title: Predictive toxicogenomics approaches reveal underlying molecular mechanisms of nongenotoxic carcinogenicity.
abstract: Toxicogenomics technology defines toxicity gene expression signatures for early predictions and hypotheses generation for mechanistic studies, which are important approaches for evaluating toxicity of drug candidate compounds. A large gene expression database built using cDNA microarrays and liver samples treated with over one hundred paradigm compounds was mined to determine gene expression signatures for nongenotoxic carcinogens (NGTCs). Data were obtained from male rats treated for 24 h. Training/testing sets of 24 NGTCs and 28 noncarcinogens were used to select genes. A semiexhaustive, nonredundant gene selection algorithm yielded six genes (nuclear transport factor 2, NUTF2; progesterone receptor membrane component 1, Pgrmc1; liver uridine diphosphate glucuronyltransferase, phenobarbital-inducible form, UDPGTr2; metallothionein 1A, MT1A; suppressor of lin-12 homolog, Sel1h; and methionine adenosyltransferase 1, alpha, Mat1a), which identified NGTCs with 88.5% prediction accuracy estimated by cross-validation. This six genes signature set also predicted NGTCs with 84% accuracy when samples were hybridized to commercially available CodeLink oligo-based microarrays. To unveil molecular mechanisms of nongenotoxic carcinogenesis, 125 differentially expressed genes (P<0.01) were selected by Student's t-test. These genes appear biologically relevant, of 71 well-annotated genes from these 125 genes, 62 were overrepresented in five biochemical pathway networks (most linked to cancer), and all of these networks were linked by one gene, c-myc. Gene expression profiling at early time points accurately predicts NGTC potential of compounds, and the same data can be mined effectively for other toxicity signatures. Predictive genes confirm prior work and suggest pathways critical for early stages of carcinogenesis.
authors.affiliation: Johnson & Johnson Pharmaceutical Research & Development, LLC, Raritan, New Jersey, USA.
authors.forename: Alex Y
authors.initials: AY
authors.lastname: Nie
authors.forename: Michael
authors.initials: M
authors.lastname: McMillian
authors.forename: J Brandon
authors.initials: JB
authors.lastname: Parker
authors.forename: Angelique
authors.initials: A
authors.lastname: Leone
authors.forename: Stewart
authors.initials: S
authors.lastname: Bryant
authors.forename: Lynn
authors.initials: L
authors.lastname: Yieh
authors.forename: Anton
authors.initials: A
authors.lastname: Bittner
authors.forename: Jay
authors.initials: J
authors.lastname: Nelson
authors.forename: Andrew
authors.initials: A
authors.lastname: Carmen
authors.forename: Jackson
authors.initials: J
authors.lastname: Wan
authors.forename: Peter G
authors.initials: PG
authors.lastname: Lord
mesh_terms: D000818:Animals; D002273:Carcinogens / Q000633:toxicity*; D002471:Cell Transformation, Neoplastic / Q000139:chemically induced* / Q000235:genetics; D015870:Gene Expression / Q000187:drug effects; D020869:Gene Expression Profiling; D052138:Genes, Neoplasm / Q000187:drug effects*; D008099:Liver / Q000187:drug effects; D008114:Liver Neoplasms, Experimental / Q000139:chemically induced* / Q000235:genetics; D008297:Male; D009152:Mutagenicity Tests; D020411:Oligonucleotide Array Sequence Analysis; D012333:RNA, Messenger / Q000032:analysis; D051381:Rats; D017207:Rats, Sprague-Dawley; D043922:Toxicogenetics
chemical_list: D002273:Carcinogens; D012333:RNA, Messenger