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Zou Z, Yoshimura Y, Yamanishi Y, Oki S. Elucidating disease-associated mechanisms triggered by pollutants via the epigenetic landscape using large-scale ChIP-Seq data. Epigenetics Chromatin 2023; 16:34. [PMID: 37743474 PMCID: PMC10518938 DOI: 10.1186/s13072-023-00510-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 09/19/2023] [Indexed: 09/26/2023] Open
Abstract
BACKGROUND Despite well-documented effects on human health, the action modes of environmental pollutants are incompletely understood. Although transcriptome-based approaches are widely used to predict associations between chemicals and disorders, the molecular cues regulating pollutant-derived gene expression changes remain unclear. Therefore, we developed a data-mining approach, termed "DAR-ChIPEA," to identify transcription factors (TFs) playing pivotal roles in the action modes of pollutants. METHODS Large-scale public ChIP-Seq data (human, n = 15,155; mouse, n = 13,156) were used to predict TFs that are enriched in the pollutant-induced differentially accessible genomic regions (DARs) obtained from epigenome analyses (ATAC-Seq). The resultant pollutant-TF matrices were then cross-referenced to a repository of TF-disorder associations to account for pollutant modes of action. We subsequently evaluated the performance of the proposed method using a chemical perturbation data set to compare the outputs of the DAR-ChIPEA and our previously developed differentially expressed gene (DEG)-ChIPEA methods using pollutant-induced DEGs as input. We then adopted the proposed method to predict disease-associated mechanisms triggered by pollutants. RESULTS The proposed approach outperformed other methods using the area under the receiver operating characteristic curve score. The mean score of the proposed DAR-ChIPEA was significantly higher than that of our previously described DEG-ChIPEA (0.7287 vs. 0.7060; Q = 5.278 × 10-42; two-tailed Wilcoxon rank-sum test). The proposed approach further predicted TF-driven modes of action upon pollutant exposure, indicating that (1) TFs regulating Th1/2 cell homeostasis are integral in the pathophysiology of tributyltin-induced allergic disorders; (2) fine particulates (PM2.5) inhibit the binding of C/EBPs, Rela, and Spi1 to the genome, thereby perturbing normal blood cell differentiation and leading to immune dysfunction; and (3) lead induces fatty liver by disrupting the normal regulation of lipid metabolism by altering hepatic circadian rhythms. CONCLUSIONS Highlighting genome-wide chromatin change upon pollutant exposure to elucidate the epigenetic landscape of pollutant responses outperformed our previously described method that focuses on gene-adjacent domains only. Our approach has the potential to reveal pivotal TFs that mediate deleterious effects of pollutants, thereby facilitating the development of strategies to mitigate damage from environmental pollution.
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Affiliation(s)
- Zhaonan Zou
- Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, 53 Shogoin Kawahara-Cho, Sakyo-Ku, Kyoto, 606-8507, Japan
| | - Yuka Yoshimura
- Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, 53 Shogoin Kawahara-Cho, Sakyo-Ku, Kyoto, 606-8507, Japan
| | - Yoshihiro Yamanishi
- Department of Complex Systems Science, Graduate School of Informatics, Nagoya University, Furo-Cho, Chikusa-Ku, Nagoya, 464-8602, Japan
| | - Shinya Oki
- Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, 53 Shogoin Kawahara-Cho, Sakyo-Ku, Kyoto, 606-8507, Japan.
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Anasamy T, Chee CF, Wong YF, Heh CH, Kiew LV, Lee HB, Chung LY. Triorganotin complexes in cancer chemotherapy: Mechanistic insights and future perspectives. Appl Organomet Chem 2020. [DOI: 10.1002/aoc.6089] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Theebaa Anasamy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy University of Malaya Kuala Lumpur Malaysia
| | - Chin Fei Chee
- Nanotechnology and Catalysis Research Centre University of Malaya Kuala Lumpur Malaysia
| | - Yuen Fei Wong
- Department of Clinical Pharmacy and Pharmacy Practice, Faculty of Pharmacy University of Malaya Kuala Lumpur Malaysia
| | - Choon Han Heh
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy University of Malaya Kuala Lumpur Malaysia
| | - Lik Voon Kiew
- Department of Pharmacology, Faculty of Medicine University of Malaya Kuala Lumpur Malaysia
| | - Hong Boon Lee
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy University of Malaya Kuala Lumpur Malaysia
- School of Biosciences, Faculty of Health and Medical Sciences Taylor's University Subang Jaya Selangor Malaysia
| | - Lip Yong Chung
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy University of Malaya Kuala Lumpur Malaysia
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Park MK, Lee CH. Effects of cerulein on keratin 8 phosphorylation and perinuclear reorganization in pancreatic cancer cells: Involvement of downregulation of protein phosphatase 2A and alpha4. ENVIRONMENTAL TOXICOLOGY 2016; 31:2090-2098. [PMID: 26303380 DOI: 10.1002/tox.22186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 07/31/2015] [Accepted: 08/05/2015] [Indexed: 06/04/2023]
Abstract
Toxicants can perturb cellular homeostasis by modifying phosphorylation-based signaling. In the present study, we examined the effects of cerulein, an inducer of acute pancreatitis, on keratin 8 (K8) phosphorylation. We found that cerulein dose-dependently induced K8 phosphorylation and perinuclear reorganization in PANC-1 cells, thus leading to migration and invasion. The extracellular signal-regulated kinases (ERK) inhibitor U0126 suppressed cerulein-induced phosphorylation of serine 431 and reorganization of K8. Cerulein reduced the expressions of protein phosphatase 2A (PP2A) via ubiqutination and alpha4. PP2A's involvement in K8 phosphorylation of PANC-1 cells was also confirmed by the observation that PP2A gene silencing resulted in K8 phosphorylation and migration of PANC-1 cells. Overall, these results suggest that cerulein induced phosphorylation and reorganization through ERK activation by downregulating PP2A and alpha4, leading to increased migration and invasion of PANC-1 cells. © 2015 Wiley Periodicals, Inc. Environ Toxicol 31: 2090-2098, 2016.
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Affiliation(s)
- Mi Kyung Park
- BK21PLUS R-FIND Team, College of Pharmacy, Dongguk University, Seoul, 100-715, Republic of Korea
| | - Chang Hoon Lee
- BK21PLUS R-FIND Team, College of Pharmacy, Dongguk University, Seoul, 100-715, Republic of Korea
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Girkin JL, Hatchwell LM, Collison AM, Starkey MR, Hansbro PM, Yagita H, Foster PS, Mattes J. TRAIL signaling is proinflammatory and proviral in a murine model of rhinovirus 1B infection. Am J Physiol Lung Cell Mol Physiol 2016; 312:L89-L99. [PMID: 27836899 DOI: 10.1152/ajplung.00200.2016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 11/04/2016] [Indexed: 02/07/2023] Open
Abstract
the aim of this study is to elucidate the role of TRAIL during rhinovirus (RV) infection in vivo. Naïve wild-type and tumor necrosis factor-related apoptosis-inducing ligand (TRAIL)-deficient (Tnfsf10-/-) BALB/c mice were infected intranasally with RV1B. In separate experiments, Tnfsf10-/- mice were sensitized and challenged via the airway route with house dust mite (HDM) to induce allergic airways disease and then challenged with RVIB or UV-RVIB. Airway hyperreactivity (AHR) was invasively assessed as total airways resistance in response to increasing methacholine challenge and inflammation was assessed in bronchoalveolar lavage fluid at multiple time points postinfection. Chemokines were quantified by ELISA of whole lung lysates and viral load was determined by quantitative RT-PCR and tissue culture infective dose (TCID50). Human airway epithelial cells (BEAS2B) were infected with RV1B and stimulated with recombinant TRAIL or neutralizing anti-TRAIL antibodies and viral titer assessed by TCID50 HDM-challenged Tnfsf10-/- mice were protected against RV-induced AHR and had suppressed cellular infiltration in the airways upon RV infection. Chemokine C-X-C-motif ligand 2 (CXCL2) production was suppressed in naïve Tnfsf10-/- mice infected with RV1B, with less RV1B detected 24 h postinfection. This was associated with reduced apoptotic cell death and a reduction of interferon (IFN)-λ2/3 but not IFN-α or IFN-β. TRAIL stimulation increased, whereas anti-TRAIL antibodies reduced viral replication in RV1B-infected BEAS2B cells in vitro. In conclusion, TRAIL promotes RV-induced AHR, inflammation and RV1B replication, implicating this molecule and its downstream signaling pathways as a possible target for the amelioration of RV1B-induced allergic and nonallergic lung inflammation and AHR.
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Affiliation(s)
- Jason L Girkin
- Experimental and Translational Respiratory Medicine Group, University of Newcastle and Hunter Medical Research Institute, Newcastle, Australia.,Priority Research Centre for Healthy Lungs, University of Newcastle and Hunter Medical Research Institute, Newcastle, Australia
| | - Luke M Hatchwell
- Experimental and Translational Respiratory Medicine Group, University of Newcastle and Hunter Medical Research Institute, Newcastle, Australia.,Priority Research Centre GrowUpWell, University of Newcastle and Hunter Medical Research Institute, Newcastle, Australia
| | - Adam M Collison
- Experimental and Translational Respiratory Medicine Group, University of Newcastle and Hunter Medical Research Institute, Newcastle, Australia.,Priority Research Centre GrowUpWell, University of Newcastle and Hunter Medical Research Institute, Newcastle, Australia
| | - Malcolm R Starkey
- Priority Research Centre for Healthy Lungs, University of Newcastle and Hunter Medical Research Institute, Newcastle, Australia.,Priority Research Centre GrowUpWell, University of Newcastle and Hunter Medical Research Institute, Newcastle, Australia.,Microbiology, Asthma, and Airways Research Group, University of Newcastle and Hunter Medical Research Institute, Newcastle, Australia
| | - Philip M Hansbro
- Priority Research Centre for Healthy Lungs, University of Newcastle and Hunter Medical Research Institute, Newcastle, Australia.,Microbiology, Asthma, and Airways Research Group, University of Newcastle and Hunter Medical Research Institute, Newcastle, Australia
| | - Hideo Yagita
- Department of Immunology, Juntendo University, School of Medicine, Tokyo, Japan; and
| | - Paul S Foster
- Priority Research Centre for Healthy Lungs, University of Newcastle and Hunter Medical Research Institute, Newcastle, Australia
| | - Joerg Mattes
- Experimental and Translational Respiratory Medicine Group, University of Newcastle and Hunter Medical Research Institute, Newcastle, Australia; .,Priority Research Centre GrowUpWell, University of Newcastle and Hunter Medical Research Institute, Newcastle, Australia.,Paediatric Respiratory and Sleep Medicine Unit, John Hunter Children's Hospital, Newcastle, Australia
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Tu WW, Ji LD, Qian HX, Zhou M, Zhao JS, Xu J. Tributyltin induces disruption of microfilament in HL7702 cells via MAPK-mediated hyperphosphorylation of VASP. ENVIRONMENTAL TOXICOLOGY 2016; 31:1530-1538. [PMID: 26018654 DOI: 10.1002/tox.22157] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 05/02/2015] [Accepted: 05/11/2015] [Indexed: 06/04/2023]
Abstract
Tributyltin (TBT) has been widely used for various industrial purposes, and it has toxic effects on multiple organs and tissues. Previous studies have found that TBT could induce cytoskeletal disruption, especially of the actin filaments. However, the underlying mechanisms remain unclear. The aim of the present study was to determine whether TBT could induce microfilament disruption using HL7702 cells and then to assess for the total levels of various microfilament-associated proteins; finally, the involvement of the MAPK pathway was investigated. The results showed that after TBT treatment, F-actin began to depolymerize and lost its characteristic filamentous structure. The protein levels of Ezrin and Cofilin remained unchanged, the actin-related protein (ARP) 2/3 levels decreased slightly, and the vasodilator-stimulated phosphoprotein (VASP) decreased dramatically. However, the phosphorylation levels of VASP increased 2.5-fold, and the ratio of phosphorylated-VASP/unphosphorylated-VASP increased 31-fold. The mitogen-activated protein kinases (MAPKs) ERK and JNK were discovered to be activated. Inhibition of ERK and JNK not only largely diminished the TBT-induced hyperphosphorylation of VASP but also recovered the cellular morphology and rescued the cells from death. In summary, this study demonstrates that TBT-induced disruption of actin filaments is caused by the hyperphosphorylation of VASP through MAPK pathways. © 2015 Wiley Periodicals, Inc. Environ Toxicol 31: 1530-1538, 2016.
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Affiliation(s)
- Wei-Wei Tu
- Department of Preventive Medicine, School of Medicine, Ningbo University, 818 Fenghua Road, Ningbo, 315211, China
| | - Lin-Dan Ji
- Department of Biochemistry, School of Medicine, Ningbo University, 818 Fenghua Road, Ningbo, 315211, China
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, 818 Fenghua Road, Ningbo, 315211, China
| | - Hai-Xia Qian
- Department of Preventive Medicine, School of Medicine, Ningbo University, 818 Fenghua Road, Ningbo, 315211, China
| | - Mi Zhou
- Department of Preventive Medicine, School of Medicine, Ningbo University, 818 Fenghua Road, Ningbo, 315211, China
| | - Jin-Shun Zhao
- Department of Preventive Medicine, School of Medicine, Ningbo University, 818 Fenghua Road, Ningbo, 315211, China
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, 818 Fenghua Road, Ningbo, 315211, China
| | - Jin Xu
- Department of Preventive Medicine, School of Medicine, Ningbo University, 818 Fenghua Road, Ningbo, 315211, China.
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, 818 Fenghua Road, Ningbo, 315211, China.
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Zhou M, Feng M, Fu LL, Ji LD, Zhao JS, Xu J. Toxicogenomic analysis identifies the apoptotic pathway as the main cause of hepatotoxicity induced by tributyltin. Food Chem Toxicol 2016; 97:316-326. [PMID: 27678064 DOI: 10.1016/j.fct.2016.09.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Revised: 09/05/2016] [Accepted: 09/23/2016] [Indexed: 10/20/2022]
Abstract
Tributyltin (TBT) is one of the most widely used organotin biocides, which has severe endocrine-disrupting effects on marine species and mammals. Given that TBT accumulates at higher levels in the liver than in any other organ, and it acts mainly as a hepatotoxic agent, it is important to clearly delineate the hepatotoxicity of TBT. However, most of the available studies on TBT have focused on observations at the cellular level, while studies at the level of genes and proteins are limited; therefore, the molecular mechanisms of TBT-induced hepatotoxicity remains largely unclear. In the present study, we applied a toxicogenomic approach to investigate the effects of TBT on gene expression in the human normal liver cell line HL7702. Gene expression profiling identified the apoptotic pathway as the major cause of hepatotoxicity induced by TBT. Flow cytometry assays confirmed that medium- and high-dose TBT treatments significantly increased the number of apoptotic cells, and more cells underwent late apoptosis in the high-dose TBT group. The genes encoding heat shock proteins (HSPs), kinases and tumor necrosis factor receptors mediated TBT-induced apoptosis. These findings revealed novel molecular mechanisms of TBT-induced hepatotoxicity, and the current microarray data may also provide clues for future studies.
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Affiliation(s)
- Mi Zhou
- Department of Preventive Medicine, School of Medicine, Ningbo University, Ningbo, Zhejiang Province, China
| | - Mei Feng
- Department of Preventive Medicine, School of Medicine, Ningbo University, Ningbo, Zhejiang Province, China
| | - Ling-Ling Fu
- Department of Preventive Medicine, School of Medicine, Ningbo University, Ningbo, Zhejiang Province, China
| | - Lin-Dan Ji
- Department of Biochemistry, School of Medicine, Ningbo University, Ningbo, Zhejiang Province, China; Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang Province, China
| | - Jin-Shun Zhao
- Department of Preventive Medicine, School of Medicine, Ningbo University, Ningbo, Zhejiang Province, China; Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang Province, China
| | - Jin Xu
- Department of Preventive Medicine, School of Medicine, Ningbo University, Ningbo, Zhejiang Province, China; Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang Province, China.
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Chen J, Wang FL, Chen WD. Modulation of apoptosis-related cell signalling pathways by curcumin as a strategy to inhibit tumor progression. Mol Biol Rep 2014; 41:4583-94. [PMID: 24604727 DOI: 10.1007/s11033-014-3329-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Accepted: 02/26/2014] [Indexed: 02/06/2023]
Abstract
A hallmark of cancer is resistance to apoptosis, with both the loss of proapoptotic signals and the gain of anti-apoptotic mechanisms contributing to tumorigenesis. As inducing apoptosis in malignant cells is one of the most challenging tasks regarding cancer, researchers increasingly focus on natural products to regulate apoptotic signaling pathways. Curcumin, a polyphenolic derivative of turmeric, is a natural compound derived from Curcuma longa, has attracted great interest in the research of cancer during the last half century. Extensive studies revealed that curcumin has chemopreventive properties, which are mainly due to its ability to arrest cell cycle and to induce apoptosis in cancer cells either alone or in combination with chemotherapeutic agents or radiation. The underlying action mechanisms of curcumin are diverse and has not been elucidated so far. By regulating multiple important cellular signalling pathways including NF-κB, TRAIL, PI3 K/Akt, JAK/STAT, Notch-1, JNK, etc., curcumin are known to activate cell death signals and induce apoptosis in pre-cancerous or cancer cells without affecting normal cells, thereby inhibiting tumor progression. Several phase I and phase II clinical trials indicate that curcumin is quite safe and may exhibit therapeutic efficacy. This article reviews the main effects of curcumin on the different apoptotic signaling pathways involved in curcumin induced apoptosis in cancer cells via cellular transduction pathways and provides an in depth assessment of its pharmacological activity in the management of tumor progression.
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Affiliation(s)
- Jin Chen
- Department of Pharmacy, The Second People's Hospital of Hefei, Hefei, 230011, Anhui, People's Republic of China,
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Zhang Y, Guo Z, Xu L. Tributyltin induces a G2/M cell cycle arrest in human amniotic cells via PP2A inhibition-mediated inactivation of the ERK1/2 cascades. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2014; 37:812-818. [PMID: 24632106 DOI: 10.1016/j.etap.2014.02.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 01/28/2014] [Accepted: 02/10/2014] [Indexed: 06/03/2023]
Abstract
The molecular mechanisms underlying the cell cycle alterations induced by tributyltin (TBT), a highly toxic environmental contaminant, remain elusive. In this study, cell cycle progression and some key regulators in G2/M phase were investigated in human amniotic cells treated with TBT. Furthermore, protein phosphatase (PP) 2A and the ERK cascades were examined. The results showed that TBT caused a G2/M cell cycle arrest that was accompanied by a decrease in the total cdc25C protein level and an increase in the p-cdc2 level in the nucleus. TBT caused a decrease in PP2A activity and inhibited the ERK cascade by inactivating Raf-1, resulting in the dephosphorylation of MEK1/2, ERK1/2, and c-Myc. Taken together, TBT leads to a G2/M cell cycle arrest in FL cells, an increase in p-cdc2 and a decrease in the levels of total cdc25C protein, which may be caused by the PP2A inhibition-mediated inactivation of the ERK1/2 cascades.
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Affiliation(s)
- Yali Zhang
- Department of Biochemistry, School of Medicine, Nantong University, 19 Qi Xiu Rode, 226001 Nantong, China; Department of Biochemistry and Genetics, School of Medicine, Zhejiang University, 388 Yu Hang Tang Road, 310058 Hangzhou, China.
| | - Zonglou Guo
- Department of Biosystem Engineering, College of Biosystem Engineering and Food Science, Zhejiang University, 388 Yu Hang Tang Road, 310058 Hangzhou, China.
| | - Lihong Xu
- Department of Biochemistry and Genetics, School of Medicine, Zhejiang University, 388 Yu Hang Tang Road, 310058 Hangzhou, China.
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