Differential Expression Analysis of A6 Cells and Tissue of Origin, the Xenopus Kidney

Cell lines are used as in vitro models for systems such as the kidney, but the extent to which they resemble the native tissue is often not well established. Similarities and differences between cell lines and tissues can be elucidated by evaluating gene expression with high throughput tools such as microarrays. Our laboratory frequently uses the A6 Xenopus laevis kidney cell line as a basis for developing imaging techniques, toxicity studies, and heterologous gene expression methods. We are interested in evaluating similarities and differences between the genetic profile of the A6 cell line and the organ of origin. To this end, we employed the Affymetrix GeneChip^® Xenopus laevis Genome Array to evaluate gene expression based on intensity values assigned to probe set identifiers (PSIDs) on the microarray. The open source Database for Annotation, Visualization and Integrated Discovery (DAVID) was implemented to impart functional significance to annotated PSIDs meeting the criterion for differential expression (ǀfold changeǀ >1.5). The DAVID cluster terms were then curated into broader categories (for example, hemoglobin was classified under blood) in order to facilitate the classification of differentially expressed PSIDs. As expected, the kidney tissue assumed higher intensity levels for PSIDs associated with organ function and whole-body homeostatic activity while cell cycle-related gene categories were predominant in the A6 cell line. Moreover, the prevalence of PSIDs lacking annotation was highlighted for PSIDs upregulated in the A6 cell line.  This characterization provides important insights affecting the utilization of the A6 cell line as an in vitro model for future heterologous gene expression methods, analysis of protein function, and cellular responses to chemical agents such as drugs and toxins. Supported by NIH P50-GM68762.