Multiplex cytological profiling assay to measure diverse

PLoS ONE

Volumn 8, Issue 12, 2013, Pages

  States, Cellular ^a   Gustafsdottir, Sigrun M ^a   Ljosa, Vebjorn ^a   Sokolnicki, Katherine L ^a,b   Wilson, J Anthony ^a,c   Walpita, Deepika ^a   Kemp, Melissa M ^a   Seiler, Kathleen Petri ^a,d   Carrel, Hyman A ^a,e   Golu, Todd R ^a   Schreiber, Stuart L ^a   Clemons, Paul A ^a   Carpenter, Anne E ^a   Shamji, Alykhan F ^a  

^a BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^b inviCRO   (United States)

^c WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d CHAMPLAIN COLLEGE   (United States)

^e ModuleQ   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CELL ASSAY; CELL COMPONENT; CELL MEMBRANE; CELL NUCLEUS; CELL STRUCTURE; CHEMICAL STRUCTURE; CYTOLOGY; ENDOPLASMIC RETICULUM; GOLGI COMPLEX; HUMAN; HUMAN CELL; IMAGE ANALYSIS; MITOCHONDRION; MULTIPLEX CYTOLOGICAL PROFILING ASSAY; NUCLEOLUS; PHENOTYPE; PROTEIN TARGETING;

CELL LINE, TUMOR; FLUORESCENT DYES; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED;

EID: 84891388151     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0080999     Document Type: Article

References (24)

1. Stegmaier K, Wong JS, Ross KN, Chow KT, Peck D et al. (2007) Signature-based small molecule screening identifies cytosine arabinoside as an EWS/FLI modulator in Ewing sarcoma. PLoS Med 4: e122. doi:10.1371/journal.pmed. 0040122. PubMed: 17425403.
2. Lamb J, Crawford ED, Peck D, Modell JW, Blat IC et al. (2006) The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science 313: 1929-1935. doi:10.1126/science.1132939. PubMed: 17008526. (Pubitemid 44497995)
3. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 102: 15545-15550. doi:10.1073/pnas.0506580102. PubMed: 16199517. (Pubitemid 41528093)
4. Adams CL, Kutsyy V, Coleman DA, Cong G, Crompton AM et al. (2006) Compound classification using image-based cellular phenotypes. Methods Enzymol 414: 440-468. doi:10.1016/S0076-6879(06)14024-0. PubMed: 17110206. (Pubitemid 44716236)
5. Tanaka M, Bateman R, Rauh D, Vaisberg E, Ramachandani S et al. (2005) An unbiased cell morphology-based screen for new, biologically active small molecules. PLoS Biol 3: e128. doi:10.1371/journal.pbio.0030128. PubMed: 15799708.
6. Carpenter AE, Jones TR, Lamprecht MR, Clarke C, Kang IH et al. (2006) CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol 7: R100. doi:10.1186/ gb-2006-7-10-r100. PubMed: 17076895.
7. Jones TR, Carpenter AE, Lamprecht MR, Moffat J, Silver SJ et al. (2009) Scoring diverse cellular morphologies in image-based screens with iterative feedback and machine learning. Proc Natl Acad Sci U S A 106: 1826-1831. doi:10.1073/pnas.0808843106. PubMed: 19188593.
8. Feng Y, Mitchison TJ, Bender A, Young DW, Tallarico JA (2009) Multiparameter phenotypic profiling: using cellular effects to characterize small-molecule compounds. Nat Rev Drug Discov 8: 567-578. doi: 10.1038/nrd2876. PubMed: 19568283.
9. Futamura Y, Kawatani M, Kazami S, Tanaka K, Muroi M et al. (2012) Morphobase, an encyclopedic cell morphology database, and its use for drug target identification. Chem Biol 19: 1620-1630. PubMed: 23261605.
10. Ljosa V, Caie PD, Ter Horst R, Sokolnicki KL, Jenkins EL et al. (. (2013)) Comparison of methods for image-based profiling of cellular morphological responses to small-molecule treatment. Nature Methods, 18: 1321-9. PubMed: 24045582.
11. Loo L-H, Wu LF, Altschuler SJ (2007) Image-based multivariate profiling of drug responses from single cells. Nat Methods 4: 445-453. PubMed: 17401369. (Pubitemid 46901279)
12. Perlman ZE, Slack MD, Feng Y, Mitchison TJ, Wu LF et al. (2004) Multidimensional drug profiling by automated microscopy. Science 306: 1194-1198. doi:10.1126/science.1100709. PubMed: 15539606. (Pubitemid 39489001)
13. Young DW, Bender A, Hoyt J, McWhinnie E, Chirn G-W et al. (2008) Integrating high-content screening and ligand-target prediction to identify mechanism of action. Nat Chem Biol 4: 59-68. doi:10.1038/nchembio.2007.53. PubMed: 18066055. (Pubitemid 350273652)
14. Roberts JR, Allison DC, Donehower RC, Rowinsky EK (1990) Development of Polyploidization in Taxol-resistant Human Leukemia Cells in Vitro. Cancer Res 50: 710-716. PubMed: 1967550. (Pubitemid 20054203)
15. Yvon AM, Wadsworth P, Jordan MA (1999) Taxol suppresses dynamics of individual microtubules in living human tumor cells. Mol Biol Cell 10: 947-959. doi:10.1091/mbc.10.4.947. PubMed: 10198049. (Pubitemid 29193723)
16. Knox C, Law V, Jewison T, Liu P, Ly S, Frolkis A, Pon A, Banco K, Mak C, Neveu V, Djoumbou Y, Eisner R, Guo AC, Wishart DS (2011) DrugBank 3.0: a comprehensive resource for 'omics' research on drugs. Nucleic Acids Res 39: D1035-1041
17. Marceau F, Bawolak M-T, Lodge R, Bouthillier J, Gagné-Henley A et al. (2012) Cation trapping by cellular acidic compartments: beyond the concept of lysosomotropic drugs. Toxicol Appl Pharmacol 259: 1-12. doi:10.1016/j.taap. 2011.12.004. PubMed: 22198553.
18. Badr CE, Wurdinger T, Nilsson J, Niers JM, Whalen M et al. (2011) Lanatoside C sensitizes glioblastoma cells to tumor necrosis factorrelated apoptosis-inducing ligand and induces an alternative cell death pathway. Neuro-Oncology 13: 1213-1224. doi:10.1093/neuonc/nor067. PubMed: 21757445.
19. Riganti C, Campia I, Kopecka J, Gazzano E, Doublier S et al. (2011) Pleiotropic Effects of Cardioactive Glycosides. Curr Med Chem 18: 872-885. doi:10.2174/092986711794927685. PubMed: 21182478.
20. Ljosa V, Carpenter A (2009) Introduction to the Quantitative Analysis of Two-Dimensional Fluorescence Microscopy Images for Cell-Based. Screening-PLOS Comput Biol 5: e1000603.
21. Li F, Yin Z, Jin G, Zhao H, Wong S (2013) Bioimage Informatics for Systems Pharmacology chapter 17. PLOS Comput Biol 9: e1003043
22. Seiler KP, Ga George, Happ MP, Bodycombe NE, Carrinski Ha et al. (2008) ChemBank: a small-molecule screening and cheminformatics resource database. Nucleic Acids Res 36: D351-D359. PubMed: 17947324. (Pubitemid 351149748)
23. Ma Harris, Clark J, Ireland a, Lomax J, Ashburner M, et al. (2004) The Gene Ontology (GO) database and informatics resource. Nucleic acids research 32: D258-261 (Pubitemid 38081651)
24. Petrone PM, Simms B, Nigsch F, Lounkine E, Kutchukian P et al. (2012) Rethinking molecular similarity: comparing compounds on the basis of biological activity. ACS Chem Biol 7: 1399-1409. doi:10.1021/cb3001028. PubMed: 22594495.