Time-resolved human kinome RNAi screen identifies a network regulating mitotic-events as early regulators of cell proliferation

• Published in: PloS one 2011-07, Vol.6 (7), p.e22176
• Main Authors: Zhang, Jitao David, Koerner, Cindy, Bechtel, Stephanie, Bender, Christian, Keklikoglou, Ioanna, Schmidt, Christian, Irsigler, Anja, Ernst, Ute, Sahin, Ozgür, Wiemann, Stefan, Tschulena, Ulrich
• Format: Article
• Language: English
• Subjects: Analysis; Bioinformatics; Biological activity; Biological analysis; Biology; Cancer; Cell cycle; Cell growth; Cell proliferation; Cell Proliferation - drug effects; Data acquisition; Data analysis; Data processing; Dynamic tests; Electrical impedance; Enzyme Assays; Gene expression; Gene Knockdown Techniques; Genes; Genetic transformation; Genomes; Growth rate; HeLa Cells; High-throughput screening; High-Throughput Screening Assays - methods; Humans; Kinases; Kinetics; Medical research; Mitosis - drug effects; Mitosis - genetics; Pharmacology; Phenotype; Phosphotransferases - antagonists & inhibitors; Phosphotransferases - metabolism; Protein Kinase Inhibitors - pharmacology; Proteins; Regulators; RNA Interference; RNA, Small Interfering - metabolism; RNA-mediated interference; Signal Transduction - drug effects; Single-Cell Analysis; Studies; Time Factors; Transformation; Websites; Yang, Cindy
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0022176

Analysis of biological processes is frequently performed with the help of phenotypic assays where data is mostly acquired in single end-point analysis. Alternative phenotypic profiling techniques are desired where time-series information is essential to the biological question, for instance to differentiate early and late regulators of cell proliferation in loss-of-function studies. So far there is no study addressing this question despite of high unmet interests, mostly due to the limitation of conventional end-point assaying technologies. We present the first human kinome screen with a real-time cell analysis system (RTCA) to capture dynamic RNAi phenotypes, employing time-resolved monitoring of cell proliferation via electrical impedance. RTCA allowed us to investigate the dynamics of phenotypes of cell proliferation instead of using conventional end-point analysis. By introducing data transformation with first-order derivative, i.e. the cell-index growth rate, we demonstrate this system suitable for high-throughput screenings (HTS). The screen validated previously identified inhibitor genes and, additionally, identified activators of cell proliferation. With the information of time kinetics available, we could establish a network of mitotic-event related genes to be among the first displaying inhibiting effects after RNAi knockdown. The time-resolved screen captured kinetics of cell proliferation caused by RNAi targeting human kinome, serving as a resource for researchers. Our work establishes RTCA technology as a novel robust tool with biological and pharmacological relevance amenable for high-throughput screening.