@article{lawrie_mitchell_dhammi_wallace_hodgson_roe_2020, title={Role of long non-coding RNA in DEET- and fipronil-mediated alteration of transcripts associated with Phase I and Phase II xenobiotic metabolism in human primary hepatocytes}, volume={167}, ISSN={["1095-9939"]}, DOI={10.1016/j.pestbp.2020.104607}, abstractNote={Human exposure to environmental chemicals both individually and in combination occurs frequently world-wide most often with unknown consequences. Use of molecular approaches to aide in the assessment of risk involved in chemical exposure is a growing field in toxicology. In this study, we examined the impact of two environmental chemicals used in and around homes, the insect repellent DEET (N,N-diethyl-m-toluamide) and the phenylpyrazole insecticide fipronil (fluocyanobenpyrazole) on transcript levels of enzymes potentially involved in xenobiotic metabolism and on long non-coding RNAs (lncRNAs). Primary human hepatocytes were treated with these two chemicals both individually and in combination. Using RNA-Seq, we found that 10 major enzyme categories involved in phase 1 and phase 2 xenobiotic metabolism were significantly (α = 0.05) up- and down-regulated (i.e., 100 μM DEET–19 transcripts, 89% up and 11% down; 10 μM fipronil–52 transcripts, 53% up and 47% down; and 100 μM DEET +10 μM fipronil–69 transcripts, 43% up and 57% down). The altered genes were then mapped to the human genome and their proximity (within 1,000,000 bp) to lncRNAs examined. Unique proximities were discovered between altered lncRNA and altered P450s (CYP) and other enzymes (DEET, 2 CYP; Fipronil, 6 CYP and 15 other; and DEET + fipronil, 7 CYP and 21 other). Many of the altered P450 transcripts were in multiple clusters in the genome with proximal altered lncRNAs, suggesting a regulator function for the lncRNA. At the gene level there was high percent identity for lncRNAs near P450 clusters, but this relationship was not found at the transcript level. The role of these altered lncRNAs associated with xenobiotic induction, human diseases and chemical mixtures is discussed.}, journal={PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY}, author={Lawrie, Roger D. and Mitchell, Robert D., III and Dhammi, Anirudh and Wallace, Andrew and Hodgson, Ernest and Roe, R. Michael}, year={2020}, month={Jul} }
 @article{mitchell_wallace_hodgson_roe_2017, title={Differential Expression Profile of lncRNAs from Primary Human Hepatocytes Following DEET and Fipronil Exposure}, volume={18}, ISSN={["1422-0067"]}, DOI={10.3390/ijms18102104}, abstractNote={While the synthesis and use of new chemical compounds is at an all-time high, the study of their potential impact on human health is quickly falling behind, and new methods are needed to assess their impact. We chose to examine the effects of two common environmental chemicals, the insect repellent N,N-diethyl-m-toluamide (DEET) and the insecticide fluocyanobenpyrazole (fipronil), on transcript levels of long non-protein coding RNAs (lncRNAs) in primary human hepatocytes using a global RNA-Seq approach. While lncRNAs are believed to play a critical role in numerous important biological processes, many still remain uncharacterized, and their functions and modes of action remain largely unclear, especially in relation to environmental chemicals. RNA-Seq showed that 100 µM DEET significantly increased transcript levels for 2 lncRNAs and lowered transcript levels for 18 lncRNAs, while fipronil at 10 µM increased transcript levels for 76 lncRNAs and decreased levels for 193 lncRNAs. A mixture of 100 µM DEET and 10 µM fipronil increased transcript levels for 75 lncRNAs and lowered transcript levels for 258 lncRNAs. This indicates a more-than-additive effect on lncRNA transcript expression when the two chemicals were presented in combination versus each chemical alone. Differentially expressed lncRNA genes were mapped to chromosomes, analyzed by proximity to neighboring protein-coding genes, and functionally characterized via gene ontology and molecular mapping algorithms. While further testing is required to assess the organismal impact of changes in transcript levels, this initial analysis links several of the dysregulated lncRNAs to processes and pathways critical to proper cellular function, such as the innate and adaptive immune response and the p53 signaling pathway.}, number={10}, journal={INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES}, author={Mitchell, Robert D., III and Wallace, Andrew D. and Hodgson, Ernest and Roe, R. Michael}, year={2017}, month={Oct} }
 @article{mitchell_dhammi_wallace_hodgson_roe_2016, title={Impact of Environmental Chemicals on the Transcriptome of Primary Human Hepatocytes: Potential for Health Effects}, volume={30}, ISSN={1095-6670}, url={http://dx.doi.org/10.1002/JBT.21801}, DOI={10.1002/jbt.21801}, abstractNote={New paradigms for human health risk assessment of environmental chemicals emphasize the use of molecular methods and human‐derived cell lines. In this study, we examined the effects of the insect repellent DEET (N,N‐diethyl‐m‐toluamide) and the phenylpyrazole insecticide fipronil (fluocyanobenpyrazole) on transcript levels in primary human hepatocytes. These chemicals were tested individually and as a mixture. RNA‐Seq showed that 100 μM DEET significantly increased transcript levels (α = 0.05) for 108 genes and lowered transcript levels for 64 genes and fipronil at 10 μM increased the levels of 2246 transcripts and decreased the levels for 1428 transcripts. Fipronil was 21‐times more effective than DEET in eliciting changes, even though the treatment concentration was 10‐fold lower for fipronil versus DEET. The mixture of DEET and fipronil produced a more than additive effect (levels increased for 3017 transcripts and decreased for 2087 transcripts). The transcripts affected for all chemical treatments were classified by GO analysis and mapped to chromosomes. The overall treatment responses, specific pathways, and individual transcripts affected were discussed at different levels of fold‐change. Changes found in transcript levels in response to treatments will require further research to understand their importance in overall cellular, organ, and organismic function.}, number={8}, journal={Journal of Biochemical and Molecular Toxicology}, publisher={Wiley}, author={Mitchell, Robert D., III and Dhammi, Anirudh and Wallace, Andrew and Hodgson, Ernest and Roe, R. Michael}, year={2016}, month={Apr}, pages={375–395} }
 @article{hodgson_wallace_shah_choi_joo_2014, title={Human Variation and Risk Assessment: Microarray and Other Studies Utilizing Human Hepatocytes and Human Liver Subcellular Preparations}, volume={28}, ISSN={["1099-0461"]}, DOI={10.1002/jbt.21534}, abstractNote={ABSTRACT}, number={1}, journal={JOURNAL OF BIOCHEMICAL AND MOLECULAR TOXICOLOGY}, author={Hodgson, Ernest and Wallace, Andrew D. and Shah, Ruchir R. and Choi, Kyoungju and Joo, Hyun}, year={2014}, month={Jan}, pages={1–10} }
 @article{zhang_wallace_du_kibbe_jafari_xie_lin_baccarelli_soares_hou_2012, title={DNA methylation alterations in response to pesticide exposure in vitro}, volume={53}, number={7}, journal={Environmental and Molecular Mutagenesis}, author={Zhang, X. and Wallace, A. D. and Du, P. and Kibbe, W. A. and Jafari, N. and Xie, H. H. and Lin, S. M. and Baccarelli, A. and Soares, M. B. and Hou, L. F.}, year={2012}, pages={542–549} }
 @article{zhang_wallace_du_lin_baccarelli_jiang_jafari_zheng_xie_soares_et al._2012, title={Genome-wide study of DNA methylation alterations in response to diazinon exposure in vitro}, volume={34}, number={3}, journal={Environmental Toxicology and Pharmacology}, author={Zhang, X. and Wallace, A. D. and Du, P. and Lin, S. M. and Baccarelli, A. A. and Jiang, H. M. and Jafari, N. and Zheng, Y. N. and Xie, H. H. and Soares, M. B. and et al.}, year={2012}, pages={959–968} }
 @misc{wallace_2012, title={Toxic endpoints in the study of human exposure to environmental chemicals}, volume={112}, journal={Toxicology and human environments}, author={Wallace, A. D.}, year={2012}, pages={89–115} }
 @article{casabar_das_dekrey_gardiner_cao_rose_wallace_2010, title={Endosulfan induces CYP2B6 and CYP3A4 by activating the pregnane X receptor}, volume={245}, number={3}, journal={Toxicology and Applied Pharmacology}, author={Casabar, R. C. T. and Das, P. C. and DeKrey, G. K. and Gardiner, C. S. and Cao, Y. and Rose, R. L. and Wallace, A. D.}, year={2010}, pages={335–343} }
 @article{croom_wallace_hodgson_2010, title={Human variation in CYP-specific chlorpyrifos metabolism}, volume={276}, ISSN={["0300-483X"]}, DOI={10.1016/j.tox.2010.08.005}, abstractNote={Chlorpyrifos, an organophophorothioate insecticide, is bioactivated to the neurotoxic metabolite, chlorpyrifos-oxon (CPO) by cytochromes P450 (CYPs). To determine the variability in chlorpyrifos bioactivation, CPO production by human liver microsomes from 17 individual donors was compared relative to phenotype and genotype. CPO production varied over 14-fold between individuals in incubations utilizing 20 μM chlorpyrifos as substrate, while CPO production varied 57-fold in incubations with 100 μM chlorpyrifos. For all but two samples, the formation of the less toxic metabolite, 3,5,6-trichloro-2-pyridinol (TCP), was greater than CPO production. TCP production varied 9-fold in incubations utilizing 20 μM chlorpyrifos as substrate and 19-fold using 100 μM chlorpyrifos. Chlorpyrifos metabolism by individual human liver microsomes was significantly correlated with CYP2B6, CYP2C19 and CYP3A4 related activity. CPO formation was best correlated with CYP2B6 related activity at low (20 μM) chlorpyrifos concentrations while CYP3A4 related activity was best correlated with CPO formation at high concentrations (100 μM) of chlorpyrifos. TCP production was best correlated with CYP3A4 activity at all substrate concentrations of chlorpyrifos. The production of both CPO and TCP was significantly lower at a concentration of 20 μM chlorpyrifos as compared to 100 μM chlorpyrifos. Calculations of percent total normalized rates (% TNR) and the chemical inhibitors ketoconazole and ticlopidine were used to confirm the importance of CYP2B6, CYP2C19, and CYP3A4 for the metabolism of chlorpyrifos. The combination of ketoconazole and ticlopidine inhibited the majority of TCP and CPO formation. CPO formation did not differ by CYP2B6 genotype. Individual variations in CPO production may need to be considered in determining the risk of chlorpyrifos poisoning.}, number={3}, journal={TOXICOLOGY}, author={Croom, Edward L. and Wallace, Andrew D. and Hodgson, Ernest}, year={2010}, month={Oct}, pages={184–191} }
 @article{hannas_wang_baldwin_li_wallace_leblanc_2010, title={Interactions of the crustacean nuclear receptors HR3 and E75 in the regulation of gene transcription}, volume={167}, ISSN={["1095-6840"]}, DOI={10.1016/j.ygcen.2010.03.025}, abstractNote={Endocrine signal transduction occurs through cascades that involve the action of both ligand-dependent and ligand-independent nuclear receptors. In insects, two such nuclear receptors are HR3 and E75 that interact to transduce signals initiated by ecdysteroids. We have cloned these nuclear receptors from the crustacean Daphnia pulex to assess their function as regulators of gene transcription in this ecologically and economically important group of organisms. Both nuclear receptors from D. pulex (DappuHR3 (group NR1F) and DappuE75 (group NR1D)) exhibit a high degree of sequence similarity to other NR1F and NR1D group members that is indicative of monomeric binding to the RORE (retinoid orphan receptor element). DappuE75 possesses key amino acid residues required for heme binding to the ligand-binding domain. Next, we developed a gene transcription reporter assay containing a luciferase reporter gene driven by the RORE. DappuHR3, but not DappuE75, activated transcription of the luciferase gene in this system. Co-transfection experiments revealed that DappuE75 suppressed DappuHR3-dependent luciferase transcription in a dose-dependent manner. Electrophoretic mobility shift assays confirmed that DappuHR3 bound to the RORE. However, we found no evidence that DappuE75 similarly bound to the response element. These experiments further demonstrated that DappuE75 prevented DappuHR3 from binding to the response element. In conclusion, DappuHR3 functions as a transcriptional activator of genes regulated by the RORE and DappuE75 is a negative regulator of this activity. DappuE75 does not suppress the action of DappuHR3 by occupying the response element but presumably interacts directly with the DappuHR3 protein. Taken together with the previous demonstration that daphnid HR3 is highly induced by 20-hydroxyecdysone, these results support the premise that HR3 is a major component of ecdysteroid signaling in some crustaceans and is under the negative regulatory control of E75.}, number={2}, journal={GENERAL AND COMPARATIVE ENDOCRINOLOGY}, author={Hannas, Bethany R. and Wang, Ying H. and Baldwin, William S. and Li, Yangchun and Wallace, Andrew D. and LeBlanc, Gerald A.}, year={2010}, month={Jun}, pages={268–278} }
 @article{wallace_cao_chandramouleeswaran_cidlowski_2010, title={Lysine 419 targets human glucocorticoid receptor for proteasomal degradation}, volume={75}, number={12}, journal={Steroids}, author={Wallace, A. D. and Cao, Y. and Chandramouleeswaran, S. and Cidlowski, J. A.}, year={2010}, pages={1016–1023} }
 @article{croom_stevens_hines_wallace_hodgson_2009, title={Human hepatic CYP2B6 developmental expression: The impact of age and genotype}, volume={78}, ISSN={["1873-2968"]}, DOI={10.1016/j.bcp.2009.03.029}, abstractNote={Although CYP2B6 is known to metabolize numerous pharmaceuticals and toxicants in adults, little is known regarding CYP2B6 ontogeny or its possible role in pediatric drug/toxicant metabolism. To address this knowledge gap, hepatic CYP2B6 protein levels were characterized in microsomal protein preparations isolated from a pediatric liver bank (N = 217). Donor ages ranged from 10 weeks gestation to 17 years of age with a median age of 1.9 months. CYP2B6 levels were measured by semi-quantitative western blotting. Overall, CYP2B6 expression was detected in 75% of samples. However, the percentage of samples with detectable CYP2B6 protein increased with age from 64% in fetal samples to 95% in samples from donors >10 years of age. There was a significant, but only 2-fold increase in median CYP2B6 expression after the neonatal period (birth to 30 days postnatal) although protein levels varied over 25-fold in both age groups. The median CYP2B6 level in samples over 30 postnatal days to 17 years of age (1.3 pmol/mg microsomal protein) was lower than previously reported adult levels (2.2–22 pmol/mg microsomal protein), however, this likely relates to the median age of these samples, i.e., 10.3 months. CYP2B6 expression did not vary significantly by gender. Furthermore, CYP2B6 levels did not correlate with CYP3A4, CYP3A5.1 or CYP3A7 activity, consistent with different mechanisms controlling the ontogeny and constitutive expression of these enzymes and the lack of significant induction in the pediatric samples.}, number={2}, journal={BIOCHEMICAL PHARMACOLOGY}, author={Croom, Edward L. and Stevens, Jeffrey C. and Hines, Ronald N. and Wallace, Andrew D. and Hodgson, Ernest}, year={2009}, month={Jul}, pages={184–190} }
 @article{cooper_cho_thompson_wallace_2008, title={Phthalate induction of CYP3A4 is dependent on glucocorticoid regulation of PXR expression}, volume={103}, ISSN={["1096-0929"]}, DOI={10.1093/toxsci/kfn047}, abstractNote={Cytochrome P450 3A4 (CYP3A4) is responsible for oxidative metabolism of more than 60% of all pharmaceuticals. CYP3A4 is inducible by xenobiotics that activate pregnane X receptor (PXR), and enhanced CYP3A4 activity has been implicated in adverse drug interactions. Recent evidence suggest that the widely used plasticizer, di-2-ethylhexyl phthalate (DEHP), and its primary metabolite mono-2-ethylhexyl phthalate (MEHP) may act as agonists for PXR. Hospital patients are uniquely exposed to high levels of DEHP as well as being administered glucocorticoids. Glucocorticoids positively regulate PXR expression in a glucocorticoid receptor (GR)-mediated mechanism. We suggest that the magnitude of CYP3A4 induction by phthalates is dependent on the expression of PXR and may be significantly higher in the presence of glucocorticoids. DEHP and MEHP induced PXR-mediated transcription of the CYP3A4 promoter in a dose-dependent fashion. Coexposure to phthalates and dexamethasone (Dex) resulted in enhanced CYP3A4 promoter activity; furthermore, this induction was abrogated by both the GR antagonist RU486 and GR small interfering ribonucleic acid. Dex induced PXR protein expression in human hepatocytes and a liver-derived rat cell line. CYP3A4 protein was highly induced by Dex and DEHP coadministration in human hepatocyte cultures. Finally, enhanced 6beta-hydroxytestosterone formation in Dex and phthalate cotreated human hepatocytes confirmed CYP3A4 enzyme induction. Concomitant exposure to glucocorticoids and phthalates resulting in enhanced metabolic activity of CYP3A4 may play a role in altered efficacy of pharmaceutical agents. Understanding the role of glucocorticoid regulation of PXR as a key determinant in the magnitude of CYP3A4 induction by xenobiotics may provide insight into adverse drug effects in a sensitive population.}, number={2}, journal={TOXICOLOGICAL SCIENCES}, publisher={Oxford University Press (OUP)}, author={Cooper, Beth W. and Cho, Taehyeon M. and Thompson, Peter M. and Wallace, Andrew D.}, year={2008}, month={Jun}, pages={268–277} }
 @article{tompkins_sit_wallace_2008, title={Unique transcription start sites and distinct promoter regions differentiate the pregnane X receptor (PXR) isoforms PXR 1 and PXR 2}, volume={36}, ISSN={["1521-009X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-42449091555&partnerID=MN8TOARS}, DOI={10.1124/dmd.107.018317}, abstractNote={The pregnane X receptor (PXR) is known as the xenosensing receptor responsible for coordinated regulation of metabolic genes in response to diverse xenobiotic challenges. In particular, the ability of the PXR to regulate CYP3A4, the enzyme capable of metabolizing more than 60% of all pharmaceuticals, defines its metabolic importance. Currently the list of PXR ligands and target genes is extensive, yet investigations into the regulation and expression of PXRs are few. After an initial review of available sequence data, we discovered discrepancies in the 5′ untranslated region (UTR) and transcriptional start site (TSS) characterizations of the human PXR gene and subsequently endeavored to define TSSs and proximal promoters for isoforms PXR 1 and PXR 2. Reverse transcriptase-polymerase chain reaction and primer extension experiments performed on RNA from human liver identified two TSSs for each receptor isoform. These results extended the 5′UTR sequence of each isoform and defined new proximal promoters for both. Candidate response elements for liver-enriched transcription factors and other receptors were found in both proximal promoters. Quantitative PCR from human liver illustrated a highly variable expression profile for total PXRs; yet PXR 2 expression represented a consistent 2 to 5% of total PXR expression, despite the observed variability. Transfection experiments demonstrated that PXR 1 and PXR 2 had comparable abilities to transcriptionally activate the CYP3A4 promoter. Collectively, comparable function, consistent expression, and independent regulation suggest that PXR 2 is capable of contributing to the cumulative function of PXRs and should be included in the larger investigations of PXR expression and regulation.}, number={5}, journal={DRUG METABOLISM AND DISPOSITION}, publisher={American Society for Pharmacology & Experimental Therapeutics (ASPET)}, author={Tompkins, Leslie M. and Sit, Tim L. and Wallace, Andrew D.}, year={2008}, month={May}, pages={923–929} }
 @article{tompkins_wallace_2007, title={Mechanisms of cytochrome P450 induction}, volume={21}, number={4}, journal={Journal of Biochemical and Molecular Toxicology}, author={Tompkins, L. M. and Wallace, A. D.}, year={2007}, pages={176–181} }