nt. However, due partly to the heterogeneity between tumors, identifying robust biomarkers and functionally linking cancer genes to drug sensitivity has been challenging. Nonetheless, catalogues describing the molecular changes Factor Xa review in the major tumor types, currently emerging from sequencing efforts, will theoretically enable systematic studies into the molecular aberrations underpinning treatment response 4, 6, 7. Another important objective of cancer research is to develop new anti-cancer treatments with increased specificity for cancer cells. For example, the monoclonal antibody Trastuzumab directly targets HER2/NEU-positive breast cancer and BRAF kinase inhibitors have recently shown promise in melanoma carrying BRAF mutations 8, 9. However, it is not Correspondence: snijmancemm.oeaw.ac.at.
These authors contributed equally to this work AUTHOR CONTRIBUTIONS S.M.N and M.K.M. conceived the study, designed experiments, analyzed data and wrote the manuscript. M.K.M. and S.M.N. with help from I.Z.U. Fingolimod 162359-56-0 and N.-M. and set up the multiplexing assay. B.V.G., I.Z.U and M.K.M. created and characterized the isogenic cell lines. J.C. and G.D. designed the analysis platform and database infrastructure for the screen. G.D. and M.K.M. analyzed the screening data and wrote R code to identify hits. M.K.M. performed the majority of experiments. C.K., M.S., H.L. and S.M.N. performed and helped with additional experiments. COMPETING FINANCIAL INTERESTS The authors declare no competing financial interests. UKPMC Funders Group Author Manuscript Nat Chem Biol. Author manuscript, available in PMC 2012 May 1.
Published in final edited form as: Nat Chem Biol. , 7 : 787�?93. doi:10.1038/nchembio.695. UKPMC Funders Group Author Manuscript UKPMC Funders Group Author Manuscript often possible to directly translate known molecular aberrations of cancer cells into targeted therapies. For instance, the oncogenic transcription factor c-MYC is overexpressed in a variety of malignancies, but because it lacks critical hydrophobic pockets it is challenging to target by small-molecule compounds 10, 11. Alternative approaches for identifying drugs that specifically target cancer cells are urgently needed. The molecular changes that occur in cancer cells can result in a dependency on gene products that are not essential in normal cells 12-14.
Inhibition of these proteins would thus result in cell cycle arrest or death of the cancer cell but would not affect fitness of their normal counterparts. This notion, which is termed synthetic sickness or lethality, induced essentiality or non-oncogene addiction, provides a framework to identify drugs that do not target the cancer gene directly yet are specific for cells that contain the aberration. Indeed, the observation that cells containing BRCA mutations are hypersensitive to inhibition of the enzyme PARP has found its way into the clinic and represents the paradigm for synthetic lethality-based therapy 15, 16. However, there are currently only a few cancer-relevant synthetic-lethal interactions that have been identified 17. Thus, a systematic analysis of the effect of individual cancer genes on the cellular response to existing and experimental drugs may identify new targeted anti-cancer therapies directly relevant for the clinic.
The challenge of such a systematic approach is the large number of combinations among drugs and genes that would have to be analyzed. The promise of insight into drug actions as exemplified by similar screens in model organisms, most notably yeast, warrants development of suitable methods in human cells 18, 19. We developed a method to multiplex cellular fitness measurements of up to one hundred isogenic cell lines using molecular barcodes to facilitate the quantitative assessment of functional drug-gene