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Liu Y, Song F, Li Z, Chen L, Xu Y, Sun H, Chang Y. A comprehensive tool for tumor precision medicine with pharmaco-omics data analysis. Front Pharmacol 2023; 14:1085765. [PMID: 36713829 PMCID: PMC9878337 DOI: 10.3389/fphar.2023.1085765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/04/2023] [Indexed: 01/14/2023] Open
Abstract
Background: Cancer precision medicine is an effective strategy to fight cancers by bridging genomics and drug discovery to provide specific treatment for patients with different genetic characteristics. Although some public databases and modelling frameworks have been developed through studies on drug response, most of them only considered the ramifications of the drug on the cell line and the effects on the patient still require a huge amount of work to integrate data from various databases and calculations, especially concerning precision treatment. Furthermore, not only efficacy but also the adverse effects of drugs on patients should be taken into account during cancer treatment. However, the adverse effects as essential indicators of drug safety assessment are always neglected. Method: A holistic estimation explores various drugs' efficacy levels by calculating their potency both in reversing and enhancing cancer-associated gene expression change. And a method for bridging the gap between cell culture and living tissue estimates the effectiveness of a drug on individual patients through the mappings of various cell lines to each person according to their genetic mutation similarities. Result: We predicted the efficacy of FDA-recommended drugs, taking into account both efficacy and toxicity, and obtained consistent results. We also provided an intuitive and easy-to-use web server called DBPOM (http://www.dbpom.net/, a comprehensive database of pharmaco-omics for cancer precision medicine), which not only integrates the above methods but also provides calculation results on more than 10,000 small molecule compounds and drugs. As a one-stop web server, clinicians and drug researchers can also analyze the overall effect of a drug or a drug combination on cancer patients as well as the biological functions that they target. DBPOM is now public, free to use with no login requirement, and contains all the data and code. Conclusion: Both the positive and negative effects of drugs during precision treatment are essential for practical application of drugs. DBPOM based on the two effects will become a vital resource and analysis platform for drug development, drug mechanism studies and the discovery of new therapies.
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Affiliation(s)
- Yijun Liu
- School of Artificial Intelligence, Jilin University, Changchun, China
| | - Fuhu Song
- School of Artificial Intelligence, Jilin University, Changchun, China
| | - Zhi Li
- Medical Oncology Department, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Liang Chen
- Department of Computer Science, College of Engineering, Shantou University, Shantou, China,Key Laboratory of Intelligent Manufacturing Technology of Ministry of Education, Shantou University, Shantou, China
| | - Ying Xu
- Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, The University of Georgia, Athens, GA, United States
| | - Huiyan Sun
- School of Artificial Intelligence, Jilin University, Changchun, China,International Center of Future Science, Jilin University, Changchun, China,*Correspondence: Huiyan Sun, ; Yi Chang,
| | - Yi Chang
- School of Artificial Intelligence, Jilin University, Changchun, China,International Center of Future Science, Jilin University, Changchun, China,*Correspondence: Huiyan Sun, ; Yi Chang,
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2
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Sager TM, Joseph P, Umbright CM, Hubbs AF, Barger M, Kashon ML, Fedan JS, Roberts JR. Biological effects of inhaled crude oil vapor. III. Pulmonary inflammation, cytotoxicity, and gene expression profile. Inhal Toxicol 2023; 35:241-253. [PMID: 37330949 PMCID: PMC10658288 DOI: 10.1080/08958378.2023.2224394] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 06/04/2023] [Indexed: 06/20/2023]
Abstract
OBJECTIVE Workers may be exposed to vapors emitted from crude oil in upstream operations in the oil and gas industry. Although the toxicity of crude oil constituents has been studied, there are very few in vivo investigations designed to mimic crude oil vapor (COV) exposures that occur in these operations. The goal of the current investigation was to examine lung injury, inflammation, oxidant generation, and effects on the lung global gene expression profile following a whole-body acute or sub-chronic inhalation exposure to COV. MATERIALS AND METHODS To conduct this investigation, rats were subjected to either a whole-body acute (6 hr) or a sub-chronic (28 d) inhalation exposure (6 hr/d × 4 d/wk × 4 wk) to COV (300 ppm; Macondo well surrogate oil). Control rats were exposed to filtered air. One and 28 d after acute exposure, and 1, 28, and 90 d following sub-chronic exposure, bronchoalveolar lavage was performed on the left lung to collect cells and fluid for analyses, the apical right lobe was preserved for histopathology, and the right cardiac and diaphragmatic lobes were processed for gene expression analyses. RESULTS No exposure-related changes were identified in histopathology, cytotoxicity, or lavage cell profiles. Changes in lavage fluid cytokines indicative of inflammation, immune function, and endothelial function after sub-chronic exposure were limited and varied over time. Minimal gene expression changes were detected only at the 28 d post-exposure time interval in both the exposure groups. CONCLUSION Taken together, the results from this exposure paradigm, including concentration, duration, and exposure chamber parameters, did not indicate significant and toxicologically relevant changes in markers of injury, oxidant generation, inflammation, and gene expression profile in the lung.
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Affiliation(s)
- Tina M Sager
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV, USA
| | - Pius Joseph
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV, USA
| | - Christina M Umbright
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV, USA
| | - Ann F Hubbs
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV, USA
| | - Mark Barger
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV, USA
| | - Michael L Kashon
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV, USA
| | - Jeffrey S Fedan
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV, USA
| | - Jenny R Roberts
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV, USA
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3
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Su R, Yang H, Wei L, Chen S, Zou Q. A multi-label learning model for predicting drug-induced pathology in multi-organ based on toxicogenomics data. PLoS Comput Biol 2022; 18:e1010402. [PMID: 36070305 PMCID: PMC9451100 DOI: 10.1371/journal.pcbi.1010402] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 07/18/2022] [Indexed: 11/18/2022] Open
Abstract
Drug-induced toxicity damages the health and is one of the key factors causing drug withdrawal from the market. It is of great significance to identify drug-induced target-organ toxicity, especially the detailed pathological findings, which are crucial for toxicity assessment, in the early stage of drug development process. A large variety of studies have devoted to identify drug toxicity. However, most of them are limited to single organ or only binary toxicity. Here we proposed a novel multi-label learning model named Att-RethinkNet, for predicting drug-induced pathological findings targeted on liver and kidney based on toxicogenomics data. The Att-RethinkNet is equipped with a memory structure and can effectively use the label association information. Besides, attention mechanism is embedded to focus on the important features and obtain better feature presentation. Our Att-RethinkNet is applicable in multiple organs and takes account the compound type, dose, and administration time, so it is more comprehensive and generalized. And more importantly, it predicts multiple pathological findings at the same time, instead of predicting each pathology separately as the previous model did. To demonstrate the effectiveness of the proposed model, we compared the proposed method with a series of state-of-the-arts methods. Our model shows competitive performance and can predict potential hepatotoxicity and nephrotoxicity in a more accurate and reliable way. The implementation of the proposed method is available at https://github.com/RanSuLab/Drug-Toxicity-Prediction-MultiLabel.
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Affiliation(s)
- Ran Su
- School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University, Tianjin, China
| | - Haitang Yang
- School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University, Tianjin, China
| | - Leyi Wei
- School of Software, Shandong University, Jinan, Shandong, China
- * E-mail: (LW); (SC); (QZ)
| | - Siqi Chen
- School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University, Tianjin, China
- * E-mail: (LW); (SC); (QZ)
| | - Quan Zou
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, Zhejiang, China
- * E-mail: (LW); (SC); (QZ)
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4
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Sohrabi SS, Rashidipour M, Sohrabi SM, Hadizadeh M, Shams MH, Mohammadi M. Genome-wide evaluation of transcriptomic responses of human tissues to smoke: A systems biology study. Gene X 2022; 820:146114. [PMID: 35077830 DOI: 10.1016/j.gene.2021.146114] [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: 07/30/2021] [Revised: 11/29/2021] [Accepted: 12/06/2021] [Indexed: 11/18/2022] Open
Abstract
The harmful compounds in various sources of smoke threaten human health. So far, many studies have investigated the effects of compounds of smoke on transcriptome changes in different human tissues. However, no study has been conducted on the effects of these compounds on transcriptome changes in different human tissues simultaneously. Hence, the present study was conducted to identify smoke-related genes (SRGs) and their response mechanisms to smoke in various human cells and tissues using systems biology based methods. A total of 6,484 SRGs were identified in the studied tissues, among which 4,095 SRGs were up-regulated and 2,389 SRGs were down-regulated. Totally, 459 SRGs were smoke-related transcription factors (SRTFs). Gene regulatory network analysis showed that the studied cells and tissues have different gene regulation and responses to compounds of smoke. The comparison of different tissues revealed no common SRG among the all studied tissues. However, the CYP1B1 gene was common among seven cells and tissues, and had the same expression trend. Network analysis showed that the CYP1B1 is a hub gene among SRGs in various cells and tissues. To the best of our knowledge, for the first time, our results showed that compounds of smoke induce and increase the expression of CYP1B1 key gene in all target and non-target tissues of human. Moreover, despite the specific characteristics of CYP1B1 gene and its identical expression trend in target and non-target tissues, it can be used as a biomarker for diagnosis and prognosis.
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Affiliation(s)
- Seyed Sajad Sohrabi
- Department of Production Engineering and Plant Genetics, Faculty of Agriculture, Lorestan University, Khorramabad, Iran; Environmental Health Research Center, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Marzieh Rashidipour
- Environmental Health Research Center, Lorestan University of Medical Sciences, Khorramabad, Iran; Nutritional Health Research Center, Lorestan University of Medical Sciences, Khorramabad, Iran.
| | - Seyyed Mohsen Sohrabi
- Department of Production Engineering and Plant Genetics, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Morteza Hadizadeh
- Physiology Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohammad-Hossein Shams
- Department of Immunology, Faculty of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Mohsen Mohammadi
- Razi Herbal Medicines Research Center and Department of Pharmacognosy and Pharmaceutical Biotechnology, Faculty of Pharmacy, Lorestan University of Medical Sciences, Khorramabad, Iran
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5
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Gauran II, Xue G, Chen C, Ombao H, Yu Z. Ridge Penalization in High-Dimensional Testing With Applications to Imaging Genetics. Front Neurosci 2022; 16:836100. [PMID: 35401090 PMCID: PMC8987922 DOI: 10.3389/fnins.2022.836100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/24/2022] [Indexed: 11/13/2022] Open
Abstract
High-dimensionality is ubiquitous in various scientific fields such as imaging genetics, where a deluge of functional and structural data on brain-relevant genetic polymorphisms are investigated. It is crucial to identify which genetic variations are consequential in identifying neurological features of brain connectivity compared to merely random noise. Statistical inference in high-dimensional settings poses multiple challenges involving analytical and computational complexity. A widely implemented strategy in addressing inference goals is penalized inference. In particular, the role of the ridge penalty in high-dimensional prediction and estimation has been actively studied in the past several years. This study focuses on ridge-penalized tests in high-dimensional hypothesis testing problems by proposing and examining a class of methods for choosing the optimal ridge penalty. We present our findings on strategies to improve the statistical power of ridge-penalized tests and what determines the optimal ridge penalty for hypothesis testing. The application of our work to an imaging genetics study and biological research will be presented.
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Affiliation(s)
- Iris Ivy Gauran
- Biostatistics Group, Computer, Electrical, Mathematical Sciences, and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Gui Xue
- Center for Brain and Learning Science, Beijing Normal University, Beijing, China
| | - Chuansheng Chen
- Department of Psychological Science, University of California, Irvine, Irvine, CA, United States
| | - Hernando Ombao
- Biostatistics Group, Computer, Electrical, Mathematical Sciences, and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Zhaoxia Yu
- Department of Statistics, University of California, Irvine, Irvine, CA, United States
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6
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Bry X, Niang N, Verron T, Bougeard S. Clusterwise elastic-net regression based on a combined information criterion. ADV DATA ANAL CLASSI 2022. [DOI: 10.1007/s11634-021-00489-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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7
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Sager TM, Umbright CM, Mustafa GM, Roberts JR, Orandle MS, Cumpston JL, McKinney WG, Boots T, Kashon ML, Joseph P. Pulmonary toxicity and gene expression changes in response to whole-body inhalation exposure to multi-walled carbon nanotubes in rats. Inhal Toxicol 2022; 34:200-218. [PMID: 35648795 PMCID: PMC9885491 DOI: 10.1080/08958378.2022.2081386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Purpose: To investigate the molecular mechanisms underlying the pulmonary toxicity induced by exposure to one form of multi-walled carbon nanotubes (MWCNT-7).Materials and methods: Rats were exposed, by whole-body inhalation, to air or an aerosol containing MWCNT-7 particles at target cumulative doses (concentration x time) ranging from 22.5 to 180 (mg/m3)h over a three-day (6 hours/day) period and toxicity and global gene expression profiles were determined in the lungs.Results: MWCNT-7 particles, associated with alveolar macrophages (AMs), were detected in rat lungs following the exposure. Mild to moderate lung pathological changes consisting of increased cellularity, thickening of the alveolar wall, alveolitis, fibrosis, and granuloma formation were detected. Bronchoalveolar lavage (BAL) toxicity parameters such as lactate dehydrogenase activity, number of AMs and polymorphonuclear leukocytes (PMNs), intracellular oxidant generation by phagocytes, and levels of cytokines were significantly (p < 0.05) increased in response to exposure to MWCNT-7. Global gene expression profiling identified several significantly differentially expressed genes (fold change >1.5 and FDR p value <0.05) in all the MWCNT-7 exposed rats. Bioinformatic analysis of the gene expression data identified significant enrichment of several diseases/biological function categories (for example, cancer, leukocyte migration, inflammatory response, mitosis, and movement of phagocytes) and canonical pathways (for example, kinetochore metaphase signaling pathway, granulocyte and agranulocyte adhesion and diapedesis, acute phase response, and LXR/RXR activation). The alterations in the lung toxicity parameters and gene expression changes exhibited a dose-response to the MWCNT exposure.Conclusions: Taken together, the data provided insights into the molecular mechanisms underlying the pulmonary toxicity induced by inhalation exposure of rats to MWCNT-7.
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Affiliation(s)
- Tina M. Sager
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, USA
| | - Christina M. Umbright
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, USA
| | - Gul Mehnaz Mustafa
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, USA
| | - Jenny R. Roberts
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, USA
| | - Marlene S. Orandle
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, USA
| | - Jared L. Cumpston
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, USA
| | - Walter G. McKinney
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, USA
| | - Theresa Boots
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, USA
| | - Michael L. Kashon
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, USA
| | - Pius Joseph
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, USA
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8
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Panel of suitable reference genes and its gender differences of fetal rat liver under physiological conditions and exposure to dexamethasone during pregnancy. Reprod Toxicol 2021; 100:74-82. [PMID: 33453333 DOI: 10.1016/j.reprotox.2021.01.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 12/17/2020] [Accepted: 01/11/2021] [Indexed: 01/04/2023]
Abstract
The panel of suitable reference genes in the fetal liver have not been reported. In this study, five commonly used reference genes (GAPDH, β-actin, Rn18 s, Rpl13a, and Rps29) were firstly selected as candidates. Bestkeeper, GeNorm, and NormFinder software were then used to screen out the panel of suitable reference genes of male and female fetal rat liver under physiological and prenatal dexamethasone exposure (PDE) conditions. Finally, we verified the reliability of the screened panel of reference genes by standardizing sterol regulatory element binding protein 1c (SREBP1c) expression with different reference genes. The results showed that GAPDH + Rn18 s and GAPDH + Rpl13a were respectively the panel of suitable reference genes in male and female rat fetal liver under the physiological model, while Rn18 s + Rps29 and GAPDH + Rn18 s were respectively under the PDE model. The results showed that different reference genes affected the statistical results of SREBP1c expression, and the screened panel of suitable reference genes under the PDE model had smaller intragroup differences, when compared with other reference genes under physiological and PDE models. In conclusion, we screened and determined that the panel of suitable reference genes were GAPDH + Rn18 s and Rn18 s + Rps29 in the male rat fetal liver under physiological and PDE models, while they were GAPDH + Rpl13a and GAPDH + Rn18 s in the females, and confirmed that the selection of the panel of suitable reference genes in the fetal liver had gender differences and pathological model specificity.
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9
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Johnson KJ, Auerbach SS, Costa E. A Rat Liver Transcriptomic Point of Departure Predicts a Prospective Liver or Non-liver Apical Point of Departure. Toxicol Sci 2020; 176:86-102. [PMID: 32384157 PMCID: PMC7357187 DOI: 10.1093/toxsci/kfaa062] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Identifying a toxicity point of departure (POD) is a required step in human health risk characterization of crop protection molecules, and this POD has historically been derived from apical endpoints across a battery of animal-based toxicology studies. Using rat transcriptome and apical data for 79 molecules obtained from Open TG-GATES (Toxicogenomics Project-Genomics Assisted Toxicity Evaluation System) (632 datasets), the hypothesis was tested that a short-term exposure, transcriptome-based liver biological effect POD (BEPOD) could estimate a longer-term exposure "systemic" apical endpoint POD. Apical endpoints considered were body weight, clinical observation, kidney weight and histopathology and liver weight and histopathology. A BMDExpress algorithm using Gene Ontology Biological Process gene sets was optimized to derive a liver BEPOD most predictive of a systemic apical POD. Liver BEPODs were stable from 3 h to 29 days of exposure; the median fold difference of the 29-day BEPOD to BEPODs from earlier time points was approximately 1 (range: 0.7-1.1). Strong positive correlation (Pearson R = 0.86) and predictive accuracy (root mean square difference = 0.41) were observed between a concurrent (29 days) liver BEPOD and the systemic apical POD. Similar Pearson R and root mean square difference values were observed for comparisons between a 29-day systemic apical POD and liver BEPODs derived from 3 h to 15 days of exposure. These data across 79 molecules suggest that a longer-term exposure study apical POD from liver and non-liver compartments can be estimated using a liver BEPOD derived from an acute or subacute exposure study.
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Affiliation(s)
- Kamin J Johnson
- Predictive Safety Center, Corteva Agriscience, Indianapolis, Indiana
| | - Scott S Auerbach
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Eduardo Costa
- Data Science and Informatics, Corteva Agriscience, Mogi Mirim, Sao Paulo, Brazil
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10
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Pannala VR, Vinnakota KC, Rawls KD, Estes SK, O'Brien TP, Printz RL, Papin JA, Reifman J, Shiota M, Young JD, Wallqvist A. Mechanistic identification of biofluid metabolite changes as markers of acetaminophen-induced liver toxicity in rats. Toxicol Appl Pharmacol 2019; 372:19-32. [PMID: 30974156 DOI: 10.1016/j.taap.2019.04.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/22/2019] [Accepted: 04/05/2019] [Indexed: 12/12/2022]
Abstract
Acetaminophen (APAP) is the most commonly used analgesic and antipyretic drug in the world. Yet, it poses a major risk of liver injury when taken in excess of the therapeutic dose. Current clinical markers do not detect the early onset of liver injury associated with excess APAP-information that is vital to reverse injury progression through available therapeutic interventions. Hence, several studies have used transcriptomics, proteomics, and metabolomics technologies, both independently and in combination, in an attempt to discover potential early markers of liver injury. However, the casual relationship between these observations and their relation to the APAP mechanism of liver toxicity are not clearly understood. Here, we used Sprague-Dawley rats orally gavaged with a single dose of 2 g/kg of APAP to collect tissue samples from the liver and kidney for transcriptomic analysis and plasma and urine samples for metabolomic analysis. We developed and used a multi-tissue, metabolism-based modeling approach to integrate these data, characterize the effect of excess APAP levels on liver metabolism, and identify a panel of plasma and urine metabolites that are associated with APAP-induced liver toxicity. Our analyses, which indicated that pathways involved in nucleotide-, lipid-, and amino acid-related metabolism in the liver were most strongly affected within 10 h following APAP treatment, identified a list of potential metabolites in these pathways that could serve as plausible markers of APAP-induced liver injury. Our approach identifies toxicant-induced changes in endogenous metabolism, is applicable to other toxicants based on transcriptomic data, and provides a mechanistic framework for interpreting metabolite alterations.
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Affiliation(s)
- Venkat R Pannala
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA; Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, MD 21702, USA.
| | - Kalyan C Vinnakota
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA; Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, MD 21702, USA
| | - Kristopher D Rawls
- Department of Biomedical Engineering, University of Virginia, Box 800759, Health System, Charlottesville, Virginia 22908, USA
| | - Shanea K Estes
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Tracy P O'Brien
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Richard L Printz
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jason A Papin
- Department of Biomedical Engineering, University of Virginia, Box 800759, Health System, Charlottesville, Virginia 22908, USA
| | - Jaques Reifman
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, MD 21702, USA
| | - Masakazu Shiota
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jamey D Young
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Chemical and Biomolecular Engineering, Vanderbilt University School of Engineering, Nashville, TN 37232, USA.
| | - Anders Wallqvist
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, MD 21702, USA.
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11
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Pannala VR, Wall ML, Estes SK, Trenary I, O'Brien TP, Printz RL, Vinnakota KC, Reifman J, Shiota M, Young JD, Wallqvist A. Metabolic network-based predictions of toxicant-induced metabolite changes in the laboratory rat. Sci Rep 2018; 8:11678. [PMID: 30076366 PMCID: PMC6076258 DOI: 10.1038/s41598-018-30149-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 07/23/2018] [Indexed: 12/11/2022] Open
Abstract
In order to provide timely treatment for organ damage initiated by therapeutic drugs or exposure to environmental toxicants, we first need to identify markers that provide an early diagnosis of potential adverse effects before permanent damage occurs. Specifically, the liver, as a primary organ prone to toxicants-induced injuries, lacks diagnostic markers that are specific and sensitive to the early onset of injury. Here, to identify plasma metabolites as markers of early toxicant-induced injury, we used a constraint-based modeling approach with a genome-scale network reconstruction of rat liver metabolism to incorporate perturbations of gene expression induced by acetaminophen, a known hepatotoxicant. A comparison of the model results against the global metabolic profiling data revealed that our approach satisfactorily predicted altered plasma metabolite levels as early as 5 h after exposure to 2 g/kg of acetaminophen, and that 10 h after treatment the predictions significantly improved when we integrated measured central carbon fluxes. Our approach is solely driven by gene expression and physiological boundary conditions, and does not rely on any toxicant-specific model component. As such, it provides a mechanistic model that serves as a first step in identifying a list of putative plasma metabolites that could change due to toxicant-induced perturbations.
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Affiliation(s)
- Venkat R Pannala
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, MD, 21702, USA.
| | - Martha L Wall
- Department of Chemical and Biomolecular Engineering, Vanderbilt University School of Engineering, Nashville, TN, 37232, USA
| | - Shanea K Estes
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Irina Trenary
- Department of Chemical and Biomolecular Engineering, Vanderbilt University School of Engineering, Nashville, TN, 37232, USA
| | - Tracy P O'Brien
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Richard L Printz
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Kalyan C Vinnakota
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, MD, 21702, USA
| | - Jaques Reifman
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, MD, 21702, USA
| | - Masakazu Shiota
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Jamey D Young
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA. .,Department of Chemical and Biomolecular Engineering, Vanderbilt University School of Engineering, Nashville, TN, 37232, USA.
| | - Anders Wallqvist
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, MD, 21702, USA.
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12
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Day PEL, Chambers KF, Winterbone MS, García-Blanco T, Vauzour D, Kroon PA. Validation of control genes and a standardised protocol for quantifying gene expression in the livers of C57BL/6 and ApoE-/- mice. Sci Rep 2018; 8:8081. [PMID: 29795401 PMCID: PMC5967315 DOI: 10.1038/s41598-018-26431-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 05/08/2018] [Indexed: 12/11/2022] Open
Abstract
The liver plays a critical role in food and drug metabolism and detoxification and accordingly influences systemic body homeostasis in health and disease. While the C57BL/6 and ApoE−/− mouse models are widely used to study gene expression changes in liver disease and metabolism, currently there are no validated stably expressed endogenous genes in these models, neither is it known how gene expression varies within and across liver lobes. Here we show regional variations in the expression of Ywhaz, Gak, Gapdh, Hmbs and Act-β endogenous genes across a liver lobe; Using homogeneous samples from the four liver lobes of 6 C57BL/6 mice we tested the stability of 12 endogenous genes and show that Act-β and Eif2-α are the most stably expressed endogenous genes in all four lobes and demonstrate lobular differences in the expression of Abca1 cholesterol efflux gene. These results suggest that sampling from a specified homogeneous powdered liver lobe is paramount in enhancing data reliability and reproducibility. The stability of the 12 endogenous genes was further tested using homogeneous samples of left liver lobes from 20 ApoE−/− mice on standard or high polyphenol diets. Act-β and Ywhaz are suitable endogenous genes for gene expression normalisation in this mouse model.
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Affiliation(s)
- Priscilla E L Day
- Food & Health Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UA, UK
| | - Karen F Chambers
- Food & Health Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UA, UK
| | - Mark S Winterbone
- Food & Health Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UA, UK
| | - Tatiana García-Blanco
- Food & Health Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UA, UK
| | - David Vauzour
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Paul A Kroon
- Food & Health Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UA, UK.
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13
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Iguchi T, Sakurai K, Tamai S, Mori K. Circulating liver-specific microRNAs in cynomolgus monkeys. J Toxicol Pathol 2017; 31:3-13. [PMID: 29479135 PMCID: PMC5820098 DOI: 10.1293/tox.2017-0036] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 08/17/2017] [Indexed: 02/06/2023] Open
Abstract
Circulating microRNAs (miRNAs) can potentially be used as sensitive and specific
biomarkers for tissue injury. However, the usefulness of circulating miRNAs as safety
biomarkers in nonclinical toxicological studies using nonhuman primates is debatable owing
to the limited information on organ-specific miRNAs. Therefore, a systematic investigation
was performed to address this point. We identified organ-specific miRNAs from cynomolgus
monkeys by next-generation sequencing analysis, which revealed that miR-122 was only
abundant in the liver, whereas miR-192 was abundant in the liver, stomach, intestines, and
kidney. The sequences of these miRNAs were identical to their human counterparts. Next,
the absolute miR-122 and miR-192 levels were qualified by quantitative reverse
transcription polymerase chain reaction (RT-qPCR) to determine the circulating levels of
the miRNAs. No significant differences in the levels of circulating miRNAs between sexes
were noted, and there was greater interindividual variation in miR-122 (20-fold variation)
than in miR-192 (8-fold variation), based on their dynamic ranges. Finally, we evaluated
the fluctuation in circulating liver-specific miRNAs in a monkey model of
acetaminophen-induced hepatotoxicity. Acetaminophen with L-buthionine-(S,R)-sulfoximine
induced hepatotoxicity in all the animals, which was characterized histopathologically by
centrilobular necrosis and vacuolation of hepatocytes. Circulating miR-122 and miR-192
levels increased more than ALT levels after 24 h, indicating that circulating miR-122 and
miR-192 may serve as sensitive biomarkers for the detection of hepatotoxicity in
cynomolgus monkeys. This review describes the fundamental profiles of circulating
liver-specific miRNAs in cynomolgus monkeys and focusses on their organ specificity,
circulating levels, and fluctuations in drug-induced hepatotoxicity.
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Affiliation(s)
- Takuma Iguchi
- Medicinal Safety Research Laboratories, Daiichi Sankyo Co., Ltd., 1-16-13 Kita-Kasai, Edogawa-ku, Tokyo 134-8630, Japan
| | - Ken Sakurai
- Medicinal Safety Research Laboratories, Daiichi Sankyo Co., Ltd., 1-16-13 Kita-Kasai, Edogawa-ku, Tokyo 134-8630, Japan
| | - Satoshi Tamai
- Medicinal Safety Research Laboratories, Daiichi Sankyo Co., Ltd., 1-16-13 Kita-Kasai, Edogawa-ku, Tokyo 134-8630, Japan
| | - Kazuhiko Mori
- Medicinal Safety Research Laboratories, Daiichi Sankyo Co., Ltd., 1-16-13 Kita-Kasai, Edogawa-ku, Tokyo 134-8630, Japan
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14
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Joseph P. Transcriptomics in toxicology. Food Chem Toxicol 2017; 109:650-662. [PMID: 28720289 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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15
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Tamai S, Iguchi T, Niino N, Mikamoto K, Sakurai K, Sayama A, Shimoda H, Takasaki W, Mori K. A monkey model of acetaminophen-induced hepatotoxicity; phenotypic similarity to human. J Toxicol Sci 2017; 42:73-84. [PMID: 28070111 DOI: 10.2131/jts.42.73] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Species-specific differences in the hepatotoxicity of acetaminophen (APAP) have been shown. To establish a monkey model of APAP-induced hepatotoxicity, which has not been previously reported, APAP at doses up to 2,000 mg/kg was administered orally to fasting male and female cynomolgus monkeys (n = 3-5/group) pretreated intravenously with or without 300 mg/kg of the glutathione biosynthesis inhibitor, L-buthionine-(S,R)-sulfoximine (BSO). In all the animals, APAP at 2,000 mg/kg with BSO but not without BSO induced hepatotoxicity, which was characterized histopathologically by centrilobular necrosis and vacuolation of hepatocytes. Plasma levels of APAP and its reactive metabolite N-acethyl-p-benzoquinone imine (NAPQI) increased 4 to 7 hr after the APAP treatment. The mean Cmax level of APAP at 2,000 mg/kg with BSO was approximately 200 µg/mL, which was comparable to high-risk cutoff value of the Rumack-Matthew nomogram. Interestingly, plasma alanine aminotransferase (ALT) did not change until 7 hr and increased 24 hr or later after the APAP treatment, indicating that this phenotypic outcome was similar to that in humans. In addition, circulating liver-specific miR-122 and miR-192 levels also increased 24 hr or later compared with ALT, suggesting that circulating miR-122 and miR-192 may serve as potential biomarkers to detect hepatotoxicity in cynomolgus monkeys. These results suggest that the hepatotoxicity induced by APAP in the monkey model shown here was translatable to humans in terms of toxicokinetics and its toxic nature, and this model would be useful to investigate mechanisms of drug-induced liver injury and also potential translational biomarkers in humans.
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Affiliation(s)
- Satoshi Tamai
- Medicinal Safety Research Laboratories, Daiichi Sankyo Co., Ltd
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16
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Sellamuthu R, Umbright C, Roberts JR, Young SH, Richardson D, McKinney W, Chen BT, Li S, Kashon M, Joseph P. Molecular mechanisms of pulmonary response progression in crystalline silica exposed rats. Inhal Toxicol 2017; 29:53-64. [PMID: 28317464 DOI: 10.1080/08958378.2017.1282064] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
An understanding of the mechanisms underlying diseases is critical for their prevention. Excessive exposure to crystalline silica is a risk factor for silicosis, a potentially fatal pulmonary disease. Male Fischer 344 rats were exposed by inhalation to crystalline silica (15 mg/m3, six hours/day, five days) and pulmonary response was determined at 44 weeks following termination of silica exposure. Additionally, global gene expression profiling in lungs and BAL cells and bioinformatic analysis of the gene expression data were done to understand the molecular mechanisms underlying the progression of pulmonary response to silica. A significant increase in lactate dehydrogenase activity and albumin content in BAL fluid (BALF) suggested silica-induced pulmonary toxicity in the rats. A significant increase in the number of alveolar macrophages and infiltrating neutrophils in the lungs and elevation in monocyte chemoattractant protein-1 (MCP-1) in BALF suggested the induction of pulmonary inflammation in the silica exposed rats. Histological changes in the lungs included granuloma formation, type II pneumocyte hyperplasia, thickening of alveolar septa and positive response to Masson's trichrome stain. Microarray analysis of global gene expression detected 94 and 225 significantly differentially expressed genes in the lungs and BAL cells, respectively. Bioinformatic analysis of the gene expression data identified significant enrichment of several disease and biological function categories and canonical pathways related to pulmonary toxicity, especially inflammation. Taken together, these data suggested the involvement of chronic inflammation as a mechanism underlying the progression of pulmonary response to exposure of rats to crystalline silica at 44 weeks following termination of exposure.
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Affiliation(s)
- Rajendran Sellamuthu
- a Health Effects Laboratory Division , National Institute for Occupational Safety and Health (NIOSH) , Morgantown , WV , USA
| | - Christina Umbright
- a Health Effects Laboratory Division , National Institute for Occupational Safety and Health (NIOSH) , Morgantown , WV , USA
| | - Jenny R Roberts
- a Health Effects Laboratory Division , National Institute for Occupational Safety and Health (NIOSH) , Morgantown , WV , USA
| | - Shih-Houng Young
- a Health Effects Laboratory Division , National Institute for Occupational Safety and Health (NIOSH) , Morgantown , WV , USA
| | - Diana Richardson
- a Health Effects Laboratory Division , National Institute for Occupational Safety and Health (NIOSH) , Morgantown , WV , USA
| | - Walter McKinney
- a Health Effects Laboratory Division , National Institute for Occupational Safety and Health (NIOSH) , Morgantown , WV , USA
| | - Bean T Chen
- a Health Effects Laboratory Division , National Institute for Occupational Safety and Health (NIOSH) , Morgantown , WV , USA
| | - Shengqiao Li
- a Health Effects Laboratory Division , National Institute for Occupational Safety and Health (NIOSH) , Morgantown , WV , USA
| | - Michael Kashon
- a Health Effects Laboratory Division , National Institute for Occupational Safety and Health (NIOSH) , Morgantown , WV , USA
| | - Pius Joseph
- a Health Effects Laboratory Division , National Institute for Occupational Safety and Health (NIOSH) , Morgantown , WV , USA
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17
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Umbright C, Sellamuthu R, Roberts JR, Young SH, Richardson D, Schwegler-Berry D, McKinney W, Chen B, Gu JK, Kashon M, Joseph P. Pulmonary toxicity and global gene expression changes in response to sub-chronic inhalation exposure to crystalline silica in rats. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2017; 80:1349-1368. [PMID: 29165057 DOI: 10.1080/15287394.2017.1384773] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/22/2017] [Indexed: 06/07/2023]
Abstract
Exposure to crystalline silica results in serious adverse health effects, most notably, silicosis. An understanding of the mechanism(s) underlying silica-induced pulmonary toxicity is critical for the intervention and/or prevention of its adverse health effects. Rats were exposed by inhalation to crystalline silica at a concentration of 15 mg/m3, 6 hr/day, 5 days/week for 3, 6 or 12 weeks. Pulmonary toxicity and global gene expression profiles were determined in lungs at the end of each exposure period. Crystalline silica was visible in lungs of rats especially in the 12-week group. Pulmonary toxicity, as evidenced by an increase in lactate dehydrogenase (LDH) activity and albumin content and accumulation of macrophages and neutrophils in the bronchoalveolar lavage (BAL), was seen in animals depending upon silica exposure duration. The most severe histological changes, noted in the 12-week exposure group, consisted of chronic active inflammation, type II pneumocyte hyperplasia, and fibrosis. Microarray analysis of lung gene expression profiles detected significant differential expression of 38, 77, and 99 genes in rats exposed to silica for 3-, 6-, or 12-weeks, respectively, compared to time-matched controls. Among the significantly differentially expressed genes (SDEG), 32 genes were common in all exposure groups. Bioinformatics analysis of the SDEG identified enrichment of functions, networks and canonical pathways related to inflammation, cancer, oxidative stress, fibrosis, and tissue remodeling in response to silica exposure. Collectively, these results provided insights into the molecular mechanisms underlying pulmonary toxicity following sub-chronic inhalation exposure to crystalline silica in rats.
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Affiliation(s)
- Christina Umbright
- a Toxicology and Molecular Biology Branch, Health Effects Laboratory Division , National Institute for Occupational Safety and Health (NIOSH) , Morgantown , WV , USA
| | - Rajendran Sellamuthu
- a Toxicology and Molecular Biology Branch, Health Effects Laboratory Division , National Institute for Occupational Safety and Health (NIOSH) , Morgantown , WV , USA
| | - Jenny R Roberts
- a Toxicology and Molecular Biology Branch, Health Effects Laboratory Division , National Institute for Occupational Safety and Health (NIOSH) , Morgantown , WV , USA
| | - Shih-Houng Young
- a Toxicology and Molecular Biology Branch, Health Effects Laboratory Division , National Institute for Occupational Safety and Health (NIOSH) , Morgantown , WV , USA
| | - Diana Richardson
- a Toxicology and Molecular Biology Branch, Health Effects Laboratory Division , National Institute for Occupational Safety and Health (NIOSH) , Morgantown , WV , USA
| | - Diane Schwegler-Berry
- a Toxicology and Molecular Biology Branch, Health Effects Laboratory Division , National Institute for Occupational Safety and Health (NIOSH) , Morgantown , WV , USA
| | - Walter McKinney
- a Toxicology and Molecular Biology Branch, Health Effects Laboratory Division , National Institute for Occupational Safety and Health (NIOSH) , Morgantown , WV , USA
| | - Bean Chen
- a Toxicology and Molecular Biology Branch, Health Effects Laboratory Division , National Institute for Occupational Safety and Health (NIOSH) , Morgantown , WV , USA
| | - Ja Kook Gu
- a Toxicology and Molecular Biology Branch, Health Effects Laboratory Division , National Institute for Occupational Safety and Health (NIOSH) , Morgantown , WV , USA
| | - Michael Kashon
- a Toxicology and Molecular Biology Branch, Health Effects Laboratory Division , National Institute for Occupational Safety and Health (NIOSH) , Morgantown , WV , USA
| | - Pius Joseph
- a Toxicology and Molecular Biology Branch, Health Effects Laboratory Division , National Institute for Occupational Safety and Health (NIOSH) , Morgantown , WV , USA
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18
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Calvano J, Edwards G, Hixson C, Burr H, Mangipudy R, Tirmenstein M. Serum microRNAs-217 and −375 as biomarkers of acute pancreatic injury in rats. Toxicology 2016; 368-369:1-9. [DOI: 10.1016/j.tox.2016.08.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 08/05/2016] [Accepted: 08/09/2016] [Indexed: 11/16/2022]
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19
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Irigoien I, Arenas C. Diagnosis using clinical/pathological and molecular information. Stat Methods Med Res 2016; 25:2878-2894. [DOI: 10.1177/0962280214534410] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In diagnosis and classification diseases multiple outcomes, both molecular and clinical/pathological are routinely gathered on patients. In recent years, many approaches have been suggested for integrating gene expression (continuous data) with clinical/pathological data (usually categorical and ordinal data). This new area of research integrates both clinical and genomic data in order to improve our knowledge about diseases, and to capture the information which is lost in independent clinical or genomic studies. The related metric scaling distance is a not well-known, but very valuable distance to integrate clinical/pathological and molecular information. In this article, we present the use of the related metric scaling distance in biomedical research. We describe how this distance works, and we also explain why it may sometimes be preferred. We discuss the choice of the related metric scaling distance and compare it with other proximity measures to include both clinical and genetic information. Furthermore, we comment the choice of the related metric scaling distance when classical clustering or discriminant analysis based on distances are performed and compare the results with more complex cluster or discriminant procedures specially constructed for integrating clinical and molecular information. The use of the related metric scaling distance is illustrated on simulated experimental and four real data sets, a heart disease, and three cancer studies. The results present the flexibility and availability of this distance which gives competitive results.
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Affiliation(s)
- Itziar Irigoien
- Department of Computation and Artificial Intelligence, Euskal Herriko Unibertsitatea UPV-EHU, Donostia, Spain
| | - Concepción Arenas
- Departament d’Estadística, Universitat de Barcelona, Barcelona, Spain
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20
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Heinloth AN, Boorman GA, Foley JF, Flagler ND, Paules RS. Gene Expression Analysis Offers Unique Advantages to Histopathology in Liver Biopsy Evaluations. Toxicol Pathol 2016; 35:276-83. [PMID: 17366322 DOI: 10.1080/01926230601178207] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Liver diseases that induce nonuniform lesions often give rise to greatly varying histopathology results in needle biopsy samples from the same patient. This study examines whether gene expression analysis of such biopsies could provide a more representative picture of the overall condition of the liver. We utilized acetaminophen (APAP) as a model hepatotoxicant that gives a multifocal pattern of necrosis following toxic doses. Rats were treated with a single toxic or subtoxic dose of APAP and sacrificed 6, 24, or 48 hours after exposure. Left liver lobes were harvested, and both gene expression and histopathological analysis were performed on biopsy-sized samples. While histopathological evaluation of such small samples revealed significant sample to sample differences after toxic doses of APAP, gene expression analysis provided a very homogeneous picture and allowed clear distinction between subtoxic and toxic doses. The main biological function differentiating animals that received sub-toxic from those that had received toxic doses was an acute stress response at 6 hours and signs of energy depletion at later time points. Our results suggest that the use of genomic analysis of biopsy samples together with histopathological analysis could provide a more precise representation of the overall condition of a patient’s liver than histopathological evaluation alone.
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Affiliation(s)
- Alexandra N Heinloth
- National Center for Toxicogenomics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
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21
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Weldon BA, Shubin SP, Smith MN, Workman T, Artemenko A, Griffith WC, Thompson B, Faustman EM. Urinary microRNAs as potential biomarkers of pesticide exposure. Toxicol Appl Pharmacol 2016; 312:19-25. [PMID: 26826490 DOI: 10.1016/j.taap.2016.01.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 01/20/2016] [Accepted: 01/26/2016] [Indexed: 01/26/2023]
Abstract
MicroRNAs (miRNAs) are post-transcriptional regulators that silence messenger RNAs. Because miRNAs are stable at room temperature and long-lived, they have been proposed as molecular biomarkers to monitor disease and exposure status. While urinary miRNAs have been used clinically as potential diagnostic markers for kidney and bladder cancers and other diseases, their utility in non-clinical settings has yet to be fully developed. Our goal was to investigate the potential for urinary miRNAs to act as biomarkers of pesticide exposure and early biological response by identifying the miRNAs present in urine from 27 parent/child, farmworker/non-farmworker pairs (16FW/11NFW) collected during two agricultural seasons (thinning and post-harvest) and characterizing the between- and within-individual variability of these miRNA epigenetic regulators. MiRNAs were isolated from archived urine samples and identified using PCR arrays. Comparisons were made between age, households, season, and occupation. Of 384 miRNAs investigated, 297 (77%) were detectable in at least one sample. Seven miRNAs were detected in at least 50% of the samples, and one miRNA was present in 96% of the samples. Principal components and hierarchical clustering analyses indicate significant differences in miRNA profiles between farmworker and non-farmworker adults as well as between seasons. Six miRNAs were observed to be positively associated with farmworkers status during the post-harvest season. Expression of five of these miRNA trended towards a positive dose response relationship with organophosphate pesticide metabolites in farmworkers. These results suggest that miRNAs may be novel biomarkers of pesticide exposure and early biological response.
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Affiliation(s)
- Brittany A Weldon
- Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, United States; Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, United States
| | - Sara Pacheco Shubin
- Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, United States; Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, United States
| | - Marissa N Smith
- Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, United States; Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, United States
| | - Tomomi Workman
- Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, United States; Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, United States
| | - Alexander Artemenko
- Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, United States; Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, United States
| | - William C Griffith
- Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, United States; Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, United States
| | - Beti Thompson
- Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Elaine M Faustman
- Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, United States; Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, United States.
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22
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Hu J, Ramshesh VK, McGill MR, Jaeschke H, Lemasters JJ. Low Dose Acetaminophen Induces Reversible Mitochondrial Dysfunction Associated with Transient c-Jun N-Terminal Kinase Activation in Mouse Liver. Toxicol Sci 2015; 150:204-15. [PMID: 26721299 DOI: 10.1093/toxsci/kfv319] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Acetaminophen (APAP) overdose causes hepatotoxicity involving mitochondrial dysfunction and c-jun N-terminal kinase (JNK) activation. Because the safe limit of APAP dosing is controversial, our aim was to evaluate the role of the mitochondrial permeability transition (MPT) and JNK in mitochondrial dysfunction after APAP dosing considered nontoxic by criteria of serum alanine aminotransferase (ALT) release and histological necrosis in vivo. C57BL/6 mice were given APAP with and without the MPT inhibitor, N-methyl-4-isoleucine cyclosporin (NIM811), or the JNK inhibitor, SP600125. Fat droplet formation, cell viability, and mitochondrial function in vivo were monitored by intravital multiphoton microscopy. Serum ALT, liver histology, total JNK, and activated phospho(p)JNK were also assessed. High APAP (300 mg/kg) caused ALT release, necrosis, irreversible mitochondrial dysfunction, and hepatocellular death. By contrast, lower APAP (150 mg/kg) caused reversible mitochondrial dysfunction and fat droplet formation in hepatocytes without ALT release or necrosis. Mitochondrial protein N-acetyl-p-benzoquinone imine adducts correlated with early JNK activation, but irreversible mitochondrial depolarization and necrosis at high dose were associated with sustained JNK activation and translocation to mitochondria. NIM811 prevented cell death and/or mitochondrial depolarization after both high and low dose APAP. After low dose, SP600125 decreased mitochondrial depolarization. In conclusion, low dose APAP produces reversible MPT-dependent mitochondrial dysfunction and steatosis in hepatocytes without causing ALT release or necrosis, whereas high dose leads to irreversible mitochondrial dysfunction and cell death associated with sustained JNK activation. Thus, nontoxic APAP has the potential to cause transient mitochondrial dysfunction that may synergize with other stresses to promote liver damage and steatosis.
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Affiliation(s)
- Jiangting Hu
- *Center for Cell Death, Injury & Regeneration; Departments of Drug Discovery & Biomedical Sciences and Biochemistry & Molecular Biology
| | - Venkat K Ramshesh
- *Center for Cell Death, Injury & Regeneration; Departments of Drug Discovery & Biomedical Sciences and Biochemistry & Molecular Biology; Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina 29425
| | - Mitchell R McGill
- Department of Pharmacology, Toxicology & Therapeutics, University of Kansas Medical Center, Kansas City, Kansas 66160; and
| | - Hartmut Jaeschke
- Department of Pharmacology, Toxicology & Therapeutics, University of Kansas Medical Center, Kansas City, Kansas 66160; and
| | - John J Lemasters
- *Center for Cell Death, Injury & Regeneration; Departments of Drug Discovery & Biomedical Sciences and Biochemistry & Molecular Biology; Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina 29425; Institute of Theoretical & Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russian Federation
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Goodson WH, Lowe L, Carpenter DO, Gilbertson M, Manaf Ali A, Lopez de Cerain Salsamendi A, Lasfar A, Carnero A, Azqueta A, Amedei A, Charles AK, Collins AR, Ward A, Salzberg AC, Colacci A, Olsen AK, Berg A, Barclay BJ, Zhou BP, Blanco-Aparicio C, Baglole CJ, Dong C, Mondello C, Hsu CW, Naus CC, Yedjou C, Curran CS, Laird DW, Koch DC, Carlin DJ, Felsher DW, Roy D, Brown DG, Ratovitski E, Ryan EP, Corsini E, Rojas E, Moon EY, Laconi E, Marongiu F, Al-Mulla F, Chiaradonna F, Darroudi F, Martin FL, Van Schooten FJ, Goldberg GS, Wagemaker G, Nangami GN, Calaf GM, Williams G, Wolf GT, Koppen G, Brunborg G, Lyerly HK, Krishnan H, Ab Hamid H, Yasaei H, Sone H, Kondoh H, Salem HK, Hsu HY, Park HH, Koturbash I, Miousse IR, Scovassi AI, Klaunig JE, Vondráček J, Raju J, Roman J, Wise JP, Whitfield JR, Woodrick J, Christopher JA, Ochieng J, Martinez-Leal JF, Weisz J, Kravchenko J, Sun J, Prudhomme KR, Narayanan KB, Cohen-Solal KA, Moorwood K, Gonzalez L, Soucek L, Jian L, D'Abronzo LS, Lin LT, Li L, Gulliver L, McCawley LJ, Memeo L, Vermeulen L, Leyns L, Zhang L, Valverde M, Khatami M, Romano MF, Chapellier M, Williams MA, Wade M, Manjili MH, Lleonart ME, Xia M, Gonzalez MJ, Karamouzis MV, Kirsch-Volders M, Vaccari M, Kuemmerle NB, Singh N, Cruickshanks N, Kleinstreuer N, van Larebeke N, Ahmed N, Ogunkua O, Krishnakumar PK, Vadgama P, Marignani PA, Ghosh PM, Ostrosky-Wegman P, Thompson PA, Dent P, Heneberg P, Darbre P, Sing Leung P, Nangia-Makker P, Cheng QS, Robey RB, Al-Temaimi R, Roy R, Andrade-Vieira R, Sinha RK, Mehta R, Vento R, Di Fiore R, Ponce-Cusi R, Dornetshuber-Fleiss R, Nahta R, Castellino RC, Palorini R, Abd Hamid R, Langie SAS, Eltom SE, Brooks SA, Ryeom S, Wise SS, Bay SN, Harris SA, Papagerakis S, Romano S, Pavanello S, Eriksson S, Forte S, Casey SC, Luanpitpong S, Lee TJ, Otsuki T, Chen T, Massfelder T, Sanderson T, Guarnieri T, Hultman T, Dormoy V, Odero-Marah V, Sabbisetti V, Maguer-Satta V, Rathmell WK, Engström W, Decker WK, Bisson WH, Rojanasakul Y, Luqmani Y, Chen Z, Hu Z. Assessing the carcinogenic potential of low-dose exposures to chemical mixtures in the environment: the challenge ahead. Carcinogenesis 2015; 36 Suppl 1:S254-96. [PMID: 26106142 PMCID: PMC4480130 DOI: 10.1093/carcin/bgv039] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Low-dose exposures to common environmental chemicals that are deemed safe individually may be combining to instigate carcinogenesis, thereby contributing to the incidence of cancer. This risk may be overlooked by current regulatory practices and needs to be vigorously investigated. Lifestyle factors are responsible for a considerable portion of cancer incidence worldwide, but credible estimates from the World Health Organization and the International Agency for Research on Cancer (IARC) suggest that the fraction of cancers attributable to toxic environmental exposures is between 7% and 19%. To explore the hypothesis that low-dose exposures to mixtures of chemicals in the environment may be combining to contribute to environmental carcinogenesis, we reviewed 11 hallmark phenotypes of cancer, multiple priority target sites for disruption in each area and prototypical chemical disruptors for all targets, this included dose-response characterizations, evidence of low-dose effects and cross-hallmark effects for all targets and chemicals. In total, 85 examples of chemicals were reviewed for actions on key pathways/mechanisms related to carcinogenesis. Only 15% (13/85) were found to have evidence of a dose-response threshold, whereas 59% (50/85) exerted low-dose effects. No dose-response information was found for the remaining 26% (22/85). Our analysis suggests that the cumulative effects of individual (non-carcinogenic) chemicals acting on different pathways, and a variety of related systems, organs, tissues and cells could plausibly conspire to produce carcinogenic synergies. Additional basic research on carcinogenesis and research focused on low-dose effects of chemical mixtures needs to be rigorously pursued before the merits of this hypothesis can be further advanced. However, the structure of the World Health Organization International Programme on Chemical Safety ‘Mode of Action’ framework should be revisited as it has inherent weaknesses that are not fully aligned with our current understanding of cancer biology.
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Affiliation(s)
- William H Goodson
- California Pacific Medical Center Research Institute, 2100 Webster Street #401, San Francisco, CA 94115, USA, Getting to Know Cancer, Room 229A, 36 Arthur Street, Truro, Nova Scotia B2N 1X5, Canada, Lancaster Environment Centre, Lancaster University, Bailrigg, Lancaster LA1 4AP, UK, Institute for Health and the Environment, University at Albany, 5 University Pl., Rensselaer, NY 12144, USA, Getting to Know Cancer, Guelph N1G 1E4, Canada, School of Biotechnology, Faculty of Agriculture Biotechnology and Food Sciences, Sultan Zainal Abidin University, Tembila Campus, 22200 Besut, Terengganu, Malaysia, Department of Pharmacology and Toxicology, Faculty of Pharmacy, University of Navarra, Pamplona 31008, Spain, Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Rutgers, State University of New Jersey, Piscataway, NJ 08854, USA, Instituto de Biomedicina de Sevilla, Consejo Superior de Investigaciones Cientificas. Hospital Universitario Virgen del Rocio, Univ. de Sevilla., Avda Manuel Siurot sn. 41013 Sevilla, Spain, Department of Experimental and Clinical Medicine, University of Firenze, Florence 50134, Italy, School of Biological Sciences, University of Reading, Hopkins Building, Reading, Berkshire RG6 6UB, UK, Department of Nutrition, University of Oslo, Oslo, Norway, Department of Biochemistry and Biology, University of Bath, Claverton Down, Bath BA2 7AY, UK, Department of Public Health Sciences, College of Medicine, Pennsylvania State University, Hershey, PA 17033, USA, Center for Environmental Carcinogenesis and Risk Assessment, Environmental Protection and Health Prevention Agency, 40126 Bologna, Italy, Department of Chemicals and Radiation, Division of Environmental Medicine, Norwegian Institute of Public Health, Oslo N-0403, Norway, Planet Biotechnologies Inc., St Albert, Alberta T8N 5K4, Canada, Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40508, USA, Spanish National Cancer Research Centre, CNI
| | - Leroy Lowe
- Getting to Know Cancer, Room 229A, 36 Arthur Street, Truro, Nova Scotia B2N 1X5, Canada, Lancaster Environment Centre, Lancaster University, Bailrigg, Lancaster LA1 4AP, UK
| | - David O Carpenter
- Institute for Health and the Environment, University at Albany, 5 University Pl., Rensselaer, NY 12144, USA
| | | | - Abdul Manaf Ali
- School of Biotechnology, Faculty of Agriculture Biotechnology and Food Sciences, Sultan Zainal Abidin University, Tembila Campus, 22200 Besut, Terengganu, Malaysia
| | | | - Ahmed Lasfar
- Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Rutgers, State University of New Jersey, Piscataway, NJ 08854, USA
| | - Amancio Carnero
- Instituto de Biomedicina de Sevilla, Consejo Superior de Investigaciones Cientificas. Hospital Universitario Virgen del Rocio, Univ. de Sevilla., Avda Manuel Siurot sn. 41013 Sevilla, Spain
| | - Amaya Azqueta
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, University of Navarra, Pamplona 31008, Spain
| | - Amedeo Amedei
- Department of Experimental and Clinical Medicine, University of Firenze, Florence 50134, Italy
| | - Amelia K Charles
- School of Biological Sciences, University of Reading, Hopkins Building, Reading, Berkshire RG6 6UB, UK
| | | | - Andrew Ward
- Department of Biochemistry and Biology, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Anna C Salzberg
- Department of Public Health Sciences, College of Medicine, Pennsylvania State University, Hershey, PA 17033, USA
| | - Annamaria Colacci
- Center for Environmental Carcinogenesis and Risk Assessment, Environmental Protection and Health Prevention Agency, 40126 Bologna, Italy
| | - Ann-Karin Olsen
- Department of Chemicals and Radiation, Division of Environmental Medicine, Norwegian Institute of Public Health, Oslo N-0403, Norway
| | - Arthur Berg
- Department of Public Health Sciences, College of Medicine, Pennsylvania State University, Hershey, PA 17033, USA
| | - Barry J Barclay
- Planet Biotechnologies Inc., St Albert, Alberta T8N 5K4, Canada
| | - Binhua P Zhou
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40508, USA
| | - Carmen Blanco-Aparicio
- Spanish National Cancer Research Centre, CNIO, Melchor Fernandez Almagro, 3, 28029 Madrid, Spain
| | - Carolyn J Baglole
- Department of Medicine, McGill University, Montreal, Quebec H4A 3J1, Canada
| | - Chenfang Dong
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40508, USA
| | - Chiara Mondello
- Istituto di Genetica Molecolare, CNR, Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Chia-Wen Hsu
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3375, USA
| | - Christian C Naus
- Department of Cellular and Physiological Sciences, Life Sciences Institute, Faculty of Medicine, The University of British Columbia, Vancouver, British Columbia V5Z 1M9, Canada
| | - Clement Yedjou
- Department of Biology, Jackson State University, Jackson, MS 39217, USA
| | - Colleen S Curran
- Department of Molecular and Environmental Toxicology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Dale W Laird
- Department of Anatomy and Cell Biology, University of Western Ontario, London, Ontario N6A 3K7, Canada
| | - Daniel C Koch
- Stanford University Department of Medicine, Division of Oncology, Stanford, CA 94305, USA
| | - Danielle J Carlin
- Superfund Research Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27560, USA
| | - Dean W Felsher
- Department of Medicine, Oncology and Pathology, Stanford University, Stanford, CA 94305, USA
| | - Debasish Roy
- Department of Natural Science, The City University of New York at Hostos Campus, Bronx, NY 10451, USA
| | - Dustin G Brown
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523-1680, USA
| | - Edward Ratovitski
- Department of Head and Neck Surgery/Head and Neck Cancer Research, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Elizabeth P Ryan
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523-1680, USA
| | - Emanuela Corsini
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, 20133 Milan, Italy
| | - Emilio Rojas
- Department of Genomic Medicine and Environmental Toxicology, Institute for Biomedical Research, National Autonomous University of Mexico, Mexico City 04510, México
| | - Eun-Yi Moon
- Department of Bioscience and Biotechnology, Sejong University, Seoul 143-747, Korea
| | - Ezio Laconi
- Department of Biomedical Sciences, University of Cagliari, 09124 Cagliari, Italy
| | - Fabio Marongiu
- Department of Biomedical Sciences, University of Cagliari, 09124 Cagliari, Italy
| | - Fahd Al-Mulla
- Department of Pathology, Kuwait University, Safat 13110, Kuwait
| | - Ferdinando Chiaradonna
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy, SYSBIO Centre of Systems Biology, Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy
| | - Firouz Darroudi
- Human Safety and Environmental Research, Department of Health Sciences, College of North Atlantic, Doha 24449, State of Qatar
| | - Francis L Martin
- Lancaster Environment Centre, Lancaster University, Bailrigg, Lancaster LA1 4AP, UK
| | - Frederik J Van Schooten
- Department of Toxicology, NUTRIM School for Nutrition, Toxicology and Metabolism, Maastricht University, Maastricht 6200, The Netherlands
| | - Gary S Goldberg
- Department of Molecular Biology, School of Osteopathic Medicine, Rowan University, Stratford, NJ 08084, USA
| | - Gerard Wagemaker
- Hacettepe University, Center for Stem Cell Research and Development, Ankara 06640, Turkey
| | - Gladys N Nangami
- Department of Biochemistry and Cancer Biology, Meharry Medical College, Nashville, TN 37208, USA
| | - Gloria M Calaf
- Center for Radiological Research, Columbia University Medical Center, New York, NY 10032, USA, Instituto de Alta Investigacion, Universidad de Tarapaca, Arica, Chile
| | - Graeme Williams
- School of Biological Sciences, University of Reading, Reading, RG6 6UB, UK
| | - Gregory T Wolf
- Department of Otolaryngology - Head and Neck Surgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Gudrun Koppen
- Environmental Risk and Health Unit, Flemish Institute for Technological Research, 2400 Mol, Belgium
| | - Gunnar Brunborg
- Department of Chemicals and Radiation, Division of Environmental Medicine, Norwegian Institute of Public Health, Oslo N-0403, Norway
| | - H Kim Lyerly
- Department of Surgery, Pathology, Immunology, Duke University Medical Center, Durham, NC 27710, USA
| | - Harini Krishnan
- Department of Molecular Biology, School of Osteopathic Medicine, Rowan University, Stratford, NJ 08084, USA
| | - Hasiah Ab Hamid
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, 43400 Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Hemad Yasaei
- Department of Life Sciences, College of Health and Life Sciences and the Health and Environment Theme, Institute of Environment, Health and Societies, Brunel University Kingston Lane, Uxbridge, Middlesex UB8 3PH, UK
| | - Hideko Sone
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibraki 3058506, Japan
| | - Hiroshi Kondoh
- Department of Geriatric Medicine, Kyoto University Hospital 54 Kawaharacho, Shogoin, Sakyo-ku Kyoto, 606-8507, Japan
| | - Hosni K Salem
- Department of Urology, Kasr Al-Ainy School of Medicine, Cairo University, El Manial, Cairo 11559, Egypt
| | - Hsue-Yin Hsu
- Department of Life Sciences, Tzu-Chi University, Hualien 970, Taiwan
| | - Hyun Ho Park
- School of Biotechnology, Yeungnam University, Gyeongbuk 712-749, South Korea
| | - Igor Koturbash
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Isabelle R Miousse
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - A Ivana Scovassi
- Istituto di Genetica Molecolare, CNR, Via Abbiategrasso 207, 27100 Pavia, Italy
| | - James E Klaunig
- Department of Environmental Health, Indiana University, School of Public Health, Bloomington, IN 47405, USA
| | - Jan Vondráček
- Department of Cytokinetics, Institute of Biophysics Academy of Sciences of the Czech Republic, Brno, CZ-61265, Czech Republic
| | - Jayadev Raju
- Regulatory Toxicology Research Division, Bureau of Chemical Safety, Food Directorate, Health Canada, Ottawa, Ontario K1A 0K9, Canada
| | - Jesse Roman
- Department of Medicine, University of Louisville, Louisville, KY 40202, USA, Robley Rex VA Medical Center, Louisville, KY 40202, USA
| | - John Pierce Wise
- Department of Applied Medical Sciences, University of Southern Maine, 96 Falmouth St., Portland, ME 04104, USA
| | - Jonathan R Whitfield
- Mouse Models of Cancer Therapies Group, Vall d'Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Jordan Woodrick
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC 20057, USA
| | - Joseph A Christopher
- Cancer Research UK. Cambridge Institute, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
| | - Josiah Ochieng
- Department of Biochemistry and Cancer Biology, Meharry Medical College, Nashville, TN 37208, USA
| | | | - Judith Weisz
- Departments of Obstetrics and Gynecology and Pathology, Pennsylvania State University College of Medicine, Hershey PA 17033, USA
| | - Julia Kravchenko
- Department of Surgery, Pathology, Immunology, Duke University Medical Center, Durham, NC 27710, USA
| | - Jun Sun
- Department of Biochemistry, Rush University, Chicago, IL 60612, USA
| | - Kalan R Prudhomme
- Environmental and Molecular Toxicology, Environmental Health Science Center, Oregon State University, Corvallis, OR 97331, USA
| | | | - Karine A Cohen-Solal
- Department of Medicine/Medical Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Kim Moorwood
- Department of Biochemistry and Biology, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Laetitia Gonzalez
- Laboratory for Cell Genetics, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Laura Soucek
- Mouse Models of Cancer Therapies Group, Vall d'Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain, Catalan Institution for Research and Advanced Studies (ICREA), Barcelona 08010, Spain
| | - Le Jian
- School of Public Health, Curtin University, Bentley, WA 6102, Australia, Department of Urology, University of California Davis, Sacramento, CA 95817, USA
| | - Leandro S D'Abronzo
- Department of Urology, University of California Davis, Sacramento, CA 95817, USA
| | - Liang-Tzung Lin
- Department of Microbiology and Immunology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
| | - Lin Li
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, The People's Republic of China
| | - Linda Gulliver
- Faculty of Medicine, University of Otago, Dunedin 9054, New Zealand
| | - Lisa J McCawley
- Department of Biomedical Engineering and Cancer Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Lorenzo Memeo
- Department of Experimental Oncology, Mediterranean Institute of Oncology, Via Penninazzo 7, Viagrande (CT) 95029, Italy
| | - Louis Vermeulen
- Center for Experimental Molecular Medicine, Academic Medical Center, Meibergdreef 9, Amsterdam 1105 AZ, The Netherlands
| | - Luc Leyns
- Laboratory for Cell Genetics, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Luoping Zhang
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA 94720-7360, USA
| | - Mahara Valverde
- Department of Genomic Medicine and Environmental Toxicology, Institute for Biomedical Research, National Autonomous University of Mexico, Mexico City 04510, México
| | - Mahin Khatami
- Inflammation and Cancer Research, National Cancer Institute (NCI) (Retired), National Institutes of Health, Bethesda, MD 20892, USA
| | - Maria Fiammetta Romano
- Department of Molecular Medicine and Medical Biotechnology, Federico II University of Naples, 80131 Naples, Italy
| | - Marion Chapellier
- Centre De Recherche En Cancerologie, De Lyon, Lyon, U1052-UMR5286, France
| | - Marc A Williams
- United States Army Institute of Public Health, Toxicology Portfolio-Health Effects Research Program, Aberdeen Proving Ground, Edgewood, MD 21010-5403, USA
| | - Mark Wade
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, Via Adamello 16, 20139 Milano, Italy
| | - Masoud H Manjili
- Department of Microbiology and Immunology, Virginia Commonwealth University, Massey Cancer Center, Richmond, VA 23298, USA
| | - Matilde E Lleonart
- Institut De Recerca Hospital Vall D'Hebron, Passeig Vall d'Hebron, 119-129, 08035 Barcelona, Spain
| | - Menghang Xia
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3375, USA
| | - Michael J Gonzalez
- University of Puerto Rico, Medical Sciences Campus, School of Public Health, Nutrition Program, San Juan 00921, Puerto Rico
| | - Michalis V Karamouzis
- Department of Biological Chemistry, Medical School, University of Athens, Institute of Molecular Medicine and Biomedical Research, 10676 Athens, Greece
| | | | - Monica Vaccari
- Center for Environmental Carcinogenesis and Risk Assessment, Environmental Protection and Health Prevention Agency, 40126 Bologna, Italy
| | - Nancy B Kuemmerle
- Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Neetu Singh
- Advanced Molecular Science Research Centre (Centre for Advanced Research), King George's Medical University, Lucknow, Uttar Pradesh 226 003, India
| | - Nichola Cruickshanks
- Departments of Neurosurgery and Biochemistry and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Nicole Kleinstreuer
- Integrated Laboratory Systems Inc., in support of the National Toxicology Program Interagency Center for the Evaluation of Alternative Toxicological Methods, RTP, NC 27709, USA
| | - Nik van Larebeke
- Analytische, Milieu en Geochemie, Vrije Universiteit Brussel, Brussel B1050, Belgium
| | - Nuzhat Ahmed
- Department of Obstetrics and Gynecology, University of Melbourne, Victoria 3052, Australia
| | - Olugbemiga Ogunkua
- Department of Biochemistry and Cancer Biology, Meharry Medical College, Nashville, TN 37208, USA
| | - P K Krishnakumar
- Center for Environment and Water, Research Institute, King Fahd University of Petroleum and Minerals, Dhahran 3126, Saudi Arabia
| | - Pankaj Vadgama
- School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Paola A Marignani
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Paramita M Ghosh
- Department of Urology, University of California Davis, Sacramento, CA 95817, USA
| | - Patricia Ostrosky-Wegman
- Department of Genomic Medicine and Environmental Toxicology, Institute for Biomedical Research, National Autonomous University of Mexico, Mexico City 04510, México
| | - Patricia A Thompson
- Department of Pathology, Stony Brook School of Medicine, Stony Brook University, The State University of New York, Stony Brook, NY 11794-8691, USA
| | - Paul Dent
- Departments of Neurosurgery and Biochemistry and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Petr Heneberg
- Charles University in Prague, Third Faculty of Medicine, CZ-100 00 Prague 10, Czech Republic
| | - Philippa Darbre
- School of Biological Sciences, The University of Reading, Whiteknights, Reading RG6 6UB, England
| | - Po Sing Leung
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, The People's Republic of China
| | | | - Qiang Shawn Cheng
- Computer Science Department, Southern Illinois University, Carbondale, IL 62901, USA
| | - R Brooks Robey
- White River Junction Veterans Affairs Medical Center, White River Junction, VT 05009, USA, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Rabeah Al-Temaimi
- Human Genetics Unit, Department of Pathology, Faculty of Medicine, Kuwait University, Jabriya 13110, Kuwait
| | - Rabindra Roy
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC 20057, USA
| | - Rafaela Andrade-Vieira
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Ranjeet K Sinha
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Rekha Mehta
- Regulatory Toxicology Research Division, Bureau of Chemical Safety, Food Directorate, Health Canada, Ottawa, Ontario K1A 0K9, Canada
| | - Renza Vento
- Department of Biological, Chemical, and Pharmaceutical Sciences and Technologies, Polyclinic Plexus, University of Palermo, Palermo 90127, Italy , Sbarro Institute for Cancer Research and Molecular Medicine, Temple University, Philadelphia, PA 19122, USA
| | - Riccardo Di Fiore
- Department of Biological, Chemical, and Pharmaceutical Sciences and Technologies, Polyclinic Plexus, University of Palermo, Palermo 90127, Italy
| | | | - Rita Dornetshuber-Fleiss
- Department of Pharmacology and Toxicology, University of Vienna, Vienna A-1090, Austria, Institute of Cancer Research, Department of Medicine, Medical University of Vienna, Wien 1090, Austria
| | - Rita Nahta
- Departments of Pharmacology and Hematology and Medical Oncology, Emory University School of Medicine and Winship Cancer Institute, Atlanta, GA 30322, USA
| | - Robert C Castellino
- Division of Hematology and Oncology, Department of Pediatrics, Children's Healthcare of Atlanta, GA 30322, USA, Department of Pediatrics, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Roberta Palorini
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy, SYSBIO Centre of Systems Biology, Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy
| | - Roslida Abd Hamid
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, 43400 Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Sabine A S Langie
- Environmental Risk and Health Unit, Flemish Institute for Technological Research, 2400 Mol, Belgium
| | - Sakina E Eltom
- Department of Biochemistry and Cancer Biology, Meharry Medical College, Nashville, TN 37208, USA
| | - Samira A Brooks
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, NC 27599, USA
| | - Sandra Ryeom
- Department of Cancer Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sandra S Wise
- Department of Applied Medical Sciences, University of Southern Maine, 96 Falmouth St., Portland, ME 04104, USA
| | - Sarah N Bay
- Program in Genetics and Molecular Biology, Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA 30322, USA
| | - Shelley A Harris
- Population Health and Prevention, Research, Prevention and Cancer Control, Cancer Care Ontario, Toronto, Ontario, M5G 2L7, Canada, Departments of Epidemiology and Occupational and Environmental Health, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, M5T 3M7, Canada
| | - Silvana Papagerakis
- Department of Otolaryngology - Head and Neck Surgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Simona Romano
- Department of Molecular Medicine and Medical Biotechnology, Federico II University of Naples, 80131 Naples, Italy
| | - Sofia Pavanello
- Department of Cardiac, Thoracic and Vascular Sciences, Unit of Occupational Medicine, University of Padova, Padova 35128, Italy
| | - Staffan Eriksson
- Department of Anatomy, Physiology and Biochemistry, The Swedish University of Agricultural Sciences, PO Box 7011, VHC, Almas Allé 4, SE-756 51, Uppsala, Sweden
| | - Stefano Forte
- Department of Experimental Oncology, Mediterranean Institute of Oncology, Via Penninazzo 7, Viagrande (CT) 95029, Italy
| | - Stephanie C Casey
- Stanford University Department of Medicine, Division of Oncology, Stanford, CA 94305, USA
| | - Sudjit Luanpitpong
- Siriraj Center of Excellence for Stem Cell Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Tae-Jin Lee
- Department of Anatomy, College of Medicine, Yeungnam University, Daegu 705-717, South Korea
| | - Takemi Otsuki
- Department of Hygiene, Kawasaki Medical School, Matsushima Kurashiki, Okayama 701-0192, Japan
| | - Tao Chen
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, United States Food and Drug Administration, Jefferson, AR 72079, USA
| | - Thierry Massfelder
- INSERM U1113, team 3 'Cell Signalling and Communication in Kidney and Prostate Cancer', University of Strasbourg, Faculté de Médecine, 67085 Strasbourg, France
| | - Thomas Sanderson
- INRS-Institut Armand-Frappier, 531 Boulevard des Prairies, Laval, QC H7V 1B7, Canada
| | - Tiziana Guarnieri
- Department of Biology, Geology and Environmental Sciences, Alma Mater Studiorum Università di Bologna, Via Francesco Selmi, 3, 40126 Bologna, Italy, Center for Applied Biomedical Research, S. Orsola-Malpighi University Hospital, Via Massarenti, 9, 40126 Bologna, Italy, National Institute of Biostructures and Biosystems, Viale Medaglie d' Oro, 305, 00136 Roma, Italy
| | - Tove Hultman
- Department of Biosciences and Veterinary Public Health, Faculty of Veterinary Medicine, Swedish University of Agricultural Sciences, PO Box 7028, 75007 Uppsala, Sweden
| | - Valérian Dormoy
- INSERM U1113, team 3 'Cell Signalling and Communication in Kidney and Prostate Cancer', University of Strasbourg, Faculté de Médecine, 67085 Strasbourg, France, Department of Cell and Developmental Biology, University of California, Irvine, CA 92697, USA
| | - Valerie Odero-Marah
- Department of Biology/Center for Cancer Research and Therapeutic Development, Clark Atlanta University, Atlanta, GA 30314, USA
| | - Venkata Sabbisetti
- Harvard Medical School/Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Veronique Maguer-Satta
- United States Army Institute of Public Health, Toxicology Portfolio-Health Effects Research Program, Aberdeen Proving Ground, Edgewood, MD 21010-5403, USA
| | - W Kimryn Rathmell
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, NC 27599, USA
| | - Wilhelm Engström
- Department of Biosciences and Veterinary Public Health, Faculty of Veterinary Medicine, Swedish University of Agricultural Sciences, PO Box 7028, 75007 Uppsala, Sweden
| | | | - William H Bisson
- Environmental and Molecular Toxicology, Environmental Health Science Center, Oregon State University, Corvallis, OR 97331, USA
| | - Yon Rojanasakul
- Department of Pharmaceutical Sciences, West Virginia University, Morgantown, WV, 26506, USA
| | - Yunus Luqmani
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kuwait University, PO Box 24923, Safat 13110, Kuwait and
| | - Zhenbang Chen
- Department of Biochemistry and Cancer Biology, Meharry Medical College, Nashville, TN 37208, USA
| | - Zhiwei Hu
- Department of Surgery, The Ohio State University College of Medicine, The James Comprehensive Cancer Center, Columbus, OH 43210, USA
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Kim SJ, Yu SY, Yoon HJ, Lee SY, Youn JP, Hwang SY. Epigenetic Regulation of miR-22 in a BPA-exposed Human Hepatoma Cell. BIOCHIP JOURNAL 2015. [DOI: 10.1007/s13206-014-9110-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Rouquié D, Heneweer M, Botham J, Ketelslegers H, Markell L, Pfister T, Steiling W, Strauss V, Hennes C. Contribution of new technologies to characterization and prediction of adverse effects. Crit Rev Toxicol 2015; 45:172-83. [DOI: 10.3109/10408444.2014.986054] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Shinde V, Stöber R, Nemade H, Sotiriadou I, Hescheler J, Hengstler J, Sachinidis A. Transcriptomics of Hepatocytes Treated with Toxicants for Investigating Molecular Mechanisms Underlying Hepatotoxicity. Methods Mol Biol 2015; 1250:225-40. [PMID: 26272146 DOI: 10.1007/978-1-4939-2074-7_16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Transcriptomics is a powerful tool for high-throughput gene expression profiling. Transcriptome microarray experiments conducted with RNA isolated from hepatocytes after exposure to toxicants enable a deep insight into the molecular mechanisms of hepatotoxicity. This understanding, along with structure-activity relationships underlying hepatotoxicity, will provide a novel strategy to design cost-effective and safer therapeutics. Transcriptomics studies conducted with established hepatotoxic drugs in various in vitro and in vivo hepatotoxicity test systems have contributed to the elucidation of the mechanistic basis of liver insults, which were later on substantiated at the proteomics and metabolomics levels. The present chapter is focused on comprehensive transcriptomics of cultured primary hepatocytes treated with chemicals by applying Affymetrix microarray technology. It also describes the detailed protocol for culturing of hepatocytes, their exposure to toxicants as well as sample collection, including RNA isolation, RNA target preparation and finally the hybridization to gene chips for microarray expression analysis.
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Affiliation(s)
- Vaibhav Shinde
- Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Robert-Koch-Str. 39, 50931, Cologne, Germany
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Adler M, Leich E, Ellinger-Ziegelbauer H, Hewitt P, Dekant W, Rosenwald A, Mally A. Application of RNA interference to improve mechanistic understanding of omics responses to a hepatotoxic drug in primary rat hepatocytes. Toxicology 2014; 326:86-95. [DOI: 10.1016/j.tox.2014.10.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 09/26/2014] [Accepted: 10/15/2014] [Indexed: 10/24/2022]
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Stamper BD. Transcriptional profiling of reactive metabolites for elucidating toxicological mechanisms: a case study of quinoneimine-forming agents. Drug Metab Rev 2014; 47:45-55. [DOI: 10.3109/03602532.2014.978081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Dueñas-Gonzalez A, Alatorre B, Gonzalez-Fierro A. The impact of DNA methylation technologies on drug toxicology. Expert Opin Drug Metab Toxicol 2014; 10:637-46. [DOI: 10.1517/17425255.2014.889682] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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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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31
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Narmada BC, Kang Y, Venkatraman L, Peng Q, Sakban RB, Nugraha B, Jiang X, Bunte RM, So PTC, Tucker-Kellogg L, Mao HQ, Yu H. Hepatic stellate cell-targeted delivery of hepatocyte growth factor transgene via bile duct infusion enhances its expression at fibrotic foci to regress dimethylnitrosamine-induced liver fibrosis. Hum Gene Ther 2013; 24:508-19. [PMID: 23527815 DOI: 10.1089/hum.2012.158] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Liver fibrosis generates fibrotic foci with abundant activated hepatic stellate cells and excessive collagen deposition juxtaposed with healthy regions. Targeted delivery of antifibrotic therapeutics to hepatic stellate cells (HSCs) might improve treatment outcomes and reduce adverse effects on healthy tissue. We delivered the hepatocyte growth factor (HGF) gene specifically to activated hepatic stellate cells in fibrotic liver using vitamin A-coupled liposomes by retrograde intrabiliary infusion to bypass capillarized hepatic sinusoids. The antifibrotic effects of DsRed2-HGF vector encapsulated within vitamin A-coupled liposomes were validated by decreases in fibrotic markers in vitro. Fibrotic cultures transfected with the targeted transgene showed a significant decrease in fibrotic markers such as transforming growth factor-β1. In rats, dimethylnitrosamine-induced liver fibrosis is manifested by an increase in collagen deposition and severe defenestration of sinusoidal endothelial cells. The HSC-targeted transgene, administered via retrograde intrabiliary infusion in fibrotic rats, successfully reduced liver fibrosis markers alpha-smooth muscle actin and collagen, accompanied by an increase in the expression of DsRed2-HGF near the fibrotic foci. Thus, targeted delivery of HGF gene to hepatic stellate cells increased the transgene expression at the fibrotic foci and strongly enhanced its antifibrotic effects.
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Elmore SA, Boyle MC, Boyle MH, Cora MC, Crabbs TA, Cummings CA, Gruebbel MM, Johnson CL, Malarkey DE, McInnes EF, Nolte T, Shackelford CC, Ward JM. Proceedings of the 2013 National Toxicology Program Satellite Symposium. Toxicol Pathol 2013; 42:12-44. [PMID: 24334674 DOI: 10.1177/0192623313508020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The 2013 annual National Toxicology Program (NTP) Satellite Symposium, entitled "Pathology Potpourri," was held in Portland, Oregon, in advance of the Society of Toxicologic Pathology's 32nd annual meeting. The goal of the NTP Symposium is to present current diagnostic pathology or nomenclature issues to the toxicologic pathology community. This article presents summaries of the speakers' presentations, including diagnostic or nomenclature issues that were presented, along with select images that were used for audience voting and discussion. Some lesions and topics covered during the symposium included a caudal tail vertebra duplication in mice; nephroblastematosis in rats; ectopic C cell tumor in a hamster; granular cell aggregates/tumor in the uterus of a hamster; Pneumocystis carinii in the lung of a rat; iatrogenic chronic inflammation in the lungs of control rats; hepatoblastoma arising within an adenoma in a mouse; humoral hypercalcemia of benignancy in a transgenic mouse; acetaminophen-induced hepatotoxicity in rats; electron microscopy images of iatrogenic intraerythrocytic inclusions in transgenic mice; questionable hepatocellular degeneration/cell death/artifact in rats; atypical endometrial hyperplasia in rats; malignant mixed Müllerian tumors/carcinosarcomas in rats; differential diagnoses of proliferative lesions of the intestine of rodents; and finally obstructive nephropathy caused by melamine poisoning in a rat.
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Affiliation(s)
- Susan A Elmore
- 1National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
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Sakai R, Kondo C, Oka H, Miyajima H, Kubo K, Uehara T. Utilization of CDKN1A/p21 gene for class discrimination of DNA damage-induced clastogenicity. Toxicology 2013; 315:8-16. [PMID: 24211769 DOI: 10.1016/j.tox.2013.10.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 10/10/2013] [Accepted: 10/29/2013] [Indexed: 11/15/2022]
Abstract
The in vitro mammalian cytogenetic tests monitor chromosomal aberrations in cultured mammalian cells to test the mutagenicity of compounds. Although these tests are especially useful for evaluating the potential clastogenic effects of chemicals, false positives associated with excessive toxicity occur frequently. There is a growing demand for mechanism-based assays to confirm positive results from cytogenetic tests. We hypothesized that a toxicogenomic approach that is based on gene expression profiles could be used to investigate mechanisms of genotoxicity. Human lymphoblastoid TK6 cells were treated with each of eight different genotoxins that included six DNA damaging compounds-mitomycin C, methyl methanesulfonate, ethyl methanesulfonate, cisplatin, etoposide, hydroxyurea-and two compounds that do not damage DNA-colchicine and adenine. Cells were exposed to each compound for 4h, and Affymetrix U133A microarrays were then used to comprehensively examine gene expression. A statistical analysis was used to select biomarker candidates, and 103 probes met our statistical criteria. Expression of cyclin-dependent kinase inhibitor 1A (CDKN1A)/p21 was ranked highest for discriminating DNA-damaging compounds. To further characterize the biological significance of alterations in gene expression, functional network analysis was performed with the 103 selected probes. Interestingly, a CDKN1A-centered interactome was identified as the most significant network. Together, these findings indicated that DNA-damaging compounds often induced changes in the expression of a large number of these 103 probes and that upregulation of CDKN1A was a common key feature of DNA damage stimuli. The utility of CDKN1A as a biomarker for assessing the genotoxicity of drug candidates was further evaluated; specifically, quantitative RT-PCR was used to assess the effects of 14 additional compounds-including DNA damaging genotoxins and genotoxins that do not damage DNA and five newly-synthesized drug candidates-on CDKN1A expression. In these assays, DNA damage-positive clastogens were clearly separated from DNA damage-negative compounds based on CDKN1A expression. In conclusion, CDKN1A may be a valuable biomarker for identifying DNA damage-inducing clastogens and as a follow-up assay for mammalian cytogenetic tests.
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Affiliation(s)
- Rina Sakai
- Drug Developmental Research Laboratories, Shionogi & Co., Ltd., 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan; Department of Veterinary Science, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-58 Rinkuu Ourai Kita, Izumisano, Osaka 598-8531, Japan
| | - Chiaki Kondo
- Drug Developmental Research Laboratories, Shionogi & Co., Ltd., 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Hiroyuki Oka
- Drug Developmental Research Laboratories, Shionogi & Co., Ltd., 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Hirofumi Miyajima
- Drug Developmental Research Laboratories, Shionogi & Co., Ltd., 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Kihei Kubo
- Department of Veterinary Science, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-58 Rinkuu Ourai Kita, Izumisano, Osaka 598-8531, Japan
| | - Takeki Uehara
- Drug Developmental Research Laboratories, Shionogi & Co., Ltd., 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan.
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Zhang R, Sun J, Zhang Y, Cheng S, Zhang X. Signal transduction disturbance related to hepatocarcinogenesis in mouse by prolonged exposure to Nanjing drinking water. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2013; 20:6468-6481. [PMID: 23591932 DOI: 10.1007/s11356-013-1695-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2012] [Accepted: 03/28/2013] [Indexed: 06/02/2023]
Abstract
Toxicogenomic approaches were used to investigate the potential hepatocarcinogenic effects on mice by oral exposure to Nanjing drinking water (NJDW). Changes in the hepatic transcriptome of 3 weeks male mice (Mus musculus) were monitored and dissected after oral exposure to NJDW for 90 days. No preneoplastic and neoplastic lesions were observed in the hepatic tissue by the end of NJDW exposure. However, total of 746 genes were changed transcriptionally. Thirty-one percent of differentially expressed genes (DEGs) were associated with the functional categories of cell cycle regulation, adhesion, growth, apoptosis, and signal transduction, which are closely implicated in tumorigenesis and progression. Interrogation of Kyoto Encyclopedia of Genes and Genomes revealed that 43 DEGs were mapped to several crucial signaling pathways implicated in the pathogenesis of hepatocellular carcinoma (HCC). In signal transduction network constructed via Genes2Networks software, Egfr, Akt1, Atf2, Ctnnb1, Hras, Mapk1, Smad2, and Ccnd1 were hubs. Direct gene-disease relationships obtained from Comparative Toxicogenomics Database and scientific literatures revealed that the hubs have direct mechanism or biomarker relationships with hepatocellular preneoplastic lesions or hepatocarcinogenesis. Therefore, prolonged intake of NJDW without employing any indoor water treatment strategy might predispose mouse to HCC. Furthermore, Egfr, Akt1, Ctnnb1, Hras, Mapk1, Smad2, and Ccnd1 were identified as promising biomarkers of the potential combined hepatocarcinogenicity.
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Affiliation(s)
- Rui Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Road, Nanjing, 210046, People's Republic of China
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Joseph P, Umbright C, Sellamuthu R. Blood transcriptomics: applications in toxicology. J Appl Toxicol 2013; 33:1193-202. [PMID: 23456664 DOI: 10.1002/jat.2861] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 12/17/2012] [Accepted: 12/21/2012] [Indexed: 02/02/2023]
Abstract
The number of new chemicals that are being synthesized each year has been steadily increasing. While chemicals are of immense benefit to mankind, many of them have a significant negative impact, primarily owing to their inherent chemistry and toxicity, on the environment as well as human health. In addition to chemical exposures, human exposures to numerous non-chemical toxic agents take place in the environment and workplace. Given that human exposure to toxic agents is often unavoidable and many of these agents are found to have detrimental human health effects, it is important to develop strategies to prevent the adverse health effects associated with toxic exposures. Early detection of adverse health effects as well as a clear understanding of the mechanisms, especially at the molecular level, underlying these effects are key elements in preventing the adverse health effects associated with human exposure to toxic agents. Recent developments in genomics, especially transcriptomics, have prompted investigations into this important area of toxicology. Previous studies conducted in our laboratory and elsewhere have demonstrated the potential application of blood gene expression profiling as a sensitive, mechanistically relevant and practical surrogate approach for the early detection of adverse health effects associated with exposure to toxic agents. The advantages of blood gene expression profiling as a surrogate approach to detect early target organ toxicity and the molecular mechanisms underlying the toxicity are illustrated and discussed using recent studies on hepatotoxicity and pulmonary toxicity. Furthermore, the important challenges this emerging field in toxicology faces are presented in this review article.
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Affiliation(s)
- Pius Joseph
- Toxicology and Molecular Biology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, USA
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Sellamuthu R, Umbright C, Roberts JR, Chapman R, Young SH, Richardson D, Cumpston J, McKinney W, Chen BT, Frazer D, Li S, Kashon M, Joseph P. Transcriptomics analysis of lungs and peripheral blood of crystalline silica-exposed rats. Inhal Toxicol 2012; 24:570-9. [PMID: 22861000 DOI: 10.3109/08958378.2012.697926] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Minimally invasive approaches to detect/predict target organ toxicity have significant practical applications in occupational toxicology. The potential application of peripheral blood transcriptomics as a practical approach to study the mechanisms of silica-induced pulmonary toxicity was investigated. Rats were exposed by inhalation to crystalline silica (15 mg/m(3), 6 h/day, 5 days) and pulmonary toxicity and global gene expression profiles of lungs and peripheral blood were determined at 32 weeks following termination of exposure. A significant elevation in bronchoalveolar lavage fluid lactate dehydrogenase activity and moderate histological changes in the lungs, including type II pneumocyte hyperplasia and fibrosis, indicated pulmonary toxicity in the rats. Similarly, significant infiltration of neutrophils and elevated monocyte chemotactic protein-1 levels in the lungs showed pulmonary inflammation in the rats. Microarray analysis of global gene expression profiles identified significant differential expression [>1.5-fold change and false discovery rate (FDR) p < 0.01] of 520 and 537 genes, respectively, in the lungs and blood of the exposed rats. Bioinformatics analysis of the differentially expressed genes demonstrated significant similarity in the biological processes, molecular networks, and canonical pathways enriched by silica exposure in the lungs and blood of the rats. Several genes involved in functions relevant to silica-induced pulmonary toxicity such as inflammation, respiratory diseases, cancer, cellular movement, fibrosis, etc, were found significantly differentially expressed in the lungs and blood of the silica-exposed rats. The results of this study suggested the potential application of peripheral blood gene expression profiling as a toxicologically relevant and minimally invasive surrogate approach to study the mechanisms underlying silica-induced pulmonary toxicity.
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Affiliation(s)
- Rajendran Sellamuthu
- Toxicology and Molecular Biology Branch, National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV 26505, USA
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Uehara T, Kosyk O, Jeannot E, Bradford BU, Tech K, Macdonald JM, Boorman GA, Chatterjee S, Mason RP, Melnyk SB, Tryndyak VP, Pogribny IP, Rusyn I. Acetaminophen-induced acute liver injury in HCV transgenic mice. Toxicol Appl Pharmacol 2012. [PMID: 23200774 DOI: 10.1016/j.taap.2012.11.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The exact etiology of clinical cases of acute liver failure is difficult to ascertain and it is likely that various co-morbidity factors play a role. For example, epidemiological evidence suggests that coexistent hepatitis C virus (HCV) infection increased the risk of acetaminophen-induced acute liver injury, and was associated with an increased risk of progression to acute liver failure. However, little is known about possible mechanisms of enhanced acetaminophen hepatotoxicity in HCV-infected subjects. In this study, we tested a hypothesis that HCV-Tg mice may be more susceptible to acetaminophen hepatotoxicity, and also evaluated the mechanisms of acetaminophen-induced liver damage in wild type and HCV-Tg mice expressing core, E1 and E2 proteins. Male mice were treated with a single dose of acetaminophen (300 or 500 mg/kg in fed animals; or 200 mg/kg in fasted animals; i.g.) and liver and serum endpoints were evaluated at 4 and 24h after dosing. Our results suggest that in fed mice, liver toxicity in HCV-Tg mice is not markedly exaggerated as compared to the wild-type mice. In fasted mice, greater liver injury was observed in HCV-Tg mice. In fed mice dosed with 300 mg/kg acetaminophen, we observed that liver mitochondria in HCV-Tg mice exhibited signs of dysfunction showing the potential mechanism for increased susceptibility.
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Affiliation(s)
- Takeki Uehara
- Department of Environmental Sciences & Engineering, University of North Carolina, Chapel Hill, NC 27599, USA
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Potential new targets involved in 1,3-dinitrobenzene induced testicular toxicity. Toxicol Lett 2012; 213:275-84. [PMID: 22841810 DOI: 10.1016/j.toxlet.2012.07.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 07/10/2012] [Accepted: 07/11/2012] [Indexed: 11/21/2022]
Abstract
1,3-Dinitrobenzene (DNB) causes testicular injury, particularly to Sertoli cells, and induces apoptosis in the surrounding germinal cells in rodents; however, the mechanisms causing this toxicity are poorly understood. Our studies, using standard and molecular tools, were conducted to better understand the pathogenesis of the testicular effects. Four daily oral doses of 0.1-8mg/kg/day caused marked testicular lesions in rats from 4mg/kg/day. Global transcriptomics revealed cell cycle and cell death as the major biological processes affected with the expression of genes associated with cell cycle progression ("mitotic roles of polo-like kinase") being particularly altered. In a single dose time course study (4mg/kg), no adverse changes were recorded; however, in contrast to the data from the multiple dose study, plasma testosterone and testicular steroidogenesis-related gene expression were affected. These steroid hormone effects were confirmed in vitro using the H295R steroidogenesis assay. With this global approach we show that DNB not only induces apoptosis and interferes with cell cycle in the testes but that DNB can also modulate steroid hormone biosynthesis, suggesting an interference with the endocrine system. However, the contribution of the endocrine changes to the severe testicular lesions is presently unknown and requires further investigation.
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Effect of chemical mutagens and carcinogens on gene expression profiles in human TK6 cells. PLoS One 2012; 7:e39205. [PMID: 22723965 PMCID: PMC3377624 DOI: 10.1371/journal.pone.0039205] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Accepted: 05/18/2012] [Indexed: 12/19/2022] Open
Abstract
Characterization of toxicogenomic signatures of carcinogen exposure holds significant promise for mechanistic and predictive toxicology. In vitro transcriptomic studies allow the comparison of the response to chemicals with diverse mode of actions under controlled experimental conditions. We conducted an in vitro study in TK6 cells to characterize gene expression signatures of exposure to 15 genotoxic carcinogens frequently used in European industries. We also examined the dose-responsive changes in gene expression, and perturbation of biochemical pathways in response to these carcinogens. TK6 cells were exposed at 3 dose levels for 24 h with and without S9 human metabolic mix. Since S9 had an impact on gene expression (885 genes), we analyzed the gene expression data from cells cultures incubated with S9 and without S9 independently. The ribosome pathway was affected by all chemical-dose combinations. However in general, no similar gene expression was observed among carcinogens. Further, pathways, i.e. cell cycle, DNA repair mechanisms, RNA degradation, that were common within sets of chemical-dose combination were suggested by clustergram. Linear trends in dose–response of gene expression were observed for Trichloroethylene, Benz[a]anthracene, Epichlorohydrin, Benzene, and Hydroquinone. The significantly altered genes were involved in the regulation of (anti-) apoptosis, maintenance of cell survival, tumor necrosis factor-related pathways and immune response, in agreement with several other studies. Similarly in S9+ cultures, Benz[a]pyrene, Styrene and Trichloroethylene each modified over 1000 genes at high concentrations. Our findings expand our understanding of the transcriptomic response to genotoxic carcinogens, revealing the alteration of diverse sets of genes and pathways involved in cellular homeostasis and cell cycle control.
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Aubert J, Begriche K, Delannoy M, Morel I, Pajaud J, Ribault C, Lepage S, McGill MR, Lucas-Clerc C, Turlin B, Robin MA, Jaeschke H, Fromenty B. Differences in early acetaminophen hepatotoxicity between obese ob/ob and db/db mice. J Pharmacol Exp Ther 2012; 342:676-87. [PMID: 22647274 DOI: 10.1124/jpet.112.193813] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Clinical investigations suggest that hepatotoxicity after acetaminophen (APAP) overdose could be more severe in the context of obesity and nonalcoholic fatty liver disease. The pre-existence of fat accumulation and CYP2E1 induction could be major mechanisms accounting for such hepatic susceptibility. To explore this issue, experiments were performed in obese diabetic ob/ob and db/db mice. Preliminary investigations performed in male and female wild-type, ob/ob, and db/db mice showed a selective increase in hepatic CYP2E1 activity in female db/db mice. However, liver triglycerides in these animals were significantly lower compared with ob/ob mice. Next, APAP (500 mg/kg) was administered in female wild-type, ob/ob, and db/db mice, and investigations were carried out 0.5, 2, 4, and 8 h after APAP intoxication. Liver injury 8 h after APAP intoxication was higher in db/db mice, as assessed by plasma transaminases, liver histology, and terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling assay. In db/db mice, however, the extent of hepatic glutathione depletion, levels of APAP-protein adducts, c-Jun N-terminal kinase activation, changes in gene expression, and mitochondrial DNA levels were not greater compared with the other genotypes. Furthermore, in the db/db genotype plasma lactate and β-hydroxybutyrate were not specifically altered, whereas the plasma levels of APAP-glucuronide were intermediary between wild-type and ob/ob mice. Thus, early APAP-induced hepatotoxicity was greater in db/db than ob/ob mice, despite less severe fatty liver and similar basal levels of transaminases. Hepatic CYP2E1 induction could have an important pathogenic role when APAP-induced liver injury occurs in the context of obesity and related metabolic disorders.
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Affiliation(s)
- Jacinthe Aubert
- Institut National de la Santé et de la Recherche Médicale, U991, Université de Rennes 1, Rennes, France
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Lardizábal MN, Nocito AL, Daniele SM, Ornella LA, Palatnik JF, Veggi LM. Reference genes for real-time PCR quantification of microRNAs and messenger RNAs in rat models of hepatotoxicity. PLoS One 2012; 7:e36323. [PMID: 22563491 PMCID: PMC3341372 DOI: 10.1371/journal.pone.0036323] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Accepted: 03/30/2012] [Indexed: 01/18/2023] Open
Abstract
Hepatotoxicity is associated with major changes in liver gene expression induced by xenobiotic exposure. Understanding the underlying mechanisms is critical for its clinical diagnosis and treatment. MicroRNAs are key regulators of gene expression that control mRNA stability and translation, during normal development and pathology. The canonical technique to measure gene transcript levels is Real-Time qPCR, which has been successfully modified to determine the levels of microRNAs as well. However, in order to obtain accurate data in a multi-step method like RT-qPCR, the normalization with endogenous, stably expressed reference genes is mandatory. Since the expression stability of candidate reference genes varies greatly depending on experimental factors, the aim of our study was to identify a combination of genes for optimal normalization of microRNA and mRNA qPCR expression data in experimental models of acute hepatotoxicity. Rats were treated with four traditional hepatotoxins: acetaminophen, carbon tetrachloride, D-galactosamine and thioacetamide, and the liver expression levels of two groups of candidate reference genes, one for microRNA and the other for mRNA normalization, were determined by RT-qPCR in compliance with the MIQE guidelines. In the present study, we report that traditional reference genes such as U6 spliceosomal RNA, Beta Actin and Glyceraldehyde-3P-dehydrogenase altered their expression in response to classic hepatotoxins and therefore cannot be used as reference genes in hepatotoxicity studies. Stability rankings of candidate reference genes, considering only those that did not alter their expression, were determined using geNorm, NormFinder and BestKeeper software packages. The potential candidates whose measurements were stable were further tested in different combinations to find the optimal set of reference genes that accurately determine mRNA and miRNA levels. Finally, the combination of MicroRNA-16/5S Ribosomal RNA and Beta 2 Microglobulin/18S Ribosomal RNA were validated as optimal reference genes for microRNA and mRNA quantification, respectively, in rat models of acute hepatotoxicity.
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Affiliation(s)
| | - Ana L. Nocito
- Facultad de Ciencias Médicas, Universidad Nacional de Rosario (UNR), Rosario, Argentina
| | - Stella M. Daniele
- Facultad de Ciencias Bioquímicas y Farmacéuticas, UNR, Rosario, Argentina
| | | | | | - Luis M. Veggi
- IFISE, CONICET-UNR, Rosario, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas, UNR, Rosario, Argentina
- * E-mail:
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42
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Ogawa S, Onodera J, Honda R, Fujimoto I. Influence of systemic administration of atelocollagen on mouse livers: an ideal biomaterial for systemic drug delivery. J Toxicol Sci 2012; 36:751-62. [PMID: 22129739 DOI: 10.2131/jts.36.751] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Atelocollagen (AC), a biomaterial with low antigenicity and high bioaffinity, has been widely used in implantable materials in clinical practice. Preclinical studies have demonstrated that AC is a potential drug carrier for local and systemic delivery of cytokines, growth factors, plasmid DNA, small interfering RNA, and microRNA. AC is also believed to have low systemic toxicity on the basis of the safety of implant usage; however, this is not enough determined. Therefore, we performed whole genome expression profiling in mouse liver after systemic administration of AC or the cationic liposome carrier DOTAP/cholesterol (LP) and compared the changes of gene expressions associated with hepatotoxicity. Microarray analysis revealed that systemic LP administration significantly increased expression of toxicity-related genes, i.e., those for lipocalin-2, cyclin-dependent kinase inhibitor 1A, serum amyloid A isoforms, chemokine ligands, and granzyme B. Alternatively, AC administration did not alter the expression of any of these genes. Further gene ontology (GO) enrichment analysis highlighted the characteristic annotations extracted from genes upregulated after LP administration, and most of them were related to toxicity annotations such as immune response, inflammatory response, and apoptosis induction. In contrast, GO enrichment analysis of genes induced after AC administration revealed that only three annotations, all of which were unrelated to toxicity. These findings indicate that AC is potentially far less hepatotoxic than LP after systemic administration, suggesting that AC may be an excellent biomaterial for nontoxic drug delivery system carriers.
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Affiliation(s)
- Shingo Ogawa
- Koken Research Institute, Koken Co., Ltd., Tokyo, Japan
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Tachibana S, Shimomura A, Inadera H. Toxicity monitoring with primary cultured hepatocytes underestimates the acetaminophen-induced inflammatory responses of the mouse liver. TOHOKU J EXP MED 2012; 225:263-72. [PMID: 22083109 DOI: 10.1620/tjem.225.263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In vitro gene expression profiling with isolated hepatocytes has been used to assess the hepatotoxicity of certain chemicals because of animal welfare issues. However, whether an in vitro system can completely replace the in vivo system has yet to be elucidated in detail. Using a focused microarray established in our laboratory, we examined gene expression profiles in the mouse liver and primary cultured hepatocytes after treatment with different doses of acetaminophen, a widely used analgesic that frequently causes liver injury. The acute hepatotoxicity of acetaminophen was confirmed by showing the induction of an oxidative stress marker, heme oxygenase-1, elevated levels of serum transaminase, and histopathological findings. In vivo microarray and network analysis showed that acetaminophen treatment provoked alterations in relation to the inflammatory response, and that tumor necrosis factor-α plays a central role in related pathway alterations. By contrast, pathway analyses in in vitro isolated hepatocytes did not find such prominent changes in the inflammation-related networks compared with the in vivo situation. Thus, although in vitro gene expression profiles are useful for evaluating the direct toxicity of chemicals, indirect toxicities including inflammatory responses mediated by cell-cell interactions or secondary toxicity due to pathophysiological changes in the whole body may be overlooked. Our results indicate that the in vitro hepatotoxicity prediction system using isolated hepatocytes does not fully reflect the in vivo cellular response. An in vitro system may be appropriate, therefore, for high throughput screening to detect the direct hepatotoxicity of a test compound.
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Um SY, Park JH, Chung MW, Kim KB, Kim SH, Choi KH, Lee HJ. Nuclear magnetic resonance-based metabolomics for prediction of gastric damage induced by indomethacin in rats. Anal Chim Acta 2012; 722:87-94. [PMID: 22444538 DOI: 10.1016/j.aca.2012.01.062] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Revised: 01/25/2012] [Accepted: 01/26/2012] [Indexed: 12/30/2022]
Abstract
Non-steroidal anti-inflammatory drugs (NSAIDs) have side effects including gastric erosions, ulceration and bleeding. In this study, pattern recognition analysis of the (1)H-nuclear magnetic resonance (NMR) spectra of urine was performed to develop surrogate biomarkers related to the gastrointestinal (GI) damage induced by indomethacin in rats. Urine was collected for 5 h after oral administration of indomethacin (25 mg kg(-1)) or co-administration with cimetidine (100 mg kg(-1)), which protects against GI damage. The (1)H-NMR urine spectra were divided into spectral bins (0.04 ppm) for global profiling, and 36 endogenous metabolites were assigned for targeted profiling. The level of gastric damage in each animal was also determined. Indomethacin caused severe gastric damage; however, indomethacin administered with cimetidine did not. Simultaneously, the patterns of changes in their endogenous metabolites were different. Multivariate data analyses were carried out to recognize the spectral pattern of endogenous metabolites related to indomethacin using partial least square-discrimination analysis. In targeted profiling, a few endogenous metabolites, 2-oxoglutarate, acetate, taurine and hippurate, were selected as putative biomarkers for the gastric damage induced by indomethacin. These metabolites changed depending on the degree of GI damage, although the same dose of indomethacin (10 mg kg(-1)) was administered to rats. The results of global and targeted profiling suggest that the gastric damage induced by NSAIDs can be screened in the preclinical stage of drug development using a NMR based metabolomics approach.
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Affiliation(s)
- So Young Um
- Department of Pharmacology, National Institute of Toxicological Research, Korea Food and Drug Administration, 643 Yeonje-ri, Gangoe-myeon, Cheongwon-gun, Chungbuk, South Korea
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Yao F, Coquery J, Lê Cao KA. Independent Principal Component Analysis for biologically meaningful dimension reduction of large biological data sets. BMC Bioinformatics 2012; 13:24. [PMID: 22305354 PMCID: PMC3298499 DOI: 10.1186/1471-2105-13-24] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Accepted: 02/03/2012] [Indexed: 11/13/2022] Open
Abstract
Background A key question when analyzing high throughput data is whether the information provided by the measured biological entities (gene, metabolite expression for example) is related to the experimental conditions, or, rather, to some interfering signals, such as experimental bias or artefacts. Visualization tools are therefore useful to better understand the underlying structure of the data in a 'blind' (unsupervised) way. A well-established technique to do so is Principal Component Analysis (PCA). PCA is particularly powerful if the biological question is related to the highest variance. Independent Component Analysis (ICA) has been proposed as an alternative to PCA as it optimizes an independence condition to give more meaningful components. However, neither PCA nor ICA can overcome both the high dimensionality and noisy characteristics of biological data. Results We propose Independent Principal Component Analysis (IPCA) that combines the advantages of both PCA and ICA. It uses ICA as a denoising process of the loading vectors produced by PCA to better highlight the important biological entities and reveal insightful patterns in the data. The result is a better clustering of the biological samples on graphical representations. In addition, a sparse version is proposed that performs an internal variable selection to identify biologically relevant features (sIPCA). Conclusions On simulation studies and real data sets, we showed that IPCA offers a better visualization of the data than ICA and with a smaller number of components than PCA. Furthermore, a preliminary investigation of the list of genes selected with sIPCA demonstrate that the approach is well able to highlight relevant genes in the data with respect to the biological experiment. IPCA and sIPCA are both implemented in the R package mixomics dedicated to the analysis and exploration of high dimensional biological data sets, and on mixomics' web-interface.
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Affiliation(s)
- Fangzhou Yao
- Queensland Facility for Advanced Bioinformatics, University of Queensland, St Lucia, Australia
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Keller DA, Juberg DR, Catlin N, Farland WH, Hess FG, Wolf DC, Doerrer NG. Identification and characterization of adverse effects in 21st century toxicology. Toxicol Sci 2012; 126:291-7. [PMID: 22262567 DOI: 10.1093/toxsci/kfr350] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The practice of toxicology is changing rapidly, as demonstrated by the response to the 2007 NRC report on "Toxicity Testing in the 21(st) Century." New assays are being developed to replace animal testing; yet the use of data from these assays in decision making is not clear. A Health and Environmental Sciences Institute committee held a May 2011 workshop to discuss approaches to identifying adverse effects in the context of the NRC report. Scientists from industry, government, academia, and NGOs discussed two case studies and explored how information from new, high data content assays developed for screening can be used to differentiate adverse effects from adaptive responses. The terms "adverse effect" and "adaptive response" were defined, as well as two new terms, the relevant pathways of toxicological concern (RPTCs) and relevant responses for regulation (RRRs). RPTCs are biochemical pathways associated with adverse events and need to be elucidated before they are used in regulatory decision making. RRRs are endpoints that are the basis for risk assessment and may or may not be at the level of pathways. Workshop participants discussed the criteria for determining whether, at the RPTC level, an effect is potentially adverse or potentially indicative of adaptability, and how the use of prototypical, data-rich compounds could lead to a greater understanding of RPTCs and their use as RRRs. Also discussed was the use of RPTCs in a weight-of-evidence approach to risk assessment. Inclusion of data at this level could decrease uncertainty in risk assessments but will require the use of detailed dosimetry and consideration of exposure context and the time and dose continuum to yield scientifically based decisions. The results of this project point to the need for an extensive effort to characterize RPTCs and their use in risk assessment to make the vision of the 2007 NRC report a reality.
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Kondo C, Aoki M, Yamamoto E, Tonomura Y, Ikeda M, Kaneto M, Yamate J, Torii M, Uehara T. Predictive genomic biomarkers for drug-induced nephrotoxicity in mice. J Toxicol Sci 2012; 37:723-37. [DOI: 10.2131/jts.37.723] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Chiaki Kondo
- Drug Developmental Research Laboratories, Shionogi & Co., Ltd
| | - Miwa Aoki
- Drug Discovery Research Laboratories, Shionogi & Co., Ltd
| | - Emi Yamamoto
- Drug Developmental Research Laboratories, Shionogi & Co., Ltd
- Department of Veterinary Pathology, Graduate School of Agriculture and Biological Science, Osaka Prefecture University
| | - Yutaka Tonomura
- Drug Developmental Research Laboratories, Shionogi & Co., Ltd
| | - Minoru Ikeda
- Department of Veterinary Pathology, Graduate School of Agriculture and Biological Science, Osaka Prefecture University
| | - Masako Kaneto
- Drug Developmental Research Laboratories, Shionogi & Co., Ltd
| | - Jyoji Yamate
- Department of Veterinary Pathology, Graduate School of Agriculture and Biological Science, Osaka Prefecture University
| | - Mikinori Torii
- Drug Developmental Research Laboratories, Shionogi & Co., Ltd
| | - Takeki Uehara
- Drug Developmental Research Laboratories, Shionogi & Co., Ltd
- Department of Veterinary Pathology, Graduate School of Agriculture and Biological Science, Osaka Prefecture University
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Zhang M, Chen M, Tong W. Is Toxicogenomics a More Reliable and Sensitive Biomarker than Conventional Indicators from Rats To Predict Drug-Induced Liver Injury in Humans? Chem Res Toxicol 2011; 25:122-9. [DOI: 10.1021/tx200320e] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Min Zhang
- Center of
Excellence for Bioinformatics, Division of
Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road,
Jefferson, Arkansas 72079, United States
| | - Minjun Chen
- Center of
Excellence for Bioinformatics, Division of
Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road,
Jefferson, Arkansas 72079, United States
| | - Weida Tong
- Center of
Excellence for Bioinformatics, Division of
Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road,
Jefferson, Arkansas 72079, United States
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Ung CY, Lam SH, Zhang X, Li H, Ma J, Zhang L, Li B, Gong Z. Existence of inverted profile in chemically responsive molecular pathways in the zebrafish liver. PLoS One 2011; 6:e27819. [PMID: 22140468 PMCID: PMC3226580 DOI: 10.1371/journal.pone.0027819] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2011] [Accepted: 10/26/2011] [Indexed: 01/09/2023] Open
Abstract
How a living organism maintains its healthy equilibrium in response to endless exposure of potentially harmful chemicals is an important question in current biology. By transcriptomic analysis of zebrafish livers treated by various chemicals, we defined hubs as molecular pathways that are frequently perturbed by chemicals and have high degree of functional connectivity to other pathways. Our network analysis revealed that these hubs were organized into two groups showing inverted functionality with each other. Intriguingly, the inverted activity profiles in these two groups of hubs were observed to associate only with toxicopathological states but not with physiological changes. Furthermore, these inverted profiles were also present in rat, mouse, and human under certain toxicopathological conditions. Thus, toxicopathological-associated anti-correlated profiles in hubs not only indicate their potential use in diagnosis but also development of systems-based therapeutics to modulate gene expression by chemical approach in order to rewire the deregulated activities of hubs back to normal physiology.
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Affiliation(s)
- Choong Yong Ung
- Department of Biological Sciences, National University of Singapore, Queenstown, Singapore
- Department of Mathematics, National University of Singapore, Queenstown, Singapore
- * E-mail: (CYU); (ZG)
| | - Siew Hong Lam
- Department of Biological Sciences, National University of Singapore, Queenstown, Singapore
| | - Xun Zhang
- Graduate School for Integrative Sciences and Engineering, National University of Singapore, Queenstown, Singapore
- Department of Physics and Centre for Computational Science and Engineering, National University of Singapore, Queenstown, Singapore
| | - Hu Li
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Jing Ma
- Graduate School for Integrative Sciences and Engineering, National University of Singapore, Queenstown, Singapore
- Department of Physics and Centre for Computational Science and Engineering, National University of Singapore, Queenstown, Singapore
| | - Louxin Zhang
- Department of Mathematics, National University of Singapore, Queenstown, Singapore
- Graduate School for Integrative Sciences and Engineering, National University of Singapore, Queenstown, Singapore
| | - Baowen Li
- Graduate School for Integrative Sciences and Engineering, National University of Singapore, Queenstown, Singapore
- Department of Physics and Centre for Computational Science and Engineering, National University of Singapore, Queenstown, Singapore
| | - Zhiyuan Gong
- Department of Biological Sciences, National University of Singapore, Queenstown, Singapore
- * E-mail: (CYU); (ZG)
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Yang X, Greenhaw J, Shi Q, Su Z, Qian F, Davis K, Mendrick DL, Salminen WF. Identification of urinary microRNA profiles in rats that may diagnose hepatotoxicity. Toxicol Sci 2011; 125:335-44. [PMID: 22112502 DOI: 10.1093/toxsci/kfr321] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Circulating microRNAs (miRNAs) have emerged as novel noninvasive biomarkers for several diseases and other types of tissue injury. This study tested the hypothesis that changes in the levels of urinary miRNAs correlate with liver injury induced by hepatotoxicants. Sprague-Dawley rats were administered acetaminophen (APAP) or carbon tetrachloride (CCl(4)) and one nonhepatotoxicant (penicillin/PCN). Urine samples were collected over a 24 h period after a single oral dose of APAP (1250 mg/kg), CCl(4) (2000 mg/kg), or PCN (2400 mg/kg). APAP and CCl(4) induced liver injury based upon increased serum alanine and aspartate aminotransferase levels and histopathological findings, including liver necrosis. APAP and CCl(4) both significantly increased the urinary levels of 44 and 28 miRNAs, respectively. In addition, 10 of the increased miRNAs were in common between APAP and CCl(4). In contrast, PCN caused a slight decrease of a different nonoverlapping set of urinary miRNAs. Cluster analysis revealed a distinct urinary miRNA pattern from the hepatotoxicant-treated groups when compared with vehicle controls and PCN. Analysis of hepatic miRNA levels suggested that the liver was the source of the increased urinary miRNAs after APAP exposure; however, the results from CCl(4) were equivocal. Computational analysis was used to predict target genes of the 10 shared hepatotoxicant-induced miRNAs. Liver gene expression profiling using whole genome microarrays identified eight putative miRNA target genes that were significantly altered in the liver of APAP- and CCl(4)-treated animals. In conclusion, the patterns of urinary miRNA may hold promise as biomarkers of hepatotoxicant-induced liver injury.
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Affiliation(s)
- Xi Yang
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 72079, USA
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