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Abedini-Nassab R, Sadeghidelouei N, Shields Iv CW. Magnetophoretic circuits: A review of device designs and implementation for precise single-cell manipulation. Anal Chim Acta 2023; 1272:341425. [PMID: 37355317 DOI: 10.1016/j.aca.2023.341425] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 05/18/2023] [Accepted: 05/24/2023] [Indexed: 06/26/2023]
Abstract
Lab-on-a-chip tools have played a pivotal role in advancing modern biology and medicine. A key goal in this field is to precisely transport single particles and cells to specific locations on a chip for quantitative analysis. To address this large and growing need, magnetophoretic circuits have been developed in the last decade to manipulate a large number of single bioparticles in a parallel and highly controlled manner. Inspired by electrical circuits, magnetophoretic circuits are composed of passive and active circuit elements to offer commensurate levels of control and automation for transporting individual bioparticles. These specifications make them unique compared to other technologies in addressing crucial bioanalytical applications and answering fundamental questions buried in highly heterogeneous cell populations. In this comprehensive review, we describe key theoretical considerations for manufacturing and simulating magnetophoretic circuits. We provide a detailed tutorial for operating magnetophoretic devices containing different circuit elements (e.g., conductors, diodes, capacitors, and transistors). Finally, we provide a critical comparison of the utility of these devices to other microchip-based platforms for cellular manipulation, and discuss how they may address unmet needs in single-cell biology and medicine.
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Affiliation(s)
- Roozbeh Abedini-Nassab
- Faculty of Mechanical Engineering, Tarbiat Modares University, Tehran, P.O. Box: 14115-111, Iran.
| | - Negar Sadeghidelouei
- Faculty of Mechanical Engineering, Tarbiat Modares University, Tehran, P.O. Box: 14115-111, Iran
| | - C Wyatt Shields Iv
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, 80303, United States
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Habano W, Miura T, Terashima J, Ozawa S. Aryl hydrocarbon receptor as a DNA methylation reader in the stress response pathway. Toxicology 2022; 470:153154. [PMID: 35301058 DOI: 10.1016/j.tox.2022.153154] [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: 10/05/2021] [Revised: 01/31/2022] [Accepted: 03/10/2022] [Indexed: 10/18/2022]
Abstract
The aryl hydrocarbon receptor (AhR) mediates various cellular responses upon exposure to exogenous and endogenous stress factors. In these responses, AhR plays a dual role as a stress sensor for detecting various AhR ligands and as a transcription factor that upregulates the expression of downstream effector genes, such as those encoding drug-metabolizing enzymes. As a transcription factor, it selectively binds to the unmethylated form of a specific sequence called the xenobiotic responsive element (XRE). We suggest that AhR is a novel DNA methylation reader, unlike classical methylation readers, such as methyl-CpG-binding protein 2, which binds to methylated sequences. Under physiological conditions of continuous exposure to endogenous AhR ligands, such as kynurenine, methylation states of the individual target XREs must be strictly regulated to select and coordinate the expression of downstream genes responsible for maintaining homeostasis in the body. In contrast, long-term exposure to AhR ligands frequently leads to changes in the methylation patterns around the XRE sequence. These data indicate that AhR may contribute to the adaptive cellular response to various stresses by modulating DNA methylation. Thus, the DNA methylation profile of AhR target genes should be dynamically controlled through a balance between robustness and flexibility under both physiological and stress conditions. AhR is a pivotal player in the regulation of stress response as it shows versatility by functioning as a stress sensor, methylation reader, and putative methylation modulator.
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Affiliation(s)
- Wataru Habano
- Division of Pharmacodynamics and Molecular Genetics, Department of Clinical Pharmaceutical Sciences, School of Pharmacy, Iwate Medical University, Shiwa 028-3694, Iwate, Japan.
| | - Toshitaka Miura
- Division of Pharmacodynamics and Molecular Genetics, Department of Clinical Pharmaceutical Sciences, School of Pharmacy, Iwate Medical University, Shiwa 028-3694, Iwate, Japan
| | - Jun Terashima
- Division of Pharmacodynamics and Molecular Genetics, Department of Clinical Pharmaceutical Sciences, School of Pharmacy, Iwate Medical University, Shiwa 028-3694, Iwate, Japan
| | - Shogo Ozawa
- Division of Pharmacodynamics and Molecular Genetics, Department of Clinical Pharmaceutical Sciences, School of Pharmacy, Iwate Medical University, Shiwa 028-3694, Iwate, Japan
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Zanardi MV, Gastiazoro MP, Kretzschmar G, Wober J, Vollmer G, Varayoud J, Durando M, Zierau O. AHR agonistic effects of 6-PN contribute to potential beneficial effects of Hops extract. Mol Cell Endocrinol 2022; 543:111540. [PMID: 34965452 DOI: 10.1016/j.mce.2021.111540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 12/14/2021] [Accepted: 12/23/2021] [Indexed: 10/19/2022]
Abstract
Hops (Humulus lupulus) is used as an alternative to hormone replacement therapy due to the phytoestrogen, 8-prenylnaringenin (8-PN). To examine the potential risks/benefits of hops extract and its compounds (8-PN and 6-prenylnaringenin, 6-PN), we aimed to evaluate the estrogen receptor α (ERα) and aryl hydrocarbon receptor (AHR) signaling pathways in human endometrial cancer cells. Hops extract, 8-PN and 6-PN showed estrogenic activity. Hops extract and 6-PN activated both ERα and AHR pathways. 6-PN increased the expression of the tumor suppressor gene (AHRR), and that of genes involved in the estrogen metabolism (CYP1A1, CYP1B1). Although 6-PN might activate the detoxification and genotoxic pathways of estrogen metabolism, hops extract as a whole only modulated the genotoxic pathway by an up-regulation of CYP1B1 mRNA expression. These data demonstrate the relevant role of 6-PN contained in the hops extract as potential modulator of estrogen metabolism due to its ERα and AHR agonist activity.
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Affiliation(s)
- María Victoria Zanardi
- Instituto de Salud y Ambiente del Litoral (ISAL), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Santa Fe, Argentina; Cátedra de Fisiología Humana, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina; Molecular Cell Physiology and Endocrinology, Institute of Zoology, Technical University Dresden, Dresden, Germany.
| | - María Paula Gastiazoro
- Instituto de Salud y Ambiente del Litoral (ISAL), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Santa Fe, Argentina; Cátedra de Fisiología Humana, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Georg Kretzschmar
- Molecular Cell Physiology and Endocrinology, Institute of Zoology, Technical University Dresden, Dresden, Germany
| | - Jannette Wober
- Molecular Cell Physiology and Endocrinology, Institute of Zoology, Technical University Dresden, Dresden, Germany
| | - Günter Vollmer
- Molecular Cell Physiology and Endocrinology, Institute of Zoology, Technical University Dresden, Dresden, Germany
| | - Jorgelina Varayoud
- Instituto de Salud y Ambiente del Litoral (ISAL), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Santa Fe, Argentina; Cátedra de Fisiología Humana, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Milena Durando
- Instituto de Salud y Ambiente del Litoral (ISAL), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Santa Fe, Argentina; Cátedra de Fisiología Humana, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Oliver Zierau
- Molecular Cell Physiology and Endocrinology, Institute of Zoology, Technical University Dresden, Dresden, Germany
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Goodman S, Chappell G, Guyton KZ, Pogribny IP, Rusyn I. Epigenetic alterations induced by genotoxic occupational and environmental human chemical carcinogens: An update of a systematic literature review. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 789:108408. [PMID: 35690411 PMCID: PMC9188653 DOI: 10.1016/j.mrrev.2021.108408] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/28/2021] [Accepted: 12/07/2021] [Indexed: 01/03/2023]
Abstract
Epigenetic alterations, such as changes in DNA methylation, histones/chromatin structure, nucleosome positioning, and expression of non-coding RNAs, are recognized among key characteristics of carcinogens; they may occur independently or concomitantly with genotoxic effects. While data on genotoxicity are collected through standardized guideline tests, data collected on epigenetic effects is far less uniform. In 2016, we conducted a systematic review of published studies of genotoxic carcinogens that reported epigenetic endpoints to better understand the evidence for epigenetic alterations of human carcinogens, and the potential association with genotoxic endpoints. Since then, the number of studies of epigenetic effects of chemicals has nearly doubled. This review stands as an update on epigenetic alterations induced by occupational and environmental human carcinogens that were previously and recently classified as Group 1 by the International Agency for Research on Cancer. We found that the evidence of epigenetic effects remains uneven across agents. Studies of DNA methylation are most abundant, while reports concerning effects on non-coding RNA have increased over the past 5 years. By contrast, mechanistic toxicology studies of histone modifications and chromatin state alterations remain few. We found that most publications of epigenetic effects of carcinogens were studies in exposed humans or human cells. Studies in rodents represent the second most common species used for epigenetic studies in toxicology, in vivo exposures being the most predominant. Future studies should incorporate dose- and time-dependent study designs and also investigate the persistence of effects following cessation of exposure, considering the dynamic nature of most epigenetic alterations.
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Affiliation(s)
- Samantha Goodman
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | | | | | - Igor P Pogribny
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Ivan Rusyn
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA.
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Johnson C, Mullen DJ, Selamat SA, Campan M, Offringa IA, Marconett CN. The Sulfotransferase SULT1C2 Is Epigenetically Activated and Transcriptionally Induced by Tobacco Exposure and Is Associated with Patient Outcome in Lung Adenocarcinoma. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 19:416. [PMID: 35010676 PMCID: PMC8744592 DOI: 10.3390/ijerph19010416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/24/2021] [Accepted: 12/27/2021] [Indexed: 01/03/2023]
Abstract
Lung cancer is the leading cause of cancer-related death. Tobacco exposure is associated with 80-90% of lung cancer cases. The SULT1C2 sulfotransferase modifies xenobiotic compounds to enhance secretion but can also render these compounds carcinogenic. To determine if SULT1C2 contributes to tobacco-related carcinogenesis in the lung, we analyzed the expression and epigenetic state of SULT1C2 in human lung adenocarcinoma (LUAD) samples and in LUAD cell lines exposed to cigarette smoke condensate (CSC). SULT1C2 expression was significantly positively correlated to overall LUAD patient survival in smokers, was elevated in LUAD tumors compared to adjacent non-tumor lung, and was significantly correlated with levels of patient exposure to tobacco smoke. SULT1C2 promoter DNA methylation was inversely correlated with expression in LUAD, and hypomethylation of the SULT1C2 promoter was observed in Asian patients, as compared to Caucasians. In vitro analysis of LUAD cell lines indicates that CSC stimulates expression of SULT1C2 in a dose-dependent and cell-line-specific manner. In vitro methylation of the SULT1C2 promoter significantly decreased transcriptional activity of a reporter plasmid, and SULT1C2 expression was activated by the DNA demethylating agent 5-Aza-2'-deoxycytidine in a cell line in which the SULT1C2 promoter was hypermethylated. An aryl hydrocarbon receptor (AHR) binding site was detected spanning critical methylation sites upstream of SULT1C2. CSC exposure significantly increased AHR binding to this predicted binding site in the SULT1C2 promoter in multiple lung cell lines. Our data suggest that CSC exposure leads to activation of the AHR transcription factor, increased binding to the SULT1C2 promoter, and upregulation of SULT1C2 expression and that this process is inhibited by DNA methylation at the SULT1C2 locus. Additionally, our results suggest that the level of SULT1C2 promoter methylation and gene expression in normal lung varies depending on the race of the patient, which could in part reflect the molecular mechanisms of racial disparities seen in lung cellular responses to cigarette smoke exposure.
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Affiliation(s)
- Candace Johnson
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9520, USA; (C.J.); (D.J.M.); (S.A.S.); (M.C.); (I.A.O.)
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9520, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9520, USA
| | - Daniel J. Mullen
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9520, USA; (C.J.); (D.J.M.); (S.A.S.); (M.C.); (I.A.O.)
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9520, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9520, USA
| | - Suhaida A. Selamat
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9520, USA; (C.J.); (D.J.M.); (S.A.S.); (M.C.); (I.A.O.)
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9520, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9520, USA
| | - Mihaela Campan
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9520, USA; (C.J.); (D.J.M.); (S.A.S.); (M.C.); (I.A.O.)
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9520, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9520, USA
| | - Ite A. Offringa
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9520, USA; (C.J.); (D.J.M.); (S.A.S.); (M.C.); (I.A.O.)
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9520, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9520, USA
| | - Crystal N. Marconett
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9520, USA; (C.J.); (D.J.M.); (S.A.S.); (M.C.); (I.A.O.)
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9520, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9520, USA
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Curcumin Suppresses the Lipid Accumulation and Oxidative Stress Induced by Benzo[a]pyrene Toxicity in HepG2 Cells. Antioxidants (Basel) 2021; 10:antiox10081314. [PMID: 34439562 PMCID: PMC8389208 DOI: 10.3390/antiox10081314] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/19/2021] [Accepted: 08/19/2021] [Indexed: 01/14/2023] Open
Abstract
Benzo[a]pyrene (B[a]P) is a potentially hepatotoxic group-1 carcinogen taken up by the body through ingestion of daily foods. B[a]P is widely known to cause DNA and protein damages, which are closely related to cell transformation. Accordingly, studies on natural bioactive compounds that attenuate such chemical-induced toxicities have significant impacts on public health. This study aimed to uncover the mechanism of curcumin, the major curcuminoid in turmeric (Curcuma longa), in modulating the lipid accumulation and oxidative stress mediated by B[a]P cytotoxicity in HepG2 cells. Curcumin treatment reduced the B[a]P-induced lipid accumulation and reactive oxygen spicies (ROS) upregulation and recovered the cell viability. Cytochrome P450 family 1 subfamily A polypeptide 1 (CYP1A1) and Cytochrome P450 subfamily B polypeptide 1 (CYP1B1) downregulation resulting from decreased aryl hydrocarbon receptor (AhR) translocation into nuclei attenuated the effects of B[a]P-induced lipid accumulation and repressed cell viability, respectively. Moreover, the curcumin-induced reduction in ROS generation decreased the nuclear translocation of Nuclear factor erythroid-2-related factor 2 (Nrf2) and the expression of phase-II detoxifying enzymes. These results indicate that curcumin suppresses B[a]P-induced lipid accumulation and ROS generation which can potentially induce nonalcoholic fatty liver disease (NAFLD) and can shed a light on the detoxifying effect of curcumin.
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Aarts JMMJG, Alink GM, Franssen HJ, Roebroeks W. Evolution of Hominin Detoxification: Neanderthal and Modern Human Ah Receptor Respond Similarly to TCDD. Mol Biol Evol 2021; 38:1292-1305. [PMID: 33230523 PMCID: PMC8042735 DOI: 10.1093/molbev/msaa287] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In studies of hominin adaptations to fire use, the role of the aryl hydrocarbon receptor (AHR) in the evolution of detoxification has been highlighted, including statements that the modern human AHR confers a significantly better capacity to deal with toxic smoke components than the Neanderthal AHR. To evaluate this, we compared the AHR-controlled induction of cytochrome P4501A1 (CYP1A1) mRNA in HeLa human cervix epithelial adenocarcinoma cells transfected with an Altai-Neanderthal or a modern human reference AHR expression construct, and exposed to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). We compared the complete AHR mRNA sequences including the untranslated regions (UTRs), maintaining the original codon usage. We observe no significant difference in CYP1A1 induction by TCDD between Neanderthal and modern human AHR, whereas a 150–1,000 times difference was previously reported in a study of the AHR coding region optimized for mammalian codon usage and expressed in rat cells. Our study exemplifies that expression in a homologous cellular background is of major importance to determine (ancient) protein activity. The Neanderthal and modern human dose–response curves almost coincide, except for a slightly higher extrapolated maximum for the Neanderthal AHR, possibly caused by a 5′-UTR G-variant known from modern humans (rs7796976). Our results are strongly at odds with a major role of the modern human AHR in the evolution of hominin detoxification of smoke components and consistent with our previous study based on 18 relevant genes in addition to AHR, which concluded that efficient detoxification alleles are more dominant in ancient hominins, chimpanzees, and gorillas than in modern humans.
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Affiliation(s)
- Jac M M J G Aarts
- Human Origins Group, Faculty of Archaeology, Leiden University, Leiden, The Netherlands.,Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, Wageningen, The Netherlands
| | - Gerrit M Alink
- Human Origins Group, Faculty of Archaeology, Leiden University, Leiden, The Netherlands
| | - Henk J Franssen
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, Wageningen, The Netherlands
| | - Wil Roebroeks
- Human Origins Group, Faculty of Archaeology, Leiden University, Leiden, The Netherlands
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Li Y, Liu S, Cheng H, Chen X, Shen X, Cai Y. Dynamic transcriptome response in Meretrix meretrix to Aroclor 1254 exposure. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 207:111485. [PMID: 33254386 DOI: 10.1016/j.ecoenv.2020.111485] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/08/2020] [Accepted: 10/09/2020] [Indexed: 06/12/2023]
Abstract
Polychlorinated biphenyls (PCBs) are well-known persistent organic pollutants; they have toxic effects on the immune system, reproductive system, and endocrine system by changing the metabolism of the body. To elucidate the underlying molecular mechanism, the clam Meretrix meretrix was exposed to 10 and 1000 ng/L Aroclor 1254 and natural seawater (control). Samples from clams exposed to natural seawater and those exposed to Aroclor 1254 for 1 and 3 days were individually collected for transcriptome analysis. After assembly, more than 535,157 transcripts with a mean length of 949 bp and an N50 length of 1279 bp were obtained; a final set of 177,142 unigenes was generated. In the present study, 5101 differentially expressed genes were identified. The differentially expressed genes were related to detoxification metabolism, oxidative stress, immune response, and endocrine system disruption. Of these genes, under the Aroclor 1254 exposure, cytochrome P450 20A1 (2.06-4.46 folds), glutathione S-transferase (2.25-3.80 folds), multidrug resistance-associated protein 1-like (1.49-2.92 folds), peroxidase-like protein (1.33-4.26 folds), lysozyme (1.61-2.05 folds), bcl-2 like 1 protein (1.14-2.29 folds) and vitellogenin (1.09-1.19 folds) showed been significantly induced expressed. At the same time, some genes were down regulated, including cytochrome P450 2J5 (-1.20 ~ -2.86 folds), cytochrome P450 3A24 (-1.40 ~ -4.08 folds), C1q (-1.27 ~ -1.66 folds), Sulfotransferase (-1.51 ~ -1.84 folds), monocarboxylate transporter 10 (-1.30 ~ -4.70 folds), 3-beta hydroxysteroid dehydrogenase (-1.43 ~ -2.81 folds) and beta-galactosidase (-1.23 ~ -2.23 folds). Furthermore, it showed that the expression levels of CYP2J5, glutathione S-transferase, 3-beta hydroxysteroid dehydrogenase and beta-galactosidase had time responses and dose responses. The present study provided insights into the toxic effects of Aroclor 1254 exposure in M. meretrix.
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Affiliation(s)
- Yongqi Li
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
| | - Shishi Liu
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
| | - Hanliang Cheng
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
| | - Xiangning Chen
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
| | - Xin Shen
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang 222005, China.
| | - Yuefeng Cai
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang 222005, China.
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Mordaunt CE, Park BY, Bakulski KM, Feinberg JI, Croen LA, Ladd-Acosta C, Newschaffer CJ, Volk HE, Ozonoff S, Hertz-Picciotto I, LaSalle JM, Schmidt RJ, Fallin MD. A meta-analysis of two high-risk prospective cohort studies reveals autism-specific transcriptional changes to chromatin, autoimmune, and environmental response genes in umbilical cord blood. Mol Autism 2019; 10:36. [PMID: 31673306 PMCID: PMC6814108 DOI: 10.1186/s13229-019-0287-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/08/2019] [Indexed: 12/17/2022] Open
Abstract
Background Autism spectrum disorder (ASD) is a neurodevelopmental disorder that affects more than 1% of children in the USA. ASD risk is thought to arise from both genetic and environmental factors, with the perinatal period as a critical window. Understanding early transcriptional changes in ASD would assist in clarifying disease pathogenesis and identifying biomarkers. However, little is known about umbilical cord blood gene expression profiles in babies later diagnosed with ASD compared to non-typically developing and non-ASD (Non-TD) or typically developing (TD) children. Methods Genome-wide transcript levels were measured by Affymetrix Human Gene 2.0 array in RNA from cord blood samples from both the Markers of Autism Risk in Babies-Learning Early Signs (MARBLES) and the Early Autism Risk Longitudinal Investigation (EARLI) high-risk pregnancy cohorts that enroll younger siblings of a child previously diagnosed with ASD. Younger siblings were diagnosed based on assessments at 36 months, and 59 ASD, 92 Non-TD, and 120 TD subjects were included. Using both differential expression analysis and weighted gene correlation network analysis, gene expression between ASD and TD, and between Non-TD and TD, was compared within each study and via meta-analysis. Results While cord blood gene expression differences comparing either ASD or Non-TD to TD did not reach genome-wide significance, 172 genes were nominally differentially expressed between ASD and TD cord blood (log2(fold change) > 0.1, p < 0.01). These genes were significantly enriched for functions in xenobiotic metabolism, chromatin regulation, and systemic lupus erythematosus (FDR q < 0.05). In contrast, 66 genes were nominally differentially expressed between Non-TD and TD, including 8 genes that were also differentially expressed in ASD. Gene coexpression modules were significantly correlated with demographic factors and cell type proportions. Limitations ASD-associated gene expression differences identified in this study are subtle, as cord blood is not the main affected tissue, it is composed of many cell types, and ASD is a heterogeneous disorder. Conclusions This is the first study to identify gene expression differences in cord blood specific to ASD through a meta-analysis across two prospective pregnancy cohorts. The enriched gene pathways support involvement of environmental, immune, and epigenetic mechanisms in ASD etiology.
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Affiliation(s)
- Charles E Mordaunt
- 1Department of Medical Microbiology and Immunology, Genome Center, and MIND Institute, University of California, Davis, CA USA
| | - Bo Y Park
- 2Department of Public Health, California State University, Fullerton, CA USA
| | - Kelly M Bakulski
- 3Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI USA
| | - Jason I Feinberg
- 4Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD USA
| | - Lisa A Croen
- 5Division of Research and Autism Research Program, Kaiser Permanente Northern California, Oakland, CA USA
| | | | - Craig J Newschaffer
- 6Department of Biobehavioral Health, College of Health and Human Development, Pennsylvania State University, University Park, PA USA
| | - Heather E Volk
- 4Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD USA
| | - Sally Ozonoff
- 7Psychiatry and Behavioral Sciences and MIND Institute, University of California, Davis, CA USA
| | - Irva Hertz-Picciotto
- 8Department of Public Health Sciences and MIND Institute, University of California, Davis, CA USA
| | - Janine M LaSalle
- 1Department of Medical Microbiology and Immunology, Genome Center, and MIND Institute, University of California, Davis, CA USA
| | - Rebecca J Schmidt
- 8Department of Public Health Sciences and MIND Institute, University of California, Davis, CA USA
| | - M Daniele Fallin
- 4Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD USA
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Flores-Pérez A, Elizondo G. Apoptosis induction and inhibition of HeLa cell proliferation by alpha-naphthoflavone and resveratrol are aryl hydrocarbon receptor-independent. Chem Biol Interact 2018; 281:98-105. [DOI: 10.1016/j.cbi.2017.12.029] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 11/30/2017] [Accepted: 12/18/2017] [Indexed: 12/20/2022]
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Regulation of Human Cytochrome P4501A1 (hCYP1A1): A Plausible Target for Chemoprevention? BIOMED RESEARCH INTERNATIONAL 2016; 2016:5341081. [PMID: 28105425 PMCID: PMC5220472 DOI: 10.1155/2016/5341081] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 11/09/2016] [Accepted: 11/13/2016] [Indexed: 12/13/2022]
Abstract
Human cytochrome P450 1A1 (hCYP1A1) has been an object of study due to its role in precarcinogen metabolism; for this reason it is relevant to know more in depth the mechanisms that rule out its expression and activity, which make this enzyme a target for the development of novel chemiopreventive agents. The aim of this work is to review the origin, regulation, and structural and functional characteristics of CYP1A1 letting us understand its role in the bioactivation of precarcinogen and the consequences of its modulation in other physiological processes, as well as guide us in the study of this important protein.
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Amenya HZ, Tohyama C, Ohsako S. Dioxin induces Ahr-dependent robust DNA demethylation of the Cyp1a1 promoter via Tdg in the mouse liver. Sci Rep 2016; 6:34989. [PMID: 27713569 PMCID: PMC5054525 DOI: 10.1038/srep34989] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/22/2016] [Indexed: 12/24/2022] Open
Abstract
The aryl hydrocarbon receptor (Ahr) is a highly conserved nuclear receptor that plays an important role in the manifestation of toxicity induced by polycyclic aromatic hydrocarbons. As a xenobiotic sensor, Ahr is involved in chemical biotransformation through activation of drug metabolizing enzymes. The activated Ahr cooperates with coactivator complexes to induce epigenetic modifications at target genes. Thus, it is conceivable that 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), a potent Ahr ligand, may elicit robust epigenetic changes in vivo at the Ahr target gene cytochrome P450 1a1 (Cyp1a1). A single dose of TCDD administered to adult mice induced Ahr-dependent CpG hypomethylation, changes in histone modifications, and thymine DNA glycosylase (Tdg) recruitment at the Cyp1a1 promoter in the liver within 24 hrs. These epigenetic changes persisted until 40 days post-TCDD treatment and there was Cyp1a1 mRNA hyperinduction upon repeat administration of TCDD at this time-point. Our demethylation assay using siRNA knockdown and an in vitro methylated plasmid showed that Ahr, Tdg, and the ten-eleven translocation methyldioxygenases Tet2 and Tet3 are required for the TCDD-induced DNA demethylation. These results provide novel evidence of Ahr-driven active DNA demethylation and epigenetic memory. The epigenetic alterations influence response to subsequent chemical exposure and imply an adaptive mechanism to xenobiotic stress.
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Affiliation(s)
- Hesbon Z Amenya
- Laboratory of Environmental Health Sciences, Center for Disease Biology and Integrative Medicine, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Chiharu Tohyama
- Laboratory of Environmental Health Sciences, Center for Disease Biology and Integrative Medicine, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan.,Experimental Biology Laboratory, Faculty of Medicine, University of Tsukuba, Tsukuba 305-8575, Japan
| | - Seiichiroh Ohsako
- Laboratory of Environmental Health Sciences, Center for Disease Biology and Integrative Medicine, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
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Cacabelos R, Torrellas C. Epigenetics of Aging and Alzheimer's Disease: Implications for Pharmacogenomics and Drug Response. Int J Mol Sci 2015; 16:30483-543. [PMID: 26703582 PMCID: PMC4691177 DOI: 10.3390/ijms161226236] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 11/16/2015] [Accepted: 12/08/2015] [Indexed: 02/07/2023] Open
Abstract
Epigenetic variability (DNA methylation/demethylation, histone modifications, microRNA regulation) is common in physiological and pathological conditions. Epigenetic alterations are present in different tissues along the aging process and in neurodegenerative disorders, such as Alzheimer’s disease (AD). Epigenetics affect life span and longevity. AD-related genes exhibit epigenetic changes, indicating that epigenetics might exert a pathogenic role in dementia. Epigenetic modifications are reversible and can potentially be targeted by pharmacological intervention. Epigenetic drugs may be useful for the treatment of major problems of health (e.g., cancer, cardiovascular disorders, brain disorders). The efficacy and safety of these and other medications depend upon the efficiency of the pharmacogenetic process in which different clusters of genes (pathogenic, mechanistic, metabolic, transporter, pleiotropic) are involved. Most of these genes are also under the influence of the epigenetic machinery. The information available on the pharmacoepigenomics of most drugs is very limited; however, growing evidence indicates that epigenetic changes are determinant in the pathogenesis of many medical conditions and in drug response and drug resistance. Consequently, pharmacoepigenetic studies should be incorporated in drug development and personalized treatments.
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Affiliation(s)
- Ramón Cacabelos
- EuroEspes Biomedical Research Center, Institute of Medical Science and Genomic Medicine, 15165-Bergondo, Corunna, Spain.
- Chair of Genomic Medicine, Camilo José Cela University, 28692-Madrid, Spain.
| | - Clara Torrellas
- EuroEspes Biomedical Research Center, Institute of Medical Science and Genomic Medicine, 15165-Bergondo, Corunna, Spain.
- Chair of Genomic Medicine, Camilo José Cela University, 28692-Madrid, Spain.
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Qian Y, Zhang S, Guo W, Ma J, Chen Y, Wang L, Zhao M, Liu S. Polychlorinated Biphenyls (PCBs) Inhibit Hepcidin Expression through an Estrogen-Like Effect Associated with Disordered Systemic Iron Homeostasis. Chem Res Toxicol 2015; 28:629-40. [DOI: 10.1021/tx500428r] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yi Qian
- College
of Biological and Environmental Engineering, Zhejiang University of Technology, Hangzhou 310032, China
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Shuping Zhang
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- Institute
for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Wenli Guo
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Juan Ma
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yue Chen
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Lei Wang
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Meirong Zhao
- College
of Biological and Environmental Engineering, Zhejiang University of Technology, Hangzhou 310032, China
| | - Sijin Liu
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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