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Ali W, Khatyan U, Sun J, Alasmari A, Alshahrani MY, Qazi IH, Wang T, Liu Z, Zou H. Mitigating effect of pomegranate peel extract against the furan induced testicular injury by apoptosis, steroidogenic enzymes and oxidative stress. CHEMOSPHERE 2024; 358:142086. [PMID: 38670510 DOI: 10.1016/j.chemosphere.2024.142086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 04/09/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024]
Abstract
Furan is generated in a wide array of heat-treated foods through thermal degradation, leading to severe impairments in the male reproductive system. The main objective of this study was to investigate the potential of pomegranate peel extract (PGPE) in mitigating testicular dysfunctions induced by furan. Male rats were categorized into four groups: control/untreated, PGPE, furan, and PGPE + furan group. The study results revealed that furan-treated rats exhibited significantly elevated aminotransferase and phosphatase activity, and also generated increased oxidative stress, and reduced antioxidative stress protein activity. Additionally, protein content levels (ALT, AST, ALP, and ACP) and activities of steroidogenic Leydig cell hydroxysteroid dehydrogenase (3β-HSD and 17β-HSD) enzymes were significantly decreased. Significant variations in testicular parameters, apoptotic genes (Bcl-2, P53, and Caspase3), inflammatory and anti-inflammatory cytokines (IL1β, IL10), male sex hormones follicle-stimulating hormone (FSH), luteinizing hormone (LH), testosterone, and sperm quality were also observed. Furthermore, testicular histological abnormalities were confirmed by biochemical and molecular modifications. Notably, PGPE pre-treated furan-intoxicated animals exhibited significant improvements in most of the assessed parameters compared to furan-treated groups. In conclusion, PGPE presents essential preventive measures and a novel pharmacological potential therapy against furan-induced testicular injury.
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Affiliation(s)
- Waseem Ali
- College of Veterinary Medicine, Yangzhou University Yangzhou, Jiangsu 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, China; Sindh Agriculture University, Tandojam, Pakistan
| | - Uzma Khatyan
- Sindh Agriculture University, Tandojam, Pakistan
| | - Jian Sun
- College of Veterinary Medicine, Yangzhou University Yangzhou, Jiangsu 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, China
| | | | - Mohammad Y Alshahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Saudi Arabia
| | | | - Tao Wang
- College of Veterinary Medicine, Yangzhou University Yangzhou, Jiangsu 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, China
| | - Zongping Liu
- College of Veterinary Medicine, Yangzhou University Yangzhou, Jiangsu 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, China.
| | - Hui Zou
- College of Veterinary Medicine, Yangzhou University Yangzhou, Jiangsu 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, China.
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Ortiz-Zamora L, Ferreira JV, de Oliveira NKS, de Molfetta FA, Hage-Melim LIS, Fernandes CP, Oliveira AEMFM. Potential implications of vouacapan compounds for insecticidal activity: an in silico study. Recent Pat Biotechnol 2022; 16:155-173. [PMID: 34994338 DOI: 10.2174/1872208316666220106110902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 08/11/2021] [Accepted: 11/30/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND From the fruits and seeds of the species of Pterodon, it is possible to obtain two main products: the essential oil and oleoresin. In oleoresin, numerous vouacapan compounds have been demonstrated to have biological potential, including insecticidal activity. OBJECTIVE In silico studies were performed to identify potential candidates for natural insecticides among the vouacapans present in the genus Pterodon. MATERIALS AND METHODS Molecular docking and molecular dynamics studies were performed to analyze the interaction of vouacapan compounds with acetylcholinesterase of Drosophila melanogaster. Pharmacokinetic parameters regarding physicochemical properties, plasma protein binding, and activity in the central nervous system were evaluated. The toxicological properties of the selected molecules were predicted using Malathion as the reference compound. RESULTS 6α,7β-dimethoxivouacapan-17-ene (15) showed a high number of interactions and scores in molecular docking studies. This result suggests that this compound exhibits an inhibitory activity of the enzyme acetylcholinesterase. Regarding physicochemical properties, this compound showed the best results, besides presenting low cutaneous permeability values, suggesting null absorption. Molecular dynamics studies demonstrated few conformational changes in the structure of the complex formed by compound 4 and acetylcholinesterase enzyme throughout the simulation time. CONCLUSION It was determined that compound 4 (vouacapan 6α,7β,17β,19-tetraol) is an excellent candidate for usage as a natural insecticide.
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Affiliation(s)
- Lisset Ortiz-Zamora
- Post-Graduate Program in Tropical Biodiversity, Amapá Federal University, Macapá, Amapá, Brazil
- Laboratory of Phytopharmaceutical Nanobiotechnology, Amapá Federal University, Macapá, Amapá, Brazil
| | - Jaderson V Ferreira
- Laboratory of Pharmaceutical and Medicinal Chemistry (PharMedChem), Federal University of Amapá, Macapá, Amapá, Brazil
| | - Nayana K S de Oliveira
- Laboratory of Pharmaceutical and Medicinal Chemistry (PharMedChem), Federal University of Amapá, Macapá, Amapá, Brazil
| | - Fábio A de Molfetta
- Institute of Exact and Natural Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Lorane I S Hage-Melim
- Laboratory of Pharmaceutical and Medicinal Chemistry (PharMedChem), Federal University of Amapá, Macapá, Amapá, Brazil
- Post-Graduate Program in Pharmaceutical Sciences, Amapá Federal University, Macapá, Amapá, Brazil
| | - Caio P Fernandes
- Post-Graduate Program in Pharmaceutical Sciences, Amapá Federal University, Macapá, Amapá, Brazil
| | - Anna E M F M Oliveira
- Post-Graduate Program in Pharmaceutical Sciences, Amapá Federal University, Macapá, Amapá, Brazil
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Rehman H, Jahan S, Ullah I, Thörnqvist PO, Jabbar M, Shoaib M, Aman F, John N. Effects of endocrine disruptor furan on reproductive physiology of Sprague Dawley rats: An F1 Extended One-Generation Reproductive Toxicity Study (EOGRTS). Hum Exp Toxicol 2020; 39:1079-1094. [PMID: 32174189 DOI: 10.1177/0960327120911416] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The present study investigated the reproductive toxicity of furan in an Extended One-Generation Reproductive Toxicity Study in rats. Sprague Dawley F0 weaning rats (30 per sex per group) were exposed to furan orally at 0, 1, 2.5, 5, and 10 mg kg-1 for 10 weeks (males) and 2 weeks (females) and then mated. Results of F0 indicated that in the furan-treated groups (5 mg kg-1 and 10 mg kg-1), body weight (bw) gain decreased during prebreed and gestational period while increased during lactation periods. F0 animals prebreeding exposure resulted in head tilt and foot splay at 10 mg kg-1. Number of live pups at birth were decreased (p < 0.001) at 10 mg kg-1. At postnatal day (PND) 70, a significant (p = 0.03) decrease in testosterone levels of male rats and estrogen levels of female rats (p = 0.05) was observed in 10 mg kg-1 furan-treated group in F1 generation. Luteinizing hormone, follicle-stimulating hormone, and progesterone levels were also reduced, but their reduction was not statistically significant in all groups. In higher dose furan group (10 mg kg-1), testicular and ovarian weights were reduced in F1 generation at PND 70, with decreased daily sperm production (p = 0.01) and disturbed estrous cyclicity (p < 0.01). Some histopathological changes were also observed in testis and ovaries in groups whose parents were previously exposed to 10 mg kg-1 bw of furan group. Based on the above results, it is suggested that exposure to food-based contaminant furan induced remarkable changes in the F0 (parental stage) and F1 (offspring, pubertal, and adult stage) generations of Sprague Dawley rats.
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Affiliation(s)
- H Rehman
- Reproductive Physiology Laboratory, Faculty of Biological Sciences, Department of Animal Sciences, Quaid-i-Azam University, Islamabad, Pakistan.,Division of Physiology, Department of Neuroscience, Uppsala Biomedical Centre (BMC), Uppsala University, Uppsala, Sweden
| | - S Jahan
- Reproductive Physiology Laboratory, Faculty of Biological Sciences, Department of Animal Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - I Ullah
- Division of Physiology, Department of Neuroscience, Uppsala Biomedical Centre (BMC), Uppsala University, Uppsala, Sweden
| | - P-O Thörnqvist
- Division of Physiology, Department of Neuroscience, Uppsala Biomedical Centre (BMC), Uppsala University, Uppsala, Sweden
| | - M Jabbar
- Department of Statistics, University of Gujrat, Gujrat, Pakistan
| | - M Shoaib
- Reproductive Physiology Laboratory, Faculty of Biological Sciences, Department of Animal Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - F Aman
- Reproductive Physiology Laboratory, Faculty of Biological Sciences, Department of Animal Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - N John
- Reproductive Physiology Laboratory, Faculty of Biological Sciences, Department of Animal Sciences, Quaid-i-Azam University, Islamabad, Pakistan
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Kaya E, Yılmaz S, Ceribasi S. Protective Role of Propolis on Low and High Dose Furan-induced Hepatotoxicity and Oxidative Stress in Rats. J Vet Res 2019; 63:423-431. [PMID: 31572824 PMCID: PMC6749730 DOI: 10.2478/jvetres-2019-0054] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 08/12/2019] [Indexed: 01/13/2023] Open
Abstract
INTRODUCTION The aim of this study was to evaluate potential protective effects of propolis on furan-induced hepatic damage by assessing the levels of malondialdehyde (MDA) and reduced glutathione (GSH), antioxidant enzyme activities, and histopathological changes in the liver. MATERIAL AND METHODS Albino Wistar rats were divided into six groups: a control, propolis-treated (100 mg/kg b.w./day), low-dose furan-treated (furan-L group; 2 mg/kg b.w./day), high-dose furan-treated (furan-H group; 16 mg/kg b.w./day), furan-L+propolis treated, and furan-H+propolis treated group. Propolis and furan were applied by gavage; propolis for 8 days, and furan for 20 days in furan-L groups and 10 days in furan-H groups. RESULTS While MDA levels were elevated in furan-treated groups, levels of GSH and activities of antioxidant enzymes decreased (p < 0.001). The levels of MDA and GSH and activities of antioxidant enzymes were normal in the furan+propolis groups, especially in the furan-L+propolis group (p < 0.001). While the aspartate transaminase, alanine transaminase, alkaline phosphatase, and lactate pdehydrogenase activities were elevated in the furan-H treated group (p < 0.05 and p < 0.001), they were unchanged in the furan-L treated group. Histopathologically, several lesions were observed in the liver tissues of the furan-treated groups, especially in the higher-dose group. It was determined that these changes were milder in both of the furan+propolis groups. CONCLUSION The results indicate that propolis exhibits good hepatoprotective and antioxidant potential against furan-induced hepatocellular damage in rats.
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Affiliation(s)
- Emre Kaya
- Department of Biochemistry, Elaziğ, Turkey
| | | | - Songul Ceribasi
- Department of Pathology, Faculty of Veterinary Medicine, Firat University, 23119, Elaziğ, Turkey
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Nguyen L, Sandoval J, De Dios R, Yihdego E, Zarate M, Castro O, McKenna S, Wright CJ. The hepatic innate immune response is lobe-specific in a murine model endotoxemia. Innate Immun 2019; 25:144-154. [PMID: 30774009 PMCID: PMC6784545 DOI: 10.1177/1753425918823900] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The liver plays a central role in the innate immune response to endotoxemia.
While previous studies have demonstrated lobe-specific transcriptional responses
to various insults, whether this is true in response to endotoxemia is unknown.
We sought to assess whether there were significant intra- and inter-lobe
differences in the murine hepatic innate immune transcriptional response to
endotoxemia. Adult male ICR mice were exposed to i.p. LPS (5 mg/kg, 30 min,
60 min, 5 h) and primary (Tnf, Cxcl1, Nfkbia, Tnfiap3) and
secondary (Il6, Nos2) innate immune response gene expression
was assessed in the left medial, right medial, left lateral, and right lateral
lobes, and the papillary and caudate processes. The expression of all innate
immune response genes increased following i.p. LPS challenge. When tested at the
early time points (30 and 60 min), the left medial lobe and caudate process
consistently demonstrated the highest induction of gene expression. Most
inter-lobe differences were attenuated at later time points (5 h). To improve
reproducibility of the study of endotoxemia induced by i.p. LPS challenge,
inclusion of appropriate methodological details regarding collection of hepatic
tissue should be included when reporting scientific results in published
manuscripts.
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Affiliation(s)
- Leanna Nguyen
- Section of Neonatology, Department of Pediatrics, University of Colorado School of Medicine, USA
| | - Jeryl Sandoval
- Section of Neonatology, Department of Pediatrics, University of Colorado School of Medicine, USA
| | - Robyn De Dios
- Section of Neonatology, Department of Pediatrics, University of Colorado School of Medicine, USA
| | - Elesa Yihdego
- Section of Neonatology, Department of Pediatrics, University of Colorado School of Medicine, USA
| | - Miguel Zarate
- Section of Neonatology, Department of Pediatrics, University of Colorado School of Medicine, USA
| | - Odalis Castro
- Section of Neonatology, Department of Pediatrics, University of Colorado School of Medicine, USA
| | - Sarah McKenna
- Section of Neonatology, Department of Pediatrics, University of Colorado School of Medicine, USA
| | - Clyde J Wright
- Section of Neonatology, Department of Pediatrics, University of Colorado School of Medicine, USA
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Borges RS, Palheta IC, Ota SSB, Morais RB, Barros VA, Ramos RS, Silva RC, Costa JDS, Silva CHTP, Campos JM, Santos CBR. Toward of Safer Phenylbutazone Derivatives by Exploration of Toxicity Mechanism. Molecules 2019; 24:molecules24010143. [PMID: 30609687 PMCID: PMC6337259 DOI: 10.3390/molecules24010143] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 12/12/2018] [Accepted: 12/15/2018] [Indexed: 12/18/2022] Open
Abstract
A drug design for safer phenylbutazone was been explored by reactivity and docking studies involving single electron transfer mechanism, as well as toxicological predictions. Several approaches about its structural properties were performed through quantum chemistry calculations at the B3LYP level of theory, together with the 6-31+G(d,p) basis sets. Molecular orbital and ionization potential were associated to electron donation capacity. The spin densities contribution showed a preferential hydroxylation at the para-positions of phenyl ring when compared to other positions. In addition, on electron abstractions the aromatic hydroxylation has more impact than alkyl hydroxylation. Docking studies indicate that six structures 1, 7, 8 and 13–15 have potential for inhibiting human as well as murine COX-2, due to regions showing similar intermolecular interactions to the observed for the control compounds (indomethacin and refecoxib). Toxicity can be related to aromatic hydroxylation. In accordance to our calculations, the derivatives here proposed are potentially more active as well safer than phenylbutazone and only structures 8 and 13–15 were the most promising. Such results can explain the biological properties of phenylbutazone and support the design of potentially safer candidates.
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Affiliation(s)
- Rosivaldo S Borges
- Núcleo de Estudos e Seleção de Moléculas Bioativas-NESBio, College of Pharmacy, Health Sciences Institute, Federal University of Pará, Belém 66075-110, PA, Brazil.
- Programa de Pós-Graduação em Química Medicinal e Modelagem Molecular, Health Science Institute, Federal University of Pará, Belém 66075-110, PA, Brazil.
| | - Ivanete C Palheta
- Núcleo de Estudos e Seleção de Moléculas Bioativas-NESBio, College of Pharmacy, Health Sciences Institute, Federal University of Pará, Belém 66075-110, PA, Brazil.
| | - Sirlene S B Ota
- Núcleo de Estudos e Seleção de Moléculas Bioativas-NESBio, College of Pharmacy, Health Sciences Institute, Federal University of Pará, Belém 66075-110, PA, Brazil.
- Programa de Pós-Graduação em Química Medicinal e Modelagem Molecular, Health Science Institute, Federal University of Pará, Belém 66075-110, PA, Brazil.
| | - Roberto B Morais
- Núcleo de Estudos e Seleção de Moléculas Bioativas-NESBio, College of Pharmacy, Health Sciences Institute, Federal University of Pará, Belém 66075-110, PA, Brazil.
- Programa de Pós-Graduação em Química Medicinal e Modelagem Molecular, Health Science Institute, Federal University of Pará, Belém 66075-110, PA, Brazil.
| | - Valéria A Barros
- Núcleo de Estudos e Seleção de Moléculas Bioativas-NESBio, College of Pharmacy, Health Sciences Institute, Federal University of Pará, Belém 66075-110, PA, Brazil.
- Programa de Pós-Graduação em Química Medicinal e Modelagem Molecular, Health Science Institute, Federal University of Pará, Belém 66075-110, PA, Brazil.
| | - Ryan S Ramos
- Programa de Pós-Graduação em Biodiversidade e Biotecnologia-Rede BIONORTE, Federal University of Amapá, Macapá 68902-280, AP, Brazil.
| | - Rai C Silva
- Programa de Pós-Graduação em Química Medicinal e Modelagem Molecular, Health Science Institute, Federal University of Pará, Belém 66075-110, PA, Brazil.
- Laboratorio de Modelagem e Química Computacional-LMQC, Federal University of Amapá, Department of Biological Sciences. Rod. Juscelino Kubitschek, Km 02, Macapá 68902-280, AP, Brazil.
| | - Josivan da S Costa
- Laboratorio de Modelagem e Química Computacional-LMQC, Federal University of Amapá, Department of Biological Sciences. Rod. Juscelino Kubitschek, Km 02, Macapá 68902-280, AP, Brazil.
| | - Carlos H T P Silva
- Laboratório Computacional de Química Farmacêutica, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, University of Sao Paulo, São Paulo 14040-903, SP, Brazil.
| | - Joaquín M Campos
- Department of Pharmaceutical Organic Chemistry, University of Granada, 18071 Granada, Spain.
| | - Cleydson B R Santos
- Programa de Pós-Graduação em Química Medicinal e Modelagem Molecular, Health Science Institute, Federal University of Pará, Belém 66075-110, PA, Brazil.
- Programa de Pós-Graduação em Biodiversidade e Biotecnologia-Rede BIONORTE, Federal University of Amapá, Macapá 68902-280, AP, Brazil.
- Laboratorio de Modelagem e Química Computacional-LMQC, Federal University of Amapá, Department of Biological Sciences. Rod. Juscelino Kubitschek, Km 02, Macapá 68902-280, AP, Brazil.
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Saracoğlu G, Baş H, Pandır D. Furan-induced cardiotoxicity in diabetic rats and protective role of lycopene. J Food Biochem 2018; 43:e12738. [PMID: 31353562 DOI: 10.1111/jfbc.12738] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 10/16/2018] [Accepted: 10/20/2018] [Indexed: 12/15/2022]
Abstract
The objective of this current study is to search the impacts of furan and lycopene on a diabetic rat's heart. Diabetes increases prevalence with a sedentary lifestyle and obesity. Furan, a carcinogen, was detected in foods that had undergone thermal treatment. Two groups were formed, such as: the control and diabetic groups. Diabetic groups fall into four allocated groups: control, lycopene, furan, and furan + lycopene. The changes in malondialdehide levels, antioxidant enzymes' activities, and histopathology of the heart were pointed out. We observed that the changes in both the MDA level and the antioxidant enzymes' activities were due to diabetes. Furan-induced increment in MDA levels, but GST, CAT, SOD, and GPx activities showed a decrease. Lycopene influenced these changes positively. In terms of the pathological studies, changes were also observed in diabetic rats. The histological damage in the diabetic furan groups was found to be very serious. Lycopene was protective against furan that caused histopathological changes. Diabetes and furan resulted into heart damages in rats and lycopene showed preventive effects. But this was not a complete protection. PRACTICAL APPLICATIONS: Furan by product of chlorinated chemical compounds production and chemical processes including combustion, are virtually ubiquitous in the environment. Because of this, furan occur potential risk for human health. Furan is known to exist at higher levels in fatty foods, such as full-fat milk and dairy products, meat and eggs. They can accumulate in the fatty tissues of animals and humans. Diabetes increase in the prevalence of a sedentary lifestyle and obesity. Diabetes with furan-induced cardiotoxicity. Foods should not be heated over and over again, especially diabetic heart patients should stay away from this situation.
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Affiliation(s)
| | - Hatice Baş
- Department of Biology, Faculty of Arts and Science, Bozok University, Yozgat, Turkey
| | - Dilek Pandır
- Department of Biology, Faculty of Arts and Science, Bozok University, Yozgat, Turkey
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8
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Awad A, Khalil SR, Farag MR, Nassan MA. Differential susceptibility of kidneys and livers to proliferative processes and transcriptional level of the genes encoding desmin, vimentin, connexin 43, and nestin in rats exposed to furan. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 162:235-244. [PMID: 29990736 DOI: 10.1016/j.ecoenv.2018.07.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 06/05/2018] [Accepted: 07/01/2018] [Indexed: 06/08/2023]
Abstract
In this study, we aimed to assess the differential toxic impact, induced by furan exposure, on the liver and kidney tissues by estimating reactive oxygen species (ROS) level, total antioxidant capacity (TAC), oxidative damage, and the tissue injury markers in a male rat model. To explain such impacts, 20 rats were assigned into two groups: a control group, where rats were administered corn oil as a vehicle, and a furan-administered group, where furan was orally administered to rats at a dose of 16 mg/kg b wt/day (five days per week over eight weeks). The transcriptional levels of intermediate filament proteins (desmin, vimentin, nestin, and connexin 43) were assessed by using quantitative real-time polymerase chain reaction (PCR), and the cell proliferation markers (proliferating cell nuclear antigen [PCNA] and proliferation-associated nuclear antigen [Ki-67]) were recognized by immunohistochemical analysis. Furthermore, the ultrastructural changes of liver and kidney were monitored using electron microscopy. Our findings showed that furan exposure could induce hepatic and renal damage to different extents. Furan can increase the ROS content, oxidative damage indices, and liver tissue injury indices but not kidney injury indices. Furthermore, it decreases the TAC in the serum of exposed rats. In addition, furan exposure was associated with changes in the mRNA expression pattern of intermediate filament proteins in both kidney and liver tissues. Moreover, furan enhances the expression of PCNA and Ki-67 in the liver tissues but not in the kidney tissues. The ultrastructure evaluation revealed the incidence of glomerular podocyte degeneration and hepatocyte injury. These results conclusively demonstrate that the deleterious effects of furan are caused by promoting fibrosis and hepatocyte proliferation in liver tissues and triggering podocyte injury in the kidney tissues.
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Affiliation(s)
- Ashraf Awad
- Animal Wealth Development Department, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Samah R Khalil
- Forensic Medicine and Toxicology, Department, Faculty of Veterinary Medicine, Zagazig University, 44511 Zagazig, Egypt.
| | - Mayada Ragab Farag
- Forensic Medicine and Toxicology, Department, Faculty of Veterinary Medicine, Zagazig University, 44511 Zagazig, Egypt
| | - Mohamed Abdo Nassan
- Department of Pathology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
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Alizadeh M, Barati M, Saleh-Ghadimi S, Roshanravan N, Zeinalian R, Jabbari M. Industrial furan and its biological effects on the body systems. J Food Biochem 2018. [DOI: 10.1111/jfbc.12597] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Mohammad Alizadeh
- Department of Nutrition; Tabriz University of Medical Sciences; Tabriz Iran
| | - Meisam Barati
- Faculty of Nutrition and Food Sciences, Student Research Committee, Cellular and Molecular Nutrition Department; Shahid Beheshti University of Medical Sciences; Tehran Iran
| | - Sevda Saleh-Ghadimi
- Student Research Committee, Talented Student Office; Tabriz University of Medical Sciences; Tabriz Iran
| | - Neda Roshanravan
- Cardiovascular Research Center; Tabriz University of Medical Sciences; Tabriz Iran
| | - Reihaneh Zeinalian
- Student Research Committee, Talented Student Office; Tabriz University of Medical Sciences; Tabriz Iran
| | - Masoumeh Jabbari
- Student Research Committee, Talented Student Office; Tabriz University of Medical Sciences; Tabriz Iran
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10
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Gill S, Kavanagh M, Cherry W, Bourque C, Caldwell D, Wang G, Bondy G. A 90-day subchronic gavage toxicity study in Fischer 344 rats with 3-methylfuran. Food Chem Toxicol 2018; 111:341-355. [DOI: 10.1016/j.fct.2017.10.055] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 10/20/2017] [Accepted: 10/30/2017] [Indexed: 12/31/2022]
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11
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Knutsen HK, Alexander J, Barregård L, Bignami M, Brüschweiler B, Ceccatelli S, Cottrill B, Dinovi M, Edler L, Grasl-Kraupp B, Hogstrand C, Hoogenboom LR, Nebbia CS, Oswald IP, Petersen A, Rose M, Roudot AC, Schwerdtle T, Vleminckx C, Vollmer G, Chipman K, De Meulenaer B, Dinovi M, Mennes W, Schlatter J, Schrenk D, Baert K, Dujardin B, Wallace H. Risks for public health related to the presence of furan and methylfurans in food. EFSA J 2017; 15:e05005. [PMID: 32625300 PMCID: PMC7009982 DOI: 10.2903/j.efsa.2017.5005] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The European Commission asked EFSA for a scientific evaluation on the risk to human health of the presence of furan and methylfurans (2-methylfuran, 3-methylfuran and 2,5-dimethylfuran) in food. They are formed in foods during thermal processing and can co-occur. Furans are produced from several precursors such as ascorbic acid, amino acids, carbohydrates, unsaturated fatty acids and carotenoids, and are found in a variety of foods including coffee and canned and jarred foods. Regarding furan occurrence, 17,056 analytical results were used in the evaluation. No occurrence data were received on methylfurans. The highest exposures to furan were estimated for infants, mainly from ready-to-eat meals. Grains and grain-based products contribute most for toddlers, other children and adolescents. In adults, elderly and very elderly, coffee is the main contributor to dietary exposure. Furan is absorbed from the gastrointestinal tract and is found in highest amounts in the liver. It has a short half-life and is metabolised by cytochrome P450 2E1 (CYP2E1) to the reactive metabolite, cis-but-2-ene-1,4-dialdehyde (BDA). BDA can bind covalently to amino acids, proteins and DNA. Furan is hepatotoxic in rats and mice with cholangiofibrosis in rats and hepatocellular adenomas/carcinomas in mice being the most prominent effects. There is limited evidence of chromosomal damage in vivo and a lack of understanding of the underlying mechanism. Clear evidence for indirect mechanisms involved in carcinogenesis include oxidative stress, gene expression alterations, epigenetic changes, inflammation and increased cell proliferation. The CONTAM Panel used a margin of exposure (MOE) approach for the risk characterisation using as a reference point a benchmark dose lower confidence limit for a benchmark response of 10% of 0.064 mg/kg body weight (bw) per day for the incidence of cholangiofibrosis in the rat. The calculated MOEs indicate a health concern. This conclusion was supported by the calculated MOEs for the neoplastic effects.
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Uçar S, Pandir D. Furan induced ovarian damage in non-diabetic and diabetic rats and cellular protective role of lycopene. Arch Gynecol Obstet 2017; 296:1027-1037. [DOI: 10.1007/s00404-017-4521-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 08/07/2017] [Indexed: 12/12/2022]
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13
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Ramm S, Limbeck E, Mally A. Functional and cellular consequences of covalent target protein modification by furan in rat liver. Toxicology 2016; 361-362:49-61. [PMID: 27402187 DOI: 10.1016/j.tox.2016.06.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 06/27/2016] [Accepted: 06/27/2016] [Indexed: 12/11/2022]
Abstract
Furan hepatotoxicity is thought to be linked to covalent binding of its reactive metabolite, cis-2-butene-1,4-dial, to hepatic proteins critical for cell homeostasis and survival. We previously identified 61 putative furan target proteins, which participate in various cellular processes including carbohydrate metabolism, fatty acid β-oxidation, adenosine triphosphate (ATP) synthesis, protein folding and maintenance of redox homeostasis. To further investigate the biological significance of target protein modification, this study was designed to determine the impact of furan on the activity of key target enzymes involved in glycolysis, β-oxidation, ATP synthesis, and redox regulation in rat liver, and to link these functional changes to alterations in cellular processes. While cis-2-butene-1,4-dial inhibited thioredoxin 1 (Txn1) in a cell-free assay, in livers of rats treated with a single high dose of furan Txn1 activity was markedly increased due to rapid up-regulation of Txn1 mRNA expression. Significant inhibition of glyceraldehyde-3-phosphate dehydrogenase and metabolic changes consistent with blocked glycolytic breakdown of glucose were observed in rat liver in response to a single high dose of furan. In contrast, furan treatment resulted in increased activity of enoyl-CoA hydratase and enhanced production of ketone bodies, indicative of increased utilization of fatty acids as energy source. Consistent with changes in TCA cycle metabolites, furan treatment resulted in a reduction of succinate dehydrogenase activity, supporting mitochondrial dysfunction as a critical event in furan toxicity. No significant changes in target protein function were observed following repeated administration of furan at lower dose (0.1 and 0.5mg/kg bw for 4 weeks) closer to estimated human exposure to furan via food. Although the relative contribution of furan mediated alterations in metabolic pathways and antioxidant defense to the overall toxic response to furan, including considerations of dose and time, remains to be established, our work contributes to mapping biological processes and toxicity pathways modulated by reactive electrophiles.
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Affiliation(s)
- Susanne Ramm
- Department of Toxicology, University of Würzburg, 97078 Würzburg, Germany
| | - Elisabeth Limbeck
- Department of Toxicology, University of Würzburg, 97078 Würzburg, Germany
| | - Angela Mally
- Department of Toxicology, University of Würzburg, 97078 Würzburg, Germany.
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Simões CJV, Almeida ZL, Costa D, Jesus CSH, Cardoso AL, Almeida MR, Saraiva MJ, Pinho E Melo TMVD, Brito RMM. A novel bis-furan scaffold for transthyretin stabilization and amyloid inhibition. Eur J Med Chem 2016; 121:823-840. [PMID: 27020050 DOI: 10.1016/j.ejmech.2016.02.074] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 02/26/2016] [Accepted: 02/29/2016] [Indexed: 12/22/2022]
Abstract
The design and synthesis of a novel bis-furan scaffold tailored for high efficiency at inhibiting transthyretin amyloid formation is reported. In vitro results show that the discovered compounds are more efficient inhibitors of amyloid formation than tafamidis, a drug currently used in the treatment of familial amyloid polyneuropathy (FAP), despite their lower molecular weight and lipophilicity. Moreover, ex vivo experiments with the strongest inhibitor in the series, conducted in human blood plasma from normal and FAP Val30Met-transthyretin carriers, disclose remarkable affinity and selectivity profiles. The promises and challenges facing further development of this compound are discussed under the light of increasing evidence implicating transthyretin stability as a key factor not only in transthyretin amyloidoses and several associated co-morbidities, but also in Alzheimer's disease.
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Affiliation(s)
- Carlos J V Simões
- BSIM(2) - Drug Discovery, Parque Tecnológico de Cantanhede, 3060-197 Cantanhede, Portugal; Centro de Química de Coimbra and Departamento de Química, Universidade de Coimbra, 3004-535 Coimbra, Portugal.
| | - Zaida L Almeida
- Centro de Química de Coimbra and Departamento de Química, Universidade de Coimbra, 3004-535 Coimbra, Portugal; Center for Neuroscience and Cell Biology, Universidade de Coimbra, 3004-504 Coimbra, Portugal
| | - Dora Costa
- Centro de Química de Coimbra and Departamento de Química, Universidade de Coimbra, 3004-535 Coimbra, Portugal
| | - Catarina S H Jesus
- Centro de Química de Coimbra and Departamento de Química, Universidade de Coimbra, 3004-535 Coimbra, Portugal; Center for Neuroscience and Cell Biology, Universidade de Coimbra, 3004-504 Coimbra, Portugal
| | - Ana L Cardoso
- Centro de Química de Coimbra and Departamento de Química, Universidade de Coimbra, 3004-535 Coimbra, Portugal
| | - Maria R Almeida
- I3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto; ICBAS - Instituto de Ciências Biomédicas de Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Maria J Saraiva
- I3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto
| | - Teresa M V D Pinho E Melo
- Centro de Química de Coimbra and Departamento de Química, Universidade de Coimbra, 3004-535 Coimbra, Portugal
| | - Rui M M Brito
- Centro de Química de Coimbra and Departamento de Química, Universidade de Coimbra, 3004-535 Coimbra, Portugal; Center for Neuroscience and Cell Biology, Universidade de Coimbra, 3004-504 Coimbra, Portugal.
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Wang E, Chen F, Hu X, Yuan Y. Protective effects of apigenin against furan-induced toxicity in mice. Food Funct 2015; 5:1804-12. [PMID: 24914499 DOI: 10.1039/c4fo00038b] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Furan, a food contaminant formed by heating, is possibly carcinogenic to humans. In this study, we discussed the effect of administration of apigenin on furan-induced toxicity by determining the ROS content, oxidative damage, cytokine levels, DNA damage, and the liver and kidney damage in a mouse model. Our data showed that apigenin administered at 5, 10, and 20 mg kg(-1) bw per day could decrease the toxicity induced by furan to different extents. On one hand, apigenin has the ability to increase the oxidative damage indexes of glutathione (GSH) and glutathione-S-transferase (GST) as well as superoxide dismutase (SOD) activities but decrease myeloperoxidase (MPO) activities and maleic dialdehyde (MDA) content in the liver and kidney of mice treated with furan. On the other hand, it could decrease cytokine levels of tumor necrosis factor α (TNF-α), interleukin (IL)-1β, and interleukin (IL)-6 but increase interleukin (IL)-10 in the serum of furan-treated mice. At the same time, the three concentrations of apigenin elected in this paper all could decrease the ROS content, DNA damage index of 8-hydroxy-desoxyguanosine (8-OHdG), the liver and kidney damage indexes of aspartate aminotransferase (AST), alanine aminotransferase (ALT), and lactic dehydrogenase (LDH), and blood urea nitrogen (BUN) and creatinine content in furan-treated mice to different extents. The protective effects of apigenin against furan-induced toxicity damage were mainly due to its excellent ability to scavenge free radicals and inhibit lipid oxidation. This is important when considering the use of apigenin as a dietary supplement for beneficial chemoprevention of furan toxicity.
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Affiliation(s)
- Enting Wang
- College of Quartermaster Technology, Jilin University, Changchun, China130062.
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16
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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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17
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Expression patterns of cell cycle proteins in the livers of rats treated with hepatocarcinogens for 28 days. Arch Toxicol 2013; 87:1141-53. [DOI: 10.1007/s00204-013-1011-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2012] [Accepted: 01/17/2013] [Indexed: 10/27/2022]
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18
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Abstract
Many xenobiotics containing a furan ring are toxic and/or carcinogenic. The harmful effects of these compounds require furan ring oxidation. This reaction generates an electrophilic intermediate. Depending on the furan ring substituents, the intermediate is either an epoxide or a cis-enedione with more ring substitution favoring epoxide formation. Either intermediate reacts with cellular nucleophiles such as protein or DNA to trigger toxicities. The reactivity of the metabolite determines which cellular nucleophiles are targeted. The toxicity of a particular furan is also influenced by the presence of competing metabolic pathways or efficient detoxification routes. GSH plays an important role in modulating the harmful effects of this class of compound by reacting with the reactive metabolite. However, this may not represent a detoxification step in all cases.
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Affiliation(s)
- Lisa A Peterson
- Division of Environmental Health Sciences, and Masonic Cancer Center, University of Minnesota , Minneapolis, Minnesota 55455, United States
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19
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Selmanoğlu G, Karacaoğlu E, Kiliç A, Koçkaya EA, Akay MT. Toxicity of food contaminant furan on liver and kidney of growing male rats. ENVIRONMENTAL TOXICOLOGY 2012; 27:613-622. [PMID: 21254322 DOI: 10.1002/tox.20673] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Revised: 10/05/2010] [Accepted: 10/09/2010] [Indexed: 05/30/2023]
Abstract
Furan is a chemical used in some industrial products and occurs naturally in heat-treated foods. We aimed to investigate the effects of orally administered furan on liver and kidney in growing Wistar male rats for 90 days. In this respect, biochemical, morphological, histopathological, and histomorphometrical examinations were performed. Three- to 4-week aged rats were divided into five groups of eight animals each; control, oil control; 2, 4, 8 mg/kg/day furan treatment groups. At the end of the experiment, antioxidant enzyme activities and serum AST, ALT, HDL, Urea, etc. levels were analyzed. Malondialdehyde (MDA) levels, superoxide dismutase (SOD), catalase (CAT), tumor necrosis factor-α (TNF-α), and interleukin-6 (IL-6) were also measured in liver homogenates. Also, liver and kidney were examined morphologically and histopathologically under light microscopy. According to the results of biochemical analysis, ALT, ALP, and LDL levels in treatment groups were significantly different compared with control groups. While LDL levels in treatment groups increased significantly, ALT and ALP levels decreased significantly. No significant changes were observed in liver MDA levels, superoxide dismutase and catalase activities in treatment groups. While IL-6 levels did not change in treatment groups, furan caused dose-dependent increases in liver TNF-α level of rats. In treatment groups, absolute and relative liver weights changed significantly, however, no significant changes were observed in kidney and relative kidney weights. Hyperemic blood vessels in the liver and congestion, edema, fibrosis, and tubular damage in the kidney of rats treated with furan were observed histopathologically. According to histomorphometric examinations, glomeruli diameters and glomerular volume decreased in the kidneys of rats in treatment groups.
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Affiliation(s)
- Güldeniz Selmanoğlu
- Department of Biology, Faculty of Science, Hacettepe University, Beytepe Campus, Ankara 06800, Turkey.
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20
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Neuwirth C, Mosesso P, Pepe G, Fiore M, Malfatti M, Turteltaub K, Dekant W, Mally A. Furan carcinogenicity: DNA binding and genotoxicity of furan in rats in vivo. Mol Nutr Food Res 2012; 56:1363-74. [PMID: 22865590 DOI: 10.1002/mnfr.201200226] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Revised: 05/21/2012] [Accepted: 06/05/2012] [Indexed: 11/09/2022]
Abstract
SCOPE Furan is a potent hepatotoxicant and liver carcinogen in rodents. However, short-term tests for genotoxicity of furan are inconclusive. The aim of this study was to assess the potential of furan to covalently bind to DNA, and to assess furan genotoxicity in rats in vivo. MATERIALS AND METHODS Accelerator mass spectrometry was used to determine the (14) C-content in DNA following administration of [3,4-(14) C]-furan (0.1 and 2.0 mg/kg bw) to F344 rats. DNA damage, micronuclei, chromosomal aberrations, and sister chromatid exchanges were analyzed in F344 rats treated with furan for up to 28 days. CONCLUSION The (14) C-content in liver DNA was significantly increased in a dose-dependent manner, with mean concentrations of 7.9 ± 3.5 amol (14) C/μg DNA and 153.3 ± 100.2 amol (14) C/μg DNA, corresponding to 16.5 ± 7.4 and 325.2 ± 212.7 adducts/10(9) nucleotides at 0.1 and 2.0 mg/kg bw, respectively. There was no evidence for genotoxicity of furan in peripheral blood and bone marrow cells. However, a dose-related increase in the incidence of chromosomal aberrations in rat splenocytes and some indication of DNA damage in liver were observed. Collectively, results from this study indicate that furan may operate-at least in part-by a genotoxic mode of action.
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Affiliation(s)
- Carolin Neuwirth
- Department of Toxicology, University of Würzburg, Würzburg, Germany
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21
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Moro S, Chipman JK, Wegener JW, Hamberger C, Dekant W, Mally A. Furan in heat-treated foods: formation, exposure, toxicity, and aspects of risk assessment. Mol Nutr Food Res 2012; 56:1197-211. [PMID: 22641279 DOI: 10.1002/mnfr.201200093] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Revised: 03/26/2012] [Accepted: 04/04/2012] [Indexed: 12/24/2022]
Abstract
Furan is formed in a variety of heat-treated foods through thermal degradation of natural food constituents. Relatively high levels of furan contamination are found in ground roasted coffee, instant coffee, and processed baby foods. European exposure estimates suggest that mean dietary exposure to furan may be as high as 1.23 and 1.01 μg/kg bw/day for adults and 3- to 12-month-old infants, respectively. Furan is a potent hepatotoxin and hepatocarcinogen in rodents, causing hepatocellular adenomas and carcinomas in rats and mice, and high incidences of cholangiocarcinomas in rats at doses ≥ 2 mg/kg bw. There is therefore a relatively low margin of exposure between estimated human exposure and doses that cause a high tumor incidence in rodents. Since a genotoxic mode of action cannot be excluded for furan-induced tumor formation, the present exposures may indicate a risk to human health and need for mitigation. This review summarizes the current knowledge on mechanisms of furan formation in food, human dietary exposure to furan, and furan toxicity, and highlights the need to establish the risk resulting from the genotoxic and carcinogenic properties of furan at doses lower than 2 mg/kg bw.
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Affiliation(s)
- Sabrina Moro
- Department of Toxicology, University of Würzburg, Würzburg, Germany
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22
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Corton JC, Bushel PR, Fostel J, O'Lone RB. Sources of variance in baseline gene expression in the rodent liver. Mutat Res 2012; 746:104-12. [PMID: 22230429 DOI: 10.1016/j.mrgentox.2011.12.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Accepted: 12/13/2011] [Indexed: 12/18/2022]
Abstract
The use of gene expression profiling in both clinical and laboratory settings would be enhanced by better characterization of variation due to individual, environmental, and technical factors. Analysis of microarray data from untreated or vehicle-treated animals within the control arm of toxicogenomics studies has yielded useful information on baseline fluctuations in liver gene expression in the rodent. Here, studies which highlight contributions of different factors to gene expression variability in the rodent liver are discussed including a large meta-analysis of rat liver, which identified genes that vary in control animals in the absence of chemical treatment. Genes and their pathways that are the most and least variable were identified in a number of these studies. Life stage, fasting, sex, diet, circadian rhythm and liver lobe source can profoundly influence gene expression in the liver. Recognition of biological and technical factors that contribute to variability of background gene expression can help the investigator in the design of an experiment that maximizes sensitivity and reduces the influence of confounders that may lead to misinterpretation of genomic changes. The factors that contribute to variability in liver gene expression in rodents are likely analogous to those contributing to human interindividual variability in drug response and chemical toxicity. Identification of batteries of genes that are altered in a variety of background conditions could be used to predict responses to drugs and chemicals in appropriate models of the human liver.
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Affiliation(s)
- J Christopher Corton
- Integrated Systems Toxicology Division, National Health and Environmental Effects Research Lab, US Environmental Protection Agency, Research Triangle Park, NC 27711, USA.
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23
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Guo NL, Wan YW, Denvir J, Porter DW, Pacurari M, Wolfarth MG, Castranova V, Qian Y. Multiwalled carbon nanotube-induced gene signatures in the mouse lung: potential predictive value for human lung cancer risk and prognosis. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2012; 75:1129-53. [PMID: 22891886 PMCID: PMC3422779 DOI: 10.1080/15287394.2012.699852] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Concerns over the potential for multiwalled carbon nanotubes (MWCNT) to induce lung carcinogenesis have emerged. This study sought to (1) identify gene expression signatures in the mouse lungs following pharyngeal aspiration of well-dispersed MWCNT and (2) determine if these genes were associated with human lung cancer risk and progression. Genome-wide mRNA expression profiles were analyzed in mouse lungs (n = 160) exposed to 0, 10, 20, 40, or 80 μg of MWCNT by pharyngeal aspiration at 1, 7, 28, and 56 d postexposure. By using pairwise statistical analysis of microarray (SAM) and linear modeling, 24 genes were selected, which have significant changes in at least two time points, have a more than 1.5-fold change at all doses, and are significant in the linear model for the dose or the interaction of time and dose. Additionally, a 38-gene set was identified as related to cancer from 330 genes differentially expressed at d 56 postexposure in functional pathway analysis. Using the expression profiles of the cancer-related gene set in 8 mice at d 56 postexposure to 10 μg of MWCNT, a nearest centroid classification accurately predicts human lung cancer survival with a significant hazard ratio in training set (n = 256) and test set (n = 186). Furthermore, both gene signatures were associated with human lung cancer risk (n = 164) with significant odds ratios. These results may lead to development of a surveillance approach for early detection of lung cancer and prognosis associated with MWCNT in the workplace.
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Affiliation(s)
- Nancy L Guo
- Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, WV 26506
- Department of Community Medicine, School of Medicine, West Virginia University, Morgantown, WV 26506
| | - Ying-Wooi Wan
- Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, WV 26506
| | - James Denvir
- Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, WV 26506
| | - Dale W Porter
- Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505
| | - Maricica Pacurari
- Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, WV 26506
| | - Michael G Wolfarth
- Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505
| | - Vincent Castranova
- Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, WV 26506
- Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505
| | - Yong Qian
- Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505
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24
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Snyder-Talkington BN, Qian Y, Castranova V, Guo NL. New perspectives for in vitro risk assessment of multiwalled carbon nanotubes: application of coculture and bioinformatics. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART B, CRITICAL REVIEWS 2012; 15:468-492. [PMID: 23190270 PMCID: PMC3513758 DOI: 10.1080/10937404.2012.736856] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Nanotechnology is a rapidly expanding field with wide application for industrial and medical use; therefore, understanding the toxicity of engineered nanomaterials is critical for their commercialization. While short-term in vivo studies have been performed to understand the toxicity profile of various nanomaterials, there is a current effort to shift toxicological testing from in vivo observational models to predictive and high-throughput in vitro models. However, conventional monoculture results of nanoparticle exposure are often disparate and not predictive of in vivo toxic effects. A coculture system of multiple cell types allows for cross-talk between cells and better mimics the in vivo environment. This review proposes that advanced coculture models, combined with integrated analysis of genome-wide in vivo and in vitro toxicogenomic data, may lead to development of predictive multigene expression-based models to better determine toxicity profiles of nanomaterials and consequent potential human health risk due to exposure to these compounds.
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Affiliation(s)
- Brandi N. Snyder-Talkington
- Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, USA
| | - Yong Qian
- Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, USA
| | - Vincent Castranova
- Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, USA
| | - Nancy L. Guo
- Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, WV 26506, USA
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25
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Amin A, Mahmoud-Ghoneim D. Texture analysis of liver fibrosis microscopic images: a study on the effect of biomarkers. Acta Biochim Biophys Sin (Shanghai) 2011; 43:193-203. [PMID: 21258076 DOI: 10.1093/abbs/gmq129] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Chronic hepatic injury results in liver fibrosis with eventual progression to irreversible cirrhosis. Liver fibrogenesis involves the activation of the quiescent hepatic stellate cell into an activated myofibroblast that is characterized by α-smooth muscle actin (α-SMA) expression and the production of collagens (types I and III). In the present study, rats were randomly divided into three groups: (i) control group, where rats were only treated with a vehicle; (ii) fibrosis group, where rats were treated with carbon tetrachloride (CCl(4)) to induce liver fibrosis; and (iii) silymarin group, where rats were protected with silymarin during CCl(4) treatment. Rats were sacrificed and sections of liver tissue were counterstained with hematoxylin and eosin and Masson's trichrome. Other sections were immunostained using collagens and α-SMA primary antibodies. Fibrosis was confirmed using serum marker measurements. Microscopic images of the stained sections were acquired and digitized. The Biomarker Index of Fibrosis (BIF) was calculated from the images by quantifying the percentage of stained fibers. Statistical methods of texture analysis (TA), namely co-occurrence and run-length matrices, were applied on the digital images followed by classification using agglomerative hierarchical clustering and linear discriminant analysis with cross validation. TA applied on different biomarkers was successful in discriminating between the groups, showing 100% sensitivity and specificity for classification between the control and fibrosis groups using any biomarker. Some classification attempts showed dependence on the biomarker used, especially for classification between the silymarin and fibrosis groups, which showed optimal results using Masson's trichrome. TA results were consistent with both BIF and serum marker measurements.
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Affiliation(s)
- Amr Amin
- Biology Department, Faculty of Science, UAE University, Al-Ain, United Arab Emirates.
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26
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Afshari CA, Hamadeh HK, Bushel PR. The evolution of bioinformatics in toxicology: advancing toxicogenomics. Toxicol Sci 2010; 120 Suppl 1:S225-37. [PMID: 21177775 DOI: 10.1093/toxsci/kfq373] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
As one reflects back through the past 50 years of scientific research, a significant accomplishment was the advance into the genomic era. Basic research scientists have uncovered the genetic code and the foundation of the most fundamental building blocks for the molecular activity that supports biological structure and function. Accompanying these structural and functional discoveries is the advance of techniques and technologies to probe molecular events, in time, across environmental and chemical exposures, within individuals, and across species. The field of toxicology has kept pace with advances in molecular study, and the past 50 years recognizes significant growth and explosive understanding of the impact of the compounds and environment to basic cellular and molecular machinery. The advancement of molecular techniques applied in a whole-genomic capacity to the study of toxicant effects, toxicogenomics, is no doubt a significant milestone for toxicological research. Toxicogenomics has also provided an avenue for advancing a joining of multidisciplinary sciences including engineering and informatics in traditional toxicological research. This review will cover the evolution of the field of toxicogenomics in the context of informatics integration its current promise, and limitations.
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Affiliation(s)
- Cynthia A Afshari
- Department of Comparative Biology and Safety Sciences, Amgen Inc., Thousand Oaks, California 91320, USA.
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Chen T, Mally A, Ozden S, Chipman JK. Low doses of the carcinogen furan alter cell cycle and apoptosis gene expression in rat liver independent of DNA methylation. ENVIRONMENTAL HEALTH PERSPECTIVES 2010; 118:1597-602. [PMID: 20562052 PMCID: PMC2974699 DOI: 10.1289/ehp.1002153] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Revised: 05/13/2010] [Accepted: 06/18/2010] [Indexed: 05/25/2023]
Abstract
BACKGROUND Evidence of potent rodent carcinogenicity via an unclear mechanism suggests that furan in various foods [leading to an intake of up to 3.5 microg/kg body weight (bw)/day] may present a potential risk to human health. OBJECTIVES We tested the hypothesis that altered expression of genes related to cell cycle control, apoptosis, and DNA damage may contribute to the carcinogenicity of furan in rodents. In addition, we investigated the reversibility of such changes and the potential role of epigenetic mechanisms in response to furan doses that approach the maximum estimated dietary intake in humans. METHODS The mRNA expression profiles of genes related to cell cycle, apoptosis, and DNA damage in rat liver treated with furan concentrations of 0.1 and 2 mg/kg bw were measured by quantitative polymerase chain reaction (PCR) arrays. We assessed epigenetic changes by analysis of global and gene-specific DNA methylation [methylation-specific PCR, combined bisulfite restriction analysis (COBRA), and methylated DNA immunoprecipitation chip] and microRNA (miRNA) analyses. RESULTS The expression profiles of apoptosis-related and cell-cycle-related genes were unchanged after 5 days of treatment, although we observed a statistically significant change in the expression of genes related to cell cycle control and apoptosis, but not DNA damage, after 4 weeks of treatment. These changes were reversed after an off-dose period of 2 weeks. None of the gene expression changes was associated with a change in DNA methylation, although we detected minor changes in the miRNA expression profile (5 miRNA alterations out of 349 measured) that may have contributed to modification of gene expression in some cases. CONCLUSION Nongenotoxic changes in gene expression may contribute to the carcinogenicity of furan in rodents. These findings highlight the need for a more comprehensive risk assessment of furan exposure in humans.
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Affiliation(s)
- Tao Chen
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Angela Mally
- Department of Toxicology, University of Würzburg, Würzburg, Germany
| | - Sibel Ozden
- Department of Toxicology, University of Würzburg, Würzburg, Germany
- Department of Pharmaceutical Toxicology, Istanbul University, Istanbul, Turkey
| | - J. Kevin Chipman
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
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Hickling KC, Hitchcock JM, Oreffo V, Mally A, Hammond TG, Evans JG, Chipman JK. Evidence of Oxidative Stress and Associated DNA Damage, Increased Proliferative Drive, and Altered Gene Expression in Rat Liver Produced by the Cholangiocarcinogenic Agent Furan. Toxicol Pathol 2010; 38:230-43. [DOI: 10.1177/0192623309357946] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Furan is a potent cholangiocarcinogen in rat by an as yet undefined mechanism. The risk to man remains unclear. Using a time-course stop study design, we have investigated the potential of furan to induce oxidative stress and DNA damage associated with inflammatory and regenerative responses in rat liver. Furan was administered via oral gavage (30 mg/kg b.w. 5 daily doses per week), and livers were analyzed at time points between eight hr and three months. A one-month recovery group previously treated for three months was also included. There was a marked association between CYP2E1 expression and DNA oxidation (8-oxo-dG) in areas of centrilobular hepatocyte necrosis seen after a single dose. After one-month recovery from three-month treatment, 8-oxo-dG was still observed in areas of furan-induced cholangiofibrosis. Furan-induced changes in the expression of various genes associated with oxidative stress, DNA damage, and cell cycle control were identified during treatment and recovery. We propose that furan-induced cholangiocarcinomas emerge from areas of cholangiofibrosis as a result of a combination of chronic, persistent indirect damage to DNA through oxygen radicals coupled with persistent proliferative signals, including loss of connexin 32, that act to convert this DNA damage to fixed mutations.
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Affiliation(s)
- K. C. Hickling
- Safety Assessment, AstraZeneca R&D Charnwood, Loughborough, United Kingdom
| | - J. M. Hitchcock
- Molecular Toxicology Drug Safety Research & Development Pfizer Ltd Sandwich, Kent, UK
| | - V. Oreffo
- Safety Assessment, AstraZeneca R&D Charnwood, Loughborough, United Kingdom
| | - A. Mally
- Department of Toxicology, University of Würzburg, Würzburg, Germany
| | - T. G. Hammond
- Safety Assessment, AstraZeneca R&D Charnwood, Loughborough, United Kingdom
| | - J. G. Evans
- Safety Assessment, AstraZeneca R&D Charnwood, Loughborough, United Kingdom
| | - J. K. Chipman
- School of Biosciences, The University of Birmingham, Birmingham, United Kingdom
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Kiyosawa N, Ando Y, Manabe S, Yamoto T. Toxicogenomic biomarkers for liver toxicity. J Toxicol Pathol 2009; 22:35-52. [PMID: 22271975 PMCID: PMC3246017 DOI: 10.1293/tox.22.35] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2008] [Accepted: 11/26/2008] [Indexed: 12/15/2022] Open
Abstract
Toxicogenomics (TGx) is a widely used technique in the preclinical stage of drug development to investigate the molecular mechanisms of toxicity. A number of candidate TGx biomarkers have now been identified and are utilized for both assessing and predicting toxicities. Further accumulation of novel TGx biomarkers will lead to more efficient, appropriate and cost effective drug risk assessment, reinforcing the paradigm of the conventional toxicology system with a more profound understanding of the molecular mechanisms of drug-induced toxicity. In this paper, we overview some practical strategies as well as obstacles for identifying and utilizing TGx biomarkers based on microarray analysis. Since clinical hepatotoxicity is one of the major causes of drug development attrition, the liver has been the best documented target organ for TGx studies to date, and we therefore focused on information from liver TGx studies. In this review, we summarize the current resources in the literature in regard to TGx studies of the liver, from which toxicologists could extract potential TGx biomarker gene sets for better hepatotoxicity risk assessment.
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Affiliation(s)
- Naoki Kiyosawa
- Medicinal Safety Research Labs., Daiichi Sankyo Co., Ltd., 717 Horikoshi, Fukuroi, Shizuoka 437-0065, Japan
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Correlation of urinary furan with plasma γ-glutamyltranspeptidase levels in healthy men and women. Food Chem Toxicol 2008; 46:1753-9. [DOI: 10.1016/j.fct.2008.01.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2007] [Revised: 12/18/2007] [Accepted: 01/09/2008] [Indexed: 11/23/2022]
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Thompson KL, Hackett J. Quality control of microarray assays for toxicogenomic and in vitro diagnostic applications. Methods Mol Biol 2008; 460:45-68. [PMID: 18449482 DOI: 10.1007/978-1-60327-048-9_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The generation of high-quality microarray data for toxicogenomics can be affected by the study design and methods used for sample acquisition, preparation, and processing. Bias can be introduced during animal treatment, tissue handling, and sample preparation. Metrics and controls used in assessing RNA integrity and the quality of microarray sample generation are reviewed in this chapter. Regulations and guidelines involved in the application of microarrays as a commercial in vitro diagnostic device are also described.
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Affiliation(s)
- Karol L Thompson
- Division of Applied Pharmacology Research, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
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Brazhnik O, Jones JF. Anatomy of data integration. J Biomed Inform 2007; 40:252-69. [PMID: 17071142 PMCID: PMC2094006 DOI: 10.1016/j.jbi.2006.09.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2005] [Revised: 09/11/2006] [Accepted: 09/19/2006] [Indexed: 01/23/2023]
Abstract
Producing reliable information is the ultimate goal of data processing. The ocean of data created with the advances of science and technologies calls for integration of data coming from heterogeneous sources that are diverse in their purposes, business rules, underlying models and enabling technologies. Reference models, Semantic Web, standards, ontology, and other technologies enable fast and efficient merging of heterogeneous data, while the reliability of produced information is largely defined by how well the data represent the reality. In this paper, we initiate a framework for assessing the informational value of data that includes data dimensions; aligning data quality with business practices; identifying authoritative sources and integration keys; merging models; uniting updates of varying frequency and overlapping or gapped data sets.
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Affiliation(s)
- Olga Brazhnik
- Center for Information Technology, National Institutes of Health, 10401 Fernwood Road, Room 3NW03, Bethesda, MD 20817, USA.
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Auman JT, Chou J, Gerrish K, Huang Q, Jayadev S, Blanchard K, Paules RS. Identification of genes implicated in methapyrilene-induced hepatotoxicity by comparing differential gene expression in target and nontarget tissue. ENVIRONMENTAL HEALTH PERSPECTIVES 2007; 115:572-8. [PMID: 17450226 PMCID: PMC1852695 DOI: 10.1289/ehp.9396] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2006] [Accepted: 01/17/2007] [Indexed: 05/15/2023]
Abstract
BACKGROUND Toxicogenomics experiments often reveal thousands of transcript alterations that are related to multiple processes, making it difficult to identify key gene changes that are related to the toxicity of interest. OBJECTIVES The objective of this study was to compare gene expression changes in a nontarget tissue to the target tissue for toxicity to help identify toxicity-related genes. METHODS Male rats were given the hepatotoxicant methapyrilene at two dose levels, with livers and kidneys removed 24 hr after one, three, and seven doses for gene expression analysis. To identify gene changes likely to be related to toxicity, we analyzed genes on the basis of their temporal pattern of change using a program developed at the National Institute of Environmental Health Sciences, termed "EPIG" (extracting gene expression patterns and identifying co-expressed genes). RESULTS High-dose methapyrilene elicited hepatic damage that increased in severity with the number of doses, whereas no treatment-related lesions were observed in the kidney. High-dose methapyrilene elicited thousands of gene changes in the liver at each time point, whereas many fewer gene changes were observed in the kidney. EPIG analysis identified patterns of gene expression correlated to the observed toxicity, including genes associated with endoplasmic reticulum stress and the unfolded protein response. CONCLUSIONS By factoring in dose level, number of doses, and tissue into the analysis of gene expression elicited by methapyrilene, we were able to identify genes likely to not be implicated in toxicity, thereby allowing us to focus on a subset of genes to identify toxicity-related processes.
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Affiliation(s)
- J. Todd Auman
- National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - Jeff Chou
- National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - Kevin Gerrish
- National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - Qihong Huang
- Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut, USA
| | - Supriya Jayadev
- Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut, USA
| | - Kerry Blanchard
- Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut, USA
| | - Richard S. Paules
- National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
- Address correspondence to R.S. Paules, NIEHS, 111 T.W. Alexander Dr., P.O. Box 12233, Mail Drop D2-03, Research Triangle Park, NC 27709 USA. Telephone: (919) 541-3710. Fax: (919) 316-4771. E-mail:
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Lobenhofer EK, Boorman GA, Phillips KL, Heinloth AN, Malarkey DE, Blackshear PE, Houle C, Hurban P. Application of visualization tools to the analysis of histopathological data enhances biological insight and interpretation. Toxicol Pathol 2007; 34:921-8. [PMID: 17178692 DOI: 10.1080/01926230601072319] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Gene expression profiling, metabolomic screens, and other high-dimensional methods have become an integral part of many biological investigations. To facilitate interpretation of these data, it is important to have detailed phenotypic data--including histopathology--to which these data can be associated, or anchored. However, as the amount of phenotypic data increases, associations within and across these data can be difficult to visualize and interpret. We have developed an approach for categorizing and clustering biologically related histopathological diagnoses to facilitate their visualization, thereby increasing the possibility of identifying associations and facilitating the comparison with other data streams. In this study, we utilize histopathological data generated as part of a standardized toxicogenomics compendium study to generate composite histopathological scores and to develop visualizations that facilitate biological insight. The validity of this approach is illustrated by the identification of transcripts that correlate with the pathology diagnoses that comprise the categories of "response to hepatocellular injury" and "repair." This approach is broadly applicable to studies in which histopathology is used to phenotypically anchor other data, and results in visualizations that facilitate biological interpretation and the identification of associations and relationships within the data.
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Affiliation(s)
- Edward K Lobenhofer
- Cogenics, Division of Clinical Data, Morrisville, North Carolina 27560, USA.
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35
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Dai X, Souza ATD, Dai H, Lewis DL, Lee CK, Spencer AG, Herweijer H, Hagstrom JE, Linsley PS, Bassett DE, Ulrich RG, He YD. PPARalpha siRNA-treated expression profiles uncover the causal sufficiency network for compound-induced liver hypertrophy. PLoS Comput Biol 2007; 3:e30. [PMID: 17335344 PMCID: PMC1808491 DOI: 10.1371/journal.pcbi.0030030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2006] [Accepted: 01/02/2007] [Indexed: 11/18/2022] Open
Abstract
Uncovering pathways underlying drug-induced toxicity is a fundamental objective in the field of toxicogenomics. Developing mechanism-based toxicity biomarkers requires the identification of such novel pathways and the order of their sufficiency in causing a phenotypic response. Genome-wide RNA interference (RNAi) phenotypic screening has emerged as an effective tool in unveiling the genes essential for specific cellular functions and biological activities. However, eliciting the relative contribution of and sufficiency relationships among the genes identified remains challenging. In the rodent, the most widely used animal model in preclinical studies, it is unrealistic to exhaustively examine all potential interactions by RNAi screening. Application of existing computational approaches to infer regulatory networks with biological outcomes in the rodent is limited by the requirements for a large number of targeted permutations. Therefore, we developed a two-step relay method that requires only one targeted perturbation for genome-wide de novo pathway discovery. Using expression profiles in response to small interfering RNAs (siRNAs) against the gene for peroxisome proliferator-activated receptor alpha (Ppara), our method unveiled the potential causal sufficiency order network for liver hypertrophy in the rodent. The validity of the inferred 16 causal transcripts or 15 known genes for PPARalpha-induced liver hypertrophy is supported by their ability to predict non-PPARalpha-induced liver hypertrophy with 84% sensitivity and 76% specificity. Simulation shows that the probability of achieving such predictive accuracy without the inferred causal relationship is exceedingly small (p < 0.005). Five of the most sufficient causal genes have been previously disrupted in mouse models; the resulting phenotypic changes in the liver support the inferred causal roles in liver hypertrophy. Our results demonstrate the feasibility of defining pathways mediating drug-induced toxicity from siRNA-treated expression profiles. When combined with phenotypic evaluation, our approach should help to unleash the full potential of siRNAs in systematically unveiling the molecular mechanism of biological events.
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Affiliation(s)
- Xudong Dai
- Informatics, Rosetta Inpharmatics, Seattle, Washington, United States of America
- * To whom correspondence should be addressed. E-mail: (XD); (YDH)
| | - Angus T. De Souza
- Preclinical Molecular Profiling, Rosetta Inpharmatics, Seattle, Washington, United States of America
| | - Hongyue Dai
- Informatics, Rosetta Inpharmatics, Seattle, Washington, United States of America
| | - David L Lewis
- Mirus Bio Corporation, Madison, Wisconsin, United States of America
| | - Chang-kyu Lee
- Informatics, Rosetta Inpharmatics, Seattle, Washington, United States of America
| | - Andy G Spencer
- Mirus Bio Corporation, Madison, Wisconsin, United States of America
| | - Hans Herweijer
- Mirus Bio Corporation, Madison, Wisconsin, United States of America
| | - Jim E Hagstrom
- Mirus Bio Corporation, Madison, Wisconsin, United States of America
| | - Peter S Linsley
- Cancer Biology, Rosetta Inpharmatics, Seattle, Washington, United States of America
| | - Douglas E Bassett
- Informatics, Rosetta Inpharmatics, Seattle, Washington, United States of America
| | - Roger G Ulrich
- Preclinical Molecular Profiling, Rosetta Inpharmatics, Seattle, Washington, United States of America
| | - Yudong D He
- Informatics, Rosetta Inpharmatics, Seattle, Washington, United States of America
- * To whom correspondence should be addressed. E-mail: (XD); (YDH)
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Abstract
Grouping of gene expression patterns across biological experiments, treatments and time-series data is performed in q-intervals of measurements using phase-shifted analysis of gene expression (PAGE); a Java-based tool to find clusters of genes that share trends of expression profiles within the dataset. The patterns and genes within q-Clusters are visualized in trend plots and compared to determine biological relevance from the gene annotations.
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Affiliation(s)
- Elo Leung
- Bioinformatics and Computational Biology, School of Computational Sciences, George Mason University, Manassas, VA 20110, USA
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Volz DC, Hinton DE, Law JM, Kullman SW. Dynamic gene expression changes precede dioxin-induced liver pathogenesis in medaka fish. Toxicol Sci 2005; 89:524-34. [PMID: 16267337 DOI: 10.1093/toxsci/kfj033] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
A major challenge for environmental genomics is linking gene expression to cellular toxicity and morphological alteration. Herein, we address complexities related to hepatic gene expression responses after a single injection of the aryl hydrocarbon receptor (AHR) agonist 2,3,7,8-tetrachlorodibenzo-p-dioxin (dioxin) and illustrate an initial stress response followed by cytologic and adaptive changes in the teleost fish medaka. Using a custom 175-gene array, we find that overall hepatic gene expression and histological changes are strongly dependent on dose and time. The most pronounced dioxin-induced gene expression changes occurred early and preceded morphologic alteration in the liver. Following a systematic search for putative Ah response elements (AHREs) (5'-CACGCA-3') within 2000 bp upstream of the predicted transcriptional start site, the majority (87%) of genes screened in this study did not contain an AHRE, suggesting that gene expression was not solely dependent on AHRE-mediated transcription. Moreover, in the highest dosage, we observed gene expression changes associated with adaptation that persisted for almost two weeks, including induction of a gene putatively identified as ependymin that may function in hepatic injury repair. These data suggest that the cellular response to dioxin involves both AHRE- and non-AHRE-mediated transcription, and that coupling gene expression profiling with analysis of morphologic pathogenesis is essential for establishing temporal relationships between transcriptional changes, toxicity, and adaptation to hepatic injury.
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Affiliation(s)
- David C Volz
- Integrated Toxicology Program and Nicholas School of the Environment and Earth Sciences, Duke University, Durham, North Carolina 27708, USA
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Ng HH, Frantz CE, Rausch L, Fairchild DC, Shimon J, Riccio E, Smith S, Mirsalis JC. Gene expression profiling of mouse host response to Listeria monocytogenes infection. Genomics 2005; 86:657-67. [PMID: 16102935 DOI: 10.1016/j.ygeno.2005.07.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2005] [Revised: 07/01/2005] [Accepted: 07/14/2005] [Indexed: 10/25/2022]
Abstract
The purpose of this study was to evaluate gene expression profiles in the liver and blood for prediction of infection severity from Listeria monocytogenes (LM). Mice were injected with medium broth (control) or a nonlethal or lethal dose of LM and sacrificed 6 h later. Gene expression changes were determined using Affymetrix MGU74Av2 GeneChips and confirmed by real-time polymerase chain reaction analysis. We identified discernable genes whose gene expression profiles can be used in pattern recognition to predict and classify samples in differently treated groups, with >or=90% accuracy in liver samples and 80% accuracy in blood at prediction; however, different genes were predictive in each tissue. Our results suggest that gene expression profiling in response to LM in mice may be able to distinguish samples in groups with varying severity of infection and provide information in finding molecular mechanisms and early biomarkers for subsequent conventional clinical endpoints.
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Affiliation(s)
- Hanna H Ng
- Biosciences Division, SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025-3493, USA.
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Lühe A, Suter L, Ruepp S, Singer T, Weiser T, Albertini S. Toxicogenomics in the pharmaceutical industry: hollow promises or real benefit? Mutat Res 2005; 575:102-15. [PMID: 15924886 DOI: 10.1016/j.mrfmmm.2005.02.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2005] [Revised: 02/24/2005] [Accepted: 02/24/2005] [Indexed: 05/02/2023]
Abstract
Almost 10 years ago, microarray technology was established as a new powerful tool for large-scale analysis of gene expression. Soon thereafter the new technology was discovered by toxicologists for the purpose of deciphering the molecular events underlying toxicity, and the term "Toxicogenomics" appeared in scientific literature. Ever since, the toxicology community was fascinated by the multiplicity of sophisticated possibilities toxicogenomics seems to offer: genome-wide analysis of toxicant-induced expression profiles may provide a means for prediction of toxicity prior to classical toxicological endpoints such as histopathology or clinical chemistry. Some researchers even speculated of the classical methods being superfluous before long. It was assumed that by using toxicogenomics it would be possible to classify compounds early in drug development and consequently save animals, time, and money in pre-clinical toxicity studies. Moreover, it seemed within reach to unravel the molecular mechanisms underlying toxicity. The feasibility of bridging data derived from in vitro and in vivo systems, identifying new biomarkers, and comparing toxicological responses "across-species" was also excessively praised. After several years of intensive application of microarray technology in the field of toxicology, not only by the pharmaceutical industry, it is now time to survey its achievements and to question how many of these wishes and promises have really come true.
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Affiliation(s)
- Anke Lühe
- F. Hoffmann-La Roche Ltd., Non-Clinical Drug Safety, 4070 Basel, Switzerland.
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Ekins S. Systems-ADME/Tox: resources and network approaches. J Pharmacol Toxicol Methods 2005; 53:38-66. [PMID: 16054403 DOI: 10.1016/j.vascn.2005.05.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2005] [Accepted: 05/23/2005] [Indexed: 01/11/2023]
Abstract
The increasing cost of drug development is partially due to our failure to identify undesirable compounds at an early enough stage of development. The application of higher throughput screening methods have resulted in the generation of very large datasets from cells in vitro or from in vivo experiments following the treatment with drugs or known toxins. In recent years the development of systems biology, databases and pathway software has enabled the analysis of the high-throughput data in the context of the whole cell. One of the latest technology paradigms to be applied alongside the existing in vitro and computational models for absorption, distribution, metabolism, excretion and toxicology (ADME/Tox) involves the integration of complex multidimensional datasets, termed toxicogenomics. The goal is to provide a more complete understanding of the effects a molecule might have on the entire biological system. However, due to the sheer complexity of this data it may be necessary to apply one or more different types of computational approaches that have as yet not been fully utilized in this field. The present review describes the data generated currently and introduces computational approaches as a component of ADME/Tox. These methods include network algorithms and manually curated databases of interactions that have been separately classified under systems biology methods. The integration of these disparate tools will result in systems-ADME/Tox and it is important to understand exactly what data resources and technologies are available and applicable. Examples of networks derived with important drug transporters and drug metabolizing enzymes are provided to demonstrate the network technologies.
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Affiliation(s)
- Sean Ekins
- GeneGo, 500 Renaissance Drive, Suite 106, St. Joseph, MI 49085, USA.
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Khoury MJ, Davis R, Gwinn M, Lindegren ML, Yoon P. Do we need genomic research for the prevention of common diseases with environmental causes? Am J Epidemiol 2005; 161:799-805. [PMID: 15840611 DOI: 10.1093/aje/kwi113] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Concerns have been raised about the value of genomic research for prevention and public health, especially for complex diseases with risk factors that are amenable to environmental modification. Given that gene-environment interactions underlie almost all human diseases, the public health significance of genomic research on common diseases with modifiable environmental risks is based not necessarily on finding new genetic "causes" but on improving existing approaches to identifying and modifying environmental risk factors to better prevent and treat disease. Such applied genomic research for environmentally caused diseases is important, because 1) it could help stratify disease risks and differentiate interventions for achieving population health benefits; 2) it could help identify new environmental risk factors for disease or help confirm suspected environmental risk factors; and 3) it could aid our understanding of disease occurrence in terms of transmission, natural history, severity, etiologic heterogeneity, and targets for intervention at the population level. While genomics is still in its infancy, opportunities exist for developing, testing, and applying the tools of genomics to clinical and public health research, especially for conditions with known or suspected environmental causes. This research is likely to lead to population-wide health promotion and disease prevention efforts, not only to interventions targeted according to genetic susceptibility.
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Affiliation(s)
- Muin J Khoury
- Office of Genomics and Disease Prevention, Coordinating Center on Health Promotion, Centers for Disease Control and Prevention, Atlanta, GA 30341, USA.
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Abstract
The early and high-throughput application of assays for non-genetic toxicity is of great interest to the pharmaceutical industry, although few systems have been validated as being of good predictive value. New technologies could enable toxicity to be studied in the context of systems biology. An important factor to be considered is the metabolism of drugs to reactive intermediates. Chemical reactions of these with cell and tissue nucleophiles are relatively well understood, but predicting how biological modifications will affect signalling and regulatory networks remains a challenge. Some of these pathways could be useful as sentinels for toxicity. This article will cover some examples of drug toxicity and the prospects for future technology development.
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Affiliation(s)
- Daniel C Liebler
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, 638 Robinson Research Building, 23rd and Pierce Avenues, Nashville, Tennessee 37232-0146, USA
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Abstract
Toxicogenomics combines transcript, protein and metabolite profiling with conventional toxicology to investigate the interaction between genes and environmental stress in disease causation. The patterns of altered molecular expression that are caused by specific exposures or disease outcomes have revealed how several toxicants act and cause disease. Despite these success stories, the field faces noteworthy challenges in discriminating the molecular basis of toxicity. We argue that toxicology is gradually evolving into a systems toxicology that will eventually allow us to describe all the toxicological interactions that occur within a living system under stress and use our knowledge of toxicogenomic responses in one species to predict the modes-of-action of similar agents in other species.
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Affiliation(s)
- Michael D Waters
- National Center for Toxicogenomics, National Institute of Environmental Health Sciences, PO Box 12233, MD F1-05, 111 Alexander Drive, Research Triangle Park, North Carolina 27709-2233, USA.
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Moggs JG, Tinwell H, Spurway T, Chang HS, Pate I, Lim FL, Moore DJ, Soames A, Stuckey R, Currie R, Zhu T, Kimber I, Ashby J, Orphanides G. Phenotypic anchoring of gene expression changes during estrogen-induced uterine growth. ENVIRONMENTAL HEALTH PERSPECTIVES 2004; 112:1589-606. [PMID: 15598610 PMCID: PMC1247656 DOI: 10.1289/txg.7345] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2004] [Accepted: 10/07/2004] [Indexed: 05/11/2023]
Abstract
A major challenge in the emerging field of toxicogenomics is to define the relationships between chemically induced changes in gene expression and alterations in conventional toxicologic parameters such as clinical chemistry and histopathology. We have explored these relationships in detail using the rodent uterotrophic assay as a model system. Gene expression levels, uterine weights, and histologic parameters were analyzed 1, 2, 4, 8, 24, 48, and 72 hr after exposure to the reference physiologic estrogen 17 beta-estradiol (E2). A multistep analysis method, involving unsupervised hierarchical clustering followed by supervised gene ontology-driven clustering, was used to define the transcriptional program associated with E2-induced uterine growth and to identify groups of genes that may drive specific histologic changes in the uterus. This revealed that uterine growth and maturation are preceded and accompanied by a complex, multistage molecular program. The program begins with the induction of genes involved in transcriptional regulation and signal transduction and is followed, sequentially, by the regulation of genes involved in protein biosynthesis, cell proliferation, and epithelial cell differentiation. Furthermore, we have identified genes with common molecular functions that may drive fluid uptake, coordinated cell division, and remodeling of luminal epithelial cells. These data define the mechanism by which an estrogen induces organ growth and tissue maturation, and demonstrate that comparison of temporal changes in gene expression and conventional toxicology end points can facilitate the phenotypic anchoring of toxicogenomic data.
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Affiliation(s)
- Jonathan G Moggs
- Syngenta Central Toxicology Laboratory, Alderley Park, Cheshire SK10 4TJ, UK
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