title: Integrating time-course microarray gene expression profiles with cytotoxicity for identification of biomarkers in primary rat hepatocytes exposed to cadmium.
abstract: BACKGROUND
  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 microM. 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.
  
  
  BACKGROUND
  Matlab source code is available upon request and DNA microarray data are available at GEO (http://www.ncbi.nlm.nih.gov/geo).
authors.affiliation: Cedars-Sinai Research Institute, Cedars-Sinai Medical Center Los Angeles, CA 90048, USA.
authors.forename: Yongxi
authors.initials: Y
authors.lastname: Tan
authors.forename: Leming
authors.initials: L
authors.lastname: Shi
authors.forename: Saber M
authors.initials: SM
authors.lastname: Hussain
authors.forename: Jun
authors.initials: J
authors.lastname: Xu
authors.forename: Weida
authors.initials: W
authors.lastname: Tong
authors.forename: John M
authors.initials: JM
authors.lastname: Frazier
authors.forename: Charles
authors.initials: C
authors.lastname: Wang
mesh_terms: D000465:Algorithms; D000818:Animals; D015415:Biomarkers / Q000737:chemistry*; D002104:Cadmium / Q000494:pharmacology*; D019295:Computational Biology / Q000379:methods*; D004305:Dose-Response Relationship, Drug; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation; D022781:Hepatocytes / Q000378:metabolism*; D007770:L-Lactate Dehydrogenase / Q000235:genetics; D008962:Models, Theoretical; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012333:RNA, Messenger / Q000378:metabolism; D051381:Rats; D012044:Regression Analysis; D015203:Reproducibility of Results; D015398:Signal Transduction; D012984:Software; D013997:Time Factors
chemical_list: D015415:Biomarkers; D012333:RNA, Messenger; D002104:Cadmium; D007770:L-Lactate Dehydrogenase