Parallel in vivo and in vitro melanoma RNAi dropout screens reveal synthetic lethality between hypoxia and DNA damage response inhibition

Cell Rep. 2014 Nov 20;9(4):1375-86. doi: 10.1016/j.celrep.2014.10.024. Epub 2014 Nov 6.


To identify factors preferentially necessary for driving tumor expansion, we performed parallel in vitro and in vivo negative-selection short hairpin RNA (shRNA) screens. Melanoma cells harboring shRNAs targeting several DNA damage response (DDR) kinases had a greater selective disadvantage in vivo than in vitro, indicating an essential contribution of these factors during tumor expansion. In growing tumors, DDR kinases were activated following hypoxia. Correspondingly, depletion or pharmacologic inhibition of DDR kinases was toxic to melanoma cells, including those that were resistant to BRAF inhibitor, and this could be enhanced by angiogenesis blockade. These results reveal that hypoxia sensitizes melanomas to targeted inhibition of the DDR and illustrate the utility of in vivo shRNA dropout screens for the identification of pharmacologically tractable targets.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cell Hypoxia / drug effects
  • Cell Proliferation / drug effects
  • Checkpoint Kinase 1
  • Checkpoint Kinase 2 / metabolism
  • DNA Damage*
  • DNA Repair* / drug effects
  • Genetic Testing*
  • HEK293 Cells
  • Humans
  • Hypoxia-Inducible Factor 1, alpha Subunit / metabolism
  • Melanoma / genetics*
  • Melanoma / pathology*
  • Mice
  • Protein Kinase Inhibitors / pharmacology
  • Protein Kinases / metabolism
  • Protein Stability / drug effects
  • RNA Interference* / drug effects
  • RNA, Small Interfering / metabolism
  • Reproducibility of Results
  • Signal Transduction / drug effects
  • Tumor Cells, Cultured
  • Xenograft Model Antitumor Assays


  • Hypoxia-Inducible Factor 1, alpha Subunit
  • Protein Kinase Inhibitors
  • RNA, Small Interfering
  • Protein Kinases
  • Checkpoint Kinase 2
  • Checkpoint Kinase 1

Associated data

  • GEO/GSE61826