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Lin MS, Varunjikar MS, Lie KK, Søfteland L, Dellafiora L, Ørnsrud R, Sanden M, Berntssen MHG, Dorne JLCM, Bafna V, Rasinger JD. Multi-tissue proteogenomic analysis for mechanistic toxicology studies in non-model species. ENVIRONMENT INTERNATIONAL 2023; 182:108309. [PMID: 37980879 DOI: 10.1016/j.envint.2023.108309] [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: 01/25/2023] [Revised: 08/15/2023] [Accepted: 11/04/2023] [Indexed: 11/21/2023]
Abstract
New approach methodologies (NAM), including omics and in vitro approaches, are contributing to the implementation of 3R (reduction, refinement and replacement) strategies in regulatory science and risk assessment. In this study, we present an integrative transcriptomics and proteomics analysis workflow for the validation and revision of complex fish genomes and demonstrate how proteogenomics expression matrices can be used to support multi-level omics data integration in non-model species in vivo and in vitro. Using Atlantic salmon as an example, we constructed proteogenomic databases from publicly available transcriptomic data and in-house generated RNA-Seq and LC-MS/MS data. Our analysis identified ∼80,000 peptides, providing direct evidence of translation for over 40,000 RefSeq structures. The data also highlighted 183 co-located peptide groups that supported a single transcript each, and in each case, either corrected a previous annotation, supported Ensembl annotations not present in RefSeq, or identified novel previously unannotated genes. Proteogenomics data-derived expression matrices revealed distinct profiles for the different tissue types analyzed. Focusing on proteins involved in defense against xenobiotics, we detected distinct expression patterns across different salmon tissues and observed homology in the expression of chemical defense proteins between in vivo and in vitro liver systems. Our study demonstrates the potential of proteogenomic analyses in extending our understanding of complex fish genomes and provides an advanced bioinformatic toolkit to support the further development of NAMs and their application in regulatory science and (eco)toxicological studies of non-model species.
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Affiliation(s)
- M S Lin
- Bioinformatics and Systems Biology Program, UC San Diego, San Diego, CA, United States.
| | | | - K K Lie
- Institute of Marine Research, Bergen, Norway.
| | - L Søfteland
- Institute of Marine Research, Bergen, Norway.
| | - L Dellafiora
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy.
| | - R Ørnsrud
- Institute of Marine Research, Bergen, Norway.
| | - M Sanden
- Institute of Marine Research, Bergen, Norway.
| | | | - J L C M Dorne
- European Food Safety Authority, Methodological and Scientific Support Unit, Via Carlo Magno 1A, 43121 Parma, Italy.
| | - V Bafna
- Computer Science & Engineering and HDSI, UC San Diego, San Diego, CA, United States.
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Dietary Selenomethionine Reduce Mercury Tissue Levels and Modulate Methylmercury Induced Proteomic and Transcriptomic Alterations in Hippocampi of Adolescent BALB/c Mice. Int J Mol Sci 2022; 23:ijms232012242. [PMID: 36293098 PMCID: PMC9603801 DOI: 10.3390/ijms232012242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/06/2022] [Accepted: 10/11/2022] [Indexed: 12/02/2022] Open
Abstract
Methylmercury (MeHg) is a well-known environmental contaminant, particularly harmful to the developing brain. The main human dietary exposure to MeHg occurs through seafood consumption. However, seafood also contains several nutrients, including selenium, which has been shown to interact with MeHg and potentially ameliorate its toxicity. The aim of this study was to investigate the combined effects of selenium (as selenomethionine; SeMet) and MeHg on mercury accumulation in tissues and the effects concomitant dietary exposure of these compounds exert on the hippocampal proteome and transcriptome in mice. Adolescent male BALB/c mice were exposed to SeMet and two different doses of MeHg through their diet for 11 weeks. Organs, including the brain, were sampled for mercury analyses. Hippocampi were collected and analyzed using proteomics and transcriptomics followed by multi-omics bioinformatics data analysis. The dietary presence of SeMet reduced the amount of mercury in several organs, including the brain. Proteomic and RNA-seq analyses showed that both protein and RNA expression patterns were inversely regulated in mice receiving SeMet together with MeHg compared to MeHg alone. Several pathways, proteins and RNA transcripts involved in conditions such as immune responses and inflammation, oxidative stress, cell plasticity and Alzheimer’s disease were affected inversely by SeMet and MeHg, indicating that SeMet can ameliorate several toxic effects of MeHg in mice.
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Proteomic analysis of hepatic effects of phenobarbital in mice with humanized liver. Arch Toxicol 2022; 96:2739-2754. [PMID: 35881160 PMCID: PMC9352639 DOI: 10.1007/s00204-022-03338-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/13/2022] [Indexed: 11/25/2022]
Abstract
Activation of the constitutive androstane receptor (CAR) may induce adaptive but also adverse effects in rodent liver, including the induction of drug-metabolizing enzymes, transient hepatocellular proliferation, and promotion of liver tumor growth. Human relevance of CAR-related adverse hepatic effects is controversially debated. Here, we used the chimeric FRG-KO mouse model with livers largely repopulated by human hepatocytes, in order to study human hepatocytes and their response to treatment with the model CAR activator phenobarbital (PB) in vivo. Mice received an intraperitoneal injection with 50 mg/kg body weight PB or saline, and were sacrificed after 72–144 h. Non-repopulated FRG-KO mice were used as additional control. Comprehensive proteomics datasets were generated by merging data obtained by targeted as well as non-targeted proteomics approaches. For the first time, a novel proteomics workflow was established to comparatively analyze the effects of PB on human and murine proteins within one sample. Analysis of merged proteome data sets and bioinformatics data mining revealed comparable responses in murine and human hepatocytes with respect to nuclear receptor activation and induction of xenobiotic metabolism. By contrast, activation of MYC, a key regulator of proliferation, was predicted only for mouse but not human hepatocytes. Analyses of 5-bromo-2′-deoxyuridine incorporation confirmed this finding. In summary, this study for the first time presents a comprehensive proteomic analysis of CAR-dependent effects in human and mouse hepatocytes from humanized FRG-KO mice. The data support the hypothesis that PB does induce adaptive metabolic responses, but not hepatocellular proliferation in human hepatocytes in vivo.
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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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Heikelä H, Ruohonen ST, Adam M, Viitanen R, Liljenbäck H, Eskola O, Gabriel M, Mairinoja L, Pessia A, Velagapudi V, Roivainen A, Zhang FP, Strauss L, Poutanen M. Hydroxysteroid (17β) dehydrogenase 12 is essential for metabolic homeostasis in adult mice. Am J Physiol Endocrinol Metab 2020; 319:E494-E508. [PMID: 32691632 DOI: 10.1152/ajpendo.00042.2020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Hydroxysteroid 17β dehydrogenase 12 (HSD17B12) is suggested to be involved in the elongation of very long chain fatty acids. Previously, we have shown a pivotal role for the enzyme during mouse development. In the present study we generated a conditional Hsd17b12 knockout (HSD17B12cKO) mouse model by breeding mice homozygous for a floxed Hsd17b12 allele with mice expressing the tamoxifen-inducible Cre recombinase at the ROSA26 locus. Gene inactivation was induced by administering tamoxifen to adult mice. The gene inactivation led to a 20% loss of body weight within 6 days, associated with drastic reduction in both white (83% males, 75% females) and brown (65% males, 60% females) fat, likely due to markedly reduced food and water intake. Furthermore, the knockout mice showed sickness behavior and signs of liver toxicity, specifically microvesicular hepatic steatosis and increased serum alanine aminotransferase (4.6-fold in males, 7.7-fold in females). The hepatic changes were more pronounced in females than males. Proinflammatory cytokines, such as interleukin-6 (IL-6), IL-17, and granulocyte colony-stimulating factor, were increased in the HSD17B12cKO mice indicating an inflammatory response. Serum lipidomics study showed an increase in the amount of dihydroceramides, despite the dramatic overall loss of lipids. In line with the proposed role for HSD17B12 in fatty acid elongation, we observed accumulation of ceramides, dihydroceramides, hexosylceramides, and lactosylceramides with shorter than 18-carbon fatty acid side chains in the serum. The results indicate that HSD17B12 is essential for proper lipid homeostasis and HSD17B12 deficiency rapidly results in fatal systemic inflammation and lipolysis in adult mice.
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Affiliation(s)
- Hanna Heikelä
- Turku Center for Disease Modeling, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Suvi T Ruohonen
- Turku Center for Disease Modeling, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Marion Adam
- Turku Center for Disease Modeling, Institute of Biomedicine, University of Turku, Turku, Finland
| | | | - Heidi Liljenbäck
- Turku Center for Disease Modeling, Institute of Biomedicine, University of Turku, Turku, Finland
- Turku PET Centre, University of Turku, Turku, Finland
| | - Olli Eskola
- Turku PET Centre, University of Turku, Turku, Finland
| | - Michael Gabriel
- Turku Center for Disease Modeling, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Laura Mairinoja
- Turku Center for Disease Modeling, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Alberto Pessia
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Vidya Velagapudi
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Anne Roivainen
- Turku Center for Disease Modeling, Institute of Biomedicine, University of Turku, Turku, Finland
- Turku PET Centre, University of Turku, Turku, Finland
- Turku PET Centre, Turku University Hospital, Turku, Finland
| | - Fu-Ping Zhang
- Turku Center for Disease Modeling, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Leena Strauss
- Turku Center for Disease Modeling, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Matti Poutanen
- Turku Center for Disease Modeling, Institute of Biomedicine, University of Turku, Turku, Finland
- Department of Internal Medicine, Institute of Medicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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Kang S, Johnston TV, Ku S, Ji GE. Acute and sub-chronic (28-day) oral toxicity profiles of newly synthesized prebiotic butyl-fructooligosaccharide in ICR mouse and Wistar rat models. Toxicol Res (Camb) 2020; 9:484-492. [PMID: 32905258 DOI: 10.1093/toxres/tfaa055] [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: 02/26/2020] [Revised: 06/19/2020] [Accepted: 07/01/2020] [Indexed: 11/13/2022] Open
Abstract
B-FOS (butyl-fructooligosaccharide) is a newly synthesized prebiotic molecule, formed by the combination of FOS and butyrate by ester bonds. B-FOS has been reported to have the potential prebiotic effect of promoting intestinal flora diversity and enhancing butyrate production. The aim of this study was to investigate the potential acute and sub-chronic toxicity of B-FOS in Institute of Cancer Research (ICR) mice and Wistar rats to verify its biosafety. ICR mice were administered a single oral gavage of B-FOS at doses of 0, 500, 1000, and 2000 mg/kg body weight and observed for signs of acute toxicity for 14 days. Sub-chronic toxicity was evaluated by repeated oral administration of B-FOS at 2000 mg/kg for 28 days, in accordance with Organization for Economic Co-operation and Development (OECD) protocol test numbers 420 and 407. No mortality or abnormal clinical signs were observed during the experimental periods after B-FOS administration. Furthermore, no significant changes in body weight, organ weight, serum biochemical parameters, or tissue histology were observed after animal sacrifice. These in vivo results indicate that B-FOS does not exert any acute or sub-chronic toxicity at a dose of 2000 mg/kg, and this novel molecule can be regarded as a safe prebiotic substance for use in the food and nutraceutical industries.
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Affiliation(s)
- Sini Kang
- Department of Food and Nutrition, Research Institute of Human Ecology, Seoul National University, Seoul 08826, Korea
| | - Tony V Johnston
- Fermentation Science Program, School of Agriculture, College of Basic and Applied Sciences, Middle Tennessee State University, Murfreesboro, TN 37132, USA
| | - Seockmo Ku
- Fermentation Science Program, School of Agriculture, College of Basic and Applied Sciences, Middle Tennessee State University, Murfreesboro, TN 37132, USA
| | - Geun Eog Ji
- Department of Food and Nutrition, Research Institute of Human Ecology, Seoul National University, Seoul 08826, Korea.,Research Center, BIFIDO Co., Ltd., Hongcheon 25117, Korea
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Merel S, Regueiro J, Berntssen MH, Hannisdal R, Ørnsrud R, Negreira N. Identification of ethoxyquin and its transformation products in salmon after controlled dietary exposure via fish feed. Food Chem 2019; 289:259-268. [DOI: 10.1016/j.foodchem.2019.03.054] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 03/11/2019] [Accepted: 03/11/2019] [Indexed: 01/08/2023]
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Berntssen MHG, Hoogenveen R, Bernhard A, Lundebye AK, Ørnsrud R, Zeilmaker MJ. Modelling of the feed-to-fillet transfer of ethoxyquin and one of its main metabolites, ethoxyquin dimer, to the fillet of farmed Atlantic salmon ( Salmon salar L.). Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2019; 36:1042-1054. [PMID: 31063084 DOI: 10.1080/19440049.2019.1605208] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Ethoxyquin (EQ) is an antioxidant supplemented to feed ingredients, mainly fish meal, which is currently under re-evaluation for use in the food production chain. EQ is partly metabolized into several metabolites of which the ethoxyquin dimer (EQDM) accumulates most in the farmed fish fillet. In this study, the feed-to-fillet transfer of dietary EQ and EQDM in Atlantic salmon fillet was investigated, and a physiologically based pharmacokinetic (PBPK-) two-compartmental model was developed, based on experimental determined EQ and EQDM uptake, metabolism, and elimination kinetics. The model was verified with an external data-set and used to simulate the long term (>1.5 years) EQ and EQDM feed-to fillet transfer in Atlantic salmon under realistic farming conditions such as the seasonal fluctuations in feed intake, growth, and fillet fat deposition. The model predictions showed that initial EQDM levels in juvenile fish are the driving factor in final levels found in food-producing animals, while for EQ the levels in feed, and seasonal variations were the driving factor for food EQ levels.
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Affiliation(s)
- M H G Berntssen
- a Department of Feed Safety , Institute of Marine Research (IMR) , Bergen , Norway
| | - R Hoogenveen
- b RIVM, National Institute for Public Health and the Environment , Bilthoven , The Netherlands
| | - A Bernhard
- a Department of Feed Safety , Institute of Marine Research (IMR) , Bergen , Norway
| | - A-K Lundebye
- a Department of Feed Safety , Institute of Marine Research (IMR) , Bergen , Norway
| | - R Ørnsrud
- a Department of Feed Safety , Institute of Marine Research (IMR) , Bergen , Norway
| | - M J Zeilmaker
- b RIVM, National Institute for Public Health and the Environment , Bilthoven , The Netherlands
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