregulation has been shown to be associated with disease states, such as cancer. Genes and pathways regulating their biogenesis remain unknown and are highly sought after. For this purpose, we have validated a multiplexed high-content assay strategy to screen for such modulators. Here, we describe its implementation that makes use of a cell-based gain-of-function reporter assay monitoring enhanced green fluorescent protein expression under the control of miRNA 21 (miR-21); combined with measures of both cell metabolic activities through the use of Alamar Blue and cell death through imaged Hoechst-stained nuclei. The strategy was validated using a panel of known genes and enabled us to successfully progress to and complete an arrayed genome-wide short interfering RNA (siRNA) screen against the Ambion Silencer Select v4.0 library containing 64,755 siRNA duplexes covering 21,565 genes. We applied a high-stringency hit analysis method, referred to as the Bhinder-Djaballah analysis method, leading to the nomination of 1,273 genes as candidate inhibitors of the miR-21 biogenesis pathway; after several iterations eliminating those genes with only one active duplex and those enriched in seed sequence mediated off-target effects. Biological classifications revealed four major control junctions among them vesicular transport via clathrin-mediated endocytosis. Altogether, our screen has uncovered a number of novel candidate regulators that are potentially good druggable targets allowing for the discovery and development of small molecules for regulating miRNA function.
authors.affiliation: High-Throughput Screening Core Facility, Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA.
authors.forename: David
authors.initials: D
authors.lastname: Shum
authors.forename: Bhavneet
authors.initials: B
authors.lastname: Bhinder
authors.forename: Christina N
authors.initials: CN
authors.lastname: Ramirez
authors.forename: Constantin
authors.initials: C
authors.lastname: Radu
authors.forename: Paul A
authors.initials: PA
authors.lastname: Calder
authors.forename: Lesslie
authors.initials: L
authors.lastname: Beauchamp
authors.forename: T
authors.initials: T
authors.lastname: Farazi
authors.forename: M
authors.initials: M
authors.lastname: Landthaler
authors.forename: T
authors.initials: T
authors.lastname: Tuschi
authors.forename: Susan
authors.initials: S
authors.lastname: Magdaleno
authors.forename: Hakim
authors.initials: H
authors.lastname: Djaballah
mesh_terms: D000465:Algorithms; D001331:Automation; D002478:Cells, Cultured; D004396:Coloring Agents; D015723:Gene Library; D018390:Gene Targeting; D049452:Green Fluorescent Proteins; D057166:High-Throughput Screening Assays; D006801:Humans; D007091:Image Processing, Computer-Assisted; D035683:MicroRNAs / Q000096:biosynthesis* / Q000187:drug effects / Q000235:genetics*; D010078:Oxazines; D016133:Polymerase Chain Reaction; D034622:RNA Interference; D034741:RNA, Small Interfering / Q000235:genetics; D015203:Reproducibility of Results; D014966:Xanthenes
chemical_list: D004396:Coloring Agents; C524940:MIRN21 microRNA, human; D035683:MicroRNAs; D010078:Oxazines; D034741:RNA, Small Interfering; D014966:Xanthenes; D049452:Green Fluorescent Proteins; C005843:resazurin