Systems analysis of quantitative shRNA-library screens identifies regulators of cell adhesion

XiaoDong Huang¹^,2^,5 , Jean YJ Wang¹^,2^,3 and Xin Lu²^,4^,6

¹Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093, USA

²Moores Cancer Center, University of California at San Diego, La Jolla, CA 92093, USA

³Division of Hematology/Oncology, Department of Medicine, School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA

⁴Department of Family and Preventive Medicine, University of California at San Diego, La Jolla, CA 92093, USA

⁵Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA

⁶Abbott Laboratories, 100 Abbott Park Rd, North Chicago, IL 60063, USA

author email corresponding author email

BMC Systems Biology 2008, 2:49doi:10.1186/1752-0509-2-49


Published:	13 June 2008

Abstract

Background

High throughput screens with RNA interference technology enable loss-of-function analyses of gene activities in mammalian cells. While the construction of genome-scale shRNA libraries has been successful, results of large-scale screening of those libraries can be difficult to analyze because of the relatively high noise levels and the fact that not all shRNAs in a library are equally effective in silencing gene expression.

Results

We have screened a library consisting of 43,828 shRNAs directed against 8,500 human genes for functions that are necessary in cell detachment induced by a constitutively activated c-Abl tyrosine kinase. To deal with the issues of noise and uncertainty of knockdown efficiencies, we employed an analytical strategy that combines quantitative data analysis with biological knowledge, i.e. Gene Ontology and pathway information, to increase the power of the RNAi screening technique. Using this strategy we found 16 candidate genes to be involved in Abl-induced disruption of cell adhesion, and verified that the knockdown of IL6ST is associated with enhanced cell attachment.

Conclusion

Our results suggest that the power of genome-wide quantitative shRNA screens can be significantly increased when analyzed using a systems biology-based approach to identify functional gene networks.