Publications
Filipovic D, Kana O, Marri D, Bhattacharya S. Unique challenges and best practices for single cell transcriptomic analysis in toxicology. Curr Opin Toxicol. 2024 Jun;38:100475. doi: 10.1016/j.cotox.2024.100475. Epub 2024 Mar 29. PMID: 38645720; PMCID: PMC11027889.
Bagga AD, Johnson BP, Zhang Q. Spatially Dependent Tissue Distribution of Thyroid Hormones by Plasma Thyroid Hormone Binding Proteins. bioRxiv [Preprint]. 2024 Apr 15:2023.12.20.572629. doi: 10.1101/2023.12.20.572629. PMID: 38187691; PMCID: PMC10769377.
Cholico GN, Fling RR, Sink WJ, Nault R, Zacharewski T. Inhibition of the urea cycle by the environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin increases serum ammonia levels in mice. J Biol Chem. 2024 Jan;300(1):105500. doi: 10.1016/j.jbc.2023.105500. Epub 2023 Nov 25. PMID: 38013089; PMCID: PMC10731612.
Rance N. How single-cell transcriptomics provides insight on hepatic responses to TCDD. Curr Opin Toxicol. 2023 Dec; 36. doi: 10.1016/j.cotox.2023.100441. PMID: 37981901; PMCID: PMC10653208.
Filipovic D, Qi W, Kana O, Marri D, LeCluyse EL, Andersen ME, Cuddapah S, Bhattacharya S. Interpretable predictive models of genome-wide aryl hydrocarbon receptor-DNA binding reveal tissue-specific binding determinants. Toxicol Sci. 2023 Nov 28;196(2):170-186. doi: 10.1093/toxsci/kfad094. PMID: 37707797; PMCID: PMC10682972.
Kumbale CM, Zhang Q, Voit EO. Hepatic cholesterol biosynthesis and dioxin-induced dysregulation: A multiscale computational approach. Food Chem Toxicol. 2023 Nov;181:114086. doi: 10.1016/j.fct.2023.114086. Epub 2023 Oct 10. PMID: 37820785; PMCID: PMC10841405.
Khan DMIO, Karmaus PWF, Bach A, Crawford RB, Kaminski NE. An in vitro model of human hematopoiesis identifies a regulatory role for the aryl hydrocarbon receptor. Blood Adv. 2023 Oct 24;7(20):6253-6265. doi: 10.1182/bloodadvances.2023010169. PMID: 37477592; PMCID: PMC10589788.
Jurgelewicz A, Nault R, Harkema J, Zacharewski TR, LaPres JJ. Characterizing the impact of simvastatin co-treatment of cell specific TCDD-induced gene expression and systemic toxicity. Sci Rep. 2023 Oct 3;13(1):16598. doi: 10.1038/s41598-023-42972-8. PMID: 37789023; PMCID: PMC10547718.
Nault R, Cave MC, Ludewig G, Moseley HNB, Pennell KG, Zacharewski T. A Case for Accelerating Standards to Achieve the FAIR Principles of Environmental Health Research Experimental Data. Environ Health Perspect. 2023 Jun;131(6):65001. doi: 10.1289/EHP11484. Epub 2023 Jun 23. PMID: 37352010; PMCID: PMC10289218.
Bagga AD, Johnson BP, Zhang Q. A minimal human physiologically based kinetic model of thyroid hormones and chemical disruption of plasma thyroid hormone binding proteins. Front Endocrinol (Lausanne). 2023 May 25;14:1168663. doi: 10.3389/fendo.2023.1168663. PMID: 37305053; PMCID: PMC10248451.
Orlowska K, Fling RR, Nault R, Schilmiller AL, Zacharewski TR. Cystine/Glutamate Xc- Antiporter Induction Compensates for Transsulfuration Pathway Repression by 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) to Ensure Cysteine for Hepatic Glutathione Biosynthesis. Chem Res Toxicol. 2023 Jun 19;36(6):900-915. doi:10.1021/acs.chemrestox.3c00017. Epub 2023 May 15. PMID: 37184393; PMCID: PMC10284067.
Steidemann MM, Liu J, Bayes K, Castro LP, Ferguson-Miller S, LaPres JJ. Evidence for crosstalk between the aryl hydrocarbon receptor and the translocator protein in mouse lung epithelial cells. Exp Cell Res. 2023 Aug 1;429(1):113617. doi: 10.1016/j.yexcr.2023.113617. Epub 2023 May 10. PMID: 37172753; PMCID: PMC10330775.
Yu K, Lv Y, Liu C, Boyd SA, Teppen BJ, Li H. Reaction of decabromodiphenyl ether with organo-modified clay-templated zero-valent iron in water-tetrahydrofuran solution: Nano- to micrometric scale effects. J Hazard Mater. 2023 Mar 5;445:130538. doi: 10.1016/j.jhazmat.2022.130538. Epub 2022 Dec 8. PMID: 37055959; PMCID: PMC10105828.
Cholico GN, Orlowska K, Fling RR, Sink WJ, Zacharewski NA, Fader KA, Nault R, Zacharewski T. Consequences of reprogramming acetyl-CoA metabolism by 2,3,7,8-tetrachlorodibenzo-p-dioxin in the mouse liver. Sci Rep. 2023 Mar 13;13(1):4138. doi: 10.1038/s41598-023-31087-9. PMID: 36914879; PMCID: PMC10011583.
Nault R, Saha S, Bhattacharya S, Sinha S, Maiti T, Zacharewski T. Single-cell transcriptomics shows dose-dependent disruption of hepatic zonation by TCDD in mice. Toxicol Sci. 2023 Jan 31;191(1):135-148. doi: 10.1093/toxsci/kfac109. PMID: 36222588; PMCID: PMC9887712.
Liu R, Zacharewski TR, Conolly RB, Zhang Q. A Physiologically Based Pharmacokinetic (PBPK) Modeling Framework for Mixtures of Dioxin-like Compounds. Toxics. 2022 Nov 17;10(11):700. doi: 10.3390/toxics10110700. PMID: 36422908; PMCID: PMC9698634.
Shi Z, Xia M, Xiao S, Zhang Q. Identification of nonmonotonic concentration-responses in Tox21 high-throughput screening estrogen receptor assays. Toxicol Appl Pharmacol. 2022 Oct 1;452:116206. doi: 10.1016/j.taap.2022.116206. Epub 2022 Aug 19. PMID: 35988584; PMCID: PMC9452481.
Orlowska K, Fling RR, Nault R, Sink WJ, Schilmiller AL, Zacharewski T. Dioxin-elicited decrease in cobalamin redirects propionyl-CoA metabolism to the β-oxidation-like pathway resulting in acrylyl-CoA conjugate buildup. J Biol Chem. 2022 Sep;298(9):102301. doi: 10.1016/j.jbc.2022.102301. Epub 2022 Aug 2. PMID: 35931118; PMCID: PMC9418907.
Liu S, Pi J, Zhang Q. Signal amplification in the KEAP1-NRF2-ARE antioxidant response pathway. Redox Biol. 2022 Aug;54:102389. doi:10.1016/j.redox.2022.102389. Epub 2022 Jun 30. PMID: 35792437; PMCID: PMC9287733.
Zhou J, Blevins LK, Crawford RB, Kaminski NE. Role of Programmed Cell Death Protein-1 and Lymphocyte Specific Protein Tyrosine Kinase in the Aryl Hydrocarbon Receptor- Mediated Impairment of the IgM Response in Human CD5+ Innate-Like B Cells. Front Immunol. 2022 Apr 26;13:884203. doi:10.3389/fimmu.2022.884203. PMID: 35558082; PMCID: PMC9088000.
Cholico GN, Nault R, Zacharewski TR. Genome-Wide ChIPseq Analysis of AhR, COUP-TF, and HNF4 Enrichment in TCDD-Treated Mouse Liver. Int J Mol Sci. 2022 Jan 29;23(3):1558. doi: 10.3390/ijms23031558. PMID: 35163483; PMCID: PMC8836158.
Nault R, Saha S, Bhattacharya S, Dodson J, Sinha S, Maiti T, Zacharewski T. Benchmarking of a Bayesian single cell RNAseq differential gene expression test for dose-response study designs. Nucleic Acids Res. 2022 May 6;50(8):e48. doi:10.1093/nar/gkac019. PMID: 35061903; PMCID: PMC9071439.
Fling RR, Zacharewski TR. Aryl Hydrocarbon Receptor (AhR) Activation by 2,3,7,8-Tetrachlorodibenzo-p-Dioxin (TCDD) Dose-Dependently Shifts the Gut Microbiome Consistent with the Progression of Non-Alcoholic Fatty Liver Disease. Int J Mol Sci. 2021 Nov 18;22(22):12431. doi: 10.3390/ijms222212431. PMID: 34830313; PMCID: PMC8625315.
Kumbale CM, Voit EO, Zhang Q. Emergence and Enhancement of Ultrasensitivity through Posttranslational Modulation of Protein Stability. Biomolecules. 2021 Nov 22;11(11):1741. doi: 10.3390/biom11111741. PMID: 34827739; PMCID: PMC8615576.
Liu S, Pi J, Zhang Q. Mathematical modeling reveals quantitative properties of KEAP1-NRF2 signaling. Redox Biol. 2021 Nov;47:102139. doi: 10.1016/j.redox.2021.102139. Epub 2021 Sep 22. PMID: 34600335; PMCID: PMC8531862.
Mutter TY, Zylstra GJ. Differential Roles of Three Different Upper Pathway meta Ring Cleavage Product Hydrolases in the Degradation of Dibenzo-p-Dioxin and Dibenzofuran by Sphingomonas wittichii Strain RW1. Appl Environ Microbiol. 2021 Oct 28;87(22):e0106721. doi: 10.1128/AEM.01067-21. Epub 2021 Sep 1. PMID: 34469199; PMCID: PMC8552877.
Cholico GN, Fling RR, Zacharewski NA, Fader KA, Nault R, Zacharewski TR. Thioesterase induction by 2,3,7,8-tetrachlorodibenzo-p-dioxin results in a futile cycle that inhibits hepatic β-oxidation. Sci Rep. 2021 Aug 3;11(1):15689. doi: 10.1038/s41598-021-95214-0. PMID: 34344994; PMCID: PMC8333094.
Williams MR, Stedtfeld RD, Stedtfeld TM, Crawford RB, Kuwahara T, Kaminski NE, Tiedje JM, Hashsham SA. MicroRNA-based host response to toxicant exposure is influenced by the presence of gut microbial populations. Sci Total Environ. 2021 Nov 25;797:149130. doi: 10.1016/j.scitotenv. 2021.149130. Epub 2021 Jul 20. PMID: 34311349; PMCID: PMC8464502.
Blevins LK, Zhou J, Crawford RB, Kaminski NE. Identification of a Sensitive Human Immunological Target of Aryl Hydrocarbon Receptor Activation: CD5+ Innate-Like B Cells. Front Immunol. 2021 Apr 15;12:635748. doi:10.3389/fimmu.2021.635748. PMID: 33936048; PMCID: PMC8082145.
Mutter TY, Zylstra GJ. Separate Upper Pathway Ring Cleavage Dioxygenases Are Required for Growth of Sphingomonas wittichii Strain RW1 on Dibenzofuran and Dibenzo-p-Dioxin. Appl Environ Microbiol. 2021 May 11;87(11):e02464-20. doi: 10.1128/AEM.02464-20. PMID: 33741618; PMCID: PMC8208143.
Jurgelewicz A, Dornbos P, Warren M, Nault R, Arkatkar A, Lin H, Threadgill DW, Zacharewski T, LaPres JJ. Genetics-Based Approach to Identify Novel Genes Regulated by the Aryl Hydrocarbon Receptor in Mouse Liver. Toxicol Sci. 2021 May 27;181(2):285-294. doi: 10.1093/toxsci/kfab032. PMID: 33720361; PMCID: PMC8599770.
Warren MR, Radulescu A, Dornbos P, Cuomo D, Zumwalt S, Bueso-Mendoza D, Nitcher M, LaPres JJ, Threadgill DW. Peanut butter as an alternative dose delivery method to prevent strain-dependent orogastric gavage-induced stress in mouse teratogenicity studies. J Pharmacol Toxicol Methods. 2021 Jan-Feb;107:106948. doi: 10.1016/j.vascn.2020.106948. Epub 2020 Dec 30. PMID: 33387613; PMCID: PMC9059485.
Gingrich J, Filipovic D, Conolly R, Bhattacharya S, Veiga-Lopez A. Pregnancy-specific physiologically-based toxicokinetic models for bisphenol A and bisphenol S. Environ Int. 2021 Feb;147:106301. doi:10.1016/j.envint.2020.106301. Epub 2020 Dec 22. PMID: 33360411; PMCID: PMC7856209.
Nault R, Fader KA, Bhattacharya S, Zacharewski TR. Single-Nuclei RNA Sequencing Assessment of the Hepatic Effects of 2,3,7,8-Tetrachlorodibenzo-p-dioxin. Cell Mol Gastroenterol Hepatol. 2021;11(1):147-159. doi: 10.1016/j.jcmgh.2020.07.012. Epub 2020 Aug 10. PMID: 32791302; PMCID: PMC7674514.
Tu YJ, Premachandra GS, Boyd SA, Sallach JB, Li H, Teppen BJ, Johnston CT. Synthesis and evaluation of Fe3O4-impregnated activated carbon for dioxin removal. Chemosphere. 2021 Jan;263:128263. doi: 10.1016/j.chemosphere.2020.128263. Epub 2020 Sep 6. PMID: 33297207; PMCID: PMC7733032.
Yuan Q, Sallach JB, Rhodes G, Bach A, Crawford R, Li H, Johnston CT, Teppen BJ, Kaminski NE, Boyd SA. Natural organic matter does not diminish the mammalian bioavailability of 2,3,7,8-tetrachlorodibenzo-p-dioxin. Chemosphere. 2021 Feb;264(Pt 1):128420. doi: 10.1016/j.chemosphere.2020.128420. Epub 2020 Sep 23. PMID: 33032214; PMCID: PMC7749823.
Fling RR, Doskey CM, Fader KA, Nault R, Zacharewski TR. 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) dysregulates hepatic one carbon metabolism during the progression of steatosis to steatohepatitis with fibrosis in mice. Sci Rep. 2020 Sep 9;10(1):14831. doi: 10.1038/s41598-020-71795-0. PMID: 32908189; PMCID: PMC7481292.
Doskey CM, Fader KA, Nault R, Lydic T, Matthews J, Potter D, Sharratt B, Williams K, Zacharewski T. 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) alters hepatic polyunsaturated fatty acid metabolism and eicosanoid biosynthesis in female Sprague-Dawley rats. Toxicol Appl Pharmacol. 2020 Jul 1;398:115034. doi: 10.1016/j.taap.2020.115034. Epub 2020 May 5. PMID: 32387183; PMCID: PMC7294678.
Dornbos P, Arkatkar AA, LaPres JJ. An Automated Method To Predict Mouse Gene and Protein Sequences Using Variant Data. G3 (Bethesda). 2020 Mar 5;10(3):925-932. doi: 10.1534/g3.119.400983. PMID: 31911484; PMCID: PMC7056971.
Josyula N, Andersen ME, Kaminski NE, Dere E, Zacharewski TR, Bhattacharya S. Gene co-regulation and co-expression in the aryl hydrocarbon receptor-mediated transcriptional regulatory network in the mouse liver. Arch Toxicol. 2020 Jan;94(1):113-126. doi: 10.1007/s00204-019-02620-5. Epub 2019 Nov 14. PMID: 31728591.
Blevins LK, Zhou J, Crawford R, Kaminski NE. TCDD-mediated suppression of naïve human B cell IgM secretion involves aryl hydrocarbon receptor-mediated reduction in STAT3 serine 727 phosphorylation and is restored by interferon-γ. Cell Signal. 2020 Jan;65:109447. doi: 10.1016/j.cellsig.2019.109447. Epub 2019 Oct 31. PMID: 31678681; PMCID: PMC6903688.
Zhang Q, Caudle WM, Pi J, Bhattacharya S, Andersen ME, Kaminski NE, Conolly RB. Embracing Systems Toxicology at Single-Cell Resolution. Curr Opin Toxicol. 2019 Aug;16:49-57. doi: 10.1016/j.cotox.2019.04.003. Epub 2019 Apr 19. PMID: 31768481; PMCID: PMC6876623.
Guo J, Quensen JF, Sun Y, Wang Q, Brown CT, Cole JR, Tiedje JM. Review, Evaluation, and Directions for Gene-Targeted Assembly for Ecological Analyses of Metagenomes. Front Genet. 2019 Oct 15;10:957. doi: 10.3389/fgene.2019.00957. PMID: 31749830; PMCID: PMC6843070.
Dornbos P, Jurgelewicz A, Fader KA, Williams K, Zacharewski TR, LaPres JJ. Characterizing the Role of HMG-CoA Reductase in Aryl Hydrocarbon Receptor-Mediated Liver Injury in C57BL/6 Mice. Sci Rep. 2019 Nov 1;9(1):15828. doi: 10.1038/s41598-019-52001-2. PMID: 31676775; PMCID: PMC6825130.
Zhuang J, Cox JG, Chung M, Hamm JA, Zwickle A, Upham BL. Risk, Stigma, Trustworthiness, and Citizen Participation-A Multifaceted Analysis of Media Coverage of Dioxin Contamination in Midland, Michigan. Int J Environ Res Public Health. 2019 Oct 29;16(21):4165. doi: 10.3390/ijerph16214165. PMID: 31671717; PMCID: PMC6862584.
Cox JG, Chung M, Hamm JA, Zwickle A, Cruz SM, Dearing JW. Working with Institutional Stakeholders: Propositions for Alternative Approaches to Community Engagement. Int J Environ Res Public Health. 2019 Oct 19;16(20):4010. doi: 10.3390/ijerph16204010. PMID: 31635112; PMCID: PMC6844076.
Zwickle A, Cox JG, Zhuang J, Hamm JA, Upham BL, Chung M, Cruz S, Dearing JW. The Effect of Dioxin Contamination and Remediation on Property Values. Int J Environ Res Public Health. 2019 Oct 15;16(20):3900. doi: 10.3390/ijerph16203900. PMID: 31618820; PMCID: PMC6843844.
Dearing JW. Scaling Up Solutions to Toxic Contamination in Communities. Int J Environ Res Public Health. 2019 Aug 22;16(17):3034. doi: 10.3390/ijerph16173034. PMID: 31443335; PMCID: PMC6747373.
Fader KA, Nault R, Doskey CM, Fling RR, Zacharewski TR. 2,3,7,8-Tetrachlorodibenzo-p-dioxin abolishes circadian regulation of hepatic metabolic activity in mice. Sci Rep. 2019 Apr 24;9(1):6514. doi: 10.1038/s41598-019-42760-3. PMID: 31015483; PMCID: PMC6478849.
Davis JD, Kumbale CM, Zhang Q, Voit EO. Dynamical systems approaches to personalized medicine. Curr Opin Biotechnol. 2019 Aug;58:168-174. doi: 10.1016/j.copbio.2019.03.005. Epub 2019 Apr 9. PMID: 30978644; PMCID: PMC7050596.
Hamm JA, Cox J, Zwickle G, Zhuang J, Cruz S, Upham BL, Chung M, Dearing JW. Trust in Whom? Dioxin, Organizations, Risk Perception, and Fish Consumption in Michigan's Saginaw Bay Watershed. J Risk Res. 2019;22(12):1624-1637. doi: 10.1080/13669877.2018.1501599. Epub 2018 Oct 11. PMID: 32336934; PMCID: PMC7182128.