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Corton JC, Ledbetter V, Cohen SM, Atlas E, Yauk CL, Liu J. A transcriptomic biomarker predictive of cell proliferation for use in adverse outcome pathway-informed testing and assessment. Toxicol Sci 2024; 201:174-189. [PMID: 39137154 DOI: 10.1093/toxsci/kfae102] [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] [Indexed: 08/15/2024] Open
Abstract
High-throughput transcriptomics (HTTr) is increasingly being used to identify molecular targets of chemicals that can be linked to adverse outcomes. Cell proliferation (CP) is an important key event in chemical carcinogenesis. Here, we describe the construction and characterization of a gene expression biomarker that is predictive of the CP status in human and rodent tissues. The biomarker was constructed from 30 genes known to be increased in expression in prostate cancers relative to surrounding tissues and in cycling human MCF-7 cells after estrogen receptor (ER) agonist exposure. Using a large compendium of gene expression profiles to test utility, the biomarker could identify increases in CP in (i) 308 out of 367 tumor vs. normal surrounding tissue comparisons from 6 human organs, (ii) MCF-7 cells after activation of ER, (iii) after partial hepatectomy in mice and rats, and (iv) the livers of mice and rats after exposure to nongenotoxic hepatocarcinogens. The biomarker identified suppression of CP (i) under conditions of p53 activation by DNA damaging agents in human cells, (ii) in human A549 lung cells exposed to therapeutic anticancer kinase inhibitors (dasatinib, nilotnib), and (iii) in the mouse liver when comparing high levels of CP at birth to the low background levels in the adult. The responses using the biomarker were similar to those observed using conventional markers of CP including PCNA, Ki67, and BrdU labeling. The CP biomarker will be a useful tool for interpretation of HTTr data streams to identify CP status after exposure to chemicals in human cells or in rodent tissues.
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Affiliation(s)
- J Christopher Corton
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, Research Triangle Park, NC 27711, United States
| | - Victoria Ledbetter
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, Research Triangle Park, NC 27711, United States
| | - Samuel M Cohen
- Department of Pathology and Microbiology and Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 69198-3135, United States
| | - Ella Atlas
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch (HECSB) Health Canada, Ottawa, ON K2K 0K9, Canada
| | - Carole L Yauk
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Jie Liu
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, Research Triangle Park, NC 27711, United States
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2
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Beal MA, Coughlan MC, Nunnikhoven A, Gagné M, Barton-Maclaren TS, Bradford LM, Rowan-Carroll A, Williams A, Meier MJ. High-throughput transcriptomics toxicity assessment of eleven data-poor bisphenol A alternatives. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 361:124827. [PMID: 39197648 DOI: 10.1016/j.envpol.2024.124827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 08/22/2024] [Accepted: 08/25/2024] [Indexed: 09/01/2024]
Abstract
Bisphenol A (BPA), a widely used chemical in the production of plastics and epoxy resins, has garnered significant attention due to its association with adverse health effects, particularly its endocrine-disrupting properties. Regulatory measures aimed at reducing human exposure to BPA have led to a proliferation of alternative chemicals used in various consumer and industrial products. While these alternatives serve to reduce BPA exposure, concerns have arisen regarding their safety and potential toxicity as regrettable substitutes. Previous efforts have demonstrated that in vitro high-throughput transcriptomics (HTTr) studies can be used to assess the endocrine-disrupting potential of BPA alternatives, and this strategy produces transcriptomic points-of-departure (tPODs) that are protective of human health when compared to the PODs from traditional rodent studies. In this study, we used in vitro HTTr to assess the potential for toxicity of eleven data-poor legacy chemicals sharing structural similarities to BPA. Human breast cancer MCF-7 cells were exposed to BPA and 11 alternatives at concentrations ranging from 0.1 to 25 μM to assess toxicity. Analysis of global transcriptomic changes and a previously characterized estrogen receptor alpha (ERα) transcriptomic biomarker signature revealed that 9 of 11 chemicals altered gene expression relative to controls. One of the chemicals (2,4'-Bisphenol A) activated the ERα biomarker at the same concentration as BPA (i.e., 4,4'-BPA) but was deemed to be more potent as it induced global transcriptomic changes at lower concentrations. These results address data gaps in support of ongoing screening assessments to identify BPA alternatives with hazard potential and help to identify potential candidates that may serve as safer alternatives.
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Affiliation(s)
- Marc A Beal
- Bureau of Chemical Safety, Health Products and Food Branch, Health Canada, Canada.
| | - Melanie C Coughlan
- Bureau of Chemical Safety, Health Products and Food Branch, Health Canada, Canada
| | - Andrée Nunnikhoven
- Bureau of Chemical Safety, Health Products and Food Branch, Health Canada, Canada
| | - Matthew Gagné
- Existing Substances Risk Assessment Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Canada
| | - Tara S Barton-Maclaren
- Existing Substances Risk Assessment Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Canada
| | - Lauren M Bradford
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Canada
| | - Andrea Rowan-Carroll
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Canada
| | - Andrew Williams
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Canada
| | - Matthew J Meier
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Canada
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3
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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.
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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.
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4
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Fenton PC, Turner CJ, Hogstrand C, Bury NR. Fluid shear stress affects the metabolic and toxicological response of the rainbow trout gill cell line RTgill-W1. Toxicol In Vitro 2023; 90:105590. [PMID: 36997009 DOI: 10.1016/j.tiv.2023.105590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/20/2023] [Accepted: 03/23/2023] [Indexed: 03/30/2023]
Abstract
The Rainbow trout gill cell-line (RTgill-W1) has been accepted by the Organisation for Economic Co-operation and Development (OECD TG249) as a replacement for fish in acute toxicity tests. In these tests cells are exposed under static conditions. In contrast, in vivo, water moves over fish gills generating fluid shear stress (FSS) that alters cell physiology and response to toxicants. The current study uses a specialised 3D printed chamber designed to house inserts and allows for the flow (0.2 dynes cm2) of water over the cells. This system was used to assess RTgill-W1 cell responses to FSS in the absence and presence of copper (Cu) over 24 h. FSS caused increased gene expression of mechanosensitive channel peizo1 and the Cu-transporter atp7a, elevated reactive oxygen species generation and increased expression of superoxidase dismutase. Cell metabolism was unaffected by Cu (0.163 μM to 2.6 μM Cu) under static conditions but significantly reduced by FSS + Cu above 1.3 μM. Differential expression of metallothionein (mt) a and b was observed with increased expression of mta under static conditions and mtb under FSS on exposure to Cu. These findings highlight toxicologically relevant mechanosensory responses by RTgill-W1 to FSS that may influence toxicological responses.
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Matteo G, Leingartner K, Rowan-Carroll A, Meier M, Williams A, Beal MA, Gagné M, Farmahin R, Wickramasuriya S, Reardon AJF, Barton-Maclaren T, Christopher Corton J, Yauk CL, Atlas E. In vitro transcriptomic analyses reveal pathway perturbations, estrogenic activities, and potencies of data-poor BPA alternative chemicals. Toxicol Sci 2023; 191:266-275. [PMID: 36534918 PMCID: PMC9936204 DOI: 10.1093/toxsci/kfac127] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Since initial regulatory action in 2010 in Canada, bisphenol A (BPA) has been progressively replaced by structurally related alternative chemicals. Unfortunately, many of these chemicals are data-poor, limiting toxicological risk assessment. We used high-throughput transcriptomics to evaluate potential hazards and compare potencies of BPA and 15 BPA alternative chemicals in cultured breast cancer cells. MCF-7 cells were exposed to BPA and 15 alternative chemicals (0.0005-100 µM) for 48 h. TempO-Seq (BioSpyder Inc) was used to examine global transcriptomic changes and estrogen receptor alpha (ERα)-associated transcriptional changes. Benchmark concentration (BMC) analysis was conducted to identify 2 global transcriptomic points of departure: (1) the lowest pathway median gene BMC and (2) the 25th lowest rank-ordered gene BMC. ERα activation was evaluated using a published transcriptomic biomarker and an ERα-specific transcriptomic point of departure was derived. Genes fitting BMC models were subjected to upstream regulator and canonical pathway analysis in Ingenuity Pathway Analysis. Biomarker analysis identified BPA and 8 alternative chemicals as ERα active. Global and ERα transcriptomic points of departure produced highly similar potency rankings with bisphenol AF as the most potent chemical tested, followed by BPA and bisphenol C. Further, BPA and transcriptionally active alternative chemicals enriched similar gene sets associated with increased cell division and cancer-related processes. These data provide support for future read-across applications of transcriptomic profiling for risk assessment of data-poor chemicals and suggest that several BPA alternative chemicals may cause hazards at similar concentrations to BPA.
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Affiliation(s)
- Geronimo Matteo
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch (HECSB) Health Canada, Ottawa, Ontario K2K 0K9, Canada.,Department of Biology, Faculty of Science, University of Ottawa, Ottawa, Ontario K1N 9A7, Canada
| | - Karen Leingartner
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch (HECSB) Health Canada, Ottawa, Ontario K2K 0K9, Canada.,Department of Biology, Faculty of Science, University of Ottawa, Ottawa, Ontario K1N 9A7, Canada
| | - Andrea Rowan-Carroll
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch (HECSB) Health Canada, Ottawa, Ontario K2K 0K9, Canada.,Department of Biology, Faculty of Science, University of Ottawa, Ottawa, Ontario K1N 9A7, Canada
| | - Matthew Meier
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch (HECSB) Health Canada, Ottawa, Ontario K2K 0K9, Canada.,Department of Biology, Faculty of Science, University of Ottawa, Ottawa, Ontario K1N 9A7, Canada
| | - Andrew Williams
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch (HECSB) Health Canada, Ottawa, Ontario K2K 0K9, Canada.,Department of Biology, Faculty of Science, University of Ottawa, Ottawa, Ontario K1N 9A7, Canada
| | - Marc A Beal
- Bureau of Chemical Safety, Health Canada.,Existing Substances Risk Assessment Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario K2K 0K9, Canada
| | - Matthew Gagné
- Existing Substances Risk Assessment Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario K2K 0K9, Canada
| | - Reza Farmahin
- Existing Substances Risk Assessment Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario K2K 0K9, Canada
| | - Shamika Wickramasuriya
- Existing Substances Risk Assessment Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario K2K 0K9, Canada
| | - Anthony J F Reardon
- Existing Substances Risk Assessment Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario K2K 0K9, Canada
| | - Tara Barton-Maclaren
- Existing Substances Risk Assessment Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario K2K 0K9, Canada
| | - J Christopher Corton
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Carole L Yauk
- Department of Biology, Faculty of Science, University of Ottawa, Ottawa, Ontario K1N 9A7, Canada
| | - Ella Atlas
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch (HECSB) Health Canada, Ottawa, Ontario K2K 0K9, Canada.,Department of Biochemistry, Faculty of Medicine, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada
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6
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Repurposing Disulfiram as an Antimicrobial Agent in Topical Infections. Antibiotics (Basel) 2022; 11:antibiotics11121752. [PMID: 36551409 PMCID: PMC9774419 DOI: 10.3390/antibiotics11121752] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/09/2022] Open
Abstract
Antimicrobial drugs applied topically offer several advantages. However, the widespread use of antibiotics has led to increasing antimicrobial resistance. One interesting approach in the drug discovery process is drug repurposing. Disulfiram, which was originally approved as an anti-alcoholism drug, offers an attractive alternative to treat topical multidrug resistance bacteria in skin human infections. This study aimed to evaluate the biopharmaceutical characteristics of the drug and the effects arising from its topical application in detail. Microdilution susceptibility testing showed antibacterial activity against Gram-positive bacteria Staphylococcus aureus and Streptococcus pyogenes. Dermal absorption revealed no permeation in pig skin. The quantification of the drug retained in pig skin demonstrated concentrations in the stratum corneum and epidermis, enough to treat skin infections. Moreover, in vitro cytotoxicity and micro-array analyses were performed to better understand the mechanism of action and revealed the importance of the drug as a metal ion chelator. Together, our findings suggest that disulfiram has the potential to be repurposed as an effective antibiotic to treat superficial human skin infections.
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7
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Corton JC, Lee JS, Liu J, Ren H, Vallanat B, DeVito M. Determinants of gene expression in the human liver: Impact of aging and sex on xenobiotic metabolism. Exp Gerontol 2022; 169:111976. [PMID: 36244585 PMCID: PMC10586520 DOI: 10.1016/j.exger.2022.111976] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 09/28/2022] [Accepted: 10/03/2022] [Indexed: 12/15/2022]
Abstract
There is a need to characterize the potential susceptibility of older adults to toxicity from environmental chemical exposures. Liver xenobiotic metabolizing enzymes (XMEs) play important roles in detoxifying and eliminating xenobiotics. We examined global gene expression in the livers of young (21-45 years) and old (69+ years) men and women. Differentially expressed genes (DEG) were identified using two-way ANOVA (p ≤ 0.05). We identified 1437 and 1670 DEGs between young and old groups in men and women, respectively. Only a minor number of the total number of genes overlapped (146 genes). Aging increased or decreased pathways involved in inflammation and intermediary metabolism, respectively. Aging led to numerous changes in the expression of XME genes or genes known to control their expression (~90 genes). Out of 10 cytochrome P450s activities examined, there were increased activities of CYP1A2 and CYP2C9 enzymes in the old groups. We also identified sex-dependent genes that were more numerous in the young group (1065) than in the old group (202) and included changes in XMEs. These studies indicate that the livers from aging humans when compared to younger adults exhibit changes in XMEs that may lead to differences in the metabolism of xenobiotics.
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Affiliation(s)
- J Christopher Corton
- Center for Computational Toxicology and Exposure, US EPA, Research Triangle Park, NC 27711, United States of America.
| | - Janice S Lee
- Center for Public Health and Environmental Assessment, US EPA, Research Triangle Park, NC 27711, United States of America.
| | - Jie Liu
- Center for Computational Toxicology and Exposure, US EPA, Research Triangle Park, NC 27711, United States of America.
| | - Hongzu Ren
- Center for Public Health and Environmental Assessment, US EPA, Research Triangle Park, NC 27711, United States of America.
| | - Beena Vallanat
- Center for Computational Toxicology and Exposure, US EPA, Research Triangle Park, NC 27711, United States of America.
| | - Michael DeVito
- Center for Computational Toxicology and Exposure, US EPA, Research Triangle Park, NC 27711, United States of America.
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Corton JC, Mitchell CA, Auerbach S, Bushel P, 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] [MESH Headings] [Grants] [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.
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Affiliation(s)
- J Christopher Corton
- Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Constance A Mitchell
- Health and Environmental Sciences Institute, Washington, District of Columbia, USA
| | - Scott Auerbach
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Pierre Bushel
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, North Carolina, USA
| | | | - Patricia A Escobar
- Safety Assessment and Laboratory Animal Resources, Merck Sharp & Dohme Corp, West Point, Pennsylvania, USA
| | - Roland Froetschl
- BfArM-Bundesinstitut für Arzneimittel und Medizinprodukte, Federal Institute for Drugs and Medical Devices, Bonn, Germany
| | - Alison H Harrill
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | | | - James E Klaunig
- Laboratory of Investigative Toxicology and Pathology, Department of Environmental and Occupational Health, Indiana School of Public Health, Indiana University, Bloomington, Indiana, USA
| | - Arun R Pandiri
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, 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, Pennsylvania, 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, Ontario, Canada
| | - Carole L Yauk
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Syril D Pettit
- Health and Environmental Sciences Institute, Washington, District of Columbia, USA
| | - Frank D Sistare
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, USA
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9
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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.
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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.
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10
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Corton JC, Liu J, Kleinstreuer N, Gwinn MR, Ryan N. Towards replacement of animal tests with in vitro assays: a gene expression biomarker predicts in vitro and in vivo estrogen receptor activity. Chem Biol Interact 2022; 363:109995. [PMID: 35697134 DOI: 10.1016/j.cbi.2022.109995] [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: 04/05/2022] [Revised: 05/02/2022] [Accepted: 05/24/2022] [Indexed: 11/18/2022]
Abstract
High-throughput transcriptomics (HTTr) has the potential to support efforts to reduce or replace some animal tests. In past studies, we described a computational approach utilizing a gene expression biomarker consisting of 46 genes to predict estrogen receptor (ER) activity after chemical exposure in ER-positive human breast cancer cells including the MCF-7 cell line. We hypothesized that the biomarker model could identify ER activities of chemicals examined by Endocrine Disruptor Screening Program (EDSP) Tier 1 screening assays in which transcript profiles of the same chemicals were examined in MCF-7 cells. For the 62 chemicals examined including 5 chemicals examined in this study using RNA-Seq, the ER biomarker model accuracy was 1) 97% for in vitro reference chemicals, 2) 76-85% for guideline uterotrophic assays, and 3) 87-88% for guideline and nonguideline uterotrophic assays. For the same chemicals, these accuracies were similar or slightly better than those of the ToxCast ER model based on 18 in vitro assays. The performance of the ER biomarker model indicates that HTTr interpreted using the ER biomarker correctly identifies active and inactive ER reference chemicals. As part of the HTTr screening program the approach could rapidly identify chemicals with potential ER bioactivities for additional screening and testing.
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Affiliation(s)
- J Christopher Corton
- Center for Computational Toxicology and Exposure, US-EPA, Research Triangle Park, NC, 27711, USA.
| | - Jie Liu
- Center for Computational Toxicology and Exposure, US-EPA, Research Triangle Park, NC, 27711, USA.
| | - Nicole Kleinstreuer
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27711, USA.
| | - Maureen R Gwinn
- Center for Computational Toxicology and Exposure, US-EPA, Research Triangle Park, NC, 27711, USA.
| | - Natalia Ryan
- Oak Ridge Institute for Science and Education (ORISE), Research Triangle Park, NC, 27711, USA.
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11
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Liu JJ, Liang Y, Zhang Y, Wu RX, Song YL, Zhang F, Shi JS, Liu J, Xu SF, Wang Z. GC-MS Profile of Hua-Feng-Dan and RNA-Seq Analysis of Induced Adaptive Responses in the Liver. Front Pharmacol 2022; 13:730318. [PMID: 35355721 PMCID: PMC8959110 DOI: 10.3389/fphar.2022.730318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 01/19/2022] [Indexed: 01/17/2023] Open
Abstract
Background: Hua-Feng-Dan is a patent Chinese medicine for stroke recovery and various diseases. This study used GC-MS to profile its ingredients and RNA-Seq to analyze the induced adaptive response in the liver. Methods: Hua-Feng-Dan was subjected to steam distillation and solvent extraction, followed by GC-MS analysis. Mice were orally administered Hua-Feng-Dan and its "Guide drug" Yaomu for 7 days. Liver pathology was examined, and total RNA isolated for RNA-Seq, followed by bioinformatic analysis and quantitative real-time PCR (qPCR). Results: Forty-four volatile and fifty liposoluble components in Hua-Feng-Dan were profiled and analyzed by the NIST library and their concentrations quantified. The major components (>1%) in volatile (5) and liposoluble (10) were highlighted. Hua-Feng-Dan and Yaomu at hepatoprotective doses did not produce liver toxicity as evidenced by histopathology and serum enzyme activities. GO Enrichment revealed that Hua-Feng-Dan affected lipid homeostasis, protein folding, and cell adhesion. KEGG showed activated cholesterol metabolism, bile secretion, and PPAR signaling pathways. Differentially expressed genes (DEGs) were identified by DESeq2 with p < 0.05 compared to controls. Hua-Feng-Dan produced more DEGs than Yaomu. qPCR on selected genes largely verified RNA-Seq results. Ingenuity Pathways Analysis of the upstream regulator revealed activation of MAPK and adaptive responses by Hua-Feng-Dan, and Yaomu was less effective. Hua-Feng-Dan-induced DEGs were highly correlated with the Gene Expression Omnibus database of chemical-induced adaptive transcriptome changes in the liver. Conclusion: GC-MS primarily profiled volatile and liposoluble components in Hua-Feng-Dan. Hua-Feng-Dan at the hepatoprotective dose did not produce liver pathological changes but induced metabolic and signaling pathway activations. The effects of Hua-Feng-Dan on liver transcriptome changes point toward induced adaptive responses to program the liver to produce hepatoprotective effects.
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Affiliation(s)
- Jia-Jia Liu
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnocentric of Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Yan Liang
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Ya Zhang
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnocentric of Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Rui-Xia Wu
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Ying-Lian Song
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Feng Zhang
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnocentric of Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Jing-Shan Shi
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnocentric of Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Jie Liu
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnocentric of Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Shang-Fu Xu
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnocentric of Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Zhang Wang
- College of Ethnomedicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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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.
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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:
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13
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Chambers B, Shah I. Evaluating adaptive stress response gene signatures using transcriptomics. COMPUTATIONAL TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2021; 20:1-9. [PMID: 37829472 PMCID: PMC10569130 DOI: 10.1016/j.comtox.2021.100179] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
Stress response pathways (SRPs) mitigate the cellular effects of chemicals, but excessive perturbation can lead to adverse outcomes. Here, we investigated a computational approach to evaluate SRP activity from transcriptomic data using gene set enrichment analysis (GSEA). We extracted published gene signatures for DNA damage response (DDR), unfolded protein response (UPR), heat shock response (HSR), response to hypoxia (HPX), metal-associated response (MTL), and oxidative stress response (OSR) from the Molecular Signatures Database (MSigDB). Next, we used a gene-frequency approach to build consensus SRP signatures of varying lengths from 50 to 477 genes. We then prepared a reference dataset from perturbagens associated with SRPs from the literature with their transcriptomic profiles retrieved from public repositories. Lastly, we used receiver-operator characteristic analysis to evaluate the GSEA scores from matching transcriptomic reference profiles to SRP signatures. Our consensus signatures performed better than or as well as published signatures for 4 out of the 6 SRPs, with the best consensus signature area under the curve (% performance relative to median of published signatures) of 1.00 for DDR (109%), 0.86 for UPR (169%), 0.99 for HTS (103%), 1.00 for HPX (104%), 0.74 for MTL (150%) and 0.83 for OSR (148%). The best matches between transcriptomic profiles and SRP signatures correctly classified perturbagens in 78% and 88% of the cases by first and second rank, respectively. We believe this approach can characterize SRP activity for new chemicals using transcriptomics with further evaluation.
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Affiliation(s)
- Bryant Chambers
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Imran Shah
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
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14
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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.
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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
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15
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Zaman MS, Barman SK, Corley SM, Wilkins MR, Malladi CS, Wu MJ. Transcriptomic insights into the zinc homeostasis of MCF-7 breast cancer cells via next-generation RNA sequencing. Metallomics 2021; 13:6271325. [PMID: 33960390 DOI: 10.1093/mtomcs/mfab026] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/18/2021] [Indexed: 11/12/2022]
Abstract
A significant gap in the knowledge of zinc homeostasis exists for breast cancer cells. In this study, we investigated the transcriptomic response of the luminal breast cancer cells (MCF-7) to the exposure of extracellular zinc using next-generation RNA sequencing. The dataset was collected for three time points (T0, T30, and T120) in the time course of zinc treatment, which revealed the dramatic increase, up to 869-fold, of the gene expression for metallothioneins (MT1B, MT1F, MT1X, and MT2A) and the zinc exporter ZnT1 (SLC30A1) at T30, continuingly through to T120. The similar dynamic expression pattern was found for the autophagy-related gene (VMP1) and numerous genes for zinc finger proteins (e.g. RNF165, ZNF365, ZBTB2, SNAI1, ZNF442, ZNF547, ZNF563, and ZNF296). These findings point to the all-hands-on-deck strategy adopted by the cancer cells for maintaining zinc homeostasis. The stress responsive genes encoding heat shock proteins (HSPA1A, HSPA1B, HSPA1L, HSPA4L, HSPA6, HSPA8, HSPH1, HSP90AA1, and HSP90AB1) and the MTF-1 biomarker genes (AKR1C2, CLU, ATF3, GDF15, HMOX1, MAP1A, MAFG, SESN2, and UBC) were also differentially up-regulated at T120, suggesting a role of heat shock proteins and the MTF-1 related stress proteins in dealing with zinc exposure. It is for the first time that the gene encoding Polo-like kinase 2 (PLK2) was found to be involved in zinc-related response. The top differentially expressed genes were validated by qRT-PCR and further extended to the basal type breast cancer cells (MDA-MB-231). It was found that the expression level of SLC30A1 in MDA-MB-231 was higher than MCF-7 in response to zinc exposure. Taken together, the findings contribute to our knowledge and understanding of zinc homeostasis in breast cancer cells.
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Affiliation(s)
- Mohammad S Zaman
- School of Science, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Shital K Barman
- School of Science, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Susan M Corley
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Marc R Wilkins
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Chandra S Malladi
- Proteomics and Lipidomics Lab, School of Medicine, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Ming J Wu
- School of Science, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
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