title: Screening a mouse liver gene expression compendium identifies modulators of the aryl hydrocarbon receptor (AhR).
abstract: The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor that mediates the biological and toxic effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), dioxin-like compounds (DLC) as well as some drugs and endogenous tryptophan metabolites. Short-term activation of AhR can lead to hepatocellular steatosis, and chronic activation can lead to liver cancer in mice and rats. Analytical approaches were developed to identify biosets in a genomic database in which AhR activity was altered. A set of 63 genes was identified (the AhR gene expression biomarker) that was dependent on AhR for regulation after exposure to TCDD or benzo[a]pyrene and includes the known AhR targets Cyp1a1 and Cyp1b1. A fold-change rank-based test (Running Fisher's test; p-value ≤ 10(-4)) was used to evaluate the similarity between the AhR biomarker and a test set of 37 and 41 biosets positive or negative, respectively for AhR activation. The test resulted in a balanced accuracy of 95%. The rank-based test was used to identify factors that activate or suppress AhR in an annotated mouse liver/mouse primary hepatocyte gene expression database of ∼ 1850 comparisons. In addition to the expected activation of AhR by TCDD and DLC, AhR was activated by AP20189 and phenformin. AhR was suppressed by phenobarbital and 1,4-Bis[2-(3,5-dichloropyridyloxy)] benzene (TCPOBOP) in a constitutive activated receptor (CAR)-dependent manner and pregnenolone-16α-carbonitrile in a pregnane X receptor (PXR)-dependent manner. Inactivation of individual genes in nullizygous models led to AhR activation (Pxr, Ghrhr, Taf10) or suppression (Ahr, Ilst6st, Hnf1a). This study describes a novel screening strategy for identifying factors in mouse liver that perturb AhR in a gene expression compendium.
authors.affiliation: NHEERL, US-EPA, Research Triangle Park, NC 27711, United States.
authors.forename: Keiyu
authors.initials: K
authors.lastname: Oshida
authors.affiliation: NHEERL, US-EPA, Research Triangle Park, NC 27711, United States.
authors.forename: Naresh
authors.initials: N
authors.lastname: Vasani
authors.affiliation: The Hamner Institutes for Health Sciences, Research Triangle Park, NC 27709, United States.
authors.forename: Russell S
authors.initials: RS
authors.lastname: Thomas
authors.affiliation: RegeneMed, San Diego, CA 92121, United States.
authors.forename: Dawn
authors.initials: D
authors.lastname: Applegate
authors.affiliation: National Cancer Institute, NIH, Bethesda, MD 20892, United States.
authors.forename: Frank J
authors.initials: FJ
authors.lastname: Gonzalez
authors.affiliation: Rutgers University, Piscataway, NJ 08854, United States.
authors.forename: Lauren M
authors.initials: LM
authors.lastname: Aleksunes
authors.affiliation: University of Kansas Medical Center, Kansas City, KS 66160, United States.
authors.forename: Curtis D
authors.initials: CD
authors.lastname: Klaassen
authors.affiliation: NHEERL, US-EPA, Research Triangle Park, NC 27711, United States. Electronic address: corton.chris@epa.gov.
authors.forename: J Christopher
authors.initials: JC
authors.lastname: Corton
mesh_terms: D000818:Animals; D004789:Enzyme Activation / Q000187:drug effects / Q000235:genetics; D015870:Gene Expression / Q000187:drug effects*; D005819:Genetic Markers; D057166:High-Throughput Screening Assays / Q000379:methods; D008099:Liver / Q000378:metabolism*; D008297:Male; D051379:Mice; D008807:Mice, Inbred BALB C; D018345:Mice, Knockout; D040081:Protein Array Analysis; D060888:Real-Time Polymerase Chain Reaction; D018336:Receptors, Aryl Hydrocarbon / Q000187:drug effects* / Q000235:genetics / Q000378:metabolism
chemical_list: D005819:Genetic Markers; D018336:Receptors, Aryl Hydrocarbon
keywords: Aryl hydrocarbon receptor; Constitutive activated receptor; Keap1; Liver cancer; Nrf2; Peroxisome proliferator-activated receptor; Pregnane X receptor; Transcript profiling