1
|
Chambers BA, Basili D, Word L, Baker N, Middleton A, Judson RS, Shah I. Searching for LINCS to Stress: Using Text Mining to Automate Reference Chemical Curation. Chem Res Toxicol 2024. [PMID: 38736322 DOI: 10.1021/acs.chemrestox.3c00335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Abstract
Adaptive stress response pathways (SRPs) restore cellular homeostasis following perturbation but may activate terminal outcomes like apoptosis, autophagy, or cellular senescence if disruption exceeds critical thresholds. Because SRPs hold the key to vital cellular tipping points, they are targeted for therapeutic interventions and assessed as biomarkers of toxicity. Hence, we are developing a public database of chemicals that perturb SRPs to enable new data-driven tools to improve public health. Here, we report on the automated text-mining pipeline we used to build and curate the first version of this database. We started with 100 reference SRP chemicals gathered from published biomarker studies to bootstrap the database. Second, we used information retrieval to find co-occurrences of reference chemicals with SRP terms in PubMed abstracts and determined pairwise mutual information thresholds to filter biologically relevant relationships. Third, we applied these thresholds to find 1206 putative SRP perturbagens within thousands of substances in the Library of Integrated Network-Based Cellular Signatures (LINCS). To assign SRP activity to LINCS chemicals, domain experts had to manually review at least three publications for each of 1206 chemicals out of 181,805 total abstracts. To accomplish this efficiently, we implemented a machine learning approach to predict SRP classifications from texts to prioritize abstracts. In 5-fold cross-validation testing with a corpus derived from the 100 reference chemicals, artificial neural networks performed the best (F1-macro = 0.678) and prioritized 2479/181,805 abstracts for expert review, which resulted in 457 chemicals annotated with SRP activities. An independent analysis of enriched mechanisms of action and chemical use class supported the text-mined chemical associations (p < 0.05): heat shock inducers were linked with HSP90 and DNA damage inducers to topoisomerase inhibition. This database will enable novel applications of LINCS data to evaluate SRP activities and to further develop tools for biomedical information extraction from the literature.
Collapse
Affiliation(s)
- Bryant A Chambers
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, United States
| | - Danilo Basili
- Unilever, Safety and Environmental Assurance Centre (SEAC), Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, U.K
| | - Laura Word
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, United States
| | - Nancy Baker
- Leidos, Research Triangle Park, North Carolina 27711, United States
| | - Alistair Middleton
- Unilever, Safety and Environmental Assurance Centre (SEAC), Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, U.K
| | - Richard S Judson
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, United States
| | - Imran Shah
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, United States
| |
Collapse
|
2
|
Corton JC, Matteo G, Chorley B, Liu J, Vallanat B, Everett L, Atlas E, Meier MJ, Williams A, Yauk CL. A 50-gene biomarker identifies estrogen receptor-modulating chemicals in a microarray compendium. Chem Biol Interact 2024; 394:110952. [PMID: 38570061 DOI: 10.1016/j.cbi.2024.110952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/01/2024] [Accepted: 03/09/2024] [Indexed: 04/05/2024]
Abstract
High throughput transcriptomics (HTTr) profiling has the potential to rapidly and comprehensively identify molecular targets of environmental chemicals that can be linked to adverse outcomes. We describe here the construction and characterization of a 50-gene expression biomarker designed to identify estrogen receptor (ER) active chemicals in HTTr datasets. Using microarray comparisons, the genes in the biomarker were identified as those that exhibited consistent directional changes when ER was activated (4 ER agonists; 4 ESR1 gene constitutively active mutants) and opposite directional changes when ER was suppressed (4 antagonist treatments; 4 ESR1 knockdown experiments). The biomarker was evaluated as a predictive tool using the Running Fisher algorithm by comparison to annotated gene expression microarray datasets including those evaluating the transcriptional effects of hormones and chemicals in MCF-7 cells. Depending on the reference dataset used, the biomarker had a predictive accuracy for activation of up to 96%. To demonstrate applicability for HTTr data analysis, the biomarker was used to identify ER activators in a set of 15 chemicals that are considered potential bisphenol A (BPA) alternatives examined at up to 10 concentrations in MCF-7 cells and analyzed by full-genome TempO-Seq. Using benchmark dose (BMD) modeling, the biomarker genes stratified the ER potency of BPA alternatives consistent with previous studies. These results demonstrate that the ER biomarker can be used to accurately identify ER activators in transcript profile data derived from MCF-7 cells.
Collapse
Affiliation(s)
- J Christopher Corton
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, Research Triangle Park, NC, 27711, USA.
| | - Geronimo Matteo
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, K1A 0K9, Canada; Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada.
| | - Brian Chorley
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, Research Triangle Park, NC, 27711, USA.
| | - Jie Liu
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, Research Triangle Park, NC, 27711, USA.
| | - Beena Vallanat
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, Research Triangle Park, NC, 27711, USA.
| | - Logan Everett
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, Research Triangle Park, NC, 27711, USA.
| | - Ella Atlas
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, K1A 0K9, Canada.
| | - Matthew J Meier
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, K1A 0K9, Canada.
| | - Andrew Williams
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, K1A 0K9, Canada.
| | - Carole Lyn Yauk
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada.
| |
Collapse
|
3
|
Shukla A, Khan MGM, Cayarga AA, Namvarpour M, Chowdhury MMH, Levesque D, Lucier JF, Boisvert FM, Ramanathan S, Ilangumaran S. The Tumor Suppressor SOCS1 Diminishes Tolerance to Oxidative Stress in Hepatocellular Carcinoma. Cancers (Basel) 2024; 16:292. [PMID: 38254783 PMCID: PMC10814246 DOI: 10.3390/cancers16020292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
SOCS1 is a tumor suppressor in hepatocellular carcinoma (HCC). Recently, we showed that a loss of SOCS1 in hepatocytes promotes NRF2 activation. Here, we investigated how SOCS1 expression in HCC cells affected oxidative stress response and modulated the cellular proteome. Murine Hepa1-6 cells expressing SOCS1 (Hepa-SOCS1) or control vector (Hepa-Vector) were treated with cisplatin or tert-butyl hydroperoxide (t-BHP). The induction of NRF2 and its target genes, oxidative stress, lipid peroxidation, cell survival and cellular proteome profiles were evaluated. NRF2 induction was significantly reduced in Hepa-SOCS1 cells. The gene and protein expression of NRF2 targets were differentially induced in Hepa-Vector cells but markedly suppressed in Hepa-SOCS1 cells. Hepa-SOCS1 cells displayed an increased induction of reactive oxygen species but reduced lipid peroxidation. Nonetheless, Hepa-SOCS1 cells treated with cisplatin or t-BHP showed reduced survival. GCLC, poorly induced in Hepa-SOCS1 cells, showed a strong positive correlation with NFE2L2 and an inverse correlation with SOCS1 in the TCGA-LIHC transcriptomic data. A proteomic analysis of Hepa-Vector and Hepa-SOCS1 cells revealed that SOCS1 differentially modulated many proteins involved in diverse molecular pathways, including mitochondrial ROS generation and ROS detoxification, through peroxiredoxin and thioredoxin systems. Our findings indicate that maintaining sensitivity to oxidative stress is an important tumor suppression mechanism of SOCS1 in HCC.
Collapse
Affiliation(s)
- Akhil Shukla
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; (A.S.); (M.G.M.K.); (A.A.C.); (M.N.); (M.M.H.C.); (D.L.); (F.-M.B.); (S.R.)
| | - Md Gulam Musawwir Khan
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; (A.S.); (M.G.M.K.); (A.A.C.); (M.N.); (M.M.H.C.); (D.L.); (F.-M.B.); (S.R.)
| | - Anny Armas Cayarga
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; (A.S.); (M.G.M.K.); (A.A.C.); (M.N.); (M.M.H.C.); (D.L.); (F.-M.B.); (S.R.)
| | - Mozhdeh Namvarpour
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; (A.S.); (M.G.M.K.); (A.A.C.); (M.N.); (M.M.H.C.); (D.L.); (F.-M.B.); (S.R.)
| | - Mohammad Mobarak H. Chowdhury
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; (A.S.); (M.G.M.K.); (A.A.C.); (M.N.); (M.M.H.C.); (D.L.); (F.-M.B.); (S.R.)
| | - Dominique Levesque
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; (A.S.); (M.G.M.K.); (A.A.C.); (M.N.); (M.M.H.C.); (D.L.); (F.-M.B.); (S.R.)
| | - Jean-François Lucier
- Department of Biology, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada;
| | - François-Michel Boisvert
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; (A.S.); (M.G.M.K.); (A.A.C.); (M.N.); (M.M.H.C.); (D.L.); (F.-M.B.); (S.R.)
| | - Sheela Ramanathan
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; (A.S.); (M.G.M.K.); (A.A.C.); (M.N.); (M.M.H.C.); (D.L.); (F.-M.B.); (S.R.)
- Centre de Recherche, Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Subburaj Ilangumaran
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; (A.S.); (M.G.M.K.); (A.A.C.); (M.N.); (M.M.H.C.); (D.L.); (F.-M.B.); (S.R.)
- Centre de Recherche, Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| |
Collapse
|
4
|
Robarts DR, Dai J, Lau C, Apte U, Corton JC. Hepatic Transcriptome Comparative In Silico Analysis Reveals Similar Pathways and Targets Altered by Legacy and Alternative Per- and Polyfluoroalkyl Substances in Mice. TOXICS 2023; 11:963. [PMID: 38133364 PMCID: PMC10748317 DOI: 10.3390/toxics11120963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/20/2023] [Accepted: 11/25/2023] [Indexed: 12/23/2023]
Abstract
Per- and poly-fluoroalkyl substances (PFAS) are a large class of fluorinated carbon chains that include legacy PFAS, such as perfluorooctane sulfonate (PFOS), perfluorooctanoic acid (PFOA), perfluorononanoic acid (PFNA), and perfluorohexane sulfonate (PFHxS). These compounds induce adverse health effects, including hepatotoxicity. Potential alternatives to the legacy PFAS (HFPO-DA (GenX), HFPO4, HFPO-TA, F-53B, 6:2 FTSA, and 6:2 FTCA), as well as a byproduct of PFAS manufacturing (Nafion BP2), are increasingly being found in the environment. The potential hazards of these new alternatives are less well known. To better understand the diversity of molecular targets of the PFAS, we performed a comparative toxicogenomics analysis of the gene expression changes in the livers of mice exposed to these PFAS, and compared these to five activators of PPARα, a common target of many PFAS. Using hierarchical clustering, pathway analysis, and predictive biomarkers, we found that most of the alternative PFAS modulate molecular targets that overlap with legacy PFAS. Only three of the 11 PFAS tested did not appreciably activate PPARα (Nafion BP2, 6:2 FTSA, and 6:2 FTCA). Predictive biomarkers showed that most PFAS (PFHxS, PFOA, PFOS, PFNA, HFPO-TA, F-53B, HFPO4, Nafion BP2) activated CAR. PFNA, PFHxS, PFOA, PFOS, HFPO4, HFPO-TA, F-53B, Nafion BP2, and 6:2 FTSA suppressed STAT5b, activated NRF2, and activated SREBP. There was no apparent relationship between the length of the carbon chain, type of head group, or number of ether linkages and the transcriptomic changes. This work highlights the similarities in molecular targets between the legacy and alternative PFAS.
Collapse
Affiliation(s)
- Dakota R. Robarts
- Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, Research Triangle Park, NC 27711, USA
| | - Jiayin Dai
- State Environmental Protection Key Laboratory of Environmental Health Impact Assessment of Emerging Contaminants, School of Environmental Sciences and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Christopher Lau
- Center for Public Health and Environmental Assessment, US Environmental Protection Agency, Research Triangle Park, NC 27711, USA
| | - Udayan Apte
- Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - J. Christopher Corton
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, Research Triangle Park, NC 27711, USA
| |
Collapse
|
5
|
Wahlang B. RISING STARS: Sex differences in toxicant-associated fatty liver disease. J Endocrinol 2023; 258:e220247. [PMID: 37074385 PMCID: PMC10330380 DOI: 10.1530/joe-22-0247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 04/19/2023] [Indexed: 04/20/2023]
Abstract
Based on biological sex, the consequential health outcomes from exposures to environmental chemicals or toxicants can differ in disease pathophysiology, progression, and severity. Due to basal differences in cellular and molecular processes resulting from sexual dimorphism of organs including the liver and additional factors influencing 'gene-environment' interactions, males and females can exhibit different responses to toxicant exposures. Associations between environmental/occupational chemical exposures and fatty liver disease (FLD) have been well-acknowledged in human epidemiologic studies and their causal relationships demonstrated in experimental models. However, studies related to sex differences in liver toxicology are still limited to draw any inferences on sex-dependent chemical toxicity. The purpose of this review is to highlight the present state of knowledge on the existence of sex differences in toxicant-associated FLD (TAFLD), discuss potential underlying mechanisms driving these differences, implications of said differences on disease susceptibility, and emerging concepts. Chemicals of interest include various categories of pollutants that have been investigated in TAFLD, namely persistent organic pollutants, volatile organic compounds, and metals. Insight into research areas requiring further development is also discussed, with the objective of narrowing the knowledge gap on sex differences in environmental liver diseases. Major conclusions from this review exercise are that biological sex influences TAFLD risks, in part due to (i) toxicant disruption of growth hormone and estrogen receptor signaling, (ii) basal sex differences in energy mobilization and storage, and (iii) differences in chemical metabolism and subsequent body burden. Finally, further sex-dependent toxicological assessments are warranted for the development of sex-specific intervention strategies.
Collapse
Affiliation(s)
- Banrida Wahlang
- Division of Gastroenterology, Hepatology & Nutrition, Department of Medicine, School of Medicine, University of Louisville, Louisville, KY, 40202, USA
- UofL Superfund Research Center, University of Louisville, Louisville, KY, 40202, USA
- The Center for Integrative Environmental Health Sciences, University of Louisville, Louisville, KY, 40202, USA
| |
Collapse
|
6
|
Sabeti Z, Ansarin A, Ansarin K, Zafari V, Seyedrezazadeh E, Shakerkhatibi M, Asghari-Jafarabadi M, Dastgiri S, Zoroufchi Benis K, Sepehri M, Khamnian Z. Sex-specific association of exposure to air pollutants and Nrf2 gene expression and inflammatory biomarkers in exhaled breath of healthy adolescents. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 326:121463. [PMID: 36958658 DOI: 10.1016/j.envpol.2023.121463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 03/13/2023] [Accepted: 03/18/2023] [Indexed: 06/18/2023]
Abstract
Studies investigating the nuclear factor erythroid 2-related factor 2 (Nrf2) expression levels in the respiratory system of healthy subjects are scarce. Moreover, separate studies on the health-related outcomes of air pollution for each sex are limited. The current panel study investigated sex-specific Nrf2 expression levels and related oxidative stress and inflammatory responses among healthy adolescents exposed to PM2.5, PM10, O3, and PM2.5-bounded metals in a high traffic region. Forty-nine healthy nonsmoking subjects participated in the study for five consecutive months (Nov. 2019 to Feb. 2020). Each subject was asked to provide 1 mL of exhaled breath condensate (EBC). Data were analyzed using linear mixed-effects models. The results showed that PM10, PM2.5, O3, and PM2.5-bounded metals were negatively linked to Nrf2 expression level in EBC of females with -58.3% (95% CI: 79.5, -15.4), -32.1% (95% CI: -50.3, -7.1), -76.2% (95% CI: -92.6, -23.9), and -1.9 (95% CI: -3.4, -0.4), respectively. While our results presented no significant association between the studied pollutants and Nrf2 gene expression in males, significant associations were observed between the pollutants and total nitric oxide (NOx), interleukins 6 (IL-6), and tumor necrosis factor-alpha (TNF-α) in the EBC of females. In the case of males, only EBC cytokines showed a significant association with air pollutants. Overall, this study suggests that exposure to ambient air pollutants may affect the respiratory system with biologically different mechanisms in males and females. PM2.5 concentration had a positive correlation with exhaled TNF-α and IL6 values in females while positive correlation with TNF-α and negative correlation with IL6 values in males. O3 had a negative correlation with TNF-α in males.
Collapse
Affiliation(s)
- Zahra Sabeti
- Health and Environment Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Atefeh Ansarin
- Tuberculosis and Lung Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Khalil Ansarin
- Tuberculosis and Lung Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Rahat Breath and Sleep Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Venus Zafari
- Department of Basic Oncology, Health Institute of Ege University, Izmir, Turkey
| | - Ensiyeh Seyedrezazadeh
- Tuberculosis and Lung Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Shakerkhatibi
- Health and Environment Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Mohammad Asghari-Jafarabadi
- Cabrini Research, Cabrini Health, Malvern, VIC, 3144, Australia; School of Public Health and Preventative Medicine, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC, 3004, Australia; Road Traffic Injury Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Saeed Dastgiri
- Tabriz Health Services Management Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Khaled Zoroufchi Benis
- Department of Chemical and Biological Engineering, University of Saskatchewan, Saskatoon, SK, Canada
| | - Maryam Sepehri
- Tabriz Health Services Management Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Zhila Khamnian
- Department of Community Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| |
Collapse
|
7
|
Ide S, Ide K, Abe K, Kobayashi Y, Kitai H, McKey J, Strausser SA, O'Brien LL, Tata A, Tata PR, Souma T. Sex differences in resilience to ferroptosis underlie sexual dimorphism in kidney injury and repair. Cell Rep 2022; 41:111610. [PMID: 36351395 PMCID: PMC9795409 DOI: 10.1016/j.celrep.2022.111610] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 08/27/2022] [Accepted: 10/14/2022] [Indexed: 11/09/2022] Open
Abstract
In both humans and mice, repair of acute kidney injury is worse in males than in females. Here, we provide evidence that this sexual dimorphism results from sex differences in ferroptosis, an iron-dependent, lipid-peroxidation-driven regulated cell death. Using genetic and single-cell transcriptomic approaches in mice, we report that female sex confers striking protection against ferroptosis, which was experimentally induced in proximal tubular (PT) cells by deleting glutathione peroxidase 4 (Gpx4). Single-cell transcriptomic analyses further identify the NFE2-related factor 2 (NRF2) antioxidant protective pathway as a female resilience mechanism against ferroptosis. Genetic inhibition and pharmacological activation studies show that NRF2 controls PT cell fate and plasticity by regulating ferroptosis. Importantly, pharmacological NRF2 activation protects male PT cells from ferroptosis and improves cellular plasticity as in females. Our data highlight NRF2 as a potential therapeutic target to prevent failed renal repair after acute kidney injury in both sexes by modulating cellular plasticity.
Collapse
Affiliation(s)
- Shintaro Ide
- Division of Nephrology, Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kana Ide
- Division of Nephrology, Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Koki Abe
- Division of Nephrology, Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Yoshihiko Kobayashi
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hiroki Kitai
- Division of Nephrology, Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jennifer McKey
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Sarah A Strausser
- Division of Nephrology, Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Lori L O'Brien
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Aleksandra Tata
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Purushothama Rao Tata
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA; Duke Regeneration Center, Duke University School of Medicine, Durham, NC 27710, USA; Duke Cancer Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Tomokazu Souma
- Division of Nephrology, Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Duke Regeneration Center, Duke University School of Medicine, Durham, NC 27710, USA.
| |
Collapse
|
8
|
Bathish B, Robertson H, Dillon JF, Dinkova-Kostova AT, Hayes JD. Nonalcoholic steatohepatitis and mechanisms by which it is ameliorated by activation of the CNC-bZIP transcription factor Nrf2. Free Radic Biol Med 2022; 188:221-261. [PMID: 35728768 DOI: 10.1016/j.freeradbiomed.2022.06.226] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 06/13/2022] [Indexed: 12/11/2022]
Abstract
Non-alcoholic steatohepatitis (NASH) represents a global health concern. It is characterised by fatty liver, hepatocyte cell death and inflammation, which are associated with lipotoxicity, endoplasmic reticulum (ER) stress, mitochondrial dysfunction, iron overload and oxidative stress. NF-E2 p45-related factor 2 (Nrf2) is a transcription factor that combats oxidative stress. Remarkably, Nrf2 is downregulated during the development of NASH, which probably accelerates disease, whereas in pre-clinical studies the upregulation of Nrf2 inhibits NASH. We now review the scientific literature that proposes Nrf2 downregulation during NASH involves its increased ubiquitylation and proteasomal degradation, mediated by Kelch-like ECH-associated protein 1 (Keap1) and/or β-transducin repeat-containing protein (β-TrCP) and/or HMG-CoA reductase degradation protein 1 (Hrd1, also called synoviolin (SYVN1)). Additionally, downregulation of Nrf2-mediated transcription during NASH may involve diminished recruitment of coactivators by Nrf2, due to increased levels of activating transcription factor 3 (ATF3) and nuclear factor-kappaB (NF-κB) p65, or competition for promoter binding due to upregulation of BTB and CNC homology 1 (Bach1). Many processes that downregulate Nrf2 are triggered by transforming growth factor-beta (TGF-β), with oxidative stress amplifying its signalling. Oxidative stress may also increase suppression of Nrf2 by β-TrCP through facilitating formation of the DSGIS-containing phosphodegron in Nrf2 by glycogen synthase kinase-3. In animal models, knockout of Nrf2 increases susceptibility to NASH, while pharmacological activation of Nrf2 by inducing agents that target Keap1 inhibits development of NASH. These inducing agents probably counter Nrf2 downregulation affected by β-TrCP, Hrd1/SYVN1, ATF3, NF-κB p65 and Bach1, by suppressing oxidative stress. Activation of Nrf2 is also likely to inhibit NASH by ameliorating lipotoxicity, inflammation, ER stress and iron overload. Crucially, pharmacological activation of Nrf2 in mice in which NASH has already been established supresses liver steatosis and inflammation. There is therefore compelling evidence that pharmacological activation of Nrf2 provides a comprehensive multipronged strategy to treat NASH.
Collapse
Affiliation(s)
- Boushra Bathish
- Jacqui Wood Cancer Centre, Division of Cellular Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, Scotland, UK
| | - Holly Robertson
- Jacqui Wood Cancer Centre, Division of Cellular Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, Scotland, UK; Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - John F Dillon
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, UK
| | - Albena T Dinkova-Kostova
- Jacqui Wood Cancer Centre, Division of Cellular Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, Scotland, UK
| | - John D Hayes
- Jacqui Wood Cancer Centre, Division of Cellular Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, Scotland, UK.
| |
Collapse
|
9
|
Corton JC, Liu J, Williams A, Cho E, Yauk CL. A gene expression biomarker identifies inhibitors of two classes of epigenome effectors in a human microarray compendium. Chem Biol Interact 2022; 365:110032. [PMID: 35777453 DOI: 10.1016/j.cbi.2022.110032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 11/03/2022]
Abstract
Biomarkers predictive of molecular and toxicological effects are needed to interpret emerging high-throughput transcriptomics (HTTr) data streams. To address the limited approaches available for identifying epigenotoxicants, we previously developed and validated an 81-gene biomarker that accurately predicts histone deacetylase inhibition (HDACi) in transcript profiles derived from chemically-treated TK6 cells. In the present study, we sought to determine if this biomarker (TGx-HDACi) could be used to identify HDACi chemicals in other cell lines using the Running Fisher correlation test. Using microarray comparisons derived from human cells exposed to HDACi, we found considerable heterogeneity in correlation with the TGx-HDACi biomarker dependent on chemical exposure conditions and tissue from which the cell line was derived. Using a defined set of conditions that overlapped with our earlier study, the biomarker was able to accurately identify HDACi chemicals (90-100% balanced accuracy). In an in silico screen of 2427 chemicals in 9660 chemical versus control comparisons, the biomarker coupled with the Running Fisher test was able to identify 14 additional HDACi chemicals as well as other chemicals not previously associated with HDACi. Most notable were 12 inhibitors of bromodomain (BRD) and extraterminal (BET) family proteins including BRD4 that bind to acetylated histones. The BET protein inhibitors could be distinguished from the HDACi based on differences in the expression of a small set of biomarker genes. Our results indicate that the TGx-HDACi biomarker will be useful for identifying inhibitors of two classes of epigenome effectors in HTTr screening studies.
Collapse
Affiliation(s)
- J Christopher Corton
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, Research Triangle Park, NC, 27711, USA.
| | - Jie Liu
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, Research Triangle Park, NC, 27711, USA.
| | - Andrew Williams
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, Canada.
| | - Eunnara Cho
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, Canada.
| | - Carole L Yauk
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada.
| |
Collapse
|
10
|
Liu A, Han N, Munoz-Muriedas J, Bender A. Deriving time-concordant event cascades from gene expression data: A case study for Drug-Induced Liver Injury (DILI). PLoS Comput Biol 2022; 18:e1010148. [PMID: 35687583 PMCID: PMC9292124 DOI: 10.1371/journal.pcbi.1010148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 07/18/2022] [Accepted: 04/26/2022] [Indexed: 01/10/2023] Open
Abstract
Adverse event pathogenesis is often a complex process which compromises multiple events ranging from the molecular to the phenotypic level. In toxicology, Adverse Outcome Pathways (AOPs) aim to formalize this as temporal sequences of events, in which event relationships should be supported by causal evidence according to the tailored Bradford-Hill criteria. One of the criteria is whether events are consistently observed in a certain temporal order and, in this work, we study this time concordance using the concept of “first activation” as data-driven means to generate hypotheses on potentially causal mechanisms. As a case study, we analysed liver data from repeat-dose studies in rats from the TG-GATEs database which comprises measurements across eight timepoints, ranging from 3 hours to 4 weeks post-treatment. We identified time-concordant gene expression-derived events preceding adverse histopathology, which serves as surrogate readout for Drug-Induced Liver Injury (DILI). We find known mechanisms in DILI to be time-concordant, and show further that significance, frequency and log fold change (logFC) of differential expression are metrics which can additionally prioritize events although not necessary to be mechanistically relevant. Moreover, we used the temporal order of transcription factor (TF) expression and regulon activity to identify transcriptionally regulated TFs and subsequently combined this with prior knowledge on functional interactions to derive detailed gene-regulatory mechanisms, such as reduced Hnf4a activity leading to decreased expression and activity of Cebpa. At the same time, also potentially novel events are identified such as Sox13 which is highly significantly time-concordant and shows sustained activation over time. Overall, we demonstrate how time-resolved transcriptomics can derive and support mechanistic hypotheses by quantifying time concordance and how this can be combined with prior causal knowledge, with the aim of both understanding mechanisms of toxicity, as well as potential applications to the AOP framework. We make our results available in the form of a Shiny app (https://anikaliu.shinyapps.io/dili_cascades), which allows users to query events of interest in more detail. Understanding mechanisms from systems-scale biological data is of great relevance in toxicology as well as drug discovery; however how to generate causal hypotheses instead of correlations is by no means clear. In this work, we study the conserved temporal order of events and present an automatable framework to quantify and characterize time concordance across a large set of time-series. We apply this concept to events derived from time-resolved gene expression and histopathology from the TG-GATEs in vivo liver data as a case study. We were able to recover known events involved in the pathogenesis of Drug-Induced Liver Injury (DILI), and identify potentially novel pathway and transcription factors (TFs) which precede adverse histopathology. As complementary sources of evidence for causality, we additionally show how time concordance and prior knowledge on plausible interactions between TFs can be combined to derive causal hypotheses on the TFs’ mode of regulation and interaction partners. Overall, the results derived in our case study can serve as valuable hypothesis-free starting points for the development of Adverse Outcome Pathways for DILI, and demonstrate that our approach provides a novel angle to prioritize mechanistically relevant events.
Collapse
Affiliation(s)
- Anika Liu
- Milner Therapeutics Institute, University of Cambridge, Cambridge, United Kingdom
- Systems Modelling and Translational Biology, Data and Computational Sciences, GSK, London, United Kingdom
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (AL); (AB)
| | - Namshik Han
- Milner Therapeutics Institute, University of Cambridge, Cambridge, United Kingdom
- Cambridge Centre for AI in Medicine, Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, United Kingdom
| | - Jordi Munoz-Muriedas
- Systems Modelling and Translational Biology, Data and Computational Sciences, GSK, London, United Kingdom
- Computer-Aided Drug Design, UCB, Slough, United Kingdom
| | - Andreas Bender
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (AL); (AB)
| |
Collapse
|
11
|
Christopher Corton J, Mitchell CA, Auerbach S, Bushel JP, Ellinger-Ziegelbauer H, Escobar PA, Froetschl R, Harrill AH, Johnson K, Klaunig JE, Pandiri AR, Podtelezhnikov AA, Rager JE, Tanis KQ, van der Laan JW, Vespa A, Yauk CL, Pettit SD, Sistare FD. A Collaborative Initiative to Establish Genomic Biomarkers for Assessing Tumorigenic Potential to Reduce Reliance on Conventional Rodent Carcinogenicity Studies. Toxicol Sci 2022; 188:4-16. [PMID: 35404422 PMCID: PMC9238304 DOI: 10.1093/toxsci/kfac041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
There is growing recognition across broad sectors of the scientific community that use of genomic biomarkers has the potential to reduce the need for conventional rodent carcinogenicity studies of industrial chemicals, agrochemicals, and pharmaceuticals through a weight-of-evidence approach. These biomarkers fall into 2 major categories: (1) sets of gene transcripts that can identify distinct tumorigenic mechanisms of action; and (2) cancer driver gene mutations indicative of rapidly expanding growth-advantaged clonal cell populations. This call-to-action article describes a collaborative approach launched to develop and qualify biomarker gene expression panels that measure widely accepted molecular pathways linked to tumorigenesis and their activation levels to predict tumorigenic doses of chemicals from short-term exposures. Growing evidence suggests that application of such biomarker panels in short-term exposure rodent studies can identify both tumorigenic hazard and tumorigenic activation levels for chemical-induced carcinogenicity. In the future, this approach will be expanded to include methodologies examining mutations in key cancer driver gene mutation hotspots as biomarkers of both genotoxic and nongenotoxic chemical tumor risk. Analytical, technical, and biological validation studies of these complementary genomic tools are being undertaken by multisector and multidisciplinary collaborative teams within the Health and Environmental Sciences Institute. Success from these efforts will facilitate the transition from current heavy reliance on conventional 2-year rodent carcinogenicity studies to more rapid animal- and resource-sparing approaches for mechanism-based carcinogenicity evaluation supporting internal and regulatory decision-making.
Collapse
Affiliation(s)
- J Christopher Corton
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, Research Triangle Park, NC, USA
| | | | - Scott Auerbach
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - J Pierre Bushel
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, USA
| | | | - Patricia A Escobar
- Safety Assessment and Laboratory Animal Resources, Merck Sharp & Dohme Corp, West Point, PA, USA
| | - Roland Froetschl
- BfArM-Bundesinstitut für Arzneimittel und Medizinprodukte, Federal Institute for Drugs and Medical Devices, Kurt-Georg-Kiesinger-Allee 3, Bonn, Germany
| | - Alison H Harrill
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | | | - James E Klaunig
- Laboratory of Investigative Toxicology and Pathology, Department of Environmental and Occupational Health, Indiana School of Public Health, Indiana University, Bloomington, IN, USA
| | - Arun R Pandiri
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | | | - Julia E Rager
- The Institute for Environmental Health Solutions, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Keith Q Tanis
- Safety Assessment and Laboratory Animal Resources, Merck Sharp & Dohme Corp, West Point, PA, USA
| | - Jan Willem van der Laan
- Section on Pharmacology, Toxicology and Kinetics, Medicines Evaluation Board, Utrecht, The Netherlands
| | - Alisa Vespa
- Therapeutic Products Directorate, Health Canada, Ottawa, Canada
| | - Carole L Yauk
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Syril D Pettit
- Health and Environmental Sciences Institute, Washington, DC, USA
| | - Frank D Sistare
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| |
Collapse
|
12
|
Korunes KL, Liu J, Huang R, Xia M, Houck KA, Corton JC. A gene expression biomarker for predictive toxicology to identify chemical modulators of NF-κB. PLoS One 2022; 17:e0261854. [PMID: 35108274 PMCID: PMC8809623 DOI: 10.1371/journal.pone.0261854] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 12/12/2021] [Indexed: 11/29/2022] Open
Abstract
The nuclear factor-kappa B (NF-κB) is a transcription factor with important roles in inflammation, immune response, and oncogenesis. Dysregulation of NF-κB signaling is associated with inflammation and certain cancers. We developed a gene expression biomarker predictive of NF-κB modulation and used the biomarker to screen a large compendia of gene expression data. The biomarker consists of 108 genes responsive to tumor necrosis factor α in the absence but not the presence of IκB, an inhibitor of NF-κB. Using a set of 450 profiles from cells treated with immunomodulatory factors with known NF-κB activity, the balanced accuracy for prediction of NF-κB activation was > 90%. The biomarker was used to screen a microarray compendium consisting of 12,061 microarray comparisons from human cells exposed to 2,672 individual chemicals to identify chemicals that could cause toxic effects through NF-κB. There were 215 and 49 chemicals that were identified as putative or known NF-κB activators or suppressors, respectively. NF-κB activators were also identified using two high-throughput screening assays; 165 out of the ~3,800 chemicals (ToxCast assay) and 55 out of ~7,500 unique compounds (Tox21 assay) were identified as potential activators. A set of 32 chemicals not previously associated with NF-κB activation and which partially overlapped between the different screens were selected for validation in wild-type and NFKB1-null HeLa cells. Using RT-qPCR and targeted RNA-Seq, 31 of the 32 chemicals were confirmed to be NF-κB activators. These results comprehensively identify a set of chemicals that could cause toxic effects through NF-κB.
Collapse
Affiliation(s)
- Katharine L. Korunes
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, Research Triangle Park, North Carolina, United States of America
- Biology Department, Duke University, Durham, North Carolina, United States of America
| | - Jie Liu
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, Research Triangle Park, North Carolina, United States of America
| | - Ruili Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Menghang Xia
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Keith A. Houck
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, Research Triangle Park, North Carolina, United States of America
| | - J. Christopher Corton
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, Research Triangle Park, North Carolina, United States of America
- * E-mail:
| |
Collapse
|
13
|
Rooney J, Wehmas LC, Ryan N, Chorley BN, Hester SD, Kenyon EM, Schmid JE, George BJ, Hughes MF, Sey YM, Tennant AH, Simmons JE, Wood CE, Corton JC. Genomic comparisons between hepatocarcinogenic and non-hepatocarcinogenic organophosphate insecticides in the mouse liver. Toxicology 2022; 465:153046. [PMID: 34813904 DOI: 10.1016/j.tox.2021.153046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 11/12/2021] [Accepted: 11/17/2021] [Indexed: 11/27/2022]
Abstract
Short-term biomarkers of toxicity have an increasingly important role in the screening and prioritization of new chemicals. In this study, we examined early indicators of liver toxicity for three reference organophosphate (OP) chemicals, which are among the most widely used insecticides in the world. The OP methidathion was previously shown to increase the incidence of liver toxicity, including hepatocellular tumors, in male mice. To provide insights into the adverse outcome pathway (AOP) that underlies these tumors, effects of methidathion in the male mouse liver were examined after 7 and 28 day exposures and compared to those of two other OPs that either do not increase (fenthion) or possibly suppress liver cancer (parathion) in mice. None of the chemicals caused increases in liver weight/body weight or histopathological changes in the liver. Parathion decreased liver cell proliferation after 7 and 28 days while the other chemicals had no effects. There was no evidence for hepatotoxicity in any of the treatment groups. Full-genome microarray analysis of the livers from the 7 and 28 day treatments demonstrated that methidathion and fenthion regulated a large number of overlapping genes, while parathion regulated a unique set of genes. Examination of cytochrome P450 enzyme activities and use of predictive gene expression biomarkers found no consistent evidence for activation of AhR, CAR, PXR, or PPARα. Parathion suppressed the male-specific gene expression pattern through STAT5b, similar to genetic and dietary conditions that decrease liver tumor incidence in mice. Overall, these findings indicate that methidathion causes liver cancer by a mechanism that does not involve common mechanisms of liver cancer induction.
Collapse
Affiliation(s)
- John Rooney
- Oak Ridge Institute for Science and Education (ORISE) Research Participant at US EPA, Office of Research and Development, Center for Computational Toxicology and Exposure (formerly NHEERL), Research Triangle Park, NC, 27711, United States; National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, United States(3).
| | - Leah C Wehmas
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, United States.
| | - Natalia Ryan
- Oak Ridge Institute for Science and Education (ORISE) Research Participant at US EPA, Office of Research and Development, Center for Computational Toxicology and Exposure (formerly NHEERL), Research Triangle Park, NC, 27711, United States; National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, United States(3).
| | - Brian N Chorley
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, United States.
| | - Susan D Hester
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, United States.
| | - Elaina M Kenyon
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, United States.
| | - Judith E Schmid
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, United States(3).
| | - Barbara Jane George
- Center for Public Health and Environmental Assessment, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, United States.
| | - Michael F Hughes
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, United States.
| | - Yusupha M Sey
- Center for Public Health and Environmental Assessment, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, United States.
| | - Alan H Tennant
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, United States.
| | - Jane Ellen Simmons
- Center for Public Health and Environmental Assessment, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, United States.
| | - Charles E Wood
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, United States(3).
| | - J Christopher Corton
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, United States.
| |
Collapse
|
14
|
Alam MS, Czajkowsky DM. SARS-CoV-2 infection and oxidative stress: Pathophysiological insight into thrombosis and therapeutic opportunities. Cytokine Growth Factor Rev 2021; 63:44-57. [PMID: 34836751 PMCID: PMC8591899 DOI: 10.1016/j.cytogfr.2021.11.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/07/2021] [Accepted: 11/08/2021] [Indexed: 01/08/2023]
Abstract
The current coronavirus disease 2019 (COVID-19) pandemic has presented unprecedented challenges to global health. Although the majority of COVID-19 patients exhibit mild-to-no symptoms, many patients develop severe disease and need immediate hospitalization, with most severe infections associated with a dysregulated immune response attributed to a cytokine storm. Epidemiological studies suggest that overall COVID-19 severity and morbidity correlate with underlying comorbidities, including diabetes, obesity, cardiovascular diseases, and immunosuppressive conditions. Patients with such comorbidities exhibit elevated levels of reactive oxygen species (ROS) and oxidative stress caused by an increased accumulation of angiotensin II and by activation of the NADPH oxidase pathway. Moreover, accumulating evidence suggests that oxidative stress coupled with the cytokine storm contribute to COVID-19 pathogenesis and immunopathogenesis by causing endotheliitis and endothelial cell dysfunction and by activating the blood clotting cascade that results in blood coagulation and microvascular thrombosis. In this review, we survey the mechanisms of how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induces oxidative stress and the consequences of this stress on patient health. We further shed light on aspects of the host immunity that are crucial to prevent the disease during the early phase of infection. A better understanding of the disease pathophysiology as well as preventive measures aimed at lowering ROS levels may pave the way to mitigate SARS-CoV-2-induced complications and decrease mortality.
Collapse
Affiliation(s)
- Mohammad Shah Alam
- Department of Anatomy and Histology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh.
| | - Daniel M Czajkowsky
- Bio-ID Centre, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| |
Collapse
|
15
|
Carter RN, Gibbins MTG, Barrios-Llerena ME, Wilkie SE, Freddolino PL, Libiad M, Vitvitsky V, Emerson B, Le Bihan T, Brice M, Su H, Denham SG, Homer NZM, Mc Fadden C, Tailleux A, Faresse N, Sulpice T, Briand F, Gillingwater T, Ahn KH, Singha S, McMaster C, Hartley RC, Staels B, Gray GA, Finch AJ, Selman C, Banerjee R, Morton NM. The hepatic compensatory response to elevated systemic sulfide promotes diabetes. Cell Rep 2021; 37:109958. [PMID: 34758301 PMCID: PMC8595646 DOI: 10.1016/j.celrep.2021.109958] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 07/06/2021] [Accepted: 10/15/2021] [Indexed: 12/12/2022] Open
Abstract
Impaired hepatic glucose and lipid metabolism are hallmarks of type 2 diabetes. Increased sulfide production or sulfide donor compounds may beneficially regulate hepatic metabolism. Disposal of sulfide through the sulfide oxidation pathway (SOP) is critical for maintaining sulfide within a safe physiological range. We show that mice lacking the liver- enriched mitochondrial SOP enzyme thiosulfate sulfurtransferase (Tst-/- mice) exhibit high circulating sulfide, increased gluconeogenesis, hypertriglyceridemia, and fatty liver. Unexpectedly, hepatic sulfide levels are normal in Tst-/- mice because of exaggerated induction of sulfide disposal, with associated suppression of global protein persulfidation and nuclear respiratory factor 2 target protein levels. Hepatic proteomic and persulfidomic profiles converge on gluconeogenesis and lipid metabolism, revealing a selective deficit in medium-chain fatty acid oxidation in Tst-/- mice. We reveal a critical role of TST in hepatic metabolism that has implications for sulfide donor strategies in the context of metabolic disease.
Collapse
Affiliation(s)
- Roderick N Carter
- University/British Heart Foundation Centre for Cardiovascular Science, University of Edinburgh, Queen's Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - Matthew T G Gibbins
- University/British Heart Foundation Centre for Cardiovascular Science, University of Edinburgh, Queen's Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - Martin E Barrios-Llerena
- University/British Heart Foundation Centre for Cardiovascular Science, University of Edinburgh, Queen's Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - Stephen E Wilkie
- University/British Heart Foundation Centre for Cardiovascular Science, University of Edinburgh, Queen's Medical Research Institute, Edinburgh EH16 4TJ, UK; Glasgow Ageing Research Network (GARNER), Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - Peter L Freddolino
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Marouane Libiad
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Victor Vitvitsky
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Barry Emerson
- University/British Heart Foundation Centre for Cardiovascular Science, University of Edinburgh, Queen's Medical Research Institute, Edinburgh EH16 4TJ, UK
| | | | - Madara Brice
- University/British Heart Foundation Centre for Cardiovascular Science, University of Edinburgh, Queen's Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - Huizhong Su
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XR, UK
| | - Scott G Denham
- University/British Heart Foundation Centre for Cardiovascular Science, University of Edinburgh, Queen's Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - Natalie Z M Homer
- University/British Heart Foundation Centre for Cardiovascular Science, University of Edinburgh, Queen's Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - Clare Mc Fadden
- University/British Heart Foundation Centre for Cardiovascular Science, University of Edinburgh, Queen's Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - Anne Tailleux
- Université de Lille, INSERM, CHU Lille, Institut Pasteur de Lille, U101-EGID, 59000, Lille, France
| | - Nourdine Faresse
- Physiogenex S.A.S, Prologue Biotech, 516 rue Pierre et Marie Curie, 31670 Labège, France
| | - Thierry Sulpice
- Physiogenex S.A.S, Prologue Biotech, 516 rue Pierre et Marie Curie, 31670 Labège, France
| | - Francois Briand
- Physiogenex S.A.S, Prologue Biotech, 516 rue Pierre et Marie Curie, 31670 Labège, France
| | - Tom Gillingwater
- College of Medicine & Veterinary Medicine, University of Edinburgh, Old Medical School (Anatomy), Teviot Place, Edinburgh EH8 9AG, UK
| | - Kyo Han Ahn
- Department of Chemistry, POSTECH, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyungbuk 37673, South Korea
| | - Subhankar Singha
- Department of Chemistry, POSTECH, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyungbuk 37673, South Korea
| | - Claire McMaster
- School of Chemistry, Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK
| | - Richard C Hartley
- School of Chemistry, Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK
| | - Bart Staels
- Université de Lille, INSERM, CHU Lille, Institut Pasteur de Lille, U101-EGID, 59000, Lille, France
| | - Gillian A Gray
- University/British Heart Foundation Centre for Cardiovascular Science, University of Edinburgh, Queen's Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - Andrew J Finch
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XR, UK
| | - Colin Selman
- Glasgow Ageing Research Network (GARNER), Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - Ruma Banerjee
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Nicholas M Morton
- University/British Heart Foundation Centre for Cardiovascular Science, University of Edinburgh, Queen's Medical Research Institute, Edinburgh EH16 4TJ, UK.
| |
Collapse
|
16
|
Cervantes PW, Corton JC. A Gene Expression Biomarker Predicts Heat Shock Factor 1 Activation in a Gene Expression Compendium. Chem Res Toxicol 2021; 34:1721-1737. [PMID: 34170685 DOI: 10.1021/acs.chemrestox.0c00510] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The United States Environmental Protection Agency (US EPA) recently developed a tiered testing strategy to use advances in high-throughput transcriptomics (HTTr) testing to identify molecular targets of thousands of environmental chemicals that can be linked to adverse outcomes. Here, we describe a method that uses a gene expression biomarker to predict chemical activation of heat shock factor 1 (HSF1), a transcription factor critical for proteome maintenance. The HSF1 biomarker was built from transcript profiles derived from A375 cells exposed to a HSF1-activating heat shock protein (HSP) 90 inhibitor in the presence or absence of HSF1 expression. The resultant 44 identified genes included those that (1) are dependent on HSF1 for regulation, (2) have direct interactions with HSF1 assessed by ChIP-Seq, and (3) are in the molecular chaperone family. To test for accuracy, the biomarker was compared in a pairwise manner to gene lists derived from treatments with known HSF1 activity (HSP and proteasomal inhibitors) using the correlation-based Running Fisher test; the balanced accuracy for prediction was 96%. A microarray compendium consisting of 12,092 microarray comparisons from human cells exposed to 2670 individual chemicals was screened using our approach; 112 and 19 chemicals were identified as putative HSF1 activators or suppressors, respectively, and most appear to be novel modulators. A large percentage of the chemical treatments that induced HSF1 also induced oxidant-activated NRF2 (∼46%). For five compounds or mixtures, we found that NRF2 activation occurred at lower concentrations or at earlier times than HSF1 activation, supporting the concept of a tiered cellular protection system dependent on the level of chemical-induced stress. The approach described here could be used to identify environmentally relevant chemical HSF1 activators in HTTr data sets.
Collapse
Affiliation(s)
- Patrick W Cervantes
- Center for Computational Toxicology and Exposure, United States Environmental Protection Agency, Research Triangle Park, North Carolina 27711, United States.,Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison 53706, Wisconsin, United States
| | - J Christopher Corton
- Center for Computational Toxicology and Exposure, United States Environmental Protection Agency, Research Triangle Park, North Carolina 27711, United States
| |
Collapse
|
17
|
Fang H, Stone KP, Forney LA, Sims LC, Gutierrez GC, Ghosh S, Gettys TW. Implementation of dietary methionine restriction using casein after selective, oxidative deletion of methionine. iScience 2021; 24:102470. [PMID: 34113817 PMCID: PMC8169944 DOI: 10.1016/j.isci.2021.102470] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/29/2021] [Accepted: 04/22/2021] [Indexed: 01/24/2023] Open
Abstract
Dietary methionine restriction (MR) is normally implemented using diets formulated from elemental amino acids (AA) that reduce methionine content to ∼0.17%. However, translational implementation of MR with elemental AA-based diets is intractable due to poor palatability. To solve this problem and restrict methionine using intact proteins, casein was subjected to mild oxidation to selectively reduce methionine. Diets were then formulated using oxidized casein, adding back methionine to produce a final concentration of 0.17%. The biological efficacy of dietary MR using the oxidized casein (Ox Cas) diet was compared with the standard elemental MR diet in terms of the behavioral, metabolic, endocrine, and transcriptional responses to the four diets. The Ox Cas MR diet faithfully reproduced the expected physiological, biochemical, and transcriptional responses in liver and inguinal white adipose tissue. Collectively, these findings demonstrate that dietary MR can be effectively implemented using casein after selective oxidative reduction of methionine.
Collapse
Affiliation(s)
- Han Fang
- Laboratory of Nutrient Sensing and Adipocyte Signaling, Pennington Biomedical Research Center, Baton Rouge, LA 70808, USA
| | - Kirsten P. Stone
- Laboratory of Nutrient Sensing and Adipocyte Signaling, Pennington Biomedical Research Center, Baton Rouge, LA 70808, USA
| | - Laura A. Forney
- Laboratory of Nutrient Sensing and Adipocyte Signaling, Pennington Biomedical Research Center, Baton Rouge, LA 70808, USA
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Landon C. Sims
- Laboratory of Nutrient Sensing and Adipocyte Signaling, Pennington Biomedical Research Center, Baton Rouge, LA 70808, USA
| | - Gabriela C. Gutierrez
- School of Nutrition and Food Sciences, Louisiana State University, Baton Rouge, LA 70809, USA
| | - Sujoy Ghosh
- Laboratory of Computational Biology, Pennington Biomedical Research Center, Baton Rouge, LA 70808, USA
- Program in Cardiovascular and Metabolic Disorders and Centre for Computational Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Thomas W. Gettys
- Laboratory of Nutrient Sensing and Adipocyte Signaling, Pennington Biomedical Research Center, Baton Rouge, LA 70808, USA
| |
Collapse
|
18
|
Rooney J, Ryan N, Liu J, Houtman R, van Beuningen R, Hsieh JH, Chang G, Chen S, Christopher Corton J. A Gene Expression Biomarker Identifies Chemical Modulators of Estrogen Receptor α in an MCF-7 Microarray Compendium. Chem Res Toxicol 2021; 34:313-329. [PMID: 33405908 PMCID: PMC10683854 DOI: 10.1021/acs.chemrestox.0c00243] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Identification of chemicals that affect hormone-regulated systems will help to predict endocrine disruption. In our previous study, a 46 gene biomarker was found to be an accurate predictor of estrogen receptor (ER) α modulation in chemically treated MCF-7 cells. Here, potential ERα modulators were identified using the biomarker by screening a microarray compendium consisting of ∼1600 gene expression comparisons representing exposure to ∼1200 chemicals. A total of ∼170 chemicals were identified as potential ERα modulators. In the Connectivity Map 2.0 collection, 75 and 39 chemicals were predicted to activate or suppress ERα, and they included 12 and six known ERα agonists and antagonists/selective ERα modulators, respectively. Nineteen and eight of the total number were also identified as active in an ERα transactivation assay carried out in an MCF-7-derived cell line used to screen the Tox21 10K chemical library in agonist or antagonist modes, respectively. Chemicals predicted to modulate ERα in MCF-7 cells were examined further using global and targeted gene expression in wild-type and ERα-null cells, transactivation assays, and cell-free ERα coregulator interaction assays. Environmental chemicals classified as weak and very weak agonists were confirmed to activate ERα including apigenin, kaempferol, and oxybenzone. Novel activators included digoxin, nabumetone, ivermectin, and six progestins. Novel suppressors included emetine, mifepristone, niclosamide, and proscillaridin. Our strategy will be useful to identify environmentally relevant ERα modulators in future high-throughput transcriptomic screens.
Collapse
Affiliation(s)
- John Rooney
- Center for Computational Toxicology and Exposure, US-EPA, Research Triangle Park, NC 27711
- Present address: Integrated Lab Services, Research Triangle Park, NC
| | - Natalia Ryan
- Center for Computational Toxicology and Exposure, US-EPA, Research Triangle Park, NC 27711
- Present address: Bayer Crop Science, Research Triangle Park, NC
| | - Jie Liu
- Center for Computational Toxicology and Exposure, US-EPA, Research Triangle Park, NC 27711
| | - René Houtman
- PamGene International B.V., Den Bosch, The Netherlands
- Present address: Precision Medicine Lab, Oss, The Netherlands
| | | | - Jui-Hua Hsieh
- Kelly Government Solutions, Research Triangle Park, North Carolina
| | - Gregory Chang
- Department of Cancer Biology, Beckman Research Institute of the City of Hope, Duarte,California 91010
| | - Shiuan Chen
- Department of Cancer Biology, Beckman Research Institute of the City of Hope, Duarte,California 91010
| | - J. Christopher Corton
- Center for Computational Toxicology and Exposure, US-EPA, Research Triangle Park, NC 27711
| |
Collapse
|
19
|
Liu J, Lickteig AJ, Zhang Y, Csanaky IL, Klaassen CD. Activation of Nrf2 decreases bile acid concentrations in livers of female mice. Xenobiotica 2021; 51:605-615. [PMID: 33522359 DOI: 10.1080/00498254.2021.1880033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
1. Nuclear factor erythroid 2-related factor 2 (Nrf2) is a master regulator of oxidative/electrophilic stress. Studies suggest a role of Nrf2 in regulating bile acid (BA) metabolism in male mice. However, whether Nrf2 is important for BA homeostasis in female mice remains undefined. In this study, we systematically investigated the effect of Nrf2 activation, either through CDDO-imidazolide (CDDO-Im) treatment or genetic modulation of Kelch-like ECH associating protein 1 (Keap1), on BA homeostasis in female mice.2. Both pharmacological and genetic Nrf2 activation increased mRNA levels of multidrug resistance-associated protein 2 and 3 (Mrp2 and Mrp3), two Nrf2 target genes, in livers and ilea of female mice. Both pharmacological and genetic activation of Nrf2 decreased BA concentrations in the liver, which did not appear to be due to increased biliary BA excretion or decreased ileal BA absorption. Importantly, both pharmacological and genetic activation of Nrf2 downregulated hepatic Cyp7a1 mRNA, which might be attributable to the upregulation of the Fxr-Fgf15 signalling in the ileum.3. To conclude, Nrf2 activation lowers BA concentrations in livers of female mice, which appears to be attributable to the decreased hepatic BA synthesis.
Collapse
Affiliation(s)
- Jing Liu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, P.R.China
| | - Andrew J Lickteig
- Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Youcai Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, P.R.China
| | - Iván L Csanaky
- Division of Clinical Pharmacology, Toxicology, and Therapeutic Innovation, Children's Mercy Hospital and Clinics, Kansas City, MO, USA.,Division of Gastroenterology, Children's Mercy Hospital and Clinics, Kansas City, MO, USA.,Department of Pediatrics, University of Kansas Medical Center, Kansas City, KS, USA
| | - Curtis D Klaassen
- Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| |
Collapse
|
20
|
Liu J, Cui JY, Lu YF, Corton JC, Klaassen CD. Sex-, Age-, and Race/Ethnicity-Dependent Variations in Drug-Processing and NRF2-Regulated Genes in Human Livers. Drug Metab Dispos 2021; 49:111-119. [PMID: 33162398 PMCID: PMC7804821 DOI: 10.1124/dmd.120.000181] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 10/20/2020] [Indexed: 12/14/2022] Open
Abstract
Individual variations in xenobiotic metabolism affect the sensitivity to diseases. In this study, the impacts of sex, age, and race/ethnicity on drug-processing genes and nuclear factor erythroid 2-related factor 2 (NRF2) genes in human livers were examined via QuantiGene multiplex suspension array (226 samples) and quantitative polymerase chain reaction (qPCR) (247 samples) to profile the expression of nuclear receptors, cytochrome P450s, conjugation enzymes, transporters, bile acid metabolism, and NRF2-regulated genes. Sex differences were found in expression of about half of the genes, but in general the differences were not large. For example, females had higher transcript levels of catalase, glutamate-cysteine ligase catalytic subunit (GCLC), heme oxygenase 1 (HO-1), Kelch-like ECH-associated protein 1 (KEAP1), superoxide dismutase 1, and thioredoxin reductase-1 compared with males via qPCR. There were no apparent differences due to age, except children had higher glutamate-cysteine ligase modifier subunit (GCLM) and elderly had higher multidrug resistance protein 3. African Americans had lower expression of farnesoid X receptor (FXR) but higher expression of HO-1, Caucasians had higher expression of organic anion transporter 2, and Hispanics had higher expression of FXR, SULT2A1, small heterodimer partner, and bile salt export pump. An examination of 34 diseased and control human liver samples showed that compared with disease-free livers, fibrotic livers had higher NAD(P)H-quinone oxidoreductase 1 (NQO1), GCLC, GCLM, and NRF2; hepatocellular carcinoma had higher transcript levels of NQO1 and KEAP1; and steatotic livers had lower GCLC, GCLM, and HO-1 expression. In summary, in drug-processing gene and NRF2 genes, sex differences were the major findings, and there were no apparent age differences, and race/ethnicity differences occurred for a few genes. These descriptive findings could add to our understanding of the sex-, age-, and race/ethnicity-dependent differences in drug-processing genes as well as NRF2 genes in normal and diseased human livers. SIGNIFICANCE STATEMENT: In human liver drug-processing and nuclear factor erythroid 2-related factor 2 genes, sex differences were the main finding. There were no apparent differences due to age, except children had higher glutamate-cysteine ligase modifier subunit, and elderly had higher multidrug resistance protein 3. African Americans had lower expression of farnesoid X receptor (FXR) but higher expression of heme oxygenase 1, Caucasians had higher expression of organic anion transporter 2, and Hispanics had higher expression of FXR, small heterodimer partner, SULT2A1, and bile salt export pump.
Collapse
Affiliation(s)
- Jie Liu
- University of Kansas Medical Center, Kansas City, Kansas (J.L., J.Y.C., Y.-F.L., C.D.K.); Zunyi Medical University, Zunyi, China (J.L.,Y.-F.L.); University of Washington, Seattle, Washington (J.Y.C); and Center for Computational Toxicology and Exposure, US EPA, Research Triangle Park, North Carolina (J.L., J.C.C.)
| | - Julia Yue Cui
- University of Kansas Medical Center, Kansas City, Kansas (J.L., J.Y.C., Y.-F.L., C.D.K.); Zunyi Medical University, Zunyi, China (J.L.,Y.-F.L.); University of Washington, Seattle, Washington (J.Y.C); and Center for Computational Toxicology and Exposure, US EPA, Research Triangle Park, North Carolina (J.L., J.C.C.)
| | - Yuan-Fu Lu
- University of Kansas Medical Center, Kansas City, Kansas (J.L., J.Y.C., Y.-F.L., C.D.K.); Zunyi Medical University, Zunyi, China (J.L.,Y.-F.L.); University of Washington, Seattle, Washington (J.Y.C); and Center for Computational Toxicology and Exposure, US EPA, Research Triangle Park, North Carolina (J.L., J.C.C.)
| | - J Christopher Corton
- University of Kansas Medical Center, Kansas City, Kansas (J.L., J.Y.C., Y.-F.L., C.D.K.); Zunyi Medical University, Zunyi, China (J.L.,Y.-F.L.); University of Washington, Seattle, Washington (J.Y.C); and Center for Computational Toxicology and Exposure, US EPA, Research Triangle Park, North Carolina (J.L., J.C.C.)
| | - Curtis D Klaassen
- University of Kansas Medical Center, Kansas City, Kansas (J.L., J.Y.C., Y.-F.L., C.D.K.); Zunyi Medical University, Zunyi, China (J.L.,Y.-F.L.); University of Washington, Seattle, Washington (J.Y.C); and Center for Computational Toxicology and Exposure, US EPA, Research Triangle Park, North Carolina (J.L., J.C.C.)
| |
Collapse
|
21
|
Mining a human transcriptome database for chemical modulators of NRF2. PLoS One 2020; 15:e0239367. [PMID: 32986742 PMCID: PMC7521735 DOI: 10.1371/journal.pone.0239367] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 09/07/2020] [Indexed: 12/14/2022] Open
Abstract
Nuclear factor erythroid-2 related factor 2 (NRF2) encoded by the NFE2L2 gene is a transcription factor critical for protecting cells from chemically-induced oxidative stress. We developed computational procedures to identify chemical modulators of NRF2 in a large database of human microarray data. A gene expression biomarker was built from statistically-filtered gene lists derived from microarray experiments in primary human hepatocytes and cancer cell lines exposed to NRF2-activating chemicals (oltipraz, sulforaphane, CDDO-Im) or in which the NRF2 suppressor Keap1 was knocked down by siRNA. Directionally consistent biomarker genes were further filtered for those dependent on NRF2 using a microarray dataset from cells after NFE2L2 siRNA knockdown. The resulting 143-gene biomarker was evaluated as a predictive tool using the correlation-based Running Fisher algorithm. Using 59 gene expression comparisons from chemically-treated cells with known NRF2 activating potential, the biomarker gave a balanced accuracy of 93%. The biomarker was comprised of many well-known NRF2 target genes (AKR1B10, AKR1C1, NQO1, TXNRD1, SRXN1, GCLC, GCLM), 69% of which were found to be bound directly by NRF2 using ChIP-Seq. NRF2 activity was assessed across ~9840 microarray comparisons from ~1460 studies examining the effects of ~2260 chemicals in human cell lines. A total of 260 and 43 chemicals were found to activate or suppress NRF2, respectively, most of which have not been previously reported to modulate NRF2 activity. Using a NRF2-responsive reporter gene in HepG2 cells, we confirmed the activity of a set of chemicals predicted using the biomarker. The biomarker will be useful for future gene expression screening studies of environmentally-relevant chemicals.
Collapse
|
22
|
Jackson AC, Liu J, Vallanat B, Jones C, Nelms MD, Patlewicz G, Corton JC. Identification of novel activators of the metal responsive transcription factor (MTF-1) using a gene expression biomarker in a microarray compendium. Metallomics 2020; 12:1400-1415. [PMID: 32661532 PMCID: PMC10776036 DOI: 10.1039/d0mt00071j] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Environmental exposure to metals is known to cause a number of human toxicities including cancer. Metal-responsive transcription factor 1 (MTF-1) is an important component of metal regulation systems in mammalian cells. Here, we describe a novel method to identify chemicals that activate MTF-1 based on microarray profiling data. MTF-1 biomarker genes were identified that exhibited consistent, robust expression across 10 microarray comparisons examining the effects of metals (zinc, nickel, lead, arsenic, mercury, and silver) on gene expression in human cells. A subset of the resulting 81 biomarker genes was shown to be altered by knockdown of the MTF1 gene including metallothionein family members and a zinc transporter. The ability to correctly identify treatment conditions that activate MTF-1 was determined by comparing the biomarker to microarray comparisons from cells exposed to reference metal activators of MTF-1 using the rank-based Running Fisher algorithm. The balanced accuracy for prediction was 93%. The biomarker was then used to identify organic chemicals that activate MTF-1 from a compendium of 11 725 human gene expression comparisons representing 2582 chemicals. There were 700 chemicals identified that included those known to interact with cellular metals, such as clioquinol and disulfiram, as well as a set of novel chemicals. All nine of the novel chemicals selected for validation were confirmed to activate MTF-1 biomarker genes in MCF-7 cells and to lesser extents in MTF1-null cells by qPCR and targeted RNA-Seq. Overall, our work demonstrates that the biomarker for MTF-1 coupled with the Running Fisher test is a reliable strategy to identify novel chemical modulators of metal homeostasis using gene expression profiling.
Collapse
Affiliation(s)
- Abigail C Jackson
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, 109 T.W. Alexander Dr. MD-B105-3, Research Triangle Park, NC 27711, USA. and Department of Chemistry, Duke University, Durham, NC 27708, USA
| | - Jie Liu
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, 109 T.W. Alexander Dr. MD-B105-3, Research Triangle Park, NC 27711, USA.
| | - Beena Vallanat
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, 109 T.W. Alexander Dr. MD-B105-3, Research Triangle Park, NC 27711, USA.
| | - Carlton Jones
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, 109 T.W. Alexander Dr. MD-B105-3, Research Triangle Park, NC 27711, USA.
| | - Mark D Nelms
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, 109 T.W. Alexander Dr. MD-B105-3, Research Triangle Park, NC 27711, USA. and Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
| | - Grace Patlewicz
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, 109 T.W. Alexander Dr. MD-B105-3, Research Triangle Park, NC 27711, USA.
| | - J Christopher Corton
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, 109 T.W. Alexander Dr. MD-B105-3, Research Triangle Park, NC 27711, USA.
| |
Collapse
|
23
|
Monroe JJ, Tanis KQ, Podtelezhnikov AA, Nguyen T, Machotka SV, Lynch D, Evers R, Palamanda J, Miller RR, Pippert T, Cabalu TD, Johnson TE, Aslamkhan AG, Kang W, Tamburino AM, Mitra K, Agrawal NGB, Sistare FD. Application of a Rat Liver Drug Bioactivation Transcriptional Response Assay Early in Drug Development That Informs Chemically Reactive Metabolite Formation and Potential for Drug-induced Liver Injury. Toxicol Sci 2020; 177:281-299. [PMID: 32559301 PMCID: PMC7553701 DOI: 10.1093/toxsci/kfaa088] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Drug-induced liver injury is a major reason for drug candidate attrition from development, denied commercialization, market withdrawal, and restricted prescribing of pharmaceuticals. The metabolic bioactivation of drugs to chemically reactive metabolites (CRMs) contribute to liver-associated adverse drug reactions in humans that often goes undetected in conventional animal toxicology studies. A challenge for pharmaceutical drug discovery has been reliably selecting drug candidates with a low liability of forming CRM and reduced drug-induced liver injury potential, at projected therapeutic doses, without falsely restricting the development of safe drugs. We have developed an in vivo rat liver transcriptional signature biomarker reflecting the cellular response to drug bioactivation. Measurement of transcriptional activation of integrated nuclear factor erythroid 2-related factor 2 (NRF2)/Kelch-like ECH-associated protein 1 (KEAP1) electrophilic stress, and nuclear factor erythroid 2-related factor 1 (NRF1) proteasomal endoplasmic reticulum (ER) stress responses, is described for discerning estimated clinical doses of drugs with potential for bioactivation-mediated hepatotoxicity. The approach was established using well benchmarked CRM forming test agents from our company. This was subsequently tested using curated lists of commercial drugs and internal compounds, anchored in the clinical experience with human hepatotoxicity, while agnostic to mechanism. Based on results with 116 compounds in short-term rat studies, with consideration of the maximum recommended daily clinical dose, this CRM mechanism-based approach yielded 32% sensitivity and 92% specificity for discriminating safe from hepatotoxic drugs. The approach adds new information for guiding early candidate selection and informs structure activity relationships (SAR) thus enabling lead optimization and mechanistic problem solving. Additional refinement of the model is ongoing. Case examples are provided describing the strengths and limitations of the approach.
Collapse
Affiliation(s)
| | | | | | | | | | - Donna Lynch
- Safety Assessment & Laboratory Animal Resources
| | - Raymond Evers
- Pharmacokinetics, Pharmacodynamics & Drug Metabolism, Merck & Co., Inc, West Point, Pennsylvania 19486
| | - Jairam Palamanda
- Pharmacokinetics, Pharmacodynamics & Drug Metabolism, Merck & Co., Inc, West Point, Pennsylvania 19486
| | - Randy R Miller
- Pharmacokinetics, Pharmacodynamics & Drug Metabolism, Merck & Co., Inc, West Point, Pennsylvania 19486
| | | | - Tamara D Cabalu
- Pharmacokinetics, Pharmacodynamics & Drug Metabolism, Merck & Co., Inc, West Point, Pennsylvania 19486
| | | | | | - Wen Kang
- Safety Assessment & Laboratory Animal Resources
| | | | - Kaushik Mitra
- Safety Assessment & Laboratory Animal Resources
- Janssen Research & Development, LLC, Spring House, PA 19486
| | - Nancy G B Agrawal
- Pharmacokinetics, Pharmacodynamics & Drug Metabolism, Merck & Co., Inc, West Point, Pennsylvania 19486
| | | |
Collapse
|
24
|
Corton JC, Hill T, Sutherland JJ, Stevens JL, Rooney J. A Set of Six Gene Expression Biomarkers Identify Rat Liver Tumorigens in Short-term Assays. Toxicol Sci 2020; 177:11-26. [PMID: 32603430 PMCID: PMC8026143 DOI: 10.1093/toxsci/kfaa101] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Chemical-induced liver cancer occurs in rodents through well-characterized adverse outcome pathways. We hypothesized that measurement of the 6 most common molecular initiating events (MIEs) in liver cancer adverse outcome pathways in short-term assays using only gene expression will allow early identification of chemicals and their associated doses that are likely to be tumorigenic in the liver in 2-year bioassays. We tested this hypothesis using transcript data from a rat liver microarray compendium consisting of 2013 comparisons of 146 chemicals administered at doses with previously established effects on rat liver tumor induction. Five MIEs were measured using previously characterized gene expression biomarkers composed of gene sets predictive for genotoxicity and activation of 1 or more xenobiotic receptors (aryl hydrocarbon receptor, constitutive activated receptor, estrogen receptor, and peroxisome proliferator-activated receptor α). Because chronic injury can be important in tumorigenesis, we also developed a biomarker for cytotoxicity that had a 96% balanced accuracy. Characterization of the genes in each biomarker set using the unsupervised TXG-MAP network model demonstrated that the genes were associated with distinct functional coexpression modules. Using the Toxicological Priority Index to rank chemicals based on their ability to activate the MIEs showed that chemicals administered at tumorigenic doses clearly gave the highest ranked scores. Balanced accuracies using thresholds derived from either TG-GATES or DrugMatrix data sets to predict tumorigenicity in independent sets of chemicals were up to 93%. These results show that a MIE-directed approach using only gene expression biomarkers could be used in short-term assays to identify chemicals and their doses that cause tumors.
Collapse
Affiliation(s)
- J Christopher Corton
- Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency (EPA), Research Triangle Park, North Carolina
| | - Thomas Hill
- Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency (EPA), Research Triangle Park, North Carolina
- Oak Ridge Institute for Science and Education (ORISE)
| | | | - James L Stevens
- Indiana Biosciences Research Institute, Indianapolis, Indiana
- Paradox Found LLC, Apex, North Carolina
| | - John Rooney
- Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency (EPA), Research Triangle Park, North Carolina
- Oak Ridge Institute for Science and Education (ORISE)
- Integrated Lab Services, Research Triangle Park, NC 27560
| |
Collapse
|
25
|
Zinovkin RA, Grebenchikov OA. Transcription Factor Nrf2 as a Potential Therapeutic Target for Prevention of Cytokine Storm in COVID-19 Patients. BIOCHEMISTRY. BIOKHIMIIA 2020; 85:833-837. [PMID: 33040727 PMCID: PMC7356136 DOI: 10.1134/s0006297920070111] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 06/04/2020] [Accepted: 06/04/2020] [Indexed: 12/17/2022]
Abstract
Nrf2 is a key transcription factor responsible for antioxidant defense in many tissues and cells, including alveolar epithelium, endothelium, and macrophages. Furthermore, Nrf2 functions as a transcriptional repressor that inhibits expression of the inflammatory cytokines in macrophages. Critically ill patients with COVID-19 infection often present signs of high oxidative stress and systemic inflammation - the leading causes of mortality. This article suggests rationale for the use of Nrf2 inducers to prevent development of an excessive inflammatory response in COVID-19 patients.
Collapse
Affiliation(s)
- R A Zinovkin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
- Institute of Mitoengineering, Lomonosov Moscow State University, Moscow, 119992, Russia
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), Moscow, 119991, Russia
| | - O A Grebenchikov
- Negovsky Research Institute of General Reanimatology, Russian Academy of Medical Sciences, Moscow, 107031, Russia
| |
Collapse
|
26
|
Haghani A, Cacciottolo M, Doty KR, D'Agostino C, Thorwald M, Safi N, Levine ME, Sioutas C, Town TC, Forman HJ, Zhang H, Morgan TE, Finch CE. Mouse brain transcriptome responses to inhaled nanoparticulate matter differed by sex and APOE in Nrf2-Nfkb interactions. eLife 2020; 9:e54822. [PMID: 32579111 PMCID: PMC7314548 DOI: 10.7554/elife.54822] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 06/12/2020] [Indexed: 12/13/2022] Open
Abstract
The neurotoxicity of air pollution is undefined for sex and APOE alleles. These major risk factors of Alzheimer's disease (AD) were examined in mice given chronic exposure to nPM, a nano-sized subfraction of urban air pollution. In the cerebral cortex, female mice had two-fold more genes responding to nPM than males. Transcriptomic responses to nPM had sex-APOE interactions in AD-relevant pathways. Only APOE3 mice responded to nPM in genes related to Abeta deposition and clearance (Vav2, Vav3, S1009a). Other responding genes included axonal guidance, inflammation (AMPK, NFKB, APK/JNK signaling), and antioxidant signaling (NRF2, HIF1A). Genes downstream of NFKB and NRF2 responded in opposite directions to nPM. Nrf2 knockdown in microglia augmented NFKB responses to nPM, suggesting a critical role of NRF2 in air pollution neurotoxicity. These findings give a rationale for epidemiologic studies of air pollution to consider sex interactions with APOE alleles and other AD-risk genes.
Collapse
Affiliation(s)
- Amin Haghani
- Leonard Davis School of Gerontology, University of Southern CaliforniaLos AngelesUnited States
| | - Mafalda Cacciottolo
- Leonard Davis School of Gerontology, University of Southern CaliforniaLos AngelesUnited States
| | - Kevin R Doty
- Zilkha Neurogenetic Institute, Department of Physiology and Neuroscience, Keck School of Medicine of the University of Southern CaliforniaLos AngelesUnited States
| | - Carla D'Agostino
- Leonard Davis School of Gerontology, University of Southern CaliforniaLos AngelesUnited States
| | - Max Thorwald
- Leonard Davis School of Gerontology, University of Southern CaliforniaLos AngelesUnited States
| | - Nikoo Safi
- Leonard Davis School of Gerontology, University of Southern CaliforniaLos AngelesUnited States
| | - Morgan E Levine
- Department of Pathology, Yale School of MedicineNew HavenUnited States
| | - Constantinos Sioutas
- Department of Civil and Environmental Engineering, Viterbi School of Engineering, University of Southern CaliforniaLos AngelesUnited States
| | - Terrence C Town
- Zilkha Neurogenetic Institute, Department of Physiology and Neuroscience, Keck School of Medicine of the University of Southern CaliforniaLos AngelesUnited States
| | - Henry Jay Forman
- Leonard Davis School of Gerontology, University of Southern CaliforniaLos AngelesUnited States
| | - Hongqiao Zhang
- Leonard Davis School of Gerontology, University of Southern CaliforniaLos AngelesUnited States
| | - Todd E Morgan
- Leonard Davis School of Gerontology, University of Southern CaliforniaLos AngelesUnited States
| | - Caleb E Finch
- Leonard Davis School of Gerontology, University of Southern CaliforniaLos AngelesUnited States
- Dornsife College, University of Southern CaliforniaLos AngelesUnited States
| |
Collapse
|
27
|
Early microRNA indicators of PPARα pathway activation in the liver. Toxicol Rep 2020; 7:805-815. [PMID: 32642447 PMCID: PMC7334544 DOI: 10.1016/j.toxrep.2020.06.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/01/2020] [Accepted: 06/19/2020] [Indexed: 12/29/2022] Open
Abstract
MicroRNAs (miRNAs) are short non-coding RNA species that play key roles in post-transcriptional regulation of gene expression. MiRNAs also serve as a promising source of early biomarkers for different environmental exposures and health effects, although there is limited information linking miRNA changes to specific target pathways. In this study, we measured liver miRNAs in male B6C3F1 mice exposed to a known chemical activator of the peroxisome proliferator-activated receptor alpha (PPARα) pathway, di(2-ethylhexyl) phthalate (DEHP), for 7 and 28 days at concentrations of 0, 750, 1500, 3000, or 6000 ppm in feed. At the highest dose tested, DEHP altered 61 miRNAs after 7 days and 171 miRNAs after 28 days of exposure, with 48 overlapping miRNAs between timepoints. Analysis of these 48 common miRNAs indicated enrichment in PPARα–related targets and other pathways related to liver injury and cancer. Four of the 10 miRNAs exhibiting a clear dose trend were linked to the PPARα pathway: mmu-miRs-125a-5p, -182−5p, -20a−5p, and -378a−3p. mmu-miRs-182−5p and -378a−3p were subsequently measured using digital drop PCR across a dose range for DEHP and two related phthalates with weaker PPARα activity, di-n-octyl phthalate and n-butyl benzyl phthalate, following 7-day exposures. Analysis of mmu-miRs-182−5p and -378a−3p by transcriptional benchmark dose analysis correctly identified DEHP as having the greatest potency. However, benchmark dose estimates for DEHP based on these miRNAs (average 163; range 126−202 mg/kg-day) were higher on average than values for PPARα target genes (average 74; range 29−183 mg/kg-day). These findings identify putative miRNA biomarkers of PPARα pathway activity and suggest that early miRNA changes may be used to stratify chemical potency.
Collapse
Key Words
- AIC, Akaike Information Criterion
- ALT, alanine aminotransferase
- AOP, adverse outcome pathway
- AST, aspartate aminotransferase
- Acox1, acyl-Coenzyme A oxidase 1
- Adverse outcome pathway (AOP)
- AhR, aryl hydrocarbon receptor
- BBP, n-butyl benzyl phthalate
- BMD, benchmark dose
- BMDA, apical-based benchmark dose
- BMDL, BMD lower confidence interval
- BMDT, transcriptional-based benchmark dose
- BMR, benchmark response
- BROD, benzyloxyresorufin O-debenzylation
- Benchmark dose (BMD)
- Biomarkers
- CAR, constitutive androstane receptor
- DEGs, differentially expressed genes
- DEHP, di (2-thylhexyl) phthalate
- DEmiRs, differentially expressed miRNAs
- DNOP, di-n-octyl phthalate
- EPA, U.S. Environmental Protection Agency
- EROD, ethoxyresorufin O-dealkylation
- GEO, Gene Expression Omnibus
- HCA, hepatocellular adenoma
- HCC, hepatocellular carcinoma
- Hepatocellular carcinoma
- IPA, Ingenuity Pathway Analysis
- Liver toxicity
- MOA, mode of action
- MicroRNAs
- Mode of action (MOA)
- Nrf2, nuclear receptor erythroid 2-like 2
- POD, point-of-departure
- PPARα, peroxisome proliferator-activated receptor alpha
- PROD, pentoxyresorufin O-depentylation
- PXR, pregnane X receptor
- Peroxisome proliferator-activated receptor alpha (PPARα)
- Phthalate
- SDH, sorbitol dehydrogenase
- TMM, trimmed mean of M-values
- ddPCR, droplet digital polymerase chain reaction
- mRNA, messenger RNA
- miRNAs, microRNAs
- mtDNA, mitochondrial
- rRNA, ribosomal RNA
- smallRNA-seq, small RNA sequencing
- tRNA, transfer RNA
Collapse
|
28
|
Rooney JP, Oshida K, Kumar R, Baldwin WS, Corton JC. Chemical Activation of the Constitutive Androstane Receptor Leads to Activation of Oxidant-Induced Nrf2. Toxicol Sci 2019; 167:172-189. [PMID: 30203046 DOI: 10.1093/toxsci/kfy231] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Exposure to environmentally relevant chemicals that activate the xenobiotic receptors aryl hydrocarbon receptor (AhR), constitutive androstane receptor (CAR), and peroxisome proliferator-activated receptor alpha (PPARα) in rodent test systems often leads to increases in oxidative stress (OS) that contributes to liver cancer induction. We hypothesized that activation of the oxidant-induced transcription factor Nrf2 could be used as a surrogate endpoint for increases in OS. We examined the relationships between activation of xenobiotic receptors and Nrf2 using previously characterized gene expression biomarkers that accurately predict modulation. Using a correlation approach (Running Fisher Test), the biomarkers were compared with microarray profiles in a mouse liver gene expression compendium. Out of the 163 chemicals examined, 47% from 53 studies activated Nrf2. We found consistent coupling between CAR and Nrf2 activation. Out of the 41 chemicals from 32 studies that activated CAR, 90% also activated Nrf2. CAR was activated earlier and at lower doses than Nrf2, indicating CAR activation preceded Nrf2 activation. Nrf2 activation by 2 CAR activators was abolished in CAR-null mice. We hypothesized that Nrf2 is activated by reactive oxygen species from the increased activity of enzymes encoded by Cyp2b family members. However, Nrf2 was similarly activated in the livers of both TCPOBOP-treated wild-type and Cyp2b9/10/13-null mice. This study provides evidence that Nrf2 activation (1) often occurs after exposure to xenobiotic chemicals, (2) is tightly linked to activation of CAR, and (3) does not require induction of 3 Cyp2b genes secondary to CAR activation.
Collapse
Affiliation(s)
- John P Rooney
- National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711.,Oak Ridge Institute for Science and Education (ORISE) participant at the National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina
| | - Keiyu Oshida
- National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711.,Toray Industries, Inc, Kanagawa, Japan
| | - Ramiya Kumar
- Environmental Toxicology Program and Biological Sciences Department, Clemson University, Clemson, South Carolina 29634
| | - William S Baldwin
- Environmental Toxicology Program and Biological Sciences Department, Clemson University, Clemson, South Carolina 29634
| | - J Christopher Corton
- National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711
| |
Collapse
|
29
|
Zhang G, Cui R, Kang Y, Qi C, Ji X, Zhang T, Guo Q, Cui H, Shi G. Testosterone propionate activated the Nrf2-ARE pathway in ageing rats and ameliorated the age-related changes in liver. Sci Rep 2019; 9:18619. [PMID: 31819135 PMCID: PMC6901587 DOI: 10.1038/s41598-019-55148-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 11/25/2019] [Indexed: 12/16/2022] Open
Abstract
The present study aimed to evaluate the protective efficacy of testosterone propionate (TP) on age-related liver changes via activation of the nuclear factor erythroid 2-related factor 2-antioxidant response element (Nrf2-ARE) pathway in aged rats. Aged rats received subcutaneous injections of TP (2 mg/kg/d, 84 days). Oxidative stress parameters and the expression levels of signal transducer and activator of transcription 5b (STAT5b), Kelch-like ECH associating protein-1 (Keap1), Nrf2, haem oxygenase-1 (HO-1) and NAD(P)H: quinone oxidoreductase-1 (NQO1) in liver tissues were examined to check whether the Nrf2-ARE pathway was involved in the age-related changes in liver. Our results showed that TP supplementation alleviated liver morphology, liver function and liver fibrosis; improved oxidative stress parameters; and increased the expression of STAT5b, Nrf2, HO-1 and NQO-1 and decreased the expression of Keap1 in the liver tissues of aged rats. These results suggested that TP increased the expression of STAT5b, and then activated the Nrf2-ARE pathway and promoted antioxidant mechanisms in aged rats. These findings may provide new therapeutic uses for TP in patients with age-related liver changes.
Collapse
Affiliation(s)
- Guoliang Zhang
- Department of Neurobiology, Hebei Medical University, Shijiazhuang, 050017, P.R. China.,Department of Human Anatomy, Hebei Medical University, Shijiazhuang, 050017, P.R. China
| | - Rui Cui
- Department of Human Anatomy, Hebei Medical University, Shijiazhuang, 050017, P.R. China
| | - Yunxiao Kang
- Department of Neurobiology, Hebei Medical University, Shijiazhuang, 050017, P.R. China
| | - Chunxiao Qi
- Department of Human Anatomy, Hebei Medical University, Shijiazhuang, 050017, P.R. China
| | - Xiaoming Ji
- Department of Neurobiology, Hebei Medical University, Shijiazhuang, 050017, P.R. China
| | - Tianyun Zhang
- Department of Neurobiology, Hebei Medical University, Shijiazhuang, 050017, P.R. China
| | - Qiqing Guo
- Department of Neurobiology, Hebei Medical University, Shijiazhuang, 050017, P.R. China
| | - Huixian Cui
- Department of Human Anatomy, Hebei Medical University, Shijiazhuang, 050017, P.R. China.,Neuroscience Research Center, Hebei Medical University, Shijiazhuang, 050017, P.R. China
| | - Geming Shi
- Department of Neurobiology, Hebei Medical University, Shijiazhuang, 050017, P.R. China. .,Neuroscience Research Center, Hebei Medical University, Shijiazhuang, 050017, P.R. China. .,Hebei Key Laboratory of Forensic Medicine, Department of Forensic Medicine, Hebei Medical University, Shijiazhuang, 050017, P.R. China.
| |
Collapse
|
30
|
Christopher Corton J. Integrating gene expression biomarker predictions into networks of adverse outcome pathways. CURRENT OPINION IN TOXICOLOGY 2019. [DOI: 10.1016/j.cotox.2019.05.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
31
|
Taguchi K, Kensler TW. Nrf2 in liver toxicology. Arch Pharm Res 2019; 43:337-349. [PMID: 31782059 DOI: 10.1007/s12272-019-01192-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 11/19/2019] [Indexed: 12/14/2022]
Abstract
Liver plays essential roles in the metabolism of many endogenous chemicals and exogenous toxicants. Mechanistic studies in liver have been at the forefront of efforts to probe the roles of bioactivation and detoxication of environmental toxins and toxicants in hepatotoxicity. Moreover, idiosyncratic hepatoxicity remains a key barrier in the clinical development of drugs. The now vast Nrf2 field emerged in part from biochemical and molecular studies on chemical inducers of hepatic detoxication enzymes and subsequent characterization of the modulation of drug/toxicant induced hepatotoxicities in mice through disruption of either Nrf2 or Keap1 genes. In general, loss of Nrf2 increases the sensitivity to such toxic chemicals, highlighting a central role of this transcription factor and its downstream target genes as a modifier to chemical stress. In this review, we summarize the impact of Nrf2 on the toxicology of multiple hepatotoxicants, and discuss efforts to utilize the Nrf2 response in predictive toxicology.
Collapse
Affiliation(s)
- Keiko Taguchi
- Department of Medical Biochemistry, Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba, Sendai, 980-8575, Japan.
| | - Thomas W Kensler
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N, Seattle, WA, 98109, USA
| |
Collapse
|
32
|
Corton JC, Kleinstreuer NC, Judson RS. Identification of potential endocrine disrupting chemicals using gene expression biomarkers. Toxicol Appl Pharmacol 2019; 380:114683. [DOI: 10.1016/j.taap.2019.114683] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 07/05/2019] [Accepted: 07/15/2019] [Indexed: 02/07/2023]
|
33
|
Schwarz M, Lossow K, Kopp JF, Schwerdtle T, Kipp AP. Crosstalk of Nrf2 with the Trace Elements Selenium, Iron, Zinc, and Copper. Nutrients 2019; 11:E2112. [PMID: 31491970 PMCID: PMC6770424 DOI: 10.3390/nu11092112] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/19/2019] [Accepted: 08/23/2019] [Indexed: 01/14/2023] Open
Abstract
Trace elements, like Cu, Zn, Fe, or Se, are important for the proper functioning of antioxidant enzymes. However, in excessive amounts, they can also act as pro-oxidants. Accordingly, trace elements influence redox-modulated signaling pathways, such as the Nrf2 pathway. Vice versa, Nrf2 target genes belong to the group of transport and metal binding proteins. In order to investigate whether Nrf2 directly regulates the systemic trace element status, we used mice to study the effect of a constitutive, whole-body Nrf2 knockout on the systemic status of Cu, Zn, Fe, and Se. As the loss of selenoproteins under Se-deprived conditions has been described to further enhance Nrf2 activity, we additionally analyzed the combination of Nrf2 knockout with feeding diets that provide either suboptimal, adequate, or supplemented amounts of Se. Experiments revealed that the Nrf2 knockout partially affected the trace element concentrations of Cu, Zn, Fe, or Se in the intestine, liver, and/or plasma. However, aside from Fe, the other three trace elements were only marginally modulated in an Nrf2-dependent manner. Selenium deficiency mainly resulted in increased plasma Zn levels. One putative mediator could be the metal regulatory transcription factor 1, which was up-regulated with an increasing Se supply and downregulated in Se-supplemented Nrf2 knockout mice.
Collapse
Affiliation(s)
- Maria Schwarz
- Department of Molecular Nutritional Physiology, Institute of Nutritional Sciences, Friedrich Schiller University Jena, Dornburger Str. 24, 07743 Jena, Germany
- TraceAge-DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly, D-13353 Potsdam-Berlin-Jena, Germany
| | - Kristina Lossow
- Department of Molecular Nutritional Physiology, Institute of Nutritional Sciences, Friedrich Schiller University Jena, Dornburger Str. 24, 07743 Jena, Germany
- TraceAge-DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly, D-13353 Potsdam-Berlin-Jena, Germany
- German Institute of Human Nutrition, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
- Department of Food Chemistry, Institute of Nutritional Science, University of Potsdam, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
| | - Johannes F Kopp
- TraceAge-DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly, D-13353 Potsdam-Berlin-Jena, Germany
- Department of Food Chemistry, Institute of Nutritional Science, University of Potsdam, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
| | - Tanja Schwerdtle
- TraceAge-DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly, D-13353 Potsdam-Berlin-Jena, Germany
- Department of Food Chemistry, Institute of Nutritional Science, University of Potsdam, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
| | - Anna P Kipp
- Department of Molecular Nutritional Physiology, Institute of Nutritional Sciences, Friedrich Schiller University Jena, Dornburger Str. 24, 07743 Jena, Germany.
- TraceAge-DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly, D-13353 Potsdam-Berlin-Jena, Germany.
| |
Collapse
|
34
|
Corton JC, Witt KL, Yauk CL. Identification of p53 Activators in a Human Microarray Compendium. Chem Res Toxicol 2019; 32:1748-1759. [PMID: 31397557 DOI: 10.1021/acs.chemrestox.9b00052] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Biomarkers predictive of molecular and toxicological effects are needed to interpret emerging high-throughput transcriptomic data streams. The previously characterized 63 gene TGx-DDI biomarker that includes 20 genes known to be regulated by p53 was previously shown to accurately predict DNA damage in chemically treated cells. We comprehensively evaluated whether the molecular basis of the DDI predictions was based on a p53-dependent response. The biomarker was compared to microarray data in a compendium derived from human cells using the Running Fisher test, a nonparametric correlation test. Using the biomarker, we identified conditions that led to p53 activation, including exposure to the chemical nutlin-3 which disrupts interactions between p53 and the negative regulator MDM2 or by knockdown of MDM2. The expression of most of the genes in the biomarker (75%) were found to depend on p53 activation status based on gene behavior after TP53 overexpression or knockdown. The biomarker identified DDI chemicals that were strong inducers of p53 in wild-type cells; these p53 responses were decreased or abolished in cells after p53 knockdown by siRNAs. Using the biomarker, we screened ∼1950 chemicals in ∼9800 human cell line chemical vs control comparisons and identified ∼100 chemicals that caused p53 activation. Among the positive chemicals were many that are known to activate p53 through direct and indirect DNA damaging mechanisms. These results contribute to the evidence that the TGx-DDI biomarker is useful for identifying chemicals that cause DDI and activate p53.
Collapse
Affiliation(s)
- J Christopher Corton
- Integrated Systems Toxicology Division, NHEERL , United States Environmental Protection Agency , Research Triangle Park, Durham , North Carolina 27711 , United States
| | - Kristine L Witt
- Division of the National Toxicology Program , National Institute of Environmental Health Sciences , Research Triangle Park, Durham , North Carolina 27709 , United States
| | - Carole L Yauk
- Environmental Health Science and Research Bureau, Health Canada , Ottawa , Ontario K1A 0K9 , Canada
| |
Collapse
|
35
|
Brown-Borg HM, Rakoczy S, Wonderlich JA, Borg KE, Rojanathammanee L. Metabolic adaptation of short-living growth hormone transgenic mice to methionine restriction and supplementation. Ann N Y Acad Sci 2019; 1418:118-136. [PMID: 29722030 DOI: 10.1111/nyas.13687] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 02/17/2018] [Accepted: 02/26/2018] [Indexed: 01/07/2023]
Abstract
Extension of mammalian health and life span has been achieved using various dietary interventions. We previously reported that restricting dietary methionine (MET) content extends life span only when growth hormone signaling is intact (no life span increase in GH deficiency or GH resistance). To understand the metabolic responses of altered dietary MET in the context of accelerated aging (high GH), the current study evaluated MET and related pathways in short-living GH transgenic (GH Tg) and wild-type mice following 8 weeks of restricted (0.16%), low (0.43%), or enriched (1.3%) MET consumption. Liver MET metabolic enzymes were suppressed in GH Tg compared to diet-matched wild-type mice. MET metabolite levels were differentially affected by GH status and diet. SAM:SAH ratios were markedly higher in GH Tg mice. Glutathione levels were lower in both genotypes consuming 0.16% MET but reduced in GH Tg mice when compared to wild type. Tissue thioredoxin and glutaredoxin were impacted by diet and GH status. The responsiveness to the different MET diets is reflected across many metabolic pathways indicating the importance of GH signaling in the ability to discriminate dietary amino acid levels and alter metabolism and life span.
Collapse
Affiliation(s)
- Holly M Brown-Borg
- Department of Biomedical Sciences, University of North Dakota School of Medicine & Health Sciences, Grand Forks, North Dakota
| | - Sharlene Rakoczy
- Department of Biomedical Sciences, University of North Dakota School of Medicine & Health Sciences, Grand Forks, North Dakota
| | - Joseph A Wonderlich
- Department of Biomedical Sciences, University of North Dakota School of Medicine & Health Sciences, Grand Forks, North Dakota.,Department of Psychology, George Mason University, Fairfax, Virginia
| | - Kurt E Borg
- Education Resources, University of North Dakota School of Medicine & Health Sciences, Grand Forks, North Dakota
| | - Lalida Rojanathammanee
- Department of Biomedical Sciences, University of North Dakota School of Medicine & Health Sciences, Grand Forks, North Dakota.,School of Sports Science, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| |
Collapse
|
36
|
Corton JC. Frequent Modulation of the Sterol Regulatory Element Binding Protein (SREBP) by Chemical Exposure in the Livers of Rats. ACTA ACUST UNITED AC 2019; 10:113-129. [PMID: 30931410 DOI: 10.1016/j.comtox.2019.01.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Inappropriate activation of sterol regulatory element-binding proteins (SREBPs) can lead to non-alcoholic fatty liver disease (NAFLD). To link chemical exposure to SREBP activity, a previously characterized gene expression biomarker (Rooney et al., 2019) was used to identify microarray comparisons from rat liver that exhibited significant positive or negative correlation to the biomarker. The effects of 620 chemicals on SREBP activity were examined across 9305 chemical-dose-time microarray comparisons. SREBP was found to be frequently modulated by chemical exposure with 54% of the chemicals affecting SREBP activity. Activators included inhibitors of cholesterogenesis that act to inhibit HMG-CoA reductase (statins) or inhibit Cyp51 (conazoles). Most chemical effects were transient, lasting usually no more than 2-4 days. Modulation of SREBP in most cases led to coordinated increases or decreases in lipogenic and cholesterogenic genes. However, 570 chemical exposure conditions were identified in which regulation was uncoupled. Most of these conditions affected cholesterogenic genes in the absence of parallel effects on lipogenic genes. Together, these findings show that SREBP is a frequent target of chemical exposure and expression of lipogenic and cholesterogenic genes can be uncoupled.
Collapse
Affiliation(s)
- J Christopher Corton
- Integrated Systems Toxicology Division, NHEERL/ORD, US-EPA, Research Triangle Park, NC 27711
| |
Collapse
|