title: Frequent sampling reveals dynamic responses by the transcriptome to routine media replacement in HepG2 cells.
abstract: Cultured cell lines are employed extensively for biological research. Large-scale differential gene expression (LSDGE) is being used to study mechanisms of toxicity in such cultures. 'Normal' gene expression dynamics could have a major impact on the design and interpretation of these studies. In order to provide understanding of such dynamics, we investigated LSDGE responses to media replacement in human hepatoblastoma cells (HepG2) using 5-minute sampling frequencies for 6 hours post routine media replacement. Each mRNA transcript was found to exhibit a characteristic 'operating range' based on signal intensity. Following media replacement, which replenishes nutrients (eg, glucose and glutamate) and removes excretory products (eg, lactate), a complex set of gene expression changes was observed. Some transcripts appeared to switch on from a quiescent state to a very active one (eg, CYP1A1), others exhibited 'clocklike' oscillations (eg, asparagine synthetase), or a synchronous burst (chirp) of expression up regulation (eg, timeless). Mathematical analysis (Fourier Transform, Singular Value Decomposition, Wavelets, Phase Analysis) of oscillating expression patterns identified cycle lengths ranging from 11.8 to 210 minutes. There were prominent 36.5- and 17.4-minute cycles, for subsets of genes, and transcript-specific differences in phase angle with respect to these cycles. The functional consequences of these novel observations remain to be determined. It is clear that dense time-course studies provide a valuable approach to the investigation of physiological responses to nutrients, toxicants, and other environmental variables. This research also highlights the need for an understanding of biological dynamics when using cell culture systems. An Excel data file representing individual transcripts from the respective Clontech cDNA arrays referred to in this article is available at http://taylorandfrancis.metapress.com/openurl.asp?genre=journal&issn=0192-6233. Rows represent data for individual transcripts and columns represent the time-points from 0 to 360 minutes. To access this file, click on the issue link for 31(4), then select this article. In order to access the full article online, you must either have an individual subscription or a member subscription accessed through www.toxpath.org.
authors.affiliation: GlaxoSmithKline, Research Triangle Park, North Carolina 27709, USA. kevin.morgan@aventis.com
authors.forename: Kevin T
authors.initials: KT
authors.lastname: Morgan
authors.forename: Warren
authors.initials: W
authors.lastname: Casey
authors.forename: Marilyn
authors.initials: M
authors.lastname: Easton
authors.forename: Don
authors.initials: D
authors.lastname: Creech
authors.forename: Hong
authors.initials: H
authors.lastname: Ni
authors.forename: Lawrence
authors.initials: L
authors.lastname: Yoon
authors.forename: Steve
authors.initials: S
authors.lastname: Anderson
authors.forename: Charles W
authors.initials: CW
authors.lastname: Qualls
authors.forename: Lynn M
authors.initials: LM
authors.lastname: Crosby
authors.forename: Alistair
authors.initials: A
authors.lastname: MacPherson
authors.forename: Peter
authors.initials: P
authors.lastname: Bloomfield
authors.forename: Timothy C
authors.initials: TC
authors.lastname: Elston
mesh_terms: D018929:Cell Culture Techniques / Q000379:methods*; D045744:Cell Line, Tumor; D003470:Culture Media; D015870:Gene Expression; D020869:Gene Expression Profiling; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D010507:Periodicity; D020133:Reverse Transcriptase Polymerase Chain Reaction; D013997:Time Factors; D014158:Transcription, Genetic
chemical_list: D003470:Culture Media