Improved detection of synthetic lethal interactions in Drosophila cells using variable dose analysis (VDA)

Proc Natl Acad Sci U S A. 2017 Dec 12;114(50):E10755-E10762. doi: 10.1073/pnas.1713362114. Epub 2017 Nov 28.

Abstract

Synthetic sick or synthetic lethal (SS/L) screens are a powerful way to identify candidate drug targets to specifically kill tumor cells, but this approach generally suffers from low consistency between screens. We found that many SS/L interactions involve essential genes and are therefore detectable within a limited range of knockdown efficiency. Such interactions are often missed by overly efficient RNAi reagents. We therefore developed an assay that measures viability over a range of knockdown efficiency within a cell population. This method, called Variable Dose Analysis (VDA), is highly sensitive to viability phenotypes and reproducibly detects SS/L interactions. We applied the VDA method to search for SS/L interactions with TSC1 and TSC2, the two tumor suppressors underlying tuberous sclerosis complex (TSC), and generated a SS/L network for TSC. Using this network, we identified four Food and Drug Administration-approved drugs that selectively affect viability of TSC-deficient cells, representing promising candidates for repurposing to treat TSC-related tumors.

Keywords: Drosophila; RNAi; drug target discovery; high-throughput screening; synthetic lethality.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Drosophila / genetics*
  • Drosophila Proteins / genetics
  • Drug Delivery Systems
  • Drug Screening Assays, Antitumor / methods*
  • Epistasis, Genetic*
  • Gene Regulatory Networks
  • Genes, Essential
  • Genes, Lethal*
  • Genes, Tumor Suppressor*
  • Humans
  • RNA Interference*
  • Tumor Cells, Cultured

Substances

  • Drosophila Proteins
  • TSC1 protein, Drosophila