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Du J, Shao J, Li S, Zhu T, Song H, Lei C, Zhang M, Cen Y. Integrated transcriptomic and proteomic analyses reveal the mechanism of easy acceptance of artificial pelleted diets during food habit domestication in Largemouth bass (Micropterus salmoides). Sci Rep 2023; 13:18461. [PMID: 37891233 PMCID: PMC10611700 DOI: 10.1038/s41598-023-45645-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/22/2023] [Indexed: 10/29/2023] Open
Abstract
Acceptance of artificial pelleted diets contributes to increasing the cultured areas and output of carnivorous fish. However, the mechanism of acceptance of artificial pelleted diets remains largely unknown. In this study, the easy acceptance of artificial pelleted diets (EAD) group and the not easy acceptance of artificial pelleted diets (NAD) group of Largemouth bass (Micropterus salmoides) were divided based on the ratios of stomach weight/body weight (SB) after 0.5 h feeding, which was bigger than 18% in the EAD group and ranged from 8 to 12% in the NAD group. Through transcriptome and proteome sequencing, a total of 2463 differentially expressed genes (DEGs) and 230 differentially expressed proteins (DEPs) were identified, respectively. Integrated analyses of transcriptome and proteome data revealed that 152 DEPs were matched with the corresponding DEGs (named co-DEGs-DEPs), and 54 co-DEGs-DEPs were enriched in 16 KEGG pathways, including the metabolic pathways, steroid biosynthesis, fatty acid biosynthesis, etc. Furthermore, 3 terpenoid backbone biosynthesis-related genes (Hmgcr, Hmgcs, and Fdps) in metabolic pathways, 10 steroid biosynthesis-related genes (Fdft1, Sqle, Lss, Cyp51a1, Tm7sf2, Nsdhl, Hsd17b7, Dhcr24, Sc5d, and Dhcr7), and 3 fatty acid biosynthesis-related genes (Acaca, Fasn, and Ascl) were all up-regulated in the EAD group, suggesting that the lipid metabolism pathway and steroid biosynthesis pathway play important roles in early food habit domestication in Largemouth bass. In addition, the detection results of randomly selected 15 DEGs and 15 DEPs indicated that both transcriptome and proteome results in the study were reliable. Our study provides useful information for further research on the mechanisms of food habit domestication in fish.
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Affiliation(s)
- Jinxing Du
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Pearl River Fisheries Research Institute, China Ministry of Agriculture, Chinese Academy of Fisheries Sciences, Guangzhou, 510380, China
| | - Jiaqi Shao
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Pearl River Fisheries Research Institute, China Ministry of Agriculture, Chinese Academy of Fisheries Sciences, Guangzhou, 510380, China
- College of Fisheries, Henan Normal University, Xinxiang, 453007, China
| | - Shengjie Li
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Pearl River Fisheries Research Institute, China Ministry of Agriculture, Chinese Academy of Fisheries Sciences, Guangzhou, 510380, China.
| | - Tao Zhu
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Pearl River Fisheries Research Institute, China Ministry of Agriculture, Chinese Academy of Fisheries Sciences, Guangzhou, 510380, China
| | - Hongmei Song
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Pearl River Fisheries Research Institute, China Ministry of Agriculture, Chinese Academy of Fisheries Sciences, Guangzhou, 510380, China
| | - Caixia Lei
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Pearl River Fisheries Research Institute, China Ministry of Agriculture, Chinese Academy of Fisheries Sciences, Guangzhou, 510380, China
| | - Meng Zhang
- College of Fisheries, Henan Normal University, Xinxiang, 453007, China
| | - Yingkun Cen
- Jiyurunda Fishery Technology Co., Ltd, Foshan, 528203, China
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Wei L, Li Y, Ye H, Xiao J, Hogstrand C, Green I, Guo Z, Han D. Dietary Trivalent Chromium Exposure Up-Regulates Lipid Metabolism in Coral Trout: The Evidence From Transcriptome Analysis. Front Physiol 2021; 12:640898. [PMID: 33732169 PMCID: PMC7959734 DOI: 10.3389/fphys.2021.640898] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 01/25/2021] [Indexed: 11/14/2022] Open
Abstract
Diet quality greatly affects an animal’s performance and metabolism. Despite the fact that trivalent chromium [Cr(III)] is considered an essential element and is widely used in nutritional supplements for animals and humans, the potential toxicity of Cr(III) is unclear. Here, liver transcriptome sequencing was performed on coral trout (Plectropomus leopardus) exposed to 200 mg kg–1 of dietary organic Cr(III) [as chromium picolinate (CrPic)] for 8 weeks. One-hundred-and thirteen differentially expressed genes (DEGs) were identified in response to Cr(III) stress, in comparison to the control, including 31 up-regulated and 82 down-regulated DEGs. Clusters of Orthologous Groups of proteins (COG) classifies DEGs into 15 functional categories, with the predominant category being related to lipid transport and metabolism (9.73%). The Kyoto Encyclopedia of Genes and Genomes (KEGG) assigned DEGs to six major categories with robust DEGs as part of the lipid metabolism pathway (18.58%). Moreover, KEGG functional enrichment analysis showed that these DEGs are primarily related to steroid biosynthesis, terpenoid backbone biosynthesis, and steroid hormone biosynthesis pathways, of which steroid biosynthesis was the most significant pathway, and 12 key up-regulated DEGs (dhcr7, dhcr24, ebp, lss, msmo1, sqle, cyp51, tm7sf2, sc5dl, fdft1, nsdhl, and hsd17b7) were found for steroid biosynthesis pathways. To validate the RNA sequencing data using quantitative real-time PCR (qRT-PCR), qRT-PCR results indicate that the expression of genes encoding HMGCR, TM7SF2, TRYP2, CTRL, EBP, LSS, and CYP51 were induced, while those encoding THRSP, LCE, and MCM5 were reduced, consistent with RNA-seq results. This findings provides the first evidence that a long-term high dose of Cr(III) intake causes lipid metabolism disorder and potential toxicity in fish. Cautious health risk assessment of dietary Cr(III) intake is therefore highly recommended for the commercial and/or natural diets of aquatic animals, which has previously largely been ignored.
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Affiliation(s)
- Lu Wei
- State Key Laboratory of Marine Resource Utilization in South China Sea, School of Life and Pharmaceutical Sciences, College of Food Science and Engineering, Hainan University, Haikou, China
| | - Yu Li
- State Key Laboratory of Marine Resource Utilization in South China Sea, School of Life and Pharmaceutical Sciences, College of Food Science and Engineering, Hainan University, Haikou, China
| | - Hengzhen Ye
- State Key Laboratory of Marine Resource Utilization in South China Sea, School of Life and Pharmaceutical Sciences, College of Food Science and Engineering, Hainan University, Haikou, China
| | - Juan Xiao
- State Key Laboratory of Marine Resource Utilization in South China Sea, School of Life and Pharmaceutical Sciences, College of Food Science and Engineering, Hainan University, Haikou, China
| | - Christer Hogstrand
- Metals Metabolism Group, School of Life Course Sciences, King's College London, London, United Kingdom
| | - Iain Green
- Department of Life and Environmental Sciences, Faculty of Science and Technology, Bournemouth University, Poole, United Kingdom
| | - Zhiqiang Guo
- State Key Laboratory of Marine Resource Utilization in South China Sea, School of Life and Pharmaceutical Sciences, College of Food Science and Engineering, Hainan University, Haikou, China
| | - Dong Han
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang, China
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Kočar E, Režen T, Rozman D. Cholesterol, lipoproteins, and COVID-19: Basic concepts and clinical applications. Biochim Biophys Acta Mol Cell Biol Lipids 2021; 1866:158849. [PMID: 33157278 PMCID: PMC7610134 DOI: 10.1016/j.bbalip.2020.158849] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/09/2020] [Accepted: 10/25/2020] [Indexed: 12/19/2022]
Abstract
Cholesterol is being recognized as a molecule involved in regulating the entry of the SARS-CoV-2 virus into the host cell. However, the data about the possible role of cholesterol carrying lipoproteins and their receptors in relation to infection are scarce and the connection of lipid-associated pathologies with COVID-19 disease is in its infancy. Herein we provide an overview of lipids and lipid metabolism in relation to COVID-19, with special attention on different forms of cholesterol. Cholesterol enriched lipid rafts represent a platform for viruses to enter the host cell by endocytosis. Generally, higher membrane cholesterol coincides with higher efficiency of COVID-19 entry. Inversely, patients with COVID-19 show lowered levels of blood cholesterol, high-density lipoproteins (HDL) and low-density lipoproteins. The modulated efficiency of viral entry can be explained by availability of SR-B1 receptor. HDL seems to have a variety of roles, from being itself a scavenger for viruses, an immune modulator and mediator of viral entry. Due to inverse roles of membrane cholesterol and lipoprotein cholesterol in COVID-19 infected patients, treatment of these patients with cholesterol lowering statins needs more attention. In conclusion, cholesterol and lipoproteins are potential markers for monitoring the viral infection status, while the lipid metabolic pathways and the composition of membranes could be targeted to selectively inhibit the life cycle of the virus as a basis for antiviral therapy.
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Affiliation(s)
- Eva Kočar
- Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Zaloška 4, 1000 Ljubljana, Slovenia.
| | - Tadeja Režen
- Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Zaloška 4, 1000 Ljubljana, Slovenia.
| | - Damjana Rozman
- Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Zaloška 4, 1000 Ljubljana, Slovenia.
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Shu L, Meng Q, Diamante G, Tsai B, Chen YW, Mikhail A, Luk H, Ritz B, Allard P, Yang X. Prenatal Bisphenol A Exposure in Mice Induces Multitissue Multiomics Disruptions Linking to Cardiometabolic Disorders. Endocrinology 2019; 160:409-429. [PMID: 30566610 PMCID: PMC6349005 DOI: 10.1210/en.2018-00817] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 12/13/2018] [Indexed: 12/21/2022]
Abstract
The health impacts of endocrine-disrupting chemicals (EDCs) remain debated, and their tissue and molecular targets are poorly understood. In this study, we leveraged systems biology approaches to assess the target tissues, molecular pathways, and gene regulatory networks associated with prenatal exposure to the model EDC bisphenol A (BPA). Prenatal BPA exposure at 5 mg/kg/d, a dose below most reported no-observed-adverse-effect levels, led to tens to thousands of transcriptomic and methylomic alterations in the adipose, hypothalamus, and liver tissues in male offspring in mice, with cross-tissue perturbations in lipid metabolism as well as tissue-specific alterations in histone subunits, glucose metabolism, and extracellular matrix. Network modeling prioritized main molecular targets of BPA, including Pparg, Hnf4a, Esr1, Srebf1, and Fasn as well as numerous less studied targets such as Cyp51 and long noncoding RNAs across tissues, Fa2h in hypothalamus, and Nfya in adipose tissue. Lastly, integrative analyses identified the association of BPA molecular signatures with cardiometabolic phenotypes in mouse and human. Our multitissue, multiomics investigation provides strong evidence that BPA perturbs diverse molecular networks in central and peripheral tissues and offers insights into the molecular targets that link BPA to human cardiometabolic disorders.
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Affiliation(s)
- Le Shu
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, California
- Molecular, Cellular, and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, Los Angeles, California
| | - Qingying Meng
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, California
| | - Graciel Diamante
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, California
| | - Brandon Tsai
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, California
| | - Yen-Wei Chen
- Molecular Toxicology Interdepartmental Program, University of California, Los Angeles, Los Angeles, California
| | - Andrew Mikhail
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, California
| | - Helen Luk
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, California
| | - Beate Ritz
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, California
- Institute for Society and Genetics, University of California, Los Angeles, Los Angeles, California
| | - Patrick Allard
- Molecular Toxicology Interdepartmental Program, University of California, Los Angeles, Los Angeles, California
- Institute for Society and Genetics, University of California, Los Angeles, Los Angeles, California
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, California
- Molecular, Cellular, and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, Los Angeles, California
- Molecular Toxicology Interdepartmental Program, University of California, Los Angeles, Los Angeles, California
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, California
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Režen T, Ogris I, Sever M, Merzel F, Golic Grdadolnik S, Rozman D. Evaluation of Selected CYP51A1 Polymorphisms in View of Interactions with Substrate and Redox Partner. Front Pharmacol 2017; 8:417. [PMID: 28713270 PMCID: PMC5492350 DOI: 10.3389/fphar.2017.00417] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Accepted: 06/13/2017] [Indexed: 01/16/2023] Open
Abstract
Cholesterol is essential for development, growth, and maintenance of organisms. Mutations in cholesterol biosynthetic genes are embryonic lethal and few polymorphisms have been so far associated with pathologies in humans. Previous analyses show that lanosterol 14α-demethylase (CYP51A1) from the late part of cholesterol biosynthesis has only a few missense mutations with low minor allele frequencies and low association with pathologies in humans. The aim of this study is to evaluate the role of amino acid changes in the natural missense mutations of the hCYP51A1 protein. We searched SNP databases for existing polymorphisms of CYP51A1 and evaluated their effect on protein function. We found rare variants causing detrimental missense mutations of CYP51A1. Some missense variants were also associated with a phenotype in humans. Two missense variants have been prepared for testing enzymatic activity in vitro but failed to produce a P450 spectrum. We performed molecular modeling of three selected missense variants to evaluate the effect of the amino acid substitution on potential interaction with its substrate and the obligatory redox partner POR. We show that two of the variants, R277L and especially D152G, have possibly lower binding potential toward obligatory redox partner POR. D152G and R431H have also potentially lower affinity toward the substrate lanosterol. We evaluated the potential effect of damaging variants also using data from other in vitro CYP51A1 mutants. In conclusion, we propose to include damaging CYP51A1 variants into personalized diagnostics to improve genetic counseling for certain rare disease phenotypes.
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Affiliation(s)
- Tadeja Režen
- Faculty of Medicine, Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry, University of LjubljanaLjubljana, Slovenia
| | - Iza Ogris
- Faculty of Medicine, Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry, University of LjubljanaLjubljana, Slovenia
| | - Marko Sever
- Department of Biomolecular Structure, National Institute of ChemistryLjubljana, Slovenia
| | - Franci Merzel
- Department of Biomolecular Structure, National Institute of ChemistryLjubljana, Slovenia
| | | | - Damjana Rozman
- Faculty of Medicine, Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry, University of LjubljanaLjubljana, Slovenia
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Urlep Ž, Lorbek G, Perše M, Jeruc J, Juvan P, Matz-Soja M, Gebhardt R, Björkhem I, Hall JA, Bonneau R, Littman DR, Rozman D. Disrupting Hepatocyte Cyp51 from Cholesterol Synthesis Leads to Progressive Liver Injury in the Developing Mouse and Decreases RORC Signalling. Sci Rep 2017; 7:40775. [PMID: 28098217 PMCID: PMC5241696 DOI: 10.1038/srep40775] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 12/12/2016] [Indexed: 11/16/2022] Open
Abstract
Development of mice with hepatocyte knockout of lanosterol 14α-demethylase (HCyp51-/-) from cholesterol synthesis is characterized by the progressive onset of liver injury with ductular reaction and fibrosis. These changes begin during puberty and are generally more aggravated in the knockout females. However, a subgroup of (pre)pubertal knockout mice (runts) exhibits a pronounced male prevalent liver dysfunction characterized by downregulated amino acid metabolism and elevated Casp12. RORC transcriptional activity is diminished in livers of all runt mice, in correlation with the depletion of potential RORC ligands subsequent to CYP51 disruption. Further evidence for this comes from the global analysis that identified a crucial overlap between hepatic Cyp51-/- and Rorc-/- expression profiles. Additionally, the reduction in RORA and RORC transcriptional activity was greater in adult HCyp51-/- females than males, which correlates well with their downregulated amino and fatty acid metabolism. Overall, we identify a global and sex-dependent transcriptional de-regulation due to the block in cholesterol synthesis during development of the Cyp51 knockout mice and provide in vivo evidence that sterol intermediates downstream of lanosterol may regulate the hepatic RORC activity.
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Affiliation(s)
- Žiga Urlep
- Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Gregor Lorbek
- Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Martina Perše
- Medical Experimental Centre, Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Jera Jeruc
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Peter Juvan
- Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Madlen Matz-Soja
- Institute of Biochemistry, Faculty of Medicine, University of Leipzig, Leipzig, Germany
| | - Rolf Gebhardt
- Institute of Biochemistry, Faculty of Medicine, University of Leipzig, Leipzig, Germany
| | - Ingemar Björkhem
- Department of Laboratory Medicine, Division of Clinical Chemistry, Karolinska Institute, Karolinska University Hospital, Huddinge, Sweden
| | - Jason A. Hall
- The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York 10016, USA
| | - Richard Bonneau
- New York University & Simons Foundation for Data Analysis, New York, NY 10010, USA
| | - Dan R. Littman
- The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York 10016, USA
- Howard Hughes Medical Institute, New York University School of Medicine, New York, New York 10016, USA
| | - Damjana Rozman
- Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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Zhan F, Watanabe Y, Shimoda A, Hamada E, Kobayashi Y, Maekawa M. Evaluation of serum bone alkaline phosphatase activity in patients with liver disease: Comparison between electrophoresis and chemiluminescent enzyme immunoassay. Clin Chim Acta 2016; 460:40-5. [DOI: 10.1016/j.cca.2016.06.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 06/08/2016] [Accepted: 06/08/2016] [Indexed: 12/20/2022]
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