title: Tracking transcriptional activities with high-content epifluorescent imaging.
abstract: High-content cell imaging based on fluorescent protein reporters has recently been used to track the transcriptional activities of multiple genes under different external stimuli for extended periods. This technology enhances our ability to discover treatment-induced regulatory mechanisms, temporally order their onsets and recognize their relationships. To fully realize these possibilities and explore their potential in biological and pharmaceutical applications, we introduce a new data processing procedure to extract information about the dynamics of cell processes based on this technology. The proposed procedure contains two parts: (1) image processing, where the fluorescent images are processed to identify individual cells and allow their transcriptional activity levels to be quantified; and (2) data representation, where the extracted time course data are summarized and represented in a way that facilitates efficient evaluation. Experiments show that the proposed procedure achieves fast and robust image segmentation with sufficient accuracy. The extracted cellular dynamics are highly reproducible and sensitive enough to detect subtle activity differences and identify mechanisms responding to selected perturbations. This method should be able to help biologists identify the alterations of cellular mechanisms that allow drug candidates to change cell behavior and thereby improve the efficiency of drug discovery and treatment design.
authors.affiliation: Translational Genomics Research Institute, 445 North Fifth Street, Phoenix, Arizona 85004, USA. jhua@tgen.org
authors.forename: Jianping
authors.initials: J
authors.lastname: Hua
authors.forename: Chao
authors.initials: C
authors.lastname: Sima
authors.forename: Milana
authors.initials: M
authors.lastname: Cypert
authors.forename: Gerald C
authors.initials: GC
authors.lastname: Gooden
authors.forename: Sonsoles
authors.initials: S
authors.lastname: Shack
authors.forename: Lalitamba
authors.initials: L
authors.lastname: Alla
authors.forename: Edward A
authors.initials: EA
authors.lastname: Smith
authors.forename: Jeffrey M
authors.initials: JM
authors.lastname: Trent
authors.forename: Edward R
authors.initials: ER
authors.lastname: Dougherty
authors.forename: Michael L
authors.initials: ML
authors.lastname: Bittner
mesh_terms: D055808:Drug Discovery; D005456:Fluorescent Dyes / Q000032:analysis / Q000378:metabolism; D017930:Genes, Reporter; D045325:HCT116 Cells; D006651:Histocytochemistry / Q000379:methods*; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D008164:Luminescent Proteins / Q000032:analysis / Q000235:genetics / Q000378:metabolism; D008856:Microscopy, Fluorescence / Q000379:methods*; D014158:Transcription, Genetic
chemical_list: D005456:Fluorescent Dyes; D008164:Luminescent Proteins