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Park HR, Lee SE, Kim H, Jeon S, Han D, Jin YH, Cho JJ, Ahn HJ, Park CS, Lee J, Park YS. Profiling of miRNA expression in mice kidney with diabetic nephropathy. Mol Cell Toxicol 2018. [DOI: 10.1007/s13273-018-0049-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Jia L, Zhang D, Huang H, Zhou Y, Zhou S, Guo J. Triazophos-induced toxicity in zebrafish: miRNA-217 inhibits nup43. Toxicol Res (Camb) 2018; 7:913-922. [PMID: 30310668 PMCID: PMC6116809 DOI: 10.1039/c8tx00065d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 05/29/2018] [Indexed: 11/21/2022] Open
Abstract
Triazophos is a highly toxic organophosphorus pesticide, causing acute toxicity to brain tissue, and neurotoxicity and embryotoxicity to animals. Therefore, triazophos is considered as a public health problem due to its acute hazard index. MicroRNAs (miRNAs), a class of endogenous noncoding RNAs, can regulate the expression of target gene(s) by mediating mRNA cleavage or translational repression in organisms exposed to environmental chemicals. We found that nup43 is targeted by miR-217, which was significantly regulated in adult zebrafish (Danio rerio) exposed to triazophos (phenyl-1,2,4-triazolyl-3-(o,o-diethyl thionophosphate)). The expression of nup43 in both mRNA and protein levels was downregulated in a dose-dependent manner upon stimulation with triazophos. A dual luciferase reporter assay demonstrated that miR-217 interacted with the 3'-untranslated regions (3'-UTR) of nup43. The expression of nup43 in both mRNA and protein level was reduced in ZF4 cells when transfected with an miR-217 mimic, but increased when transfected with an miR-217 inhibitor. As a result, nup43 is targeted by miR-217 upon triazophos exposure. We suggest that miR-217 could be a potential toxicological biomarker for triazophos.
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Affiliation(s)
- Longlue Jia
- College of Life Sciences , Zhejiang Sci-Tech University , Hangzhou , 310018 , China .
| | - Danyan Zhang
- College of Life Sciences , Zhejiang Sci-Tech University , Hangzhou , 310018 , China .
| | - Hannian Huang
- Department of Applied Engineering , Zhejiang Economic & Trade Polytechnic , Hangzhou , 310018 , China
| | - Yongyong Zhou
- College of Life Sciences , Zhejiang Sci-Tech University , Hangzhou , 310018 , China .
| | - Shengli Zhou
- Environmental Monitoring Center of Zhejiang Province , Hangzhou , 310015 , China
| | - Jiangfeng Guo
- College of Life Sciences , Zhejiang Sci-Tech University , Hangzhou , 310018 , China .
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MicroRNA Expression Analysis of Human Pulmonary Fibroblasts Treated with Acrolein. BIOCHIP JOURNAL 2018. [DOI: 10.1007/s13206-017-2304-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Joseph P. Transcriptomics in toxicology. Food Chem Toxicol 2017; 109:650-662. [PMID: 28720289 PMCID: PMC6419952 DOI: 10.1016/j.fct.2017.07.031] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 07/12/2017] [Accepted: 07/14/2017] [Indexed: 12/11/2022]
Abstract
Xenobiotics, of which many are toxic, may enter the human body through multiple routes. Excessive human exposure to xenobiotics may exceed the body's capacity to defend against the xenobiotic-induced toxicity and result in potentially fatal adverse health effects. Prevention of the adverse health effects, potentially associated with human exposure to the xenobiotics, may be achieved by detecting the toxic effects at an early, reversible and, therefore, preventable stage. Additionally, an understanding of the molecular mechanisms underlying the toxicity may be helpful in preventing and/or managing the ensuing adverse health effects. Human exposures to a large number of xenobiotics are associated with hepatotoxicity or pulmonary toxicity. Global gene expression changes taking place in biological systems, in response to exposure to xenobiotics, may represent the early and mechanistically relevant cellular events contributing to the onset and progression of xenobiotic-induced adverse health outcomes. Hepatotoxicity and pulmonary toxicity resulting from exposure to xenobiotics are discussed as specific examples to demonstrate the potential application of transcriptomics or global gene expression analysis in the prevention of adverse health effects associated with exposure to xenobiotics.
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Affiliation(s)
- Pius Joseph
- Molecular Carcinogenesis Laboratory, Toxicology and Molecular Biology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, USA.
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Hong JY, Yu SY, Kim GW, Ahn JJ, Kim Y, Lim S, Son SW, Hwang SY. Identification of time-dependent biomarkers and effects of exposure to volatile organic compounds using high-throughput analysis. ENVIRONMENTAL TOXICOLOGY 2016; 31:1563-1570. [PMID: 26018793 DOI: 10.1002/tox.22160] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 05/11/2015] [Accepted: 05/16/2015] [Indexed: 06/04/2023]
Abstract
Volatile organic compounds (VOCs) can be easily taken up by humans, leading to various diseases, such as respiratory system and central nervous system disorders. Environmental risk assessment is generally conducted using traditional tests, which may be time-consuming and technically challenging. Therefore, analysis of the effects of VOCs, such as toluene, ethylbenzene, and xylene, may be improved by use of novel, high-throughput methods, such as microarray analysis. In this study, we examined the effects of VOCs exposure in humans on gene expression and methylation using microarray analysis. We recruited participants who had short-term exposure, long-term exposure, or no exposure. We then analyzed changes in gene expression in blood samples from these participants. A total of 866 genes were upregulated, while 366 genes were downregulated in the short-term exposure group. Similarly, in the long-term exposure group, a total of 852 and 480 genes were up- or downregulated, respectively. Hierarchical clustering analysis was used to divide the clustered genes into nine clusters to investigate the expression of variations in accordance with the exposure period. And the methylation microarray was performed at the same time to see whether this expression variation is related to the epigenetic study. Finally, we have 5 genes that were upregulated and 12 genes that were downregulated, gradually and respectively, so these genes are expected to function as biomarkers of the duration of exposure to VOCs. Further research is required to determine the time-dependent effects of VOCs on epigenetic regulation of gene expression. © 2015 Wiley Periodicals, Inc. Environ Toxicol 31: 1563-1570, 2016.
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Affiliation(s)
- Ji Young Hong
- Department of Bio-Nanotechnology, Hanyang University, Sangnok-Gu, Ansan, Gyeonggi-Do, Korea
| | - So Yeon Yu
- Department of Molecular & Life Science, Hanyang University, Sangnok-Gu, Ansan, Gyeonggi-Do, Korea
| | - Gi Won Kim
- Department of Molecular & Life Science, Hanyang University, Sangnok-Gu, Ansan, Gyeonggi-Do, Korea
| | - Jeong Jin Ahn
- Department of Bio-Nanotechnology, Hanyang University, Sangnok-Gu, Ansan, Gyeonggi-Do, Korea
| | - Youngjoo Kim
- Department of Bio-Nanotechnology, Hanyang University, Sangnok-Gu, Ansan, Gyeonggi-Do, Korea
| | - Seri Lim
- Department of Molecular & Life Science, Hanyang University, Sangnok-Gu, Ansan, Gyeonggi-Do, Korea
| | - Sang Wook Son
- Department of Dermatology, Korea University Medical Center, Seoul, South Korea
| | - Seung Yong Hwang
- Department of Bio-Nanotechnology, Hanyang University, Sangnok-Gu, Ansan, Gyeonggi-Do, Korea.
- Department of Molecular & Life Science, Hanyang University, Sangnok-Gu, Ansan, Gyeonggi-Do, Korea.
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Li L, Wu J, Luo M, Sun Y, Wang G. The effect of heat stress on gene expression, synthesis of steroids, and apoptosis in bovine granulosa cells. Cell Stress Chaperones 2016; 21:467-75. [PMID: 26847372 PMCID: PMC4837181 DOI: 10.1007/s12192-016-0673-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 01/21/2016] [Accepted: 01/22/2016] [Indexed: 11/26/2022] Open
Abstract
Summer heat stress (HS) is a major contributing factor in low fertility in lactating dairy cows in hot environments. Heat stress inhibits ovarian follicular development leading to diminished reproductive efficiency of dairy cows during summer. Ovarian follicle development is a complex process. During follicle development, granulosa cells (GCs) replicate, secrete hormones, and support the growth of the oocyte. To obtain an overview of the effects of heat stress on GCs, digital gene expression profiling was employed to screen and identify differentially expressed genes (DEGs; false discovery rate (FDR) ≤ 0.001, fold change ≥2) of cultured GCs during heat stress. A total of 1211 DEGs including 175 upregulated and 1036 downregulated ones were identified, of which DEGs can be classified into Gene Ontology (GO) categories and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The results suggested that heat stress triggers a dramatic and complex program of altered gene expression in GCs. We hypothesized that heat stress could induce the apoptosis and dysfunction of GCs. Real-time reverse transcription-polymerase chain reaction (RT-PCR) was used to evaluate the expression of steroidogenic genes (steroidogenic acute regulatory protein (Star), cytochrome P-450 (CYP11A1), CYP19A1, and steroidogenic factor 1 (SF-1)) and apoptosis-related genes (caspase-3, BCL-2, and BAX). Radio immunoassay (RIA) was used to analyze the level of 17β-estradiol (E2) and progesterone (P4). We also assessed the apoptosis of GCs by flow cytometry. Our data suggested that heat stress induced GC apoptosis through the BAX/BCL-2 pathway and reduced the steroidogenic gene messenger RNA (mRNA) expression and E2 synthesis. These results suggest that the decreased function of GCs may cause ovarian dysfunction and offer an improved understanding of the molecular mechanism responsible for the low fertility in cattle in summer.
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Affiliation(s)
- Lian Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
| | - Jie Wu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Man Luo
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Yu Sun
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Genlin Wang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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Park HR, Lee SE, Son GW, Yun HD, Park YS. Integrated analysis of changed microRNA expression in crotonaldehyde-exposed human endothelial cells. BIOCHIP JOURNAL 2016. [DOI: 10.1007/s13206-016-0210-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Sun S, Ge X, Zhu J, Zhang W, Xuan F. De novo assembly of the blunt snout bream (Megalobrama amblycephala) gill transcriptome to identify ammonia exposure associated microRNAs and their targets. RESULTS IN IMMUNOLOGY 2016; 6:21-7. [PMID: 27504260 PMCID: PMC4969262 DOI: 10.1016/j.rinim.2016.03.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Revised: 02/24/2016] [Accepted: 03/09/2016] [Indexed: 01/01/2023]
Abstract
De novo transcriptome sequencing is a robust method for microRNA (miRNA) target gene prediction, especially for organisms without reference genomes. Following exposure of Megalobrama amblycephala to ammonia (0.1 or 20 mg L−1 ), two cDNA libraries were constructed from the fish gills and sequenced using Illumina HiSeq 2000. Over 90 million reads were generated and de novo assembled into 46, 615 unigenes, which were then extensively annotated by comparing to different protein databases, followed by biochemical pathway prediction. The expression of 2666 unigenes significantly differed; 1961 were up-regulated, while 975 were down-regulated. Among these, 250 unigenes were identified as the targets for 10 conserved and 4 putative novel miRNA families by miRNA target computational prediction. We examined expression of ssa-miRNA-21 and its target genes by real-time quantitative PCR and found agreement with the sequencing data. This study demonstrates the feasibility of identifying miRNA targets by transcriptome analysis. The transcriptome assembly data represent a substantial increase in the genomic resources available for Megalobrama amblycephala and will be useful for gene expression profile analysis and miRNA functional annotation. Several differentially expressed genes and miRNA were identified. Target prediction indicated that a number of miRNAs involved in immunity. The study provides an understanding of molecular mechanisms of ammonia-induced toxicology in fish.
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Affiliation(s)
- Shengming Sun
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, PR China
| | - Xianping Ge
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, PR China
- Corresponding author.
| | - Jian Zhu
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, PR China
| | - Wuxiao Zhang
- Wuxi Fishery College Nanjing Agricultural University, Wuxi 214081, PR China
| | - Fujun Xuan
- Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Yancheng Teachers University, Yancheng 224051, PR China
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Williams TD, Mirbahai L, Chipman JK. The toxicological application of transcriptomics and epigenomics in zebrafish and other teleosts. Brief Funct Genomics 2014; 13:157-71. [DOI: 10.1093/bfgp/elt053] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
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Kure EH, Sæbø M, Stangeland AM, Hamfjord J, Hytterød S, Heggenes J, Lydersen E. Molecular responses to toxicological stressors: profiling microRNAs in wild Atlantic salmon (Salmo salar) exposed to acidic aluminum-rich water. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2013; 138-139:98-104. [PMID: 23728355 DOI: 10.1016/j.aquatox.2013.04.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 04/09/2013] [Accepted: 04/14/2013] [Indexed: 06/02/2023]
Abstract
Atlantic salmon (Salmo salar) is among the most sensitive organisms toward acidic, aluminum exposure. Main documented responses to this type of stress are a combination of hypoxia and loss of blood plasma ions. Physiological responses to stress in fish are often grouped into primary, secondary and tertiary responses, where the above mentioned effects are secondary responses, while primary responses include endocrine changes as measurable levels of catecholamines and corticosteroids. In this study we have exposed young (14 months) Atlantic salmon to acid/Al water (pH ≈ 5.6, Al(i) ≈ 80 μg L⁻¹) for 3 days, and obtained clear and consistent decrease of Na⁺ and Cl⁻ ions, and increases of glucose in blood plasma, hematocrit and P(CO₂) in blood. We did not measure plasma cortisol (primary response compound), but analyzed effects on microRNA level (miRNA) in muscle tissue, as this may represent initial markers of primary stress responses. miRNAs regulate diverse biological processes, many are evolutionarily conserved, and hundreds have been identified in various animals, although only in a few fish species. We used a novel high-throughput sequencing (RNA-Seq) method to identify miRNAs in Atlantic salmon and specific miRNAs as potential early markers for stress. A total of 18 miRNAs were significantly differentially expressed (FDR<0.1) in exposed compared to control fish, four down-regulated and 14 up-regulated. An unsupervised hierarchical clustering of significant miRNAs revealed two clusters representing exposed and non-exposed individuals. Utilizing the genome of the zebrafish and bioinformatic tools, we identified 224 unique miRNAs in the Atlantic salmon samples sequenced. Additional laboratory studies focusing on function, stress dose-responses and temporal expression of the identified miRNAs will facilitate their use as initial markers for stress responses.
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Affiliation(s)
- Elin H Kure
- Telemark University College, Department of Environmental and Health Studies, 3800 Bø, Norway
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Yang H, Kim GD, Park HR, Park YS. Comparative mRNA and microRNA expression profiling of methylglyoxal-exposed human endothelial cells. BIOCHIP JOURNAL 2013. [DOI: 10.1007/s13206-013-7207-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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An YR, Kim SJ, Oh MJ, Kim HM, Shim IS, Kim PJ, Choi K, Hwang SY. Analysis of microRNA and gene expression profiling in triazole fungicide-treated HepG2 cell line. Toxicology 2013; 303:94-8. [DOI: 10.1016/j.tox.2012.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Revised: 10/08/2012] [Accepted: 11/06/2012] [Indexed: 02/04/2023]
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Choi EK, Kim KS, Yang HJ, Shin MH, Suh HW, Lee KB, Ahn KS, Um JY, Lee SG, Lee BC, Jang HJ. Hexane fraction of Citrus aurantium L. stimulates glucagon-like peptide-1 (GLP-1) secretion via membrane depolarization in NCI-H716 cells. BIOCHIP JOURNAL 2012. [DOI: 10.1007/s13206-012-6106-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Identification of time-dependent biomarkers by EndoTox Array in cells exposed to nonylphenol. Mol Cell Toxicol 2012. [DOI: 10.1007/s13273-011-0050-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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