title: Cross-species hybridization of woodchuck hepatitis viral infection-induced woodchuck hepatocellular carcinoma using human, rat and mouse oligonucleotide microarrays.
abstract: OBJECTIVE
  We aimed to evaluate the transcriptional characteristics of viral infection-induced woodchuck hepatocellular carcinoma (HCC), to compare the use of human, rat and mouse gene arrays for cross-species hybridization, and to look into gene expression profiles in woodchuck HCC by the combined use of these arrays.
  
  
  METHODS
  Commercially available human, rat and mouse oligonucleotide microarrays were used to determine the gene expression profiles on the same woodchuck liver samples. Differentially expressed genes between HCC and the surrounding hepatic tissues found in the arrays were selected for quantitative reverse transcription polymerase chain reaction.
  
  
  RESULTS
  Despite the difference in the number of the probes from each array, the percentage of genes that were detectable was similar. Stringent microarray data analysis using both supervised and unsupervised methods identified 281 differentially expressed genes via the human array with a false discovery rate (FDR) of 0.99%, 107 genes via the rat array with an FDR of 1.85% and 78 genes via the mouse array with an FDR of 7.41%. Eleven genes were differentially changed in all three arrays that include the upregulation of NPM1, H2AFZ, EEF1G, HNRPAB, RPS18, EIF5, CKS2, ARIH1, RPS12 and RPS10, and the downregulation of EGR1. The quantitative reverse transcription polymerase chain reaction with woodchuck-specific primers confirmed the reliability of the microarray results.
  
  
  CONCLUSIONS
  This study further demonstrated the utility of cross-species hybridization of microarrays on woodchuck HCC. A combined use of three types of arrays identified more differential genes in HCC than individual arrays with the human array providing the richest information among the three arrays used.
authors.affiliation: Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, USA.
authors.forename: Fangjing
authors.initials: F
authors.lastname: Wang
authors.forename: Yu
authors.initials: Y
authors.lastname: Kuang
authors.forename: Nicolas
authors.initials: N
authors.lastname: Salem
authors.forename: Paul W
authors.initials: PW
authors.lastname: Anderson
authors.forename: Zhenghong
authors.initials: Z
authors.lastname: Lee
mesh_terms: D000818:Animals; D006528:Carcinoma, Hepatocellular / Q000235:genetics* / Q000821:virology; D016000:Cluster Analysis; D005240:Feasibility Studies; D020869:Gene Expression Profiling / Q000379:methods*; D015972:Gene Expression Regulation, Neoplastic; D006509:Hepatitis B / Q000150:complications* / Q000821:virology; D017919:Hepatitis B Virus, Woodchuck / Q000472:pathogenicity*; D006524:Hepatitis, Viral, Animal / Q000150:complications* / Q000821:virology; D006801:Humans; D008113:Liver Neoplasms / Q000235:genetics* / Q000821:virology; D008392:Marmota; D051379:Mice; D000090243:Nucleophosmin; D020411:Oligonucleotide Array Sequence Analysis; D051381:Rats; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction; D013045:Species Specificity