Title:Modulators of the microRNA Biogenesis Pathway via Arrayed Lentiviral Enabled RNAi Screening for Drug and Biomarker Discovery
VOLUME: 16 ISSUE: 10
Author(s):David Shum, Bhavneet Bhinder and Hakim Djaballah
Affiliation:HTS Core Facility, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA.
Keywords:BDA method, biogenesis, biomarker, diagnostics, DROSHA, H score, HCA, HCS, miRNA 21, miRNA, RNAi,
shRNA.
Abstract:MicroRNAs (miRNAs) are small endogenous and conserved non-coding RNA molecules that regulate gene
expression. Although the first miRNA was discovered well over sixteen years ago, little is known about their biogenesis
and it is only recently that we have begun to understand their scope and diversity. For this purpose, we performed an
RNAi screen aimed at identifying genes involved in their biogenesis pathway with a potential use as biomarkers. Using a
previously developed miRNA 21 (miR-21) EGFP-based biosensor cell based assay monitoring green fluorescence
enhancements, we performed an arrayed short hairpin RNA (shRNA) screen against a lentiviral particle ready TRC1
library covering 16,039 genes in 384-well plate format, and interrogating the genome one gene at a time building a
panoramic view of endogenous miRNA activity. Using the BDA method for RNAi data analysis, we nominate 497 gene
candidates the knockdown of which increased the EGFP fluorescence and yielding an initial hit rate of 3.09%; of which
only 22, with reported validated clones, are deemed high-confidence gene candidates. An unexpected and surprising result
was that only DROSHA was identified as a hit out of the seven core essential miRNA biogenesis genes; suggesting that
perhaps intracellular shRNA processing into the correct duplex may be cell dependent and with differential outcome.
Biological classification revealed several major control junctions among them genes involved in transport and vesicular
trafficking. In summary, we report on 22 high confidence gene candidate regulators of miRNA biogenesis with potential
use in drug and biomarker discovery.
