Integrating time-course microarray gene expression profiles with cytotoxicity for identification of biomarkers in primary rat hepatocytes exposed to cadmium

• Published in: Bioinformatics 2006-01, Vol.22 (1), p.77-87
• Main Authors: Tan, Yongxi, Shi, Leming, Hussain, Saber M., Xu, Jun, Tong, Weida, Frazier, John M., Wang, Charles
• Format: Article
• Language: English
• Subjects: Algorithms; Animals; Biological and medical sciences; Biomarkers - chemistry; Cadmium - pharmacology; Computational Biology - methods; Dose-Response Relationship, Drug; Fundamental and applied biological sciences. Psychology; Gene Expression Profiling - methods; Gene Expression Regulation; General aspects; Hepatocytes - metabolism; L-Lactate Dehydrogenase - genetics; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Models, Theoretical; Oligonucleotide Array Sequence Analysis - methods; Rats; Regression Analysis; Reproducibility of Results; RNA, Messenger - metabolism; Signal Transduction; Software; Time Factors
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/bti737

Motivation: DNA microarrays can provide information about the expression levels of thousands of genes simultaneously at the transcriptomic level, while conventional cell viability and cytotoxicity measurement methods provide information about the biological functions at the cellular level. Integrating these data at different levels provides a promising approach for evaluating or predicting how cells respond to chemical exposure. It is important to investigate the multi-scale biological system in a systematic way to better understand the gene regulation networks and signal transduction pathways involved in the cellular responses to environmental factors. Results: Primary rat hepatocytes were exposed to cadmium acetate at 0, 1.25 and 2 μM. mRNA expression profiles at 0, 3, 6, 12 and 24 h were measured using the Affymetrix RatTox U34 GeneChip® arrays. Simultaneously, cytotoxicity was assessed by lactase dehydrogenase leakage assay. Gene expression profiles at different time points were used to evaluate cytotoxicity at subsequent time points using partial least squares, and it was found that gene expression profiles at 0 h had the best prediction accuracy for the cytotoxicity observed at 12 h. Some biomarkers whose expression profiles showed strong relationship with cytotoxicity were identified and the underlying pathways were reconstructed to illustrate how hepatocytes respond to cadmium exposure. Permutation studies were also applied to assess the reliability of the predictive models. Availability: Matlab source code is available upon request and DNA microarray data are available at GEO (). Contact: [e-mail] Supplementary information: Supplementary data are available at Bioinformatics online.