Deducing the mechanism of action of compounds identified in phenotypic screens by integrating their multiparametric profiles with a reference genetic screen

Nature Protocols

Volumn 9, Issue 2, 2014, Pages 474-490

  Sundaramurthy, Varadharajan ^a   Barsacchi, Rico ^a   Chernykh, Mikhail ^a   Stöter, Martin ^a   Tomschke, Nadine ^a   Bickle, Marc ^a   Kalaidzidis, Yannis ^a,b   Zerial, Marino ^a  

^a MAX PLANCK INSTITUTE OF MOLECULAR CELL BIOLOGY AND GENETICS   (Germany)

^b MOSCOW STATE UNIVERSITY   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL BIOLOGY; ENDOCYTOSIS; GENETIC TESTING; HELA CELLS; HUMANS; MYCOBACTERIACEAE; RNA INTERFERENCE; SMALL MOLECULE LIBRARIES;

EID: 84893302643     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2014.027     Document Type: Article

References (37)

1. Collinet, C. et al. Systems survey of endocytosis by multiparametric image analysis. Nature 464, 243-249 (2010).
2. Danuser, G. Computer vision in cell biology. Cell 147, 973-978 (2011).
3. Stockwell, B.R. Chemical genetics: ligand-based discovery of gene function. Nat. Rev. Genet. 1, 116-125 (2000).
4. Bickle, M. The beautiful cell: high-content screening in drug discovery. Anal. Bioanal. Chem. 398, 219-226 (2010).
5. Young, D.W. et al. Integrating high-content screening and ligand-target prediction to identify mechanism of action. Nat. Chem. Biol. 4, 59-68 (2008).
6. Swinney, D.C. & Anthony, J. How were new medicines discovered? Nat. Rev. Drug Discov. 10, 507-519 (2011).
7. Merino, A., Bronowska, A.K., Jackson, D.B. & Cahill, D.J. Drug profling: knowing where it hits. Drug Discov. Today 15, 749-756 (2010).
8. Cong, F., Cheung, A.K. & Huang, S.M. Chemical genetics-based target identifcation in drug discovery. Annu. Rev. Pharmacol. Toxicol. 52, 57-78 (2012).
9. Stockwell, B.R. Exploring biology with small organic molecules. Nature 432, 846-854 (2004).
10. Schenone, M., Dancik, V., Wagner, B.K. & Clemons, P.A. Target identifcation and mechanism of action in chemical biology and drug discovery. Nat. Chem. Biol. 9, 232-240 (2013).
11. Sundaramurthy, V. et al. Integration of chemical and RNAi multiparametric profles identifes triggers of intracellular mycobacterial killing. Cell Host Microbe 13, 129-142 (2013).
12. Kittler, R. et al. Genome-scale RNAi profling of cell division in human tissue culture cells. Nat. Cell Biol. 9, 1401-1412 (2007).
13. Neumann, B. et al. Phenotypic profling of the human genome by time-lapse microscopy reveals cell division genes. Nature 464, 721-727 (2010).
14. Pelkmans, L. et al. Genome-wide analysis of human kinases in clathrin-and caveolae/raft-mediated endocytosis. Nature 436, 78-86 (2005).
15. Paul, P. et al. A Genome-wide multidimensional RNAi screen reveals pathways controlling MHC class II antigen presentation. Cell 145, 268-283 (2011).
16. Yin, Z. et al. A screen for morphological complexity identifes regulators of switch-like transitions between discrete cell shapes. Nat. Cell Biol. 15, 860-871 (2013).
17. WHO. Global Tuberculosis Report. (World Health Organization, 2013).
18. Zumla, A., Nahid, P. & Cole, S.T. Advances in the development of new tuberculosis drugs and treatment regimens. Nat. Rev. Drug Discov. 12, 388-404 (2013).
19. Goodwin, P.J., Meyerhardt, J.A. & Hursting, S.D. Host factors and cancer outcome. J. Clin. Oncol. 28, 4019-4021 (2010).
20. Gutierrez, M.G. et al. Autophagy is a defense mechanism inhibiting BCG and Mycobacterium tuberculosis survival in infected macrophages. Cell 119, 753-766 (2004).
21. Kumar, D. et al. Genome-wide analysis of the host intracellular network that regulates survival of Mycobacterium tuberculosis. Cell 140, 731-743 (2010).
22. Armstrong, J.A. & Hart, P.D. Response of cultured macrophages to Mycobacterium tuberculosis, with observations on fusion of lysosomes with phagosomes. J. Exp. Med. 134, 713-740 (1971).
23. Russell, D.G. Mycobacterium tuberculosis: here today, and here tomorrow. Nat. Rev. Mol. Cell Biol. 2, 569-577 (2001).
24. Jayachandran, R. et al. Survival of mycobacteria in macrophages is mediated by coronin 1-dependent activation of calcineurin. Cell 130, 37-50 (2007).
25. Koul, A., Herget, T., Klebl, B. & Ullrich, A. Interplay between mycobacteria and host signalling pathways. Nat. Rev. Microbiol. 2, 189-202 (2004).
26. Behar, S.M., Divangahi, M. & Remold, H.G. Evasion of innate immunity by Mycobacterium tuberculosis: is death an exit strategy? Nat. Rev. Microbiol. 8, 668-674 (2010).
27. Chen, M., Gan, H. & Remold, H.G. A mechanism of virulence: virulent Mycobacterium tuberculosis strain H37Rv, but not attenuated H37Ra, causes signifcant mitochondrial inner membrane disruption in macrophages leading to necrosis. J. Immunol. 176, 3707-3716 (2006).
28. Keane, J., Remold, H.G. & Kornfeld, H. Virulent Mycobacterium tuberculosis strains evade apoptosis of infected alveolar macrophages. J. Immunol. 164, 2016-2020 (2000).
29. Agaisse, H. et al. Genome-wide RNAi screen for host factors required for intracellular bacterial infection. Science 309, 1248-1251 (2005).
30. Philips, J.A., Rubin, E.J. & Perrimon, N. Drosophila RNAi screen reveals CD36 family member required for mycobacterial infection. Science 309, 1251-1253 (2005).
31. Dhandayuthapani, S. et al. Green fuorescent protein as a marker for gene expression and cell biology of mycobacterial interactions with macrophages. Mol. Microbiol. 17, 901-912 (1995).
32. Carpenter, A.E. et al. CellProfler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol. 7, R100 (2006).
33. Kamentsky, L. et al. Improved structure, function and compatibility for CellProfler: modular high-throughput image analysis software. Bioinformatics 27, 1179-1180 (2011).
34. Berthold, MR et al. KNIME: The Konstanz Information Miner (Springer, 2007).
35. Stoter, M. et al. CellProfler and KNIME: open source tools for high content screening. Methods Mol. Biol. 986, 105-122 (2013).
36. Kittler, R. et al. Genome-wide resources of endoribonuclease-prepared short interfering RNAs for specifc loss-of-function studies. Nat. Methods 4, 337-344 (2007).
37. Huang da, W., Sherman, B.T. & Lempicki, R.A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44-57 (2009).