Modulators of the microRNA biogenesis pathway via arrayed lentiviral enabled RNAi screening for drug and biomarker discovery Journal Article


Authors: Shum, D.; Bhinder, B.; Djaballah, H.
Article Title: Modulators of the microRNA biogenesis pathway via arrayed lentiviral enabled RNAi screening for drug and biomarker discovery
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.
Keywords: proteins; biomarker; resistance; biogenesis; breast-cancer; expression; cells; complex; rnai; mirna; diagnostics; roles; drosha; shrna; bda method; h score; hcs; hca; mirna 21; impairs
Journal Title: Combinatorial Chemistry and High Throughput Screening
Volume: 16
Issue: 10
ISSN: 1386-2073
Publisher: Bentham Science Publishers  
Date Published: 2013-12-01
Start Page: 791
End Page: 805
Language: English
ACCESSION: WOS:000327439500006
PROVIDER: wos
PMCID: PMC3884689
PUBMED: 23977983
DOI: 10.2174/1386207311301010004
Notes: Article -- Source: Wos
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  1. Bhavneet Bhinder
    31 Bhinder
  2. Hakim Djaballah
    101 Djaballah
  3. David Shum
    54 Shum