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Dang L, Dong Y, Zhang C, Su B, Ning N, Zhou S, Zhang M, Huang Q, Li Y, Wang S. Zishen Yutai pills restore fertility in premature ovarian failure through regulating arachidonic acid metabolism and the ATK pathway. JOURNAL OF ETHNOPHARMACOLOGY 2024; 324:117782. [PMID: 38272104 DOI: 10.1016/j.jep.2024.117782] [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: 11/29/2023] [Revised: 01/08/2024] [Accepted: 01/15/2024] [Indexed: 01/27/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The Zishen Yutai pills (ZYP), a Chinese medicinal formulation derived from the Qing Dynasty prescription "Shou Tai pills", have been documented to exhibit beneficial effects in clinical observations treating premature ovarian failure (POF). However, the anti-POF effects and its comprehensive systemic mechanism have not yet been clarified. AIM OF THE REVIEW Therapeutic effects and systemic mechanism of ZYP in POF were evaluated. MATERIALS AND METHODS After pulverization, sieving, and stirring, ZYP was administered intragastrically to cisplatin-induced POF mice at a dose of 1.95 mg/kg/d for 14 days. The anti-POF effects of ZYP were investigated by assessing the number of ovarian follicles at different developmental stages, as well as measuring serum estradiol (E2) levels and ovarian-expressed anti-Müllerian hormone (AMH). Reproductive performance and offspring health were evaluated to predict fertility restoration. Furthermore, a combination of proteomic and metabolomic profiling was employed to elucidate the underlying molecular mechanism of ZYP in treating POF. Western blot (WB) analyses and real-time quantitative polymerase chain reaction (RT-qPCR) were conducted to explore the mechanisms through which ZYP exerted its anti-POF effects. RESULTS We have demonstrated that oral administration of ZYP reversed the reduction in follicles at different developmental stages and stimulated the expressions of serum E2 and ovarian-expressed AMH in a cisplatin-induced POF model. Additionally, ZYP ameliorated follicle apoptosis in ovaries affected by cisplatin-induced POF. Furthermore, treatment with ZYP restored the quantity and quality of oocytes, as well as enhanced fertility. Our results revealed 62 differentially expressed proteins (DEPs) through proteomic analyses and identified 26 differentially expressed metabolites (DEMs) through metabolomic analyses. Both DEPs and DEMs were highly enriched in the arachidonic acid (AA) metabolism pathway. ZYP treatment effectively upregulated the protein and mRNA expression of critical targets in AA metabolism and the AKT pathway, including CYP17α1, HSD3β1, LHR, STAR, and AKT, in cisplatin-induced POF mice. CONCLUSIONS These results indicated that ZYP exerted protective effects against POF and restored fertility from cisplatin-induced apoptosis. ZYP could be a satisfying alternative treating POF.
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Affiliation(s)
- Lei Dang
- Department of Obstetrics and Gynaecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China; Guangzhou Baiyunshan Zhongyi Pharmaceutical Co. Ltd, Guangzhou, Guangdong, China; Postdoctoral Research Center of Guangzhou Pharmaceutical Holdings Ltd., Guangzhou, China
| | - Yingying Dong
- Department of Obstetrics and Gynaecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Chunbo Zhang
- Guangzhou Baiyunshan Zhongyi Pharmaceutical Co. Ltd, Guangzhou, Guangdong, China; Postdoctoral Research Center of Guangzhou Pharmaceutical Holdings Ltd., Guangzhou, China
| | - Biru Su
- Guangzhou Baiyunshan Zhongyi Pharmaceutical Co. Ltd, Guangzhou, Guangdong, China
| | - Na Ning
- Guangzhou Baiyunshan Zhongyi Pharmaceutical Co. Ltd, Guangzhou, Guangdong, China
| | - Su Zhou
- Department of Obstetrics and Gynaecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Minli Zhang
- Department of Obstetrics and Gynaecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Qiuling Huang
- Guangzhou Baiyunshan Zhongyi Pharmaceutical Co. Ltd, Guangzhou, Guangdong, China
| | - Yan Li
- Department of Obstetrics and Gynaecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| | - Shixuan Wang
- Department of Obstetrics and Gynaecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
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Qiao Y, Ji X, Guo H, Zheng W, Yao W. Complementary transcriptomic and proteomic analyses elucidate the toxicological molecular mechanisms of deoxynivalenol-induced contractile dysfunction in enteric smooth muscle cells. Food Chem Toxicol 2024; 186:114545. [PMID: 38403181 DOI: 10.1016/j.fct.2024.114545] [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: 01/02/2024] [Revised: 02/18/2024] [Accepted: 02/22/2024] [Indexed: 02/27/2024]
Abstract
Deoxynivalenol (DON) is one of the frequent Fusarium mycotoxins and poses a serious threat to public health worldwide. DON-induced weight loss is tightly connected with its ability to decrease feed intake by influencing gastrointestinal tract (GIT) motility. Our previous reports indicated that DON interfered with intestinal motility by injuring the contractility of enteric smooth muscle cells (SMC). Here, we further explored the potential mechanisms by employing a complementary method of transcriptomics and proteomics using the porcine enteric smooth muscle cell line (PISMC) as an experimental model. The transcriptomic and proteomic data uncover that the expression of numerous extracellular matrix (ECM) proteins and multiple integrin subunits were downregulated in PISMC under DON exposure, suppressing the ECM-integrin receptor interaction and its mediated signaling. Furthermore, DON treatment could depress actin polymerization, as reflected by the upregulated expression of Rho GTPase-activating proteins and cofilin in PISMC. Meanwhile, the expression levels of downstream contractile apparatus genes were significantly inhibited after challenge with DON. Taken together, the current results suggest that DON inhibits enteric SMC contractility by regulating the ECM-integrin-actin polymerization signaling pathway. Our findings provide novel insights into the potential mechanisms behind the DON toxicological effects in the GIT of humans and animals.
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Affiliation(s)
- Yu Qiao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China; Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Science and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Xu Ji
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Science and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Huiduo Guo
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212018, China
| | - Weijiang Zheng
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wen Yao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China; Key Lab of Animal Physiology and Biochemistry, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Nanjing Agricultural University, Nanjing, 210095, China.
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3
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Tseng CY, Custer CM, Custer TW, Dummer PM, Karouna-Renier N, Matson CW. Multi-omics responses in tree swallow (Tachycineta bicolor) nestlings from the Maumee Area of Concern, Maumee River, Ohio. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:159130. [PMID: 36183771 DOI: 10.1016/j.scitotenv.2022.159130] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 09/26/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
A multi-omics approach was utilized to identify altered biological responses and functions, and to prioritize contaminants to assess the risks of chemical mixtures in the Maumee Area of Concern (AOC), Maumee River, OH, USA. The Maumee AOC is designated by the United States Environmental Protection Agency as having significant beneficial use impairments, including degradation of fish and wildlife populations, bird or animal deformities or reproduction problems, and loss of fish and wildlife habitat. Tree swallow (Tachycineta bicolor) nestlings were collected at five sites along the Maumee River, which included wastewater treatment plants (WWTPs) and industrial land-use sites. Polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), polycyclic aromatic hydrocarbons (PAHs), polychlorinated dibenzo p dioxins and furans (PCDD/Fs), and chlorinated pesticide concentrations were elevated in Maumee tree swallows, relative to a remote reference site, Star Lake, WI, USA. Liver tissue was utilized for non-targeted transcriptome and targeted metabolome evaluation. A significantly differentially expressed gene cluster related to a downregulation in cell growth and cell cycle regulation was identified when comparing all Maumee River sites with the reference site. There was an upregulation of lipogenesis genes, such as PPAR signaling (HMGCS2, SLC22A5), biosynthesis of unsaturated fatty acids (FASN, SCD, ELOVL2, and FADS2), and higher lipogenesis related metabolites, such as docosapentaenoic acid (DPA), docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA), and arachidonic acid (AA) at two industrial land-use sites, Ironhead and Maumee, relative to WWTP sites (Perrysburg and SideCut), and the reference site. Toledo Water, in the vicinity of the other two industrial sites and also adjacent to a WWTP, showed a mix of signals between industrial land-use and WWTP land-use. PAHs, oxychlordane, and PBDEs were determined to be the most likely causes of the differentiation in biological responses, including de novo lipogenesis and biosynthesis of unsaturated fatty acids.
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Affiliation(s)
- Chi Yen Tseng
- Department of Environmental Science, The Institute of Ecological, Earth, and Environmental Sciences (TIE3S), the Center for Reservoir and Aquatic Systems Research (CRASR), Baylor University, Waco, TX 76798, United States
| | - Christine M Custer
- Upper Midwest Environmental Sciences Center, U.S. Geological Survey, La Crosse, WI 54603, United States
| | - Thomas W Custer
- Upper Midwest Environmental Sciences Center, U.S. Geological Survey, La Crosse, WI 54603, United States
| | - Paul M Dummer
- Upper Midwest Environmental Sciences Center, U.S. Geological Survey, La Crosse, WI 54603, United States
| | - Natalie Karouna-Renier
- U.S. Geological Survey, Eastern Ecological Science Center (EESC) at Patuxent, Beltsville, MD 20705, United States
| | - Cole W Matson
- Department of Environmental Science, The Institute of Ecological, Earth, and Environmental Sciences (TIE3S), the Center for Reservoir and Aquatic Systems Research (CRASR), Baylor University, Waco, TX 76798, United States.
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Wilson LB, McClure RS, Waters KM, Simonich MT, Tanguay RL. Concentration-response gene expression analysis in zebrafish reveals phenotypically-anchored transcriptional responses to retene. FRONTIERS IN TOXICOLOGY 2022; 4:950503. [PMID: 36093370 PMCID: PMC9453431 DOI: 10.3389/ftox.2022.950503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/12/2022] [Indexed: 11/13/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous environmental contaminants and are associated with human disease. Canonically, many PAHs induce toxicity via activation of the aryl hydrocarbon receptor (AHR) pathway. While the interaction between PAHs and the AHR is well-established, understanding which AHR-regulated transcriptional effects directly result in observable phenotypes and which are adaptive or benign is important to better understand PAH toxicity. Retene is a frequently detected PAH in environmental sampling and has been associated with AHR2-dependent developmental toxicity in zebrafish, though its mechanism of toxicity has not been fully elucidated. To interrogate transcriptional changes causally associated with retene toxicity, we conducted whole-animal RNA sequencing at 48 h post-fertilization after exposure to eight retene concentrations. We aimed to identify the most sensitive transcriptomic responses and to determine whether this approach could uncover gene sets uniquely differentially expressed at concentrations which induce a phenotype. We identified a concentration-response relationship for differential gene expression in both number of differentially expressed genes (DEGs) and magnitude of expression change. Elevated expression of cyp1a at retene concentrations below the threshold for teratogenicity suggested that while cyp1a expression is a sensitive biomarker of AHR activation, it may be too sensitive to serve as a biomarker of teratogenicity. Genes differentially expressed at only non-teratogenic concentrations were enriched for transforming growth factor-β (TGF-β) signaling pathway disruption while DEGs identified at only teratogenic concentrations were significantly enriched for response to xenobiotic stimulus and reduction-oxidation reaction activity. DEGs which spanned both non-teratogenic and teratogenic concentrations showed similar disrupted biological processes to those unique to teratogenic concentrations, indicating these processes were disrupted at low exposure concentrations. Gene co-expression network analysis identified several gene modules, including those associated with PAHs and AHR2 activation. One, Module 7, was strongly enriched for AHR2-associated genes and contained the strongest responses to retene. Benchmark concentration (BMC) of Module seven genes identified a median BMC of 7.5 µM, nearly the highest retene concentration with no associated teratogenicity, supporting the hypothesis that Module seven genes are largely responsible for retene toxicity.
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Affiliation(s)
- Lindsay B. Wilson
- Department of Environmental and Molecular Toxicology, Sinnhuber Aquatic Research Laboratory, Oregon State University, Corvallis, OR, United States
| | - Ryan S. McClure
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Katrina M. Waters
- Department of Environmental and Molecular Toxicology, Sinnhuber Aquatic Research Laboratory, Oregon State University, Corvallis, OR, United States
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Michael T. Simonich
- Department of Environmental and Molecular Toxicology, Sinnhuber Aquatic Research Laboratory, Oregon State University, Corvallis, OR, United States
| | - Robyn L. Tanguay
- Department of Environmental and Molecular Toxicology, Sinnhuber Aquatic Research Laboratory, Oregon State University, Corvallis, OR, United States
- *Correspondence: Robyn L. Tanguay,
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La Barbera G, Nommesen KD, Cuparencu C, Stanstrup J, Dragsted LO. A Comprehensive Database for DNA Adductomics. Front Chem 2022; 10:908572. [PMID: 35692690 PMCID: PMC9184683 DOI: 10.3389/fchem.2022.908572] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 04/22/2022] [Indexed: 11/25/2022] Open
Abstract
The exposure of human DNA to genotoxic compounds induces the formation of covalent DNA adducts, which may contribute to the initiation of carcinogenesis. Liquid chromatography (LC) coupled with high-resolution mass spectrometry (HRMS) is a powerful tool for DNA adductomics, a new research field aiming at screening known and unknown DNA adducts in biological samples. The lack of databases and bioinformatics tool in this field limits the applicability of DNA adductomics. Establishing a comprehensive database will make the identification process faster and more efficient and will provide new insight into the occurrence of DNA modification from a wide range of genotoxicants. In this paper, we present a four-step approach used to compile and curate a database for the annotation of DNA adducts in biological samples. The first step included a literature search, selecting only DNA adducts that were unequivocally identified by either comparison with reference standards or with nuclear magnetic resonance (NMR), and tentatively identified by tandem HRMS/MS. The second step consisted in harmonizing structures, molecular formulas, and names, for building a systematic database of 279 DNA adducts. The source, the study design and the technique used for DNA adduct identification were reported. The third step consisted in implementing the database with 303 new potential DNA adducts coming from different combinations of genotoxicants with nucleobases, and reporting monoisotopic masses, chemical formulas, .cdxml files, .mol files, SMILES, InChI, InChIKey and IUPAC nomenclature. In the fourth step, a preliminary spectral library was built by acquiring experimental MS/MS spectra of 15 reference standards, generating in silico MS/MS fragments for all the adducts, and reporting both experimental and predicted fragments into interactive web datatables. The database, including 582 entries, is publicly available (https://gitlab.com/nexs-metabolomics/projects/dna_adductomics_database). This database is a powerful tool for the annotation of DNA adducts measured in (HR)MS. The inclusion of metadata indicating the source of DNA adducts, the study design and technique used, allows for prioritization of the DNA adducts of interests and/or to enhance the annotation confidence. DNA adducts identification can be further improved by integrating the present database with the generation of authentic MS/MS spectra, and with user-friendly bioinformatics tools.
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Hippocampal proteins discovery of diabetes-induced central neuropathy based on proteomics. Neuroreport 2022; 33:354-362. [PMID: 35594437 DOI: 10.1097/wnr.0000000000001790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
OBJECTIVES Growing evidence suggests that diabetes can cause multifactorial damage to the central nervous system (CNS) and may lead to dementia. However, the underlying mechanism of diabetes-induced central neuropathy remains sparse. In recent years, proteomics has provided better methods and means in analyzing the molecular mechanisms of disease. We applied proteomics to investigate the changes of hippocampal proteins in diabetic rats, with a view to discover the biomarkers of diabetes-induced central neuropathy and elucidated the potential biological relationships. METHODS Male Wistar rats were randomly divided into the control group and model group. The model group rats were injected intraperitoneally with streptozotocin. Morris water maze test was performed to evaluate the learning and memory of rats, and the hippocampus was taken out. Proteomics were adopted to investigate the changes of differentially expressed proteins. RESULTS Compared with the control group, the escape latency of the diabetic rats was significantly increased (P < 0.01, P < 0.05). It was presented that four differentially expressed proteins might be the potential biomarkers of diabetes-induced central neuropathy: septin 5, GRB2 related binding protein 2 (GAB2), casein kinase 1ε (CK1ε), aquaporin 4 (AQP4). These differentially expressed proteins were mainly involved in the following signaling pathways: apoptosis, glycine/serine/threonine metabolic and GTPase signaling pathway. CONCLUSIONS These findings provided reference insights into the underlying molecular pathogenesis of diabetes-induced CNS neuropathy.
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7
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Chang Y, Rager JE, Tilton SC. Linking Coregulated Gene Modules with Polycyclic Aromatic Hydrocarbon-Related Cancer Risk in the 3D Human Bronchial Epithelium. Chem Res Toxicol 2021; 34:1445-1455. [PMID: 34048650 PMCID: PMC8560124 DOI: 10.1021/acs.chemrestox.0c00333] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Exposure to polycyclic aromatic hydrocarbons (PAHs) often occurs as complex chemical mixtures, which are linked to numerous adverse health outcomes in humans, with cancer as the greatest concern. The cancer risk associated with PAH exposures is commonly evaluated using the relative potency factor (RPF) approach, which estimates PAH mixture carcinogenic potential based on the sum of relative potency estimates of individual PAHs, compared to benzo[a]pyrene (BAP), a reference carcinogen. The present study evaluates molecular mechanisms related to PAH cancer risk through integration of transcriptomic and bioinformatic approaches in a 3D human bronchial epithelial cell model. Genes with significant differential expression from human bronchial epithelium exposed to PAHs were analyzed using a weighted gene coexpression network analysis (WGCNA) two-tiered approach: first to identify gene sets comodulated to RPF and second to link genes to a more comprehensive list of regulatory values, including inhalation-specific risk values. Over 3000 genes associated with processes of cell cycle regulation, inflammation, DNA damage, and cell adhesion processes were found to be comodulated with increasing RPF with pathways for cell cycle S phase and cytoskeleton actin identified as the most significantly enriched biological networks correlated to RPF. In addition, comodulated genes were linked to additional cancer-relevant risk values, including inhalation unit risks, oral cancer slope factors, and cancer hazard classifications from the World Health Organization's International Agency for Research on Cancer (IARC). These gene sets represent potential biomarkers that could be used to evaluate cancer risk associated with PAH mixtures. Among the values tested, RPF values and IARC categorizations shared the most similar responses in positively and negatively correlated gene modules. Together, we demonstrated a novel manner of integrating gene sets with chemical toxicity equivalence estimates through WGCNA to understand potential mechanisms.
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Affiliation(s)
- Yvonne Chang
- Environmental and Molecular Toxicology Department, Oregon State University, Corvallis, OR, United States
| | - Julia E. Rager
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina, Chapel Hill, NC, United States
- Institute for Environmental Health Solutions, and Curriculum in Toxicology, The University of North Carolina, Chapel Hill, NC, United States
| | - Susan C. Tilton
- Environmental and Molecular Toxicology Department, Oregon State University, Corvallis, OR, United States
- Superfund Research Program, Oregon State University, Corvallis, OR, United States
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Acclimation and adaptation to elevated pCO 2 increase arsenic resilience in marine diatoms. THE ISME JOURNAL 2021; 15:1599-1613. [PMID: 33452476 PMCID: PMC8163839 DOI: 10.1038/s41396-020-00873-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 11/28/2020] [Accepted: 12/07/2020] [Indexed: 01/29/2023]
Abstract
Arsenic pollution is a widespread threat to marine life, but the ongoing rise pCO2 levels is predicted to decrease bio-toxicity of arsenic. However, the effects of arsenic toxicity on marine primary producers under elevated pCO2 are not well characterized. Here, we studied the effects of arsenic toxicity in three globally distributed diatom species (Phaeodactylum tricornutum, Thalassiosira pseudonana, and Chaetoceros mulleri) after short-term acclimation (ST, 30 days), medium-term exposure (MT, 750 days), and long-term (LT, 1460 days) selection under ambient (400 µatm) and elevated (1000 and 2000 µatm) pCO2. We found that elevated pCO2 alleviated arsenic toxicity even after short acclimation times but the magnitude of the response decreased after mid and long-term adaptation. When fed with these elevated pCO2 selected diatoms, the scallop Patinopecten yessoensis had significantly lower arsenic content (3.26-52.83%). Transcriptomic and biochemical analysis indicated that the diatoms rapidly developed arsenic detoxification strategies, which included upregulation of transporters associated with shuttling harmful compounds out of the cell to reduce arsenic accumulation, and upregulation of proteins involved in synthesizing glutathione (GSH) to chelate intracellular arsenic to reduce arsenic toxicity. Thus, our results will expand our knowledge to fully understand the ecological risk of trace metal pollution under increasing human activity induced ocean acidification.
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Mellingen RM, Myrmel LS, Lie KK, Rasinger JD, Madsen L, Nøstbakken OJ. RNA sequencing and proteomic profiling reveal different alterations by dietary methylmercury in the hippocampal transcriptome and proteome in BALB/c mice. Metallomics 2021; 13:mfab022. [PMID: 33890672 PMCID: PMC8716076 DOI: 10.1093/mtomcs/mfab022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 01/02/2023]
Abstract
Methylmercury (MeHg) is a highly neurotoxic form of mercury (Hg) present in seafood. Here, we recorded and compared proteomic and transcriptomic changes in hippocampus of male BALB/c mice exposed to two doses of MeHg. Mice were fed diets spiked with 0.28 mg MeHg kg-1, 5 mg MeHg kg-1, or an unspiked control diet for 77 days. Total mercury content was significantly (P < 0.05) increased in brain tissue of both MeHg-exposed groups (18 ± 2 mg Hg kg-1 and 0.56 ± 0.06 mg Hg kg-1). Hippocampal protein and ribonucleic acid (RNA) expression levels were significantly altered both in tissues from mice receiving a low dose MeHg (20 proteins/294 RNA transcripts) and a high dose MeHg (61 proteins/876 RNA transcripts). The majority but not all the differentially expressed features in hippocampus were dose dependent. The combined use of transcriptomic and proteomic profiling data provided insight on the influence of MeHg on neurotoxicity, energy metabolism, and oxidative stress through several regulated features and pathways, including RXR function and superoxide radical degradation.
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Affiliation(s)
- Ragnhild Marie Mellingen
- Institute of Marine Research, Bergen, Norway
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | | | | | | | - Lise Madsen
- Institute of Marine Research, Bergen, Norway
- Department of Biology, University of Copenhagen, København, Denmark
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Ren Y, Sivaganesan S, Clark NA, Zhang L, Biesiada J, Niu W, Plas DR, Medvedovic M. Predicting mechanism of action of cellular perturbations with pathway activity signatures. Bioinformatics 2021; 36:4781-4788. [PMID: 32653926 DOI: 10.1093/bioinformatics/btaa590] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 06/15/2020] [Accepted: 07/03/2020] [Indexed: 12/16/2022] Open
Abstract
MOTIVATION Misregulation of signaling pathway activity is etiologic for many human diseases, and modulating activity of signaling pathways is often the preferred therapeutic strategy. Understanding the mechanism of action (MOA) of bioactive chemicals in terms of targeted signaling pathways is the essential first step in evaluating their therapeutic potential. Changes in signaling pathway activity are often not reflected in changes in expression of pathway genes which makes MOA inferences from transcriptional signatures (TSeses) a difficult problem. RESULTS We developed a new computational method for implicating pathway targets of bioactive chemicals and other cellular perturbations by integrated analysis of pathway network topology, the Library of Integrated Network-based Cellular Signature TSes of genetic perturbations of pathway genes and the TS of the perturbation. Our methodology accurately predicts signaling pathways targeted by the perturbation when current pathway analysis approaches utilizing only the TS of the perturbation fail. AVAILABILITY AND IMPLEMENTATION Open source R package paslincs is available at https://github.com/uc-bd2k/paslincs. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yan Ren
- Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45267-0056, USA
| | - Siva Sivaganesan
- Department of Mathematical Sciences, University of Cincinnati, Cincinnati, OH 45221-0025, USA
| | - Nicholas A Clark
- Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45267-0056, USA
| | - Lixia Zhang
- Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45267-0056, USA
| | - Jacek Biesiada
- Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45267-0056, USA
| | - Wen Niu
- Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45267-0056, USA
| | - David R Plas
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0521, USA
| | - Mario Medvedovic
- Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45267-0056, USA
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Franzosa JA, Bonzo JA, Jack J, Baker NC, Kothiya P, Witek RP, Hurban P, Siferd S, Hester S, Shah I, Ferguson SS, Houck KA, Wambaugh JF. High-throughput toxicogenomic screening of chemicals in the environment using metabolically competent hepatic cell cultures. NPJ Syst Biol Appl 2021; 7:7. [PMID: 33504769 PMCID: PMC7840683 DOI: 10.1038/s41540-020-00166-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 10/15/2020] [Indexed: 01/30/2023] Open
Abstract
The ToxCast in vitro screening program has provided concentration-response bioactivity data across more than a thousand assay endpoints for thousands of chemicals found in our environment and commerce. However, most ToxCast screening assays have evaluated individual biological targets in cancer cell lines lacking integrated physiological functionality (such as receptor signaling, metabolism). We evaluated differentiated HepaRGTM cells, a human liver-derived cell model understood to effectively model physiologically relevant hepatic signaling. Expression of 93 gene transcripts was measured by quantitative polymerase chain reaction using Fluidigm 96.96 dynamic arrays in response to 1060 chemicals tested in eight-point concentration-response. A Bayesian framework quantitatively modeled chemical-induced changes in gene expression via six transcription factors including: aryl hydrocarbon receptor, constitutive androstane receptor, pregnane X receptor, farnesoid X receptor, androgen receptor, and peroxisome proliferator-activated receptor alpha. For these chemicals the network model translates transcriptomic data into Bayesian inferences about molecular targets known to activate toxicological adverse outcome pathways. These data also provide new insights into the molecular signaling network of HepaRGTM cell cultures.
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Affiliation(s)
- Jill A Franzosa
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. EPA, Research Triangle Park, NC, 27711, USA
| | - Jessica A Bonzo
- Cell Biology, Biosciences Division, Thermo Fisher Scientific, Frederick, MD, 21703, USA
| | - John Jack
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. EPA, Research Triangle Park, NC, 27711, USA
| | | | - Parth Kothiya
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. EPA, Research Triangle Park, NC, 27711, USA
| | - Rafal P Witek
- Cell Biology, Biosciences Division, Thermo Fisher Scientific, Frederick, MD, 21703, USA
| | | | | | - Susan Hester
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. EPA, Research Triangle Park, NC, 27711, USA
| | - Imran Shah
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. EPA, Research Triangle Park, NC, 27711, USA
| | - Stephen S Ferguson
- Division of National Toxicology Program, National Institutes of Environmental Health Sciences of National Institutes of Health, Durham, NC, 27709, USA
| | - Keith A Houck
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. EPA, Research Triangle Park, NC, 27711, USA
| | - John F Wambaugh
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. EPA, Research Triangle Park, NC, 27711, USA.
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12
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Abdul NS, Chuturgoon AA. Fumonisin B 1 regulates LDL receptor and ABCA1 expression in an LXR dependent mechanism in liver (HepG2) cells. Toxicon 2020; 190:58-64. [PMID: 33338448 DOI: 10.1016/j.toxicon.2020.12.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/30/2020] [Accepted: 12/13/2020] [Indexed: 12/22/2022]
Abstract
The metabolic toxicity of Fumonisin B1 (FB1) converges at the accumulation of sphingoid bases and reduced ceramide levels. Several studies have alluded to a hypercholesterolemic endpoint after FB1 exposure, yet the molecular mechanisms remain elusive. Cell surface receptors are important regulators of cholesterol metabolism by regulating influx of lipids and efflux of cholesterol. Western blot analysis showed that FB1 elevates the expression of ABCA1 (a cholesterol efflux promoter) in an LXR dependent mechanism. We further highlight the potential role of PCSK9 in the degradation of LDL receptor. These data provide important evidence for the mechanism underlying hypercholesterolemia in FB1 treated models. The disruption of lipid homeostasis by FB1 is beginning to shift away from canonical ceramide synthase inhibition, and this changed perspective may shed light on diseases caused by dysregulated cholesterol metabolism such as cancer initiation and promotion.
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Affiliation(s)
- Naeem Sheik Abdul
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa; Applied Microbial and Health Biotechnology Institute, Cape Peninsula University of Technology, Cape Town, 7535, South Africa
| | - Anil A Chuturgoon
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa.
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13
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Kennedy RB, Ovsyannikova IG, Palese P, Poland GA. Current Challenges in Vaccinology. Front Immunol 2020; 11:1181. [PMID: 32670279 PMCID: PMC7329983 DOI: 10.3389/fimmu.2020.01181] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 05/13/2020] [Indexed: 12/12/2022] Open
Abstract
The development of vaccines, which prime the immune system to respond to future infections, has led to global declines in morbidity and mortality from dreadful infectious communicable diseases. However, many pathogens of public health importance are highly complex and/or rapidly evolving, posing unique challenges to vaccine development. Several of these challenges include an incomplete understanding of how immunity develops, host and pathogen genetic variability, and an increased societal skepticism regarding vaccine safety. In particular, new high-dimensional omics technologies, aided by bioinformatics, are driving new vaccine development (vaccinomics). Informed by recent insights into pathogen biology, host genetic diversity, and immunology, the increasing use of genomic approaches is leading to new models and understanding of host immune system responses that may provide solutions in the rapid development of novel vaccine candidates.
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Affiliation(s)
- Richard B Kennedy
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, MN, United States
| | - Inna G Ovsyannikova
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, MN, United States
| | - Peter Palese
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Gregory A Poland
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, MN, United States
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14
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Adeyemi JA, Sorgi CA, Machado ART, Ogunjimi AT, Gardinassi LGA, Nardini V, Faccioli LH, Antunes LMG, Barbosa F. Phospholipids modifications in human hepatoma cell lines (HepG2) exposed to silver and iron oxide nanoparticles. Arch Toxicol 2020; 94:2625-2636. [PMID: 32474618 DOI: 10.1007/s00204-020-02789-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 05/20/2020] [Indexed: 12/25/2022]
Abstract
Metallic nanoparticles such as silver (Ag NPs) and iron oxide (Fe3O4 NPs) nanoparticles are high production volume materials due to their applications in various consumer products, and in nanomedicine. However, their inherent toxicities to human cells remain a challenge. The present study was aimed at combining lipidomics data with common phenotypically-based toxicological assays to gain better understanding into cellular response to Ag NPs and Fe3O4 NPs exposure. HepG2 cells were exposed to different concentrations (3.125, 6.25, 12.5, 25, 50 and 100 µg/ml) of the nanoparticles for 24 h, after which they were assayed for toxic effects using toxicological assays like cytotoxicity, mutagenicity, apoptosis and oxidative stress. The cell membrane phospholipid profile of the cells was also performed using shotgun tandem mass spectrometry. The results showed that nanoparticles exposure resulted in concentration-dependent cytotoxicity as well as reduced cytokinesis-block proliferation index (CBPI). Also, there was an increase in the production of ROS and superoxide anions in exposed cells compared to the negative control. The lipidomics data revealed that nanoparticles exposure caused a modulation of the phospholipidome of the cells. A total of 155 lipid species were identified, out of which the fold changes of 23 were significant. The high number of differentially changed phosphatidylcholine species could be an indication that inflammation is one of the major mechanisms of toxicity of the nanoparticles to the cells.
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Affiliation(s)
- Joseph A Adeyemi
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida Do Café S/nº, Ribeirão Preto, São Paulo, 14040-903, Brazil. .,Department of Biology, School of Sciences, Federal University of Technology, P.M.B. 704, Akure, Ondo State, Nigeria.
| | - Carlos Arterio Sorgi
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida Do Café S/nº, Ribeirão Preto, São Paulo, 14040-903, Brazil
| | - Ana Rita Thomazela Machado
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida Do Café S/nº, Ribeirão Preto, São Paulo, 14040-903, Brazil
| | - Abayomi T Ogunjimi
- Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, University of Iowa, 115 S Grand Avenue, Iowa City, Iowa, USA
| | - Luiz Gustavo Araujo Gardinassi
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida Do Café S/nº, Ribeirão Preto, São Paulo, 14040-903, Brazil
| | - Viviani Nardini
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida Do Café S/nº, Ribeirão Preto, São Paulo, 14040-903, Brazil
| | | | - Lusania Maria Greggi Antunes
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida Do Café S/nº, Ribeirão Preto, São Paulo, 14040-903, Brazil
| | - Fernando Barbosa
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida Do Café S/nº, Ribeirão Preto, São Paulo, 14040-903, Brazil.
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15
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O’Donnell ST, Ross RP, Stanton C. The Progress of Multi-Omics Technologies: Determining Function in Lactic Acid Bacteria Using a Systems Level Approach. Front Microbiol 2020; 10:3084. [PMID: 32047482 PMCID: PMC6997344 DOI: 10.3389/fmicb.2019.03084] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 12/20/2019] [Indexed: 12/12/2022] Open
Abstract
Lactic Acid Bacteria (LAB) have long been recognized as having a significant impact ranging from commercial to health domains. A vast amount of research has been carried out on these microbes, deciphering many of the pathways and components responsible for these desirable effects. However, a large proportion of this functional information has been derived from a reductionist approach working with pure culture strains. This provides limited insight into understanding the impact of LAB within intricate systems such as the gut microbiome or multi strain starter cultures. Whole genome sequencing of strains and shotgun metagenomics of entire systems are powerful techniques that are currently widely used to decipher function in microbes, but they also have their limitations. An available genome or metagenome can provide an image of what a strain or microbiome, respectively, is potentially capable of and the functions that they may carry out. A top-down, multi-omics approach has the power to resolve the functional potential of an ecosystem into an image of what is being expressed, translated and produced. With this image, it is possible to see the real functions that members of a system are performing and allow more accurate and impactful predictions of the effects of these microorganisms. This review will discuss how technological advances have the potential to increase the yield of information from genomics, transcriptomics, proteomics and metabolomics. The potential for integrated omics to resolve the role of LAB in complex systems will also be assessed. Finally, the current software approaches for managing these omics data sets will be discussed.
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Affiliation(s)
- Shane Thomas O’Donnell
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- Department of Microbiology, University College Cork – National University of Ireland, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - R. Paul Ross
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- Department of Microbiology, University College Cork – National University of Ireland, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Catherine Stanton
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- APC Microbiome Ireland, Cork, Ireland
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16
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Li Y, Zhang X, Meng J, Chen J, You X, Shi Q, Wang WX. Molecular responses of an estuarine oyster to multiple metal contamination in Southern China revealed by RNA-seq. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 701:134648. [PMID: 31704403 DOI: 10.1016/j.scitotenv.2019.134648] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/05/2019] [Accepted: 09/23/2019] [Indexed: 06/10/2023]
Abstract
The estuarine oysters Crassostrea hongkongensis hyper-accumulate many metals and survive under high levels of metal exposure. In the present study, three natural populations of oysters with various levels of accumulated metals (mainly Cu and Zn) were collected from Southern China. The morphological characteristics and metal concentrations revealed their phenotypic differentiation. Further transcripts sequences acquired from their gill tissues were analyzed and 44,801 genes (with effective reads) were obtained via de novo assembly. The principal component analysis (PCA) revealed that the gene expression patterns also displayed differentiation among the three populations. A total of 3,199 differentially expressed genes (DEGs) was identified in the contaminated oysters as compared to the 'clean' oysters, which were used to explain the molecular mechanisms of metal accumulation and toxicity. GO and KEGG enrichment analysis revealed that energy production and cytoskeleton metabolism-related genes were particularly enriched in the contaminated sites during chronic metal exposure. Besides, increasing expressions of Zn/Cu transporters and metallothionein may explain their high accumulation in contaminated populations. We showed that oysters with less metal accumulation tended to cope with metal stress actively, but severe contamination destroyed part of the normal function. Our study analyzed the gene expression patterns of C. hongkongensis in Southern China and demonstrated the phenotypic differentiation of oysters under chronical metal exposure in the field.
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Affiliation(s)
- Yunlong Li
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology (HKUST), Clear Water Bay, Kowloon, Hong Kong, China
| | - Xinhui Zhang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Jie Meng
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, Shandong, China
| | - Jieming Chen
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Xinxin You
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Wen-Xiong Wang
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology (HKUST), Clear Water Bay, Kowloon, Hong Kong, China.
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17
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Banoei MM, Iupe I, Bazaz RD, Campos M, Vogel HJ, Winston BW, Mirsaeidi M. Metabolomic and metallomic profile differences between Veterans and Civilians with Pulmonary Sarcoidosis. Sci Rep 2019; 9:19584. [PMID: 31863066 PMCID: PMC6925242 DOI: 10.1038/s41598-019-56174-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 12/03/2019] [Indexed: 12/18/2022] Open
Abstract
Sarcoidosis is a disorder characterized by granulomatous inflammation of unclear etiology. In this study we evaluated whether veterans with sarcoidosis exhibited different plasma metabolomic and metallomic profiles compared with civilians with sarcoidosis. A case control study was performed on veteran and civilian patients with confirmed sarcoidosis. Proton nuclear magnetic resonance spectroscopy (1H NMR), hydrophilic interaction liquid chromatography mass spectrometry (HILIC-MS) and inductively coupled plasma mass spectrometry (ICP-MS) were applied to quantify metabolites and metal elements in plasma samples. Our results revealed that the veterans with sarcoidosis significantly differed from civilians, according to metabolic and metallomics profiles. Moreover, the results showed that veterans with sarcoidosis and veterans with COPD were similar to each other in metabolomics and metallomics profiles. This study suggests the important role of environmental risk factors in the development of different molecular phenotypic responses of sarcoidosis. In addition, this study suggests that sarcoidosis in veterans may be an occupational disease.
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Affiliation(s)
| | - Isabella Iupe
- Department of Medicine, University of Miami, Miami, FL, USA
| | - Reza Dowlatabadi Bazaz
- Department of Biological Science, Bio-NMR-metabolomics Research center, University of Calgary, Calgary, Canada
- Departments of Critical Care Medicine, Medicine and Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
| | - Michael Campos
- Section of Pulmonary, Miami VA Healthcare System, Miami, FL, USA
- Division of Pulmonary and Critical Care, University of Miami, Miami, FL, USA
| | - Hans J Vogel
- Department of Biological Science, Bio-NMR-metabolomics Research center, University of Calgary, Calgary, Canada
- Departments of Critical Care Medicine, Medicine and Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
| | - Brent W Winston
- Department of Biological Science, Bio-NMR-metabolomics Research center, University of Calgary, Calgary, Canada
- Departments of Critical Care Medicine, Medicine and Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
| | - Mehdi Mirsaeidi
- Section of Pulmonary, Miami VA Healthcare System, Miami, FL, USA.
- Division of Pulmonary and Critical Care, University of Miami, Miami, FL, USA.
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18
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Kuijpers TJM, Wolters JEJ, Kleinjans JCS, Jennen DGJ. DynOVis: a web tool to study dynamic perturbations for capturing dose-over-time effects in biological networks. BMC Bioinformatics 2019; 20:417. [PMID: 31409281 PMCID: PMC6693283 DOI: 10.1186/s12859-019-2995-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 07/16/2019] [Indexed: 01/11/2023] Open
Abstract
Background The development of high throughput sequencing techniques provides us with the possibilities to obtain large data sets, which capture the effect of dynamic perturbations on cellular processes. However, because of the dynamic nature of these processes, the analysis of the results is challenging. Therefore, there is a great need for bioinformatics tools that address this problem. Results Here we present DynOVis, a network visualization tool that can capture dynamic dose-over-time effects in biological networks. DynOVis is an integrated work frame of R packages and JavaScript libraries and offers a force-directed graph network style, involving multiple network analysis methods such as degree threshold, but more importantly, it allows for node expression animations as well as a frame-by-frame view of the dynamic exposure. Valuable biological information can be highlighted on the nodes in the network, by the integration of various databases within DynOVis. This information includes pathway-to-gene associations from ConsensusPathDB, disease-to-gene associations from the Comparative Toxicogenomics databases, as well as Entrez gene ID, gene symbol, gene synonyms and gene type from the NCBI database. Conclusions DynOVis could be a useful tool to analyse biological networks which have a dynamic nature. It can visualize the dynamic perturbations in biological networks and allows the user to investigate the changes over time. The integrated data from various online databases makes it easy to identify the biological relevance of nodes in the network. With DynOVis we offer a service that is easy to use and does not require any bioinformatics skills to visualize a network.
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Affiliation(s)
- T J M Kuijpers
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, P.O. Box 616, Maastricht, 6200 MD, The Netherlands.
| | - J E J Wolters
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, P.O. Box 616, Maastricht, 6200 MD, The Netherlands.,Present Address: School for Mental Health and Neuroscience (MHeNS), University Eye clinic Maastricht, Maastricht University Medical Centre + (MUMC+), P.O. Box 5800, Maastricht, 6229 HX, The Netherlands
| | - J C S Kleinjans
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, P.O. Box 616, Maastricht, 6200 MD, The Netherlands
| | - D G J Jennen
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, P.O. Box 616, Maastricht, 6200 MD, The Netherlands
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19
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Jelaković B, Dika Ž, Arlt VM, Stiborova M, Pavlović NM, Nikolić J, Colet JM, Vanherweghem JL, Nortier JL. Balkan Endemic Nephropathy and the Causative Role of Aristolochic Acid. Semin Nephrol 2019; 39:284-296. [DOI: 10.1016/j.semnephrol.2019.02.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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20
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McBride EM, Lawrence RJ, McGee K, Mach PM, Demond PS, Busch MW, Ramsay JW, Hussey EK, Glaros T, Dhummakupt ES. Rapid liquid chromatography tandem mass spectrometry method for targeted quantitation of human performance metabolites in saliva. J Chromatogr A 2019; 1601:205-213. [PMID: 31060786 DOI: 10.1016/j.chroma.2019.04.071] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 04/23/2019] [Accepted: 04/28/2019] [Indexed: 02/09/2023]
Abstract
Saliva is increasingly being targeted for metabolic studies due to its non-invasive collection methods. Tracing levels of certain metabolites within biofluids can provide indications for a myriad of physiological conditions. This study was performed on a panel of eight analytes found in saliva that have shown associations with physiological conditions of human performance, such as stress, inflammation, and circadian rhythm. This dual polarity liquid chromatography tandem mass spectrometric (LCMS/MS) method was developed to accommodate a diverse group of analytes including steroids, alkaloids, and neurotransmitters. Samples collected during field exercises from soldiers were compared to those of civilians and baseline levels of each of these compounds was determined in saliva. Although most analytes showed no significant differences between the two populations, relative cortisol levels were higher for soldiers than for civilians. This developed dual polarity LCMS/MS method can be applied to very diverse groups of salivary analytes simultaneously.
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Affiliation(s)
- Ethan M McBride
- Combat Capabilities Development Command (CCDC) Chemical Biological Center, Aberdeen Proving Ground, MD 21010, USA.
| | - Richard J Lawrence
- Combat Capabilities Development Command (CCDC) Chemical Biological Center, Aberdeen Proving Ground, MD 21010, USA.
| | - Kirstin McGee
- Combat Capabilities Development Command (CCDC) Chemical Biological Center, Aberdeen Proving Ground, MD 21010, USA.
| | - Phillip M Mach
- Combat Capabilities Development Command (CCDC) Chemical Biological Center, Aberdeen Proving Ground, MD 21010, USA.
| | - Paul S Demond
- Excet, Inc., 6225 Brandon Ave, Suite 360, Springfield, VA 22150, USA.
| | - Michael W Busch
- Excet, Inc., 6225 Brandon Ave, Suite 360, Springfield, VA 22150, USA.
| | - John W Ramsay
- Combat Capabilities Development Command (CCDC) Soldier Center, Natick, MA 01760, USA.
| | - Erika K Hussey
- Combat Capabilities Development Command (CCDC) Soldier Center, Natick, MA 01760, USA.
| | - Trevor Glaros
- Combat Capabilities Development Command (CCDC) Chemical Biological Center, Aberdeen Proving Ground, MD 21010, USA.
| | - Elizabeth S Dhummakupt
- Combat Capabilities Development Command (CCDC) Chemical Biological Center, Aberdeen Proving Ground, MD 21010, USA.
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21
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Prieto P, Baird AW, Blaauboer BJ, Castell Ripoll JV, Corvi R, Dekant W, Dietl P, Gennari A, Gribaldo L, Griffin JL, Hartung T, Heindel JJ, Hoet P, Jennings P, Marocchio L, Noraberg J, Pazos P, Westmoreland C, Wolf A, Wright J, Pfaller W. The Assessment of Repeated Dose ToxicityIn Vitro: A Proposed Approach. Altern Lab Anim 2019; 34:315-41. [PMID: 16831063 DOI: 10.1177/026119290603400307] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Pilar Prieto
- ECVAM, Institute for Health & Consumer Protection, European Joint Research Centre, 21020 Ispra (VA), Italy
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22
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Li Y, Zhang Y, Wang Y, Li Y, Yang F, Zhang P, Zhang Y, Liu C. A strategy for the discovery and validation of toxicity quality marker of Chinese medicine based on network toxicology. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2019; 54:365-370. [PMID: 30217547 DOI: 10.1016/j.phymed.2018.01.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 11/14/2017] [Accepted: 01/21/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Considering that the quality control indicators in Chinese medicine (CM) are disconnected from safety and effectiveness, Prof. Chang-xiao Liu et al. has proposed a concept regarding the quality marker (Q-marker) of CM to promote the healthy development of the CM industry and improve the CM quality control method. PURPOSE In this study, we proposed a strategy to discover and verify the toxicity Q-marker of CM based on network toxicology. METHODS First, traditional biochemical pathology indicators and sensitive biomarkers were used to predict the toxicity of CM. Next, the chemical composition of toxic CMs and their metabolites were rapidly identified by multidimensional detection techniques. Subsequently, the interaction network between "toxicity - toxic chemical composition - toxic target - effect pathway" was built through network toxicology, and the potential toxicity Q-marker of CM was initially screened. Finally, the chemical properties of toxicity Q-markers were verified by traceability and testability. RESULTS Based on the predicted results of network toxicology, the toxic compounds of CM were preliminarily identified, and the toxic mechanism was comprehensively interpreted. In the context of definite biological properties and chemical properties, the toxicity Q-marker was finally confirmed. CONCLUSION This extensive review provides a study method for the toxicity Q-marker of CM, which helps to systemically and thoroughly reveal the internal toxicity mechanism of CM. The in-depth study of the toxicity Q-marker provides the material basis and technical support for the safety evaluation of CM.
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Affiliation(s)
- Yubo Li
- Tianjin State Key Laboratory of Modern Chinese Medicine, School of Traditional Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, 312 Anshan west Road, Tianjin 300193, China
| | - Yani Zhang
- Tianjin State Key Laboratory of Modern Chinese Medicine, School of Traditional Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, 312 Anshan west Road, Tianjin 300193, China
| | - Yuming Wang
- Tianjin State Key Laboratory of Modern Chinese Medicine, School of Traditional Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, 312 Anshan west Road, Tianjin 300193, China
| | - Yamei Li
- Tianjin State Key Laboratory of Modern Chinese Medicine, School of Traditional Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, 312 Anshan west Road, Tianjin 300193, China
| | - Feifan Yang
- Tianjin State Key Laboratory of Modern Chinese Medicine, School of Traditional Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, 312 Anshan west Road, Tianjin 300193, China
| | - Pengjie Zhang
- Tianjin State Key Laboratory of Modern Chinese Medicine, School of Traditional Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, 312 Anshan west Road, Tianjin 300193, China
| | - Yanjun Zhang
- Tianjin State Key Laboratory of Modern Chinese Medicine, School of Traditional Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, 312 Anshan west Road, Tianjin 300193, China.
| | - Changxiao Liu
- The State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, 308 Anshan west Road, Tianjin 300193, China
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23
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GC-MS metabolomics reveals disturbed metabolic pathways in primary mouse hepatocytes exposed to subtoxic levels of 3,4-methylenedioxymethamphetamine (MDMA). Arch Toxicol 2018; 92:3307-3323. [PMID: 30255327 DOI: 10.1007/s00204-018-2314-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 09/19/2018] [Indexed: 12/23/2022]
Abstract
3,4-Methylenedioxymethamphetamine (MDMA, ecstasy) is a well-known hepatotoxic drug. Although its toxicity has been thoroughly studied at high concentrations, there is still insufficient knowledge on possible alterations of cell function at subtoxic concentrations, which are in fact more representative concentrations of intoxication scenarios. In this study, a gas chromatography-mass spectrometry (GC-MS) metabolomics approach was used to investigate the metabolic changes in primary mouse hepatocytes (PMH) exposed to two subtoxic concentrations of MDMA (LC01 and LC10) for 24 h. Metabolomic profiling of both intracellular metabolites and volatile metabolites in the extracellular medium of PMH was performed. Multivariate analysis showed that the metabolic pattern of cells exposed to MDMA discriminates from the controls in a concentration-dependent manner. Exposure to LC10 MDMA induces a significant increase in some intracellular metabolites, including oleic acid and palmitic acid, and a decrease in glutamate, aspartate, 5-oxoproline, fumarate, malate, phosphoric acid, α-ketoglutarate and citrate. Extracellular metabolites such as acetophenone, formaldehyde, pivalic acid, glyoxal and 2-butanone were found significantly increased after exposure to MDMA, compared to controls, whereas 4-methylheptane, 2,4-dimethyl-1-heptene, nonanal, among others, were found significantly decreased. The panel of discriminatory metabolites is mainly involved in tricarboxylic acid (TCA) cycle, fatty acid metabolism, glutamate metabolism, antioxidant defenses and possibly changes in the liver enzyme machinery. Overall, these results highlight the potential of the intra- and extracellular metabolome to study alterations triggered by subtoxic concentrations of MDMA in hepatic cell functions, which represents a more realistic appraisal of early toxicity events posed by exposure to this drug. In addition, these results also revealed some metabolites that may be used as potential biomarkers indicative of early events in the hepatotoxicity induced by MDMA.
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Alexander-Dann B, Pruteanu LL, Oerton E, Sharma N, Berindan-Neagoe I, Módos D, Bender A. Developments in toxicogenomics: understanding and predicting compound-induced toxicity from gene expression data. Mol Omics 2018; 14:218-236. [PMID: 29917034 PMCID: PMC6080592 DOI: 10.1039/c8mo00042e] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/08/2018] [Indexed: 12/12/2022]
Abstract
The toxicogenomics field aims to understand and predict toxicity by using 'omics' data in order to study systems-level responses to compound treatments. In recent years there has been a rapid increase in publicly available toxicological and 'omics' data, particularly gene expression data, and a corresponding development of methods for its analysis. In this review, we summarize recent progress relating to the analysis of RNA-Seq and microarray data, review relevant databases, and highlight recent applications of toxicogenomics data for understanding and predicting compound toxicity. These include the analysis of differentially expressed genes and their enrichment, signature matching, methods based on interaction networks, and the analysis of co-expression networks. In the future, these state-of-the-art methods will likely be combined with new technologies, such as whole human body models, to produce a comprehensive systems-level understanding of toxicity that reduces the necessity of in vivo toxicity assessment in animal models.
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Affiliation(s)
- Benjamin Alexander-Dann
- University of Cambridge
, Centre for Molecular Informatics
, Department of Chemistry
,
Lensfield Road
, Cambridge CB2 1EW
, UK
.
;
| | - Lavinia Lorena Pruteanu
- University of Cambridge
, Centre for Molecular Informatics
, Department of Chemistry
,
Lensfield Road
, Cambridge CB2 1EW
, UK
.
;
- Babeş-Bolyai University
, Institute for Doctoral Studies
,
1 Kogălniceanu Street
, Cluj-Napoca 400084
, Romania
- University of Medicine and Pharmacy “Iuliu Haţieganu”
, MedFuture Research Centre for Advanced Medicine
,
23 Marinescu Street/4-6 Pasteur Street
, Cluj-Napoca 400337
, Romania
| | - Erin Oerton
- University of Cambridge
, Centre for Molecular Informatics
, Department of Chemistry
,
Lensfield Road
, Cambridge CB2 1EW
, UK
.
;
| | - Nitin Sharma
- University of Cambridge
, Centre for Molecular Informatics
, Department of Chemistry
,
Lensfield Road
, Cambridge CB2 1EW
, UK
.
;
| | - Ioana Berindan-Neagoe
- University of Medicine and Pharmacy “Iuliu Haţieganu”
, MedFuture Research Centre for Advanced Medicine
,
23 Marinescu Street/4-6 Pasteur Street
, Cluj-Napoca 400337
, Romania
- University of Medicine and Pharmacy “Iuliu Haţieganu”
, Research Center for Functional Genomics
, Biomedicine and Translational Medicine
,
23 Marinescu Street
, Cluj-Napoca 400337
, Romania
- The Oncology Institute “Prof. Dr Ion Chiricuţă”
, Department of Functional Genomics and Experimental Pathology
,
34-36 Republicii Street
, Cluj-Napoca 400015
, Romania
| | - Dezső Módos
- University of Cambridge
, Centre for Molecular Informatics
, Department of Chemistry
,
Lensfield Road
, Cambridge CB2 1EW
, UK
.
;
| | - Andreas Bender
- University of Cambridge
, Centre for Molecular Informatics
, Department of Chemistry
,
Lensfield Road
, Cambridge CB2 1EW
, UK
.
;
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25
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Tian Y, Jiang F, Li Y, Jiang H, Chu Y, Zhu L, Guo W. Evaluation of the anti-hypertensive effect of Tengfu Jiangya tablet by combination of UPLC-Q-exactive-MS-based metabolomics and iTRAQ-based proteomics technology. Biomed Pharmacother 2018; 100:324-334. [DOI: 10.1016/j.biopha.2018.02.025] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 02/07/2018] [Accepted: 02/09/2018] [Indexed: 12/11/2022] Open
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26
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Gajski G, Gerić M, Oreščanin V, Garaj-Vrhovac V. Cytokinesis-block micronucleus cytome assay parameters in peripheral blood lymphocytes of the general population: Contribution of age, sex, seasonal variations and lifestyle factors. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 148:561-570. [PMID: 29127818 DOI: 10.1016/j.ecoenv.2017.11.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 09/26/2017] [Accepted: 11/01/2017] [Indexed: 06/07/2023]
Abstract
The cytokinesis-block micronucleus cytome (CBMN Cyt) assay was used to evaluate the baseline frequency of cytogenetic damage in peripheral blood lymphocytes of the general population (average age, 38.28 ± 12.83 years) in relation to age, sex, body mass index, seasonal variations (season of sampling, period of sampling and different meteorological parameters) and lifestyle factors (smoking habit, alcohol consumption, exposure to medications and diagnostic radiation, physical activity, and family history of cancer). The background frequency of micronuclei (MNi) for the 200 subjects assayed was 5.06 ± 3.11 per 1000 binucleated cells, while the mean frequency of nucleoplasmic bridges (NPBs) was 1.21 ± 1.46 and of nuclear buds (NBUDs) 3.48 ± 2.14. The background frequency of apoptosis and necrosis was 1.58 ± 1.50 and 1.39 ± 1.56, respectively, while the mean nuclear division index (NDI) was 1.99 ± 0.14. The cut-off value, which corresponds to the 95th percentile of the distribution of 200 individual values, was 11 MNi, 4 NPBs and 7 NBUDs. The study also confirmed an association of the above mentioned parameters with age, sex and several lifestyle factors. Moreover, significant confounders based on our results are also sampling season, sampling period and different meteorological parameters that were dependent on the CBMN Cyt assay parameters. In line with the above mentioned, several factors should be taken into account when it comes to the monitoring of exposed populations using cytogenetic biomarkers. Moreover, the normal and cut-off values obtained in this study present background data for the general population, and can later serve as baseline values for further biomonitoring studies.
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Affiliation(s)
- Goran Gajski
- Institute for Medical Research and Occupational Health, Mutagenesis Unit, 10000 Zagreb, Croatia.
| | - Marko Gerić
- Institute for Medical Research and Occupational Health, Mutagenesis Unit, 10000 Zagreb, Croatia.
| | | | - Vera Garaj-Vrhovac
- Institute for Medical Research and Occupational Health, Mutagenesis Unit, 10000 Zagreb, Croatia.
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Abstract
The genome revolution represents a complete change on our view of biological systems. The quantitative determination of changes in all major molecular components of the living cells, the "omics" approach, opened whole new fields for all health sciences. Genomics, transcriptomics, proteomics, metabolomics, and others, together with appropriate prediction and modeling tools, will mark the future of developmental toxicity assessment both for wildlife and humans. This is especially true for disciplines, like teratology, which rely on studies in model organisms, as studies at lower levels of organization are difficult to implement. Rodents and frogs have been the favorite models for studying human reproductive and developmental disorders for decades. Recently, the study of the development of zebrafish embryos (ZE) is becoming a major alternative tool to adult animal testing. ZE intrinsic characteristics makes this model a unique system to analyze in vivo developmental alterations that only can be studied applying in toto approaches. Moreover, under actual legislations, ZE is considered as a replacement model (and therefore, excluded from animal welfare regulations) during the first 5 days after fertilization. Here we review the most important components of the zebrafish toolbox available for analyzing early stages of embryotoxic events that could eventually lead to teratogenesis.
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28
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Piña B, Raldúa D, Barata C, Portugal J, Navarro-Martín L, Martínez R, Fuertes I, Casado M. Functional Data Analysis: Omics for Environmental Risk Assessment. COMPREHENSIVE ANALYTICAL CHEMISTRY 2018. [DOI: 10.1016/bs.coac.2018.07.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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29
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Abstract
Omics technologies have been developed in recent decades and applied to different subjects, although the greatest advancements have been achieved in human biology and disease. Genome sequencing and the exploration of its coding and noncoding regions are rapidly yielding meaningful answers to diverse questions, relating genome information to protein activity to environmental changes. In the past, marine mammal genetic and transcriptional studies have been restricted due to the lack of reference genomes. But the advance of high-throughput sequencing is revolutionizing the life sciences technologies. As long-lived organisms, at the top of the food chain, marine mammals play an important role in marine ecosystems and while their protected status is in favor of conservation of the species, it also complicates the researcher's approach to traditional measurements of health. Omics data generated by high-throughput technologies will represent an important key for improving the scientific basis for understanding both marine mammal and environment health.
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30
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Theoretical and mathematical foundation of the Virtual Cell Based Assay – A review. Toxicol In Vitro 2017; 45:209-221. [DOI: 10.1016/j.tiv.2016.07.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 07/20/2016] [Accepted: 07/21/2016] [Indexed: 11/16/2022]
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31
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Bafor EE, Rowan EG, Edrada-Ebel R. Metabolomics-Coupled Functional Pharmacology of Chlorophyll Compounds Isolated From the Leaves of Ficus Exasperata Vahl (Moraceae) Provides Novel Pathways on Myometrial Activity. Reprod Sci 2017; 25:923-937. [DOI: 10.1177/1933719117732159] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Enitome E. Bafor
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, Scotland, United Kingdom
- Department of Pharmacology and Toxicology, University of Benin, Benin City, Nigeria
| | - Edward G. Rowan
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, Scotland, United Kingdom
| | - RuAngelie Edrada-Ebel
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, Scotland, United Kingdom
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32
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Zheng PP, Li J, Kros JM. Breakthroughs in modern cancer therapy and elusive cardiotoxicity: Critical research-practice gaps, challenges, and insights. Med Res Rev 2017; 38:325-376. [PMID: 28862319 PMCID: PMC5763363 DOI: 10.1002/med.21463] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 07/14/2017] [Accepted: 07/15/2017] [Indexed: 12/16/2022]
Abstract
To date, five cancer treatment modalities have been defined. The three traditional modalities of cancer treatment are surgery, radiotherapy, and conventional chemotherapy, and the two modern modalities include molecularly targeted therapy (the fourth modality) and immunotherapy (the fifth modality). The cardiotoxicity associated with conventional chemotherapy and radiotherapy is well known. Similar adverse cardiac events are resurging with the fourth modality. Aside from the conventional and newer targeted agents, even the most newly developed, immune‐based therapeutic modalities of anticancer treatment (the fifth modality), e.g., immune checkpoint inhibitors and chimeric antigen receptor (CAR) T‐cell therapy, have unfortunately led to potentially lethal cardiotoxicity in patients. Cardiac complications represent unresolved and potentially life‐threatening conditions in cancer survivors, while effective clinical management remains quite challenging. As a consequence, morbidity and mortality related to cardiac complications now threaten to offset some favorable benefits of modern cancer treatments in cancer‐related survival, regardless of the oncologic prognosis. This review focuses on identifying critical research‐practice gaps, addressing real‐world challenges and pinpointing real‐time insights in general terms under the context of clinical cardiotoxicity induced by the fourth and fifth modalities of cancer treatment. The information ranges from basic science to clinical management in the field of cardio‐oncology and crosses the interface between oncology and onco‐pharmacology. The complexity of the ongoing clinical problem is addressed at different levels. A better understanding of these research‐practice gaps may advance research initiatives on the development of mechanism‐based diagnoses and treatments for the effective clinical management of cardiotoxicity.
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Affiliation(s)
- Ping-Pin Zheng
- Cardio-Oncology Research Group, Erasmus Medical Center, Rotterdam, the Netherlands.,Department of Pathology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Jin Li
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Johan M Kros
- Department of Pathology, Erasmus Medical Center, Rotterdam, the Netherlands
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33
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Selvaraj C, Sakkiah S, Tong W, Hong H. Molecular dynamics simulations and applications in computational toxicology and nanotoxicology. Food Chem Toxicol 2017; 112:495-506. [PMID: 28843597 DOI: 10.1016/j.fct.2017.08.028] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 08/08/2017] [Accepted: 08/22/2017] [Indexed: 12/13/2022]
Abstract
Nanotoxicology studies toxicity of nanomaterials and has been widely applied in biomedical researches to explore toxicity of various biological systems. Investigating biological systems through in vivo and in vitro methods is expensive and time taking. Therefore, computational toxicology, a multi-discipline field that utilizes computational power and algorithms to examine toxicology of biological systems, has gained attractions to scientists. Molecular dynamics (MD) simulations of biomolecules such as proteins and DNA are popular for understanding of interactions between biological systems and chemicals in computational toxicology. In this paper, we review MD simulation methods, protocol for running MD simulations and their applications in studies of toxicity and nanotechnology. We also briefly summarize some popular software tools for execution of MD simulations.
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Affiliation(s)
- Chandrabose Selvaraj
- Division of Bioinformatics and Biostatistics, National Center for Toxicology Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
| | - Sugunadevi Sakkiah
- Division of Bioinformatics and Biostatistics, National Center for Toxicology Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicology Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicology Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA.
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34
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Peng W, Datta P, Ayan B, Ozbolat V, Sosnoski D, Ozbolat IT. 3D bioprinting for drug discovery and development in pharmaceutics. Acta Biomater 2017; 57:26-46. [PMID: 28501712 DOI: 10.1016/j.actbio.2017.05.025] [Citation(s) in RCA: 158] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 05/05/2017] [Accepted: 05/09/2017] [Indexed: 02/08/2023]
Abstract
Successful launch of a commercial drug requires significant investment of time and financial resources wherein late-stage failures become a reason for catastrophic failures in drug discovery. This calls for infusing constant innovations in technologies, which can give reliable prediction of efficacy, and more importantly, toxicology of the compound early in the drug discovery process before clinical trials. Though computational advances have resulted in more rationale in silico designing, in vitro experimental studies still require gaining industry confidence and improving in vitro-in vivo correlations. In this quest, due to their ability to mimic the spatial and chemical attributes of native tissues, three-dimensional (3D) tissue models have now proven to provide better results for drug screening compared to traditional two-dimensional (2D) models. However, in vitro fabrication of living tissues has remained a bottleneck in realizing the full potential of 3D models. Recent advances in bioprinting provide a valuable tool to fabricate biomimetic constructs, which can be applied in different stages of drug discovery research. This paper presents the first comprehensive review of bioprinting techniques applied for fabrication of 3D tissue models for pharmaceutical studies. A comparative evaluation of different bioprinting modalities is performed to assess the performance and ability of fabricating 3D tissue models for pharmaceutical use as the critical selection of bioprinting modalities indeed plays a crucial role in efficacy and toxicology testing of drugs and accelerates the drug development cycle. In addition, limitations with current tissue models are discussed thoroughly and future prospects of the role of bioprinting in pharmaceutics are provided to the reader. STATEMENT OF SIGNIFICANCE Present advances in tissue biofabrication have crucial role to play in aiding the pharmaceutical development process achieve its objectives. Advent of three-dimensional (3D) models, in particular, is viewed with immense interest by the community due to their ability to mimic in vivo hierarchical tissue architecture and heterogeneous composition. Successful realization of 3D models will not only provide greater in vitro-in vivo correlation compared to the two-dimensional (2D) models, but also eventually replace pre-clinical animal testing, which has their own shortcomings. Amongst all fabrication techniques, bioprinting- comprising all the different modalities (extrusion-, droplet- and laser-based bioprinting), is emerging as the most viable fabrication technique to create the biomimetic tissue constructs. Notwithstanding the interest in bioprinting by the pharmaceutical development researchers, it can be seen that there is a limited availability of comparative literature which can guide the proper selection of bioprinting processes and associated considerations, such as the bioink selection for a particular pharmaceutical study. Thus, this work emphasizes these aspects of bioprinting and presents them in perspective of differential requirements of different pharmaceutical studies like in vitro predictive toxicology, high-throughput screening, drug delivery and tissue-specific efficacies. Moreover, since bioprinting techniques are mostly applied in regenerative medicine and tissue engineering, a comparative analysis of similarities and differences are also expounded to help researchers make informed decisions based on contemporary literature.
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35
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Wang X, Ma Y, Liu J, Yin X, Zhang Z, Wang C, Li Y, Wang H. Reproductive toxicity of β-diketone antibiotic mixtures to zebrafish (Danio rerio). ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2017; 141:160-170. [PMID: 28342328 DOI: 10.1016/j.ecoenv.2017.02.042] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 02/23/2017] [Accepted: 02/24/2017] [Indexed: 05/03/2023]
Abstract
So far, few data are available on the reproductive toxicological assessment of β-diketone antibiotics (DKAs), a class of ubiquitous pseudo-persistent pollutant, in zebrafish (Danio rerio). Herein, we reported the reproductive effects of DKAs by means of transcriptome analysis (F1-zebrafish), changes in a series of reproductive indices (F0-zebrafish) and histopathological observations. A total of 1170, 983 and 1399 genes were found to be differentially expressed when compared control vs. 6.25mg/L, control vs. 12.5mg/L and 6.25 vs. 12.5mg/L DKA-exposure treatments, respectively. Among three comparison groups, 670, 569 and 821 genes were respectively assigned for GO analyses based on matches with sequences of known functions. In 149 KEGG-noted metabolic pathways, the preferential one was the MAPK (mitogen-activated protein kinase) signaling pathway, followed by oxidative phosphorylation, neuroactive ligand-receptor interaction and so on. By qPCR verification, 6 genes (c6ast4, igfbp1b, mrpl42, tnnc2, emc4 and ddit4) showed consistent gene expression with those identified by transcriptome sequencing. Due to DKA-exposure, the concentrations of plasma estradiol and testosterone, and the gonado-somatic index were significantly dose-dependently declined. Also, DKA-exposure led to declining in zebrafish reproductive capacity, reflecting in fertilization, hatchability and egg production. Histopathological observations demonstrated that zebrafish ovary and testis suffered serious damage after DKA-exposure. The 4-oxo-TEMP signals increased obviously with increasing DKA-exposed concentrations, implying disruption of balance between generation and clearance of 1O2. In summary, DKAs not only produce reproductive toxicological effects on F0-zebrafish, but also result in adverse consequences for growth and development of F1-zebrafish.
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Affiliation(s)
- Xuedong Wang
- Key Lab of Watershed Sciences and Health of Zhejiang Province, Wenzhou Medical University, Wenzhou 325035, China
| | - Yan Ma
- College of Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Jinfeng Liu
- College of Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Xiaohan Yin
- Key Lab of Watershed Sciences and Health of Zhejiang Province, Wenzhou Medical University, Wenzhou 325035, China
| | - Zhiheng Zhang
- College of Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Caihong Wang
- College of Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Yanyan Li
- Key Lab of Watershed Sciences and Health of Zhejiang Province, Wenzhou Medical University, Wenzhou 325035, China
| | - Huili Wang
- College of Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.
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36
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Integrating 3-omics data analyze rat lung tissue of COPD states and medical intervention by delineation of molecular and pathway alterations. Biosci Rep 2017; 37:BSR20170042. [PMID: 28450497 PMCID: PMC5479022 DOI: 10.1042/bsr20170042] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 04/25/2017] [Accepted: 04/27/2017] [Indexed: 12/30/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a serious health problem. However, the molecular pathogenesis of COPD remains unknown. Here, we explored the molecular effects of cigarette smoke and bacterial infection in lung tissues of COPD rats. We also investigated therapeutic effects of aminophylline (APL) on the COPD rats and integrated transcriptome, proteome, and metabolome data for a global view of molecular mechanisms of COPD progression. Using molecular function and pathway analyses, the genes and proteins regulated in COPD and APL-treated rats were mainly attributed to oxidoreductase, antioxidant activity, energy and fatty acid metabolism. Furthermore, we identified hub proteins such as Gapdh (glyceraldehyde-3-phosphate dehydrogenase), Pkm (pyruvate kinase isozymes M1/M2), and Sod1 (superoxide dismutase 1), included in energy metabolism and oxidative stress. Then, we identified the significantly regulated metabolic pathways in lung tissues of COPD- and APL-treated rats, such as arachidonic acid, linoleic acid, and α-linolenic acid metabolism, which belong to the lipid metabolism. In particular, we picked the arachidonic acid metabolism for a more detailed pathway analysis of transcripts, proteins, and metabolites. We could observe an increase in metabolites and genes involved in arachidonic acid metabolism in COPD rats and the decrease in these in APL-treated rats, suggesting that inflammatory responses were up-regulated in COPD rats and down-regulated in APL-treated rats. In conclusion, these system-wide results suggested that COPD progression and its treatment might be associated with oxidative stress, lipid and energy metabolism disturbance. Additionally, we demonstrated the power of integrated omics for the elucidation of genes, proteins, and metabolites’ changes and disorders that were associated with COPD.
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37
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Zhang H, Wang J, Li L, Chai N, Chen Y, Wu F, Zhang W, Wang L, Shi S, Zhang L, Bian S, Xu C, Tian Y, Zhao Y. Spermine and spermidine reversed age-related cardiac deterioration in rats. Oncotarget 2017; 8:64793-64808. [PMID: 29029392 PMCID: PMC5630292 DOI: 10.18632/oncotarget.18334] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 05/21/2017] [Indexed: 01/08/2023] Open
Abstract
Aging is the most important risk factor for cardiovascular disease (CVD). Slowing or reversing the physiological impact of heart aging may reduce morbidity and mortality associated with age-related CVD. The polyamines, spermine (SP) and spermidine (SPD) are essential for cell growth, differentiation and apoptosis, and levels of both decline with age. To explore the effects of these polyamines on heart aging, we administered SP or SPD intraperitoneally to 22- to 24-month-old rats for 6 weeks. Both treatments reversed and inhibited age-related myocardial morphology alterations, myocardial fibrosis, and cell apoptosis. Using combined proteomics and metabolomics analyses, we identified proteins and metabolites up- or downregulated by SP and SPD in aging rat hearts. SP upregulated 51 proteins and 28 metabolites while downregulating 80 proteins and 29 metabolites. SPD upregulated 44 proteins and 24 metabolites and downregulated 84 proteins and 176 metabolites. These molecules were mainly associated with immune responses, blood coagulation, lipid metabolism, and glutathione metabolism pathways. Our study provides novel molecular information on the cardioprotective effects of polyamines in the aging heart, and supports the notion that SP and SPD are potential clinical therapeutics targeting heart disease.
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Affiliation(s)
- Hao Zhang
- Department of Pathophysiology, The Key Laboratory of Cardiovascular Pathophysiology, Harbin Medical University, Harbin, China
| | - Junying Wang
- Department of Pathophysiology, The Key Laboratory of Cardiovascular Pathophysiology, Harbin Medical University, Harbin, China
| | - Lingxu Li
- Department of Pathophysiology, The Key Laboratory of Cardiovascular Pathophysiology, Harbin Medical University, Harbin, China
| | - Nannan Chai
- Department of Pathophysiology, The Key Laboratory of Cardiovascular Pathophysiology, Harbin Medical University, Harbin, China.,College of Nursing, Medical School of Chifeng University, Chifeng, China
| | - Yuhan Chen
- Department of Pathophysiology, The Key Laboratory of Cardiovascular Pathophysiology, Harbin Medical University, Harbin, China
| | - Feixiang Wu
- Department of Pathophysiology, The Key Laboratory of Cardiovascular Pathophysiology, Harbin Medical University, Harbin, China
| | - Weihua Zhang
- Department of Pathophysiology, The Key Laboratory of Cardiovascular Pathophysiology, Harbin Medical University, Harbin, China.,Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Ministry of Education, Harbin, China
| | - Lina Wang
- Department of Pathophysiology, The Key Laboratory of Cardiovascular Pathophysiology, Harbin Medical University, Harbin, China
| | - Sa Shi
- Department of Pathophysiology, The Key Laboratory of Cardiovascular Pathophysiology, Harbin Medical University, Harbin, China
| | - Li Zhang
- Department of Pathophysiology, The Key Laboratory of Cardiovascular Pathophysiology, Harbin Medical University, Harbin, China
| | - Shuling Bian
- Experiment Center of Function, Harbin Medical University, Harbin, China
| | - Changqing Xu
- Department of Pathophysiology, The Key Laboratory of Cardiovascular Pathophysiology, Harbin Medical University, Harbin, China.,Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Ministry of Education, Harbin, China
| | - Ye Tian
- Department of Pathophysiology, The Key Laboratory of Cardiovascular Pathophysiology, Harbin Medical University, Harbin, China.,Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Ministry of Education, Harbin, China
| | - Yajun Zhao
- Department of Pathophysiology, The Key Laboratory of Cardiovascular Pathophysiology, Harbin Medical University, Harbin, China.,Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Ministry of Education, Harbin, China
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Integrating Transcriptomics, Proteomics, and Metabolomics Profiling with System Pharmacology for the Delineation of Long-Term Therapeutic Mechanisms of Bufei Jianpi Formula in Treating COPD. BIOMED RESEARCH INTERNATIONAL 2017; 2017:7091087. [PMID: 28424787 PMCID: PMC5382313 DOI: 10.1155/2017/7091087] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 01/22/2017] [Indexed: 12/19/2022]
Abstract
In previous work, we identified 145 active compounds from Bufei Jianpi formula (BJF) by system pharmacology and found that BJF showed short-term effect on chronic obstructive pulmonary disease (COPD) rats. Here, we applied the transcriptomic, proteomic, and metabolomics approaches to illustrate the long-term anti-COPD action and its system mechanism of BJF. BJF has obvious anti-COPD effect through decreasing inflammatory cytokines level, preventing protease-antiprotease imbalance and collagen deposition on week 32 by continuous oral administration to rats from weeks 9 to 20. Subsequently, applying the transcriptomic, proteomic, and metabolomics techniques, we detected a number of regulated genes, proteins, and metabolites, mainly related to antioxidant activity, focal adhesion, or lipid metabolism, in lung tissues of COPD and BJF-treated rats. Afterwards, we integrated system pharmacology target, transcript, protein, and metabolite data sets and found that many genes, proteins, and metabolites in rats BJF-treated group and the target proteins of BJF were mainly attributed to lipid metabolism, inflammatory response, oxidative stress, and focal adhesion. Taken together, BJF displays long-term anti-COPD effect probably by system regulation of the lipid metabolism, inflammatory response pathways oxidative stress, and focal adhesion.
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Wang H, Yin X, Li F, Dahlgren RA, Zhang Y, Zhang H, Wang X. Chronic toxicological effects of β-diketone antibiotics on Zebrafish (Danio rerio) using transcriptome profiling of deep sequencing. ENVIRONMENTAL TOXICOLOGY 2016; 31:1357-1371. [PMID: 25846866 DOI: 10.1002/tox.22141] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Revised: 03/10/2015] [Accepted: 03/18/2015] [Indexed: 06/04/2023]
Abstract
Transcriptome analysis is important for interpreting the functional elements of the genome and revealing the molecular constituents of cells and tissues. Herein, differentially transcribed genes were identified by deep sequencing after zebrafish (Danio rerio) were exposed to β-diketone antibiotics (DKAs); 23,129 and 23,550 mapped genes were detected in control and treatment groups, a total of 3238 genes were differentially expressed between control and treatment groups. Of these genes, 328 genes (213 up- and 115 down-regulation) had significant differential expression (p < 0.05) and an expression ratio (control/treatment) of >2 or <0.5. Additionally, we performed Gene Ontology (GO) category and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses, and found 266 genes in the treatment group with annotation terms linked to the GO category. A total of 77 differentially expressed transcriptional genes were associated with 132 predicted KEGG metabolic pathways. Serious liver tissue damage was reflected and consistent with the differences in genetic classification and function from the transcriptome analysis. These results enhance our understanding of zebrafish developmental processes under exposure to DKA stress. © 2015 Wiley Periodicals, Inc. Environ Toxicol 31: 1357-1371, 2016.
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Affiliation(s)
- Huili Wang
- Department of biochemistry and molecular biology, College of Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Xiaohan Yin
- Department of Environmental Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Fanghui Li
- Department of Environmental Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Randy A Dahlgren
- Department of Land, Air and Water Resources, University of California, Davis, California, 95616
| | - Yuna Zhang
- Department of Environmental Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Hongqin Zhang
- Department of biochemistry and molecular biology, College of Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Xuedong Wang
- Department of Environmental Sciences, Wenzhou Medical University, Wenzhou, 325035, China.
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Bafor EE, Rowan EG, Edrada-Ebel R. Toward Understanding Myometrial Regulation: Metabolomic Investigation Reveals New Pathways of Oxytocin and Ritodrine Activity on the Myometrium. Reprod Sci 2016; 24:691-705. [DOI: 10.1177/1933719116667224] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Enitome E. Bafor
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, Scotland, United Kingdom
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, University of Benin, Benin, Edo State, Nigeria
| | - Edward G. Rowan
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, Scotland, United Kingdom
| | - RuAngelie Edrada-Ebel
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, Scotland, United Kingdom
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41
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The metabolomic signature of hematologic malignancies. Leuk Res 2016; 49:22-35. [PMID: 27526405 DOI: 10.1016/j.leukres.2016.08.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Revised: 08/04/2016] [Accepted: 08/08/2016] [Indexed: 12/17/2022]
Abstract
The ongoing accumulation of knowledge raises hopes that understanding tumor metabolism will provide new ways for predicting, diagnosing, and even treating cancers. Some metabolic biomarkers are at present routinely utilized to diagnose cancer and metabolic alterations of tumors are being confirmed as therapeutic targets. The growing utilization of metabolomics in clinical research may rapidly turn it into one of the most potent instruments used to detect and fight tumor. In fact, while the current state and trends of high throughput metabolomics profiling focus on the purpose of discovering biomarkers and hunting for metabolic mechanism, a prospective direction, namely reprogramming metabolomics, highlights the way to use metabolomics approach for the aim of treatment of disease by way of reconstruction of disturbed metabolic pathways. In this review, we present an ample summary of the current clinical appliances of metabolomics in hematological malignancies.
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Saturno G, Pesenti M, Cavazzoli C, Rossi A, Giusti AM, Gierke B, Pawlak M, Venturi M. Expression of Serine/Threonine Protein-Kinases and Related Factors in Normal Monkey and Human Retinas: The Mechanistic Understanding of a CDK2 Inhibitor Induced Retinal Toxicity. Toxicol Pathol 2016; 35:972-83. [DOI: 10.1080/01926230701748271] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Protein-kinase inhibitors are among the most advanced compounds in development using the new drug discovery paradigm of developing small-molecule drugs against specific molecular targets in cancer. After treatment with a cyclin dependent kinase CDK2 inhibitor in monkey, histopathological analysis of the eye showed specific cellular damage in the photoreceptor layer. Since this CDK2 inhibitor showed activity also on other CDKs, in order to investigate the mechanism of toxicity of this compound, we isolated cones and rods from the retina of normal monkey and humans by Laser Capture Microdissection. Using Real-Time PCR we first measured the expression of cyclin dependent protein-kinases (CDK)1, 2, 4, 5, Glycogen synthase kinase 3β (GSK3β) and microtubule associated protein TAU. We additionally verified the presence of these proteins in monkey eye sections by immunohistochemistry and immunofluorescence analysis and afterwards quantified GSK3β , phospho-GSK3β and TAU by Reverse Phase Protein Microarrays. With this work we demonstrate how complementary gene expression and protein-based technologies constitute a powerful tool for the understanding of the molecular mechanism of a CDK2 inhibitor induced toxicity. Moreover, this investigative approach is helpful to better understand and characterize the mechanism of species-specific toxicities and further support a rational, molecular mechanism-based safety assessment in humans.
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Affiliation(s)
- Grazia Saturno
- Nerviano Medical Sciences (NMS), Accelera, v.le Pasteur 10, 20014 Nerviano MI, Italy
| | - Manuela Pesenti
- Nerviano Medical Sciences (NMS), Accelera, v.le Pasteur 10, 20014 Nerviano MI, Italy
| | - Cristiano Cavazzoli
- Nerviano Medical Sciences (NMS), Accelera, v.le Pasteur 10, 20014 Nerviano MI, Italy
| | - Anna Rossi
- Nerviano Medical Sciences (NMS), Accelera, v.le Pasteur 10, 20014 Nerviano MI, Italy
| | - Anna M. Giusti
- Nerviano Medical Sciences (NMS), Accelera, v.le Pasteur 10, 20014 Nerviano MI, Italy
| | - Berthold Gierke
- Natural and Medical Sciences Institute (NMI), at the University of Tuebingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany
| | - Michael Pawlak
- Natural and Medical Sciences Institute (NMI), at the University of Tuebingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany
| | - Miro Venturi
- Nerviano Medical Sciences (NMS), Accelera, v.le Pasteur 10, 20014 Nerviano MI, Italy
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Bouhifd M, Beger R, Flynn T, Guo L, Harris G, Hogberg H, Kaddurah-Daouk R, Kamp H, Kleensang A, Maertens A, Odwin-DaCosta S, Pamies D, Robertson D, Smirnova L, Sun J, Zhao L, Hartung T. Quality assurance of metabolomics. ALTEX-ALTERNATIVES TO ANIMAL EXPERIMENTATION 2016; 32:319-26. [PMID: 26536290 PMCID: PMC5578451 DOI: 10.14573/altex.1509161] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Indexed: 12/15/2022]
Abstract
Metabolomics promises a holistic phenotypic characterization of biological responses to toxicants. This technology is based on advanced chemical analytical tools with reasonable throughput, including mass-spectroscopy and NMR. Quality assurance, however – from experimental design, sample preparation, metabolite identification, to bioinformatics data-mining – is urgently needed to assure both quality of metabolomics data and reproducibility of biological models. In contrast to microarray-based transcriptomics, where consensus on quality assurance and reporting standards has been fostered over the last two decades, quality assurance of metabolomics is only now emerging. Regulatory use in safety sciences, and even proper scientific use of these technologies, demand quality assurance. In an effort to promote this discussion, an expert workshop discussed the quality assurance needs of metabolomics. The goals for this workshop were 1) to consider the challenges associated with metabolomics as an emerging science, with an emphasis on its application in toxicology and 2) to identify the key issues to be addressed in order to establish and implement quality assurance procedures in metabolomics-based toxicology. Consensus has still to be achieved regarding best practices to make sure sound, useful, and relevant information is derived from these new tools.
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Affiliation(s)
- Mounir Bouhifd
- Johns Hopkins University, Bloomberg School of Public Health, Center for Alternatives to Animal Testing, Baltimore, MD, USA
| | - Richard Beger
- US Food and Drug Administration, National Center for Toxicological Research, Division of Systems Biology, Jefferson, AR, USA
| | - Thomas Flynn
- US Food and Drug Administration, Center for Food Safety and Applied Nutrition, Laurel, MD, USA
| | | | - Georgina Harris
- Johns Hopkins University, Bloomberg School of Public Health, Center for Alternatives to Animal Testing, Baltimore, MD, USA
| | - Helena Hogberg
- Johns Hopkins University, Bloomberg School of Public Health, Center for Alternatives to Animal Testing, Baltimore, MD, USA
| | - Rima Kaddurah-Daouk
- Department of Psychiatry and Behavioral Sciences, Duke Institute for Brain Sciences, Duke University, Durham, NC, USA
| | - Hennicke Kamp
- Experimental Toxicology and Ecology, BASF SE, Ludwigshafen am Rhein, Germany
| | - Andre Kleensang
- Johns Hopkins University, Bloomberg School of Public Health, Center for Alternatives to Animal Testing, Baltimore, MD, USA
| | - Alexandra Maertens
- Johns Hopkins University, Bloomberg School of Public Health, Center for Alternatives to Animal Testing, Baltimore, MD, USA
| | - Shelly Odwin-DaCosta
- Johns Hopkins University, Bloomberg School of Public Health, Center for Alternatives to Animal Testing, Baltimore, MD, USA
| | - David Pamies
- Johns Hopkins University, Bloomberg School of Public Health, Center for Alternatives to Animal Testing, Baltimore, MD, USA
| | | | - Lena Smirnova
- Johns Hopkins University, Bloomberg School of Public Health, Center for Alternatives to Animal Testing, Baltimore, MD, USA
| | - Jinchun Sun
- US Food and Drug Administration, National Center for Toxicological Research, Division of Systems Biology, Jefferson, AR, USA
| | - Liang Zhao
- Johns Hopkins University, Bloomberg School of Public Health, Center for Alternatives to Animal Testing, Baltimore, MD, USA
| | - Thomas Hartung
- Johns Hopkins University, Bloomberg School of Public Health, Center for Alternatives to Animal Testing, Baltimore, MD, USA.,CAAT-Europe, University of Konstanz, Germany
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Abstract
Until recently, the study of mycobacterial diseases was trapped in culture-based technology that is more than a century old. The use of nucleic acid amplification is changing this, and powerful new technologies are on the horizon. Metabolomics, which is the study of sets of metabolites of both the bacteria and host, is being used to clarify mechanisms of disease, and can identify changes leading to better diagnosis, treatment, and prognostication of mycobacterial diseases. Metabolomic profiles are arrays of biochemical products of genes in their environment. These complex patterns are biomarkers that can allow a more complete understanding of cell function, dysfunction, and perturbation than genomics or proteomics. Metabolomics could herald sweeping advances in personalized medicine and clinical trial design, but the challenges in metabolomics are also great. Measured metabolite concentrations vary with the timing within a condition, the intrinsic biology, the instruments, and the sample preparation. Metabolism profoundly changes with age, sex, variations in gut microbial flora, and lifestyle. Validation of biomarkers is complicated by measurement accuracy, selectivity, linearity, reproducibility, robustness, and limits of detection. The statistical challenges include analysis, interpretation, and description of the vast amount of data generated. Despite these drawbacks, metabolomics provides great opportunity and the potential to understand and manage mycobacterial diseases.
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45
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Zhang Y, Wang X, Yin X, Shi M, Dahlgren RA, Wang H. Toxicity assessment of combined fluoroquinolone and tetracycline exposure in zebrafish (Danio rerio). ENVIRONMENTAL TOXICOLOGY 2016; 31:736-50. [PMID: 25504783 DOI: 10.1002/tox.22087] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 11/20/2014] [Accepted: 11/21/2014] [Indexed: 05/06/2023]
Abstract
Fluoroquinolones (FQs) and tetracyclines (TCs), the two β-diketone antibiotics (DKAs), are two frequently detected pollutants in the environment; however, little data are available on their combined toxicity to zebrafish (Danio rerio). This study reports that toxicologic effects of combined DKA (FQs-TCs) exposure on zebrafish were comparable with or slightly less than those of TCs alone, showing that TCs played a major toxicologic role in the mixtures. The effects of FQs, TCs, and DKAs on malformation rates of zebrafish were dose dependent, with EC50 values of 481.3, 16.4, and 135.1 mg/L, respectively. According to the combined effects of DKAs on zebrafish hatching, mortality, and malformation rates, the interaction between FQs and TCs was shown to be antagonistic based on three assessment methods: Toxic Unit, Additional Index, and Mixture Toxic Index. The 1.56 mg/L TC and 9.38 mg/L DKA treatments resulted in higher zebrafish basal swimming rate compared with the control group at 120 hours postfertilization (hpf). in both light and light-to-dark photoperiod experiments. Under conditions of no obvious abnormality in cardiac development, the heart beats were decreased significantly because of DKA exposure, such as decreasing by ∼20% at 150 mg/L DKAs. Transmission electron microscopy observation of myocytes from DKA-exposed hearts displayed prominent interruptions and myofibrillar disorganization of the normal parallel alignment of thick and thin filaments, and partial edematous and dissolved membranes of cell nuclear tissues. At 90 mg/L DKAs, the transcriptional levels of the acta1a, myl7, and gle1b genes, related to heart development and skeletal muscle formation, were significantly changed. This is consistent with the swimming behavior and histopathologic results obtained by transmission electron microscopy. In summary, the toxicity of the combined DKAs to zebrafish was comparable with or less than that of TCs alone and had the ability to impair individual behaviors that are of great importance in the assessment of their ecologic fitness. © 2014 Wiley Periodicals, Inc. Environ Toxicol 31: 736-750, 2016.
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Affiliation(s)
- Yuna Zhang
- Wenzhou Applied Technology & Environmental Research Institute, Wenzhou Medical University, University-Town, Wenzhou, Zhejiang, 325035, China
| | - Xuedong Wang
- Wenzhou Applied Technology & Environmental Research Institute, Wenzhou Medical University, University-Town, Wenzhou, Zhejiang, 325035, China
| | - Xiaohan Yin
- Wenzhou Applied Technology & Environmental Research Institute, Wenzhou Medical University, University-Town, Wenzhou, Zhejiang, 325035, China
| | - Mengru Shi
- School of Life Sciences, Wenzhou Medical University, University-Town, Wenzhou, Zhejiang, 325035, China
| | - Randy Alan Dahlgren
- Department of Land, Air and Water Resources, University of California, Davis, California, 95616, USA
| | - Huili Wang
- School of Life Sciences, Wenzhou Medical University, University-Town, Wenzhou, Zhejiang, 325035, China
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46
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Model-based contextualization of in vitro toxicity data quantitatively predicts in vivo drug response in patients. Arch Toxicol 2016; 91:865-883. [PMID: 27161439 PMCID: PMC5306109 DOI: 10.1007/s00204-016-1723-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/20/2016] [Indexed: 12/13/2022]
Abstract
Understanding central mechanisms underlying drug-induced toxicity plays a crucial role in drug development and drug safety. However, a translation of cellular in vitro findings to an actual in vivo context remains challenging. Here, physiologically based pharmacokinetic (PBPK) modeling was used for in vivo contextualization of in vitro toxicity data (PICD) to quantitatively predict in vivo drug response over time by integrating multiple levels of biological organization. Explicitly, in vitro toxicity data at the cellular level were integrated into whole-body PBPK models at the organism level by coupling in vitro drug exposure with in vivo drug concentration–time profiles simulated in the extracellular environment within the organ. PICD was exemplarily applied on the hepatotoxicant azathioprine to quantitatively predict in vivo drug response of perturbed biological pathways and cellular processes in rats and humans. The predictive accuracy of PICD was assessed by comparing in vivo drug response predicted for rats with observed in vivo measurements. To demonstrate clinical applicability of PICD, in vivo drug responses of a critical toxicity-related pathway were predicted for eight patients following acute azathioprine overdoses. Moreover, acute liver failure after multiple dosing of azathioprine was investigated in a patient case study by use of own clinical data. Simulated pharmacokinetic profiles were therefore related to in vivo drug response predicted for genes associated with observed clinical symptoms and to clinical biomarkers measured in vivo. PICD provides a generic platform to investigate drug-induced toxicity at a patient level and thus may facilitate individualized risk assessment during drug development.
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Li J, Zhao P, Yang L, Li Y, Tian Y, Li S. System biology analysis of long-term effect and mechanism of Bufei Yishen on COPD revealed by system pharmacology and 3-omics profiling. Sci Rep 2016; 6:25492. [PMID: 27146975 PMCID: PMC4857103 DOI: 10.1038/srep25492] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 04/18/2016] [Indexed: 01/22/2023] Open
Abstract
System pharmacology identified 195 potential targets of Bufei Yishen formula (BYF), and BYF was proven to have a short-term therapeutic effect on chronic obstructive pulmonary disease (COPD) rats previously. However, the long-term effect and mechanism of BYF on COPD is still unclear. Herein, we explored its long-term effect and underlying mechanism at system level. We administered BYF to COPD rats from week 9 to 20, and found that BYF could prevent COPD by inhibiting the inflammatory cytokines expression, protease-antiprotease imbalance and collagen deposition on week 32. Then, using transcriptomics, proteomics and metabolomics analysis, we identified significant regulated genes, proteins and metabolites in lung tissues of COPD and BYF-treated rats, which could be mainly attributed to oxidoreductase-antioxidant activity, focal adhesion, tight junction or lipid metabolism. Finally, based on the comprehensive analysis of system pharmacology target, transcript, protein and metabolite data sets, we found a number of genes, proteins, metabolites regulated in BYF-treated rats and the target proteins of BYF were involved in lipid metabolism, inflammatory response, oxidative stress and focal adhension. In conclusion, BYF exerts long-term therapeutic action on COPD probably through modulating the lipid metabolism, oxidative stress, cell junction and inflammatory response pathways at system level.
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Affiliation(s)
- Jiansheng Li
- Henan University of Traditional Chinese Medicine, Zhengzhou 450046, China.,Collaborative Innovation Center for Respiratory Disease Diagnosis and Treatment &Chinese Medicine Development of Henan Province, Zhengzhou 450046, China
| | - Peng Zhao
- Henan University of Traditional Chinese Medicine, Zhengzhou 450046, China.,Collaborative Innovation Center for Respiratory Disease Diagnosis and Treatment &Chinese Medicine Development of Henan Province, Zhengzhou 450046, China
| | - Liping Yang
- Henan University of Traditional Chinese Medicine, Zhengzhou 450046, China.,Collaborative Innovation Center for Respiratory Disease Diagnosis and Treatment &Chinese Medicine Development of Henan Province, Zhengzhou 450046, China
| | - Ya Li
- Henan University of Traditional Chinese Medicine, Zhengzhou 450046, China.,Collaborative Innovation Center for Respiratory Disease Diagnosis and Treatment &Chinese Medicine Development of Henan Province, Zhengzhou 450046, China
| | - Yange Tian
- Henan University of Traditional Chinese Medicine, Zhengzhou 450046, China.,Collaborative Innovation Center for Respiratory Disease Diagnosis and Treatment &Chinese Medicine Development of Henan Province, Zhengzhou 450046, China
| | - Suyun Li
- Collaborative Innovation Center for Respiratory Disease Diagnosis and Treatment &Chinese Medicine Development of Henan Province, Zhengzhou 450046, China.,Department of Respiratory Diseases, the First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou 450000, China
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48
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Chan WK, Tan LTH, Chan KG, Lee LH, Goh BH. Nerolidol: A Sesquiterpene Alcohol with Multi-Faceted Pharmacological and Biological Activities. Molecules 2016; 21:molecules21050529. [PMID: 27136520 PMCID: PMC6272852 DOI: 10.3390/molecules21050529] [Citation(s) in RCA: 184] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 04/14/2016] [Accepted: 04/14/2016] [Indexed: 11/16/2022] Open
Abstract
Nerolidol (3,7,11-trimethyl-1,6,10-dodecatrien-3-ol) is a naturally occurring sesquiterpene alcohol that is present in various plants with a floral odor. It is synthesized as an intermediate in the production of (3E)-4,8-dimethy-1,3,7-nonatriene (DMNT), a herbivore-induced volatile that protects plants from herbivore damage. Chemically, nerolidol exists in two geometric isomers, a trans and a cis form. The usage of nerolidol is widespread across different industries. It has been widely used in cosmetics (e.g., shampoos and perfumes) and in non-cosmetic products (e.g., detergents and cleansers). In fact, U.S. Food and Drug Administration (FDA) has also permitted the use of nerolidol as a food flavoring agent. The fact that nerolidol is a common ingredient in many products has attracted researchers to explore more medicinal properties of nerolidol that may exert beneficial effect on human health. Therefore, the aim of this review is to compile and consolidate the data on the various pharmacological and biological activities displayed by nerolidol. Furthermore, this review also includes pharmacokinetic and toxicological studies of nerolidol. In summary, the various pharmacological and biological activities demonstrated in this review highlight the prospects of nerolidol as a promising chemical or drug candidate in the field of agriculture and medicine.
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Affiliation(s)
- Weng-Keong Chan
- School of Pharmacy, Monash University Malaysia, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia.
- Biomedical Research Laboratory, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia.
| | - Loh Teng-Hern Tan
- School of Pharmacy, Monash University Malaysia, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia.
- Biomedical Research Laboratory, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia.
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia.
| | - Learn-Han Lee
- School of Pharmacy, Monash University Malaysia, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia.
- Biomedical Research Laboratory, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia.
- Center of Health Outcomes Research and Therapeutic Safety (Cohorts), School of Pharmaceutical Sciences, University of Phayao, 56000 Phayao, Thailand.
| | - Bey-Hing Goh
- School of Pharmacy, Monash University Malaysia, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia.
- Biomedical Research Laboratory, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia.
- Center of Health Outcomes Research and Therapeutic Safety (Cohorts), School of Pharmaceutical Sciences, University of Phayao, 56000 Phayao, Thailand.
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49
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Zhao P, Yang L, Li J, Li Y, Tian Y, Li S. Combining systems pharmacology, transcriptomics, proteomics, and metabolomics to dissect the therapeutic mechanism of Chinese herbal Bufei Jianpi formula for application to COPD. Int J Chron Obstruct Pulmon Dis 2016; 11:553-66. [PMID: 27042044 PMCID: PMC4801132 DOI: 10.2147/copd.s100352] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Bufei Jianpi formula (BJF) has long been used as a therapeutic agent in the treatment of COPD. Systems pharmacology identified 145 active compounds and 175 potential targets of BJF in a previous study. Additionally, BJF was previously shown to effectively prevent COPD and its comorbidities, such as ventricular hypertrophy, by inhibition of inflammatory cytokine production, matrix metalloproteinases expression, and other cytokine production, in vivo. However, the system-level mechanism of BJF for the treatment of COPD is still unclear. The aim of this study was to gain insight into its system-level mechanisms by integrating transcriptomics, proteomics, and metabolomics together with systems pharmacology datasets. Using molecular function, pathway, and network analyses, the genes and proteins regulated in COPD rats and BJF-treated rats could be mainly attributed to oxidoreductase activity, antioxidant activity, focal adhesion, tight junction, or adherens junction. Furthermore, a comprehensive analysis of systems pharmacology, transcript, protein, and metabolite datasets is performed. The results showed that a number of genes, proteins, metabolites regulated in BJF-treated rats and potential target proteins of BJF were involved in lipid metabolism, cell junction, oxidative stress, and inflammatory response, which might be the system-level therapeutic mechanism of BJF treatment.
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Affiliation(s)
- Peng Zhao
- Key Laboratory of Chinese Internal Medicine, Henan University of Traditional Chinese Medicine, Zhengzhou, People's Republic of China; Collaborative Innovation Center for Respiratory Disease Diagnosis and Treatment and Chinese Medicine Development of Henan Province, The First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, People's Republic of China
| | - Liping Yang
- Key Laboratory of Chinese Internal Medicine, Henan University of Traditional Chinese Medicine, Zhengzhou, People's Republic of China; Collaborative Innovation Center for Respiratory Disease Diagnosis and Treatment and Chinese Medicine Development of Henan Province, The First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, People's Republic of China
| | - Jiansheng Li
- Key Laboratory of Chinese Internal Medicine, Henan University of Traditional Chinese Medicine, Zhengzhou, People's Republic of China; Collaborative Innovation Center for Respiratory Disease Diagnosis and Treatment and Chinese Medicine Development of Henan Province, The First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, People's Republic of China
| | - Ya Li
- Key Laboratory of Chinese Internal Medicine, Henan University of Traditional Chinese Medicine, Zhengzhou, People's Republic of China; Collaborative Innovation Center for Respiratory Disease Diagnosis and Treatment and Chinese Medicine Development of Henan Province, The First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, People's Republic of China
| | - Yange Tian
- Key Laboratory of Chinese Internal Medicine, Henan University of Traditional Chinese Medicine, Zhengzhou, People's Republic of China; Collaborative Innovation Center for Respiratory Disease Diagnosis and Treatment and Chinese Medicine Development of Henan Province, The First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, People's Republic of China
| | - Suyun Li
- Collaborative Innovation Center for Respiratory Disease Diagnosis and Treatment and Chinese Medicine Development of Henan Province, The First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, People's Republic of China; Department of Respiratory Diseases, The First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, People's Republic of China
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Blaauboer BJ, Boobis AR, Bradford B, Cockburn A, Constable A, Daneshian M, Edwards G, Garthoff JA, Jeffery B, Krul C, Schuermans J. Considering new methodologies in strategies for safety assessment of foods and food ingredients. Food Chem Toxicol 2016; 91:19-35. [PMID: 26939913 DOI: 10.1016/j.fct.2016.02.019] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 02/25/2016] [Indexed: 12/28/2022]
Abstract
Toxicology and safety assessment are changing and require new strategies for evaluating risk that are less depending on apical toxicity endpoints in animal models and relying more on knowledge of the mechanism of toxicity. This manuscript describes a number of developments that could contribute to this change and implement this in a stepwise roadmap that can be applied for the evaluation of food and food ingredients. The roadmap was evaluated in four case studies by using literature and existing data. This preliminary evaluation was shown to be useful. However, this experience should be extended by including examples where experimental work needs to be included. To further implement these new insights in toxicology and safety assessment for the area of food and food ingredients, the recommendation is that stakeholders take action in addressing gaps in our knowledge, e.g. with regard to the applicability of the roadmap for mixtures and food matrices. Further development of the threshold of toxicological concern is needed, as well as cooperation with other sectors where similar schemes are under development. Moreover, a more comprehensive evaluation of the roadmap, also including the identification of the need for in vitro experimental work is recommended.
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Affiliation(s)
- Bas J Blaauboer
- Utrecht University, Division of Toxicology, Institute for Risk Assessment Sciences, PO Box 80.177, 3508 TD, Utrecht, The Netherlands
| | - Alan R Boobis
- Imperial College London, Department of Medicine, Centre for Pharmacology & Therapeutics, London, W12 0NN, United Kingdom
| | - Bobbie Bradford
- Unilever, Safety & Environmental Assurance Centre, London, EC4Y 0DY, United Kingdom
| | - Andrew Cockburn
- University of Newcastle, Toxico-Logical Consulting Ltd, The Old Boiler House, Moor Place Park, Kettle Green Lane, Much Hadham, Hertfordshire, SG10 6AA, United Kingdom
| | - Anne Constable
- Nestlé Research Centre, Vers-Chez-les-Blanc, 1000, Lausanne 26, Switzerland
| | - Mardas Daneshian
- University of Konstanz, Center for Alternatives to Animal Testing-Europe CAAT-Europe, 78457, Konstanz, Germany
| | - Gareth Edwards
- Consultant, 63 Woodlands Road., Sonning Common, Reading, Berkshire, RG4 9TD, United Kingdom
| | | | - Brett Jeffery
- Mars, Global Chemical Food Safety Group, Slough, SL1 4JX, United Kingdom
| | - Cyrille Krul
- University of Applied Sciences, Research Centre Technology & Innovation, Dept. Innovative Testing in Life Sciences & Chemistry, PO Box 12011, 3501 AA, Utrecht, The Netherlands; TNO Healthy Living, PO box 360, 3700 AJ Zeist, The Netherlands
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