Improved detection of synthetic lethal interactions in Drosophila cells using variable dose analysis (VDA).
Benjamin E HousdenZhongchi LiColleen KelleyYuanli WangYanhui HuAlexander J ValvezanBrendan D ManningNorbert PerrimonPublished in: Proceedings of the National Academy of Sciences of the United States of America (2017)
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.
Keyphrases
- induced apoptosis
- drug administration
- genome wide
- high throughput
- cell cycle arrest
- single cell
- stem cells
- endoplasmic reticulum stress
- signaling pathway
- oxidative stress
- emergency department
- gene expression
- dna methylation
- cell death
- cell proliferation
- risk assessment
- drug induced
- high resolution
- bone marrow
- pi k akt
- label free
- human health
- tandem mass spectrometry
- genome wide identification