Complex phenotypic assays in high-throughput screening

Current Opinion in Chemical Biology

Volumn 8, Issue 3, 2004, Pages 334-338

  Clemons, Paul A ^a  

^a HARVARD UNIVERSITY   (United States)

Author keywords

EC; embryonic carcinoma; HCS; high content screening; high throughput screening; HTS; IDF; interdigitated (electrode) fingers; MEF; mouse embryonic fibroblast; pRb; retinoblastoma protein

Indexed keywords

ANALYTIC METHOD; BIOMEDICINE; COMBINATORIAL CHEMISTRY; COMPLEX FORMATION; DATA ANALYSIS; FLUORESCENCE MICROSCOPY; GENETIC ENGINEERING; HIGH THROUGHPUT SCREENING; INFORMATION SCIENCE; MASS SPECTROMETRY; MEDICAL TECHNOLOGY; MEDICINE; NONHUMAN; PHENOTYPE; REVIEW; STRUCTURE ACTIVITY RELATION; VIDEORECORDING; ZEBRA FISH;

COMBINATORIAL CHEMISTRY TECHNIQUES; DRUG DESIGN; DRUG EVALUATION, PRECLINICAL; GENETIC ENGINEERING; MEDICAL INFORMATICS; PATTERN RECOGNITION, AUTOMATED; PHENOTYPE; SPECTROMETRY, FLUORESCENCE;

DANIO RERIO;

EID: 2942616604     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cbpa.2004.04.002     Document Type: Review

References (51)

1. Sundberg S.A. High-throughput and ultra-high-throughput screening: solution- and cell-based approaches. Curr Opin Biotechnol. 11:2000;47-53
2. Khandurina J., Guttman A. Microchip-based high-throughput screening analysis of combinatorial libraries. Curr Opin Chem Biol. 6:2002;359-366
3. Bochner B.R. New technologies to assess genotype-phenotype relationships. Nat Rev Genet. 4:2003;309-314
4. MacRae C.A., Peterson R.T. Zebrafish-based small molecule discovery. Chem Biol. 10:2003;901-908
5. Burbaum J.J., Sigal N.H. New technologies for high-throughput screening. Curr Opin Chem Biol. 1:1997;72-78
6. Silverman L., Campbell R., Broach J.R. New assay technologies for high-throughput screening. Curr Opin Chem Biol. 2:1998;397-403
7. Sittampalam G.S., Kahl S.D., Janzen W.P. High-throughput screening: advances in assay technologies. Curr Opin Chem Biol. 1:1997;384-391
8. Fernandes P.B. Technological advances in high-throughput screening. Curr Opin Chem Biol. 2:1998;597-603
9. Zemanova L., Schenk A., Valler M.J., Nienhaus G.U., Heilker R. Confocal optics microscopy for biochemical and cellular high-throughput screening. Drug Discov Today. 8:2003;1085-1093
10. Eggeling C., Brand L., Ullmann D., Jager S. Highly sensitive fluorescence detection technology currently available for HTS. Drug Discov Today. 8:2003;632-641
11. Engels M.F., Venkatarangan P. Smart screening: approaches to efficient HTS. Curr Opin Drug Discov Devel. 4:2001;275-283
12. Battersby B.J., Trau M. Novel miniaturized systems in high-throughput screening. Trends Biotechnol. 20:2002;167-173
13. Dove A. Drug screening-beyond the bottleneck. Nat Biotechnol. 17:1999;859-863
14. Dove A. Screening for content-the evolution of high throughput. Nat Biotechnol. 21:2003;859-864
15. Brown E.D. Screening in academe: a perspective on implementation of university-based small molecule screening. J Biomol Screen. 8:2003;377-379
16. Schreiber S.L. The small-molecule approach to biology: chemical genetics and diversity-oriented organic synthesis make possible the systematic exploration of biology. Chem Eng News. 81:2003;51-61
17. Stein R.L. High-throughput screening in academia: the Harvard experience. J Biomol Screen. 8:2003;615-619
18. Kamme F., Erlander M.G. Global gene expression analysis of single cells. Curr Opin Drug Discov Devel. 6:2003;231-236
19. Xiang Z., Yang Y., Ma X., Ding W. Microarray expression profiling: analysis and applications. Curr Opin Drug Discov Devel. 6:2003;384-395
20. Forster T., Roy D., Ghazal P. Experiments using microarray technology: limitations and standard operating procedures. J Endocrinol. 178:2003;195-204
21. Haggarty S.J., Clemons P.A., Schreiber S.L. Chemical genomic profiling of biological networks using graph theory and combinations of small molecule perturbations. J Am Chem Soc. 125:2003;10543-10545 Seminal example of perturbational profiling of biological systems using combinations of small molecules in 11 different yeast genetic backgrounds.
22. Giaever G., Flaherty P., Kumm J., Proctor M., Nislow C., Jaramillo D.F., Chu A.M., Jordan M.I., Arkin A.P., Davis R.W. Chemogenomic profiling: Identifying the functional interactions of small molecules in yeast. Proc Natl Acad Sci USA. 101:2004;793-798
23. Nielsen U.B., Cardone M.H., Sinskey A.J., MacBeath G., Sorger P.K. Profiling receptor tyrosine kinase activation by using Ab microarrays. Proc Natl Acad Sci USA. 100:2003;9330-9335
24. Ding S., Wu T.Y., Brinker A., Peters E.C., Hur W., Gray N.S., Schultz P.G. Synthetic small molecules that control stem cell fate. Proc Natl Acad Sci USA. 100:2003;7632-7637 Reporter-based screen for molecules inducing differentiation of stem cell precursors down a neuronal lineage.
25. Kung Sutherland M.S., Lipps S.G., Patnaik N., Gayo-Fung L.M., Khammungkune S., Xie W., Brady H.A., Barbosa M.S., Anderson D.W., Stein B. SP500263, a novel SERM, blocks osteoclastogenesis in a human bone cell model: role of IL-6 and GM-CSF. Cytokine. 23:2003;1-14 Move toward more relevant disease models using cell co-culture to screen for inhibitors of osteoclast differentiation in a high-throughput format.
26. Koeller K.M., Haggarty S.J., Perkins B.D., Leykin I., Wong J.C., Kao M.C., Schreiber S.L. Chemical genetic modifier screens: small molecule trichostatin suppressors as probes of intracellular histone and tubulin acetylation. Chem Biol. 10:2003;397-410 Rationale for using chemical-genetic modifier screens to annotate further small molecules emerging from high-throughput phenotypic screens.
27. Stockwell B.R., Haggarty S.J., Schreiber S.L. High-throughput screening of small molecules in miniaturized mammalian cell-based assays involving post-translational modifications. Chem Biol. 6:1999;71-83
28. Barrie S.E., Eno-Amooquaye E., Hardcastle A., Platt G., Richards J., Bedford D., Workman P., Aherne W., Mittnacht S., Garrett M.D. High-throughput screening for the identification of small-molecule inhibitors of retinoblastoma protein phosphorylation in cells. Anal Biochem. 320:2003;66-74 Cytoblot assay for a particular post-translational modification using time-resolved fluorescence detection.
29. Dolma S., Lessnick S.L., Hahn W.C., Stockwell B.R. Identification of genotype-selective antitumor agents using synthetic lethal chemical screening in engineered human tumor cells. Cancer Cell. 3:2003;285-296 Screen for cytotoxic compounds in a heavily engineered cell line potentially relevant to cancer.
30. Einav Y., Shistik E., Shenfeld M., Simons A.H., Melton D.W., Canaani D. Replication and episomal maintenance of Epstein-Barr virus-based vectors in mouse embryonal fibroblasts enable synthetic lethality screens. Mol Cancer Ther. 2:2003;1121-1128 Exceptional genetic engineering facilitates a general method for performing single-gene synthetic lethality experiments in embryonic fibroblasts.
31. Simons A.H., Dafni N., Dotan I., Oron Y., Canaani D. Genetic synthetic lethality screen at the single gene level in cultured human cells. Nucleic Acids Res. 29:2001;E100
32. Simons A., Dafni N., Dotan I., Oron Y., Canaani D. Establishment of a chemical synthetic lethality screen in cultured human cells. Genome Res. 11:2001;266-273
33. Fantin V.R., Berardi M.J., Scorrano L., Korsmeyer S.J., Leder P. A novel mitochondriotoxic small molecule that selectively inhibits tumor cell growth. Cancer Cell. 2:2002;29-42 Example of parallel screening for synthetic lethal phenotypes relevant to cancer and mitochondrial metabolism.
34. Rosania G.R., Lee J.W., Ding L., Yoon H.S., Chang Y.T. Combinatorial approach to organelle-targeted fluorescent library based on the styryl scaffold. J Am Chem Soc. 125:2003;1130-1131 Attempt to correlate biological properties, particularly subcellular localization, with reagent choices made during combinatorial library synthesis.
35. Haggarty S.J., Koeller K.M., Wong J.C., Butcher R.A., Schreiber S.L. Multidimensional chemical genetic analysis of diversity-oriented synthesis-derived deacetylase inhibitors using cell-based assays. Chem Biol. 10:2003;383-396 Excellent analytical approach to dealing with data from parallel phenotypic assays, resulting in characterization of discriminatory deacetylase inhibitors.
36. Li Z., Yan Y., Powers E.A., Ying X., Janjua K., Garyantes T., Baron B. Identification of gap junction blockers using automated fluorescence microscopy imaging. J Biomol Screen. 8:2003;489-499 Co-culture assay system with a requirement for detection using microscopy-based methods reveals modulators of gap-junction communication.
37. Yarrow J.C., Feng Y., Perlman Z.E., Kirchhausen T., Mitchison T.J. Phenotypic screening of small molecule libraries by high throughput cell imaging. Comb Chem High Throughput Screen. 6:2003;279-286 Seminal example of microscopy-based high-content screening in academia.
38. Haggarty S.J., Mayer T.U., Miyamoto D.T., Fathi R., King R.W., Mitchison T.J., Schreiber S.L. Dissecting cellular processes using small molecules: identification of colchicine-like, taxol-like and other small molecules that perturb mitosis. Chem Biol. 7:2000;275-286
39. Mayer T.U., Kapoor T.M., Haggarty S.J., King R.W., Schreiber S.L., Mitchison T.J. Small molecule inhibitor of mitotic spindle bipolarity identified in a phenotype-based screen. Science. 286:1999;971-974
40. Burnett P., Robertson J.K., Palmer J.M., Ryan R.R., Dubin A.E., Zivin R.A. Fluorescence imaging of electrically stimulated cells. J Biomol Screen. 8:2003;660-667 Promising technology for neurobiology allowing direct manipulation of membrane potential in cell culture adaptable to HTS.
41. Biran I., Walt D.R. Optical imaging fiber-based single live cell arrays: a high-density cell assay platform. Anal Chem. 74:2002;3046-3054
42. Peterson R.T., Link B.A., Dowling J.E., Schreiber S.L. Small molecule developmental screens reveal the logic and timing of vertebrate development. Proc Natl Acad Sci USA. 97:2000;12965-12969
43. Peterson R.T., Mably J.D., Chen J.N., Fishman M.C. Convergence of distinct pathways to heart patterning revealed by the small molecule concentramide and the mutation heart-and-soul. Curr Biol. 11:2001;1481-1491
44. Khersonsky S.M., Jung D.W., Kang T.W., Walsh D.P., Moon H.S., Jo H., Jacobson E.M., Shetty V., Neubert T.A., Chang Y.T. Facilitated forward chemical genetics using a tagged triazine library and zebrafish embryo screening. J Am Chem Soc. 125:2003;11804-11805 Excellent example of anticipating the target identification problem during combinatorial library synthesis.
45. Milan D.J., Peterson T.A., Ruskin J.N., Peterson R.T., MacRae C.A. Drugs that induce repolarization abnormalities cause bradycardia in zebrafish. Circulation. 107:2003;1355-1358 Use of continuous video recording as a HTS method for modulators of heart-rate in zebrafish.
46. Koehler A.N., Shamji A.F., Schreiber S.L. Discovery of an inhibitor of a transcription factor using small molecule microarrays and diversity-oriented synthesis. J Am Chem Soc. 125:2003;8420-8421
47. Bochner B.R., Gadzinski P., Panomitros E. Phenotype microarrays for high-throughput phenotypic testing and assay of gene function. Genome Res. 11:2001;1246-1255
48. Zhou L., Lei X.H., Bochner B.R., Wanner B.L. Phenotype microarray analysis of Escherichia coli K-12 mutants with deletions of all two-component systems. J Bacteriol. 185:2003;4956-4972
49. Fischer H.P., Brunner N.A., Wieland B., Paquette J., Macko L., Ziegelbauer K., Freiberg C. Identification of antibiotic stress-inducible promoters: a systematic approach to novel pathway-specific reporter assays for antibacterial drug discovery. Genome Res. 14:2004;90-98
50. Giot L., Bader J.S., Brouwer C., Chaudhuri A., Kuang B., Li Y., Hao Y.L., Ooi C.E., Godwin B., Vitols E., et al. A protein interaction map of Drosophila melanogaster. Science. 302:2003;1727-1736
51. Li S., Armstrong C.M., Bertin N., Ge H., Milstein S., Boxem M., Vidalain P.O., Han J.D., Chesneau A., Hao T., et al. A map of the interactome network of the metazoan C. elegans. Science. 303:2004;540-543