1
|
Li R, Zhao Y, Liang B, Pu Y, Jiang L, Ma Y. Genome-Wide Signal Selection Analysis Revealing Genes Potentially Related to Sheep-Milk-Production Traits. Animals (Basel) 2023; 13:ani13101654. [PMID: 37238084 DOI: 10.3390/ani13101654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
Natural selection and domestication have shaped modern sheep populations into a vast range of phenotypically diverse breeds. Among these breeds, dairy sheep have a smaller population than meat sheep and wool sheep, and less research is performed on them, but the lactation mechanism in dairy sheep is critically important for improving animal-production methods. In this study, whole-genome sequences were generated from 10 sheep breeds, including 57 high-milk-yield sheep and 44 low-milk-yield sheep, to investigate the genetic signatures of milk production in dairy sheep, and 59,864,820 valid SNPs (Single Nucleotide Polymorphisms) were kept after quality control to perform population-genetic-structure analyses, gene-detection analyses, and gene-function-validation analyses. For the population-genetic-structure analyses, we carried out PCA (Principal Component Analysis), as well as neighbor-joining tree and structure analyses to classify different sheep populations. The sheep used in our study were well distributed in ten groups, with the high-milk-yield-group populations close to each other and the low-milk-yield-group populations showing similar classifications. To perform an exact signal-selection analysis, we used three different methods to find SNPs to perform gene-annotation analyses within the 995 common regions derived from the fixation index (FST), nucleotide diversity (Ɵπ), and heterozygosity rate (ZHp) results. In total, we found 553 genes that were located in these regions. These genes mainly participate in the protein-binding pathway and the nucleoplasm-interaction pathway, as revealed by the GO- and KEGG-function-enrichment analyses. After the gene selection and function analyses, we found that FCGR3A, CTSK, CTSS, ARNT, GHR, SLC29A4, ROR1, and TNRC18 were potentially related to sheep-milk-production traits. We chose the strongly selected genes, FCGR3A, CTSK, CTSS, and ARNT during the signal-selection analysis to perform a RT-qPCR (Reale time Quantitative Polymerase Chain Reaction) experiment to validate their expression-level relationship with milk production, and the results showed that FCGR3A has a significant negative relationship with sheep-milk production, while other three genes did not show any positive or negative relations. In this study, it was discovered and proven that the candidate gene FCGR3A potentially contributes to the milk production of dairy sheep and a basis was laid for the further study of the genetic mechanism underlying the strong milk-production traits of sheep.
Collapse
Affiliation(s)
- Ruonan Li
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
- Teaching and Research Centre (TERRA), Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium
| | - Yuhetian Zhao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Benmeng Liang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Yabin Pu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Lin Jiang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Yuehui Ma
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| |
Collapse
|
2
|
Induction by Phenobarbital of Phase I and II Xenobiotic-Metabolizing Enzymes in Bovine Liver: An Overall Catalytic and Immunochemical Characterization. Int J Mol Sci 2022; 23:ijms23073564. [PMID: 35408925 PMCID: PMC8998613 DOI: 10.3390/ijms23073564] [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: 02/14/2022] [Revised: 03/14/2022] [Accepted: 03/21/2022] [Indexed: 12/15/2022] Open
Abstract
In cattle, phenobarbital (PB) upregulates target drug-metabolizing enzyme (DME) mRNA levels. However, few data about PB's post-transcriptional effects are actually available. This work provides the first, and an almost complete, characterization of PB-dependent changes in DME catalytic activities in bovine liver using common probe substrates and confirmatory immunoblotting investigations. As expected, PB increased the total cytochrome P450 (CYP) content and the extent of metyrapone binding; moreover, an augmentation of protein amounts and related enzyme activities was observed for known PB targets such as CYP2B, 2C, and 3A, but also CYP2E1. However, contradictory results were obtained for CYP1A, while a decreased catalytic activity was observed for flavin-containing monooxygenases 1 and 3. The barbiturate had no effect on the chosen hydrolytic and conjugative DMEs. For the first time, we also measured the 26S proteasome activity, and the increase observed in PB-treated cattle would suggest this post-translational event might contribute to cattle DME regulation. Overall, this study increased the knowledge of cattle hepatic drug metabolism, and further confirmed the presence of species differences in DME expression and activity between cattle, humans, and rodents. This reinforced the need for an extensive characterization and understanding of comparative molecular mechanisms involved in expression, regulation, and function of DMEs.
Collapse
|
3
|
Trego ML, Hoh E, Whitehead A, Kellar NM, Lauf M, Datuin DO, Lewison RL. Contaminant Exposure Linked to Cellular and Endocrine Biomarkers in Southern California Bottlenose Dolphins. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:3811-3822. [PMID: 30852886 DOI: 10.1021/acs.est.8b06487] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Cetaceans in the Southern California Bight (SCB) are exposed to high levels of halogenated organic contaminants (HOCs), which have previously been linked to impaired reproductive health and immune responses. We used a combination of molecular tools to examine the potential physiological impacts of HOC exposure in two bottlenose dolphin ( Tursiops truncatus) ecotypes in the SCB. We quantified 25 HOCs in the blubber of 22 biopsies collected from males between 2012 and 2016. We then analyzed genome-wide gene expression in skin using RNA-sequencing and measured blubber testosterone to compare HOC exposure with cellular and endocrine biomarkers. We found high levels of HOCs in both ecotypes with significantly higher total polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), tris(4-chlorophenyl)methanol (TCPMOH), and chlordane-related compounds in the coastal ecotype versus the offshore ecotype. We found evidence of PBDE bioaccumulation in both ecotypes, however, the pattern of bioaccumulation or endocrine disruption for other HOCs was different between the ecotypes, suggesting potential endocrine disruption in the coastal ecotype. We also observed correlations between HOCs and gene coexpression networks enriched for xenobiotic metabolism, hormone metabolism, and immune response that could indicate cellular effects from HOC exposure. By integrating measurements of HOC load with both transcriptome profiling and endocrine biomarkers, our approach provides insight into HOC exposure and potential impacts on wild cetacean health in southern California.
Collapse
Affiliation(s)
- Marisa L Trego
- Department of Biology , San Diego State University , 5500 Campanile Drive , San Diego , California 92182 , United States
- Department of Environmental Toxicology , University of California-Davis , 1 Shields Avenue , Davis , California 95616 , United States
| | - Eunha Hoh
- School of Public Health , San Diego State University , 5500 Campanile Drive , San Diego , California 92182 , United States
| | - Andrew Whitehead
- Department of Environmental Toxicology , University of California-Davis , 1 Shields Avenue , Davis , California 95616 , United States
| | - Nicholas M Kellar
- Ocean Associates, Incorporated, under contract to the Southwest Fisheries Science Center, National Marine Fisheries Service , National Oceanic and Atmospheric Administration , Arlington , Virginia 22207 , United States
| | - Morgane Lauf
- Ocean Associates, Incorporated, under contract to the Southwest Fisheries Science Center, National Marine Fisheries Service , National Oceanic and Atmospheric Administration , Arlington , Virginia 22207 , United States
| | - Dana O Datuin
- School of Public Health , San Diego State University , 5500 Campanile Drive , San Diego , California 92182 , United States
| | - Rebecca L Lewison
- Department of Biology , San Diego State University , 5500 Campanile Drive , San Diego , California 92182 , United States
| |
Collapse
|
4
|
Leijs MM, Esser A, Amann PM, Schettgen T, Heise R, Fietkau K, Gube M, Merk HF, Kraus T, Baron JM. Expression of CYP1A1, CYP1B1 and IL-1β in PBMCs and skin samples of PCB exposed individuals. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 642:1429-1438. [PMID: 30045523 DOI: 10.1016/j.scitotenv.2018.06.136] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Revised: 06/11/2018] [Accepted: 06/11/2018] [Indexed: 06/08/2023]
Abstract
Polychlorinated biphenyls (PCBs) are well- known man-made persistent environmental pollutants and endocrine disruptors. As a result of mass production in the past, background levels of these compounds can be measured in human blood worldwide. In 2010 high internal levels of PCBs were discovered in workers of a transformer-recycling company in Germany. Our aim was to measure, whether the expression of CYP1A1, CYP1B1, and IL-1β is dysregulated in peripheral blood mononuclear cells (PBMCs) of the exposed individuals (n = max 308). Further, we measured the regulation of CYP1A1, CYP1B1, AHRR (aromatic hydrocarbon receptor repressor) and IL-1β in skin samples of 25 workers with elevated plasma PCB levels using quantitative PCR (q-RT-PCR). We found a significant correlation between the regulation of IL-1β in skin samples and lipid adjusted PCB levels. In the PBMCs, the expression levels of CYP1A1, CYP1B1 and IL-1β decreased over time with decreasing PCB plasma levels. The upregulation of the cytokine IL-1β in exposed individuals with higher PCB plasma levels warrants further investigation in order to examine its role in the pathophysiology of autoimmune disorders and tumor promotion.
Collapse
Affiliation(s)
- Marike M Leijs
- Department of Dermatology and Allergology, RWTH Aachen University, 52074 Aachen, Germany.
| | - André Esser
- Institute for Occupational and Social Medicine, RWTH Aachen University, 52074 Aachen, Germany
| | - Philipp M Amann
- Department of Dermatology and Allergology, RWTH Aachen University, 52074 Aachen, Germany; Department of Dermatology, SLK Hospital Heilbronn, Germany
| | - Thomas Schettgen
- Institute for Occupational and Social Medicine, RWTH Aachen University, 52074 Aachen, Germany
| | - Ruth Heise
- Department of Dermatology and Allergology, RWTH Aachen University, 52074 Aachen, Germany
| | - Katharina Fietkau
- Department of Dermatology and Allergology, RWTH Aachen University, 52074 Aachen, Germany
| | - Monika Gube
- Institute for Occupational and Social Medicine, RWTH Aachen University, 52074 Aachen, Germany; Health Office of the city and area of Aachen, Trierer Straße 1, 52078 Aachen, Germany
| | - Hans F Merk
- Department of Dermatology and Allergology, RWTH Aachen University, 52074 Aachen, Germany
| | - Thomas Kraus
- Institute for Occupational and Social Medicine, RWTH Aachen University, 52074 Aachen, Germany
| | - Jens M Baron
- Department of Dermatology and Allergology, RWTH Aachen University, 52074 Aachen, Germany
| |
Collapse
|
5
|
Girolami F, Badino P, Spalenza V, Manzini L, Renzone G, Salzano AM, Dal Piaz F, Scaloni A, Rychen G, Nebbia C. Identification of candidate biomarkers of the exposure to PCBs in contaminated cattle: A gene expression- and proteomic-based approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 640-641:22-30. [PMID: 29852444 DOI: 10.1016/j.scitotenv.2018.05.284] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 05/23/2018] [Accepted: 05/23/2018] [Indexed: 06/08/2023]
Abstract
Dioxins and polychlorinated biphenyls (PCBs) are widespread and persistent contaminants. Through a combined gene expression/proteomic-based approach, candidate biomarkers of the exposure to such environmental pollutants in cattle subjected to a real eco-contamination event were identified. Animals were removed from the polluted area and fed a standard ration for 6 months. The decontamination was monitored by evaluating dioxin and PCB levels in pericaudal fat two weeks after the removal from the contaminated area (day 0) and then bimonthly for six months (days 59, 125 and 188). Gene expression measurements demonstrated that CYP1B1 expression was significantly higher in blood lymphocytes collected in contaminated animals (day 0), and decreased over time during decontamination. mRNA levels of interleukin 2 showed an opposite quantitative trend. MALDI-TOF-MS polypeptide profiling of serum samples ascertained a progressive decrease (from day 0 to 188) of serum levels of fibrinogen β-chain and serpin A3-7-like fragments, apolipoprotein (APO) C-II and serum amyloid A-4 protein, along with an augmented representation of transthyretin isoforms, as well as APOC-III and APOA-II proteins during decontamination. When differentially represented species were combined with serum antioxidant, acute phase and proinflammatory protein levels already ascertained in the same animals (Cigliano et al., 2016), bioinformatics unveiled an interaction network linking together almost all components. This suggests the occurrence of a complex PCB-responsive mechanism associated with animal contamination/decontamination, including a cohort of protein/polypeptide species involved in blood redox homeostasis, inflammation and lipid transport. All together, these results suggest the use in combination of such biomarkers for identifying PCB-contaminated animals, and for monitoring the restoring of their healthy condition following a decontamination process.
Collapse
Affiliation(s)
- F Girolami
- Department of Veterinary Sciences, University of Torino, Largo P. Braccini 2, Grugliasco, Italy
| | - P Badino
- Department of Veterinary Sciences, University of Torino, Largo P. Braccini 2, Grugliasco, Italy
| | - V Spalenza
- Department of Veterinary Sciences, University of Torino, Largo P. Braccini 2, Grugliasco, Italy
| | - L Manzini
- Department of Veterinary Sciences, University of Torino, Largo P. Braccini 2, Grugliasco, Italy
| | - G Renzone
- Proteomics and Mass Spectrometry Laboratory, ISPAAM, National Research Council, Via Argine 1085, Napoli, Italy
| | - A M Salzano
- Proteomics and Mass Spectrometry Laboratory, ISPAAM, National Research Council, Via Argine 1085, Napoli, Italy
| | - F Dal Piaz
- Department of Medicine and Surgery, University of Salerno, Via Giovanni Paolo II 132, Fisciano, Italy
| | - A Scaloni
- Proteomics and Mass Spectrometry Laboratory, ISPAAM, National Research Council, Via Argine 1085, Napoli, Italy
| | - G Rychen
- Unité de Recherches Animal et Fonctionnalités des Produits Animaux, INRA-Université de Lorraine, 2 av de la forêt de Haye, Vandoeuvre-lès-Nancy Cedex, France
| | - C Nebbia
- Department of Veterinary Sciences, University of Torino, Largo P. Braccini 2, Grugliasco, Italy.
| |
Collapse
|
6
|
Wimmerová S, van den Berg M, Chovancová J, Patayová H, Jusko TA, van Duursen MBM, Palkovičová Murínová Ľ, Canton RF, van Ede KI, Trnovec T. Relative effect potency estimates of dioxin-like activity for dioxins, furans, and dioxin-like PCBs in adults based on cytochrome P450 1A1 and 1B1 gene expression in blood. ENVIRONMENT INTERNATIONAL 2016; 96:24-33. [PMID: 27588699 PMCID: PMC6047354 DOI: 10.1016/j.envint.2016.08.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 08/22/2016] [Accepted: 08/22/2016] [Indexed: 05/04/2023]
Abstract
BACKGROUND In the risk assessment of PCDDs, PCDFs, and dioxin-like (DL) PCBs, regulatory authorities support the use of the toxic equivalency factor (TEF)-scheme derived from a heterogeneous data set of the relative effect potency (REPs) estimates. OBJECTIVES We sought to determine REPs for dioxin-like compounds (DLCs) using expression of cytochrome P450 (CYP) 1A1 and 1B1 mRNA in human peripheral blood mononuclear cells representing two different pathways. METHODS We used a sex and age adjusted regression-based approach comparing the strength of association between each DLC and the cytochrome P450 (CYP) 1A1 and 1B1 mRNA expression in 320 adults residing in an organochlorine-polluted area of eastern Slovakia. RESULTS We calculated REPs based on CYP1A1 expression for 4 PCDDs, 8 PCDFs, and 1 PCB congener, and based on CYP1B1 expression for 5 PCDFs and 11 PCB congeners. REPs from CYP1A1 correlated with REPs previously derived from thyroid volume (ρ=0.85; p<0.001) and serum FT4 (ρ=0.77; p=0.009). The 13 log REPs from CYP1A1 correlated with log WHO-TEFs (r=0.63; p=0.015) and 11 log PCB REPs with PCB consensus toxicity factors (CTFs) for compounds with WHO-TEFs (r=0.80; p=0.003). The complete set of derived 56 log REPs correlated with the log CTFs (r=0.77; p=0.001) and log WHO-TEFs (r=0.81; p<0.001). CONCLUSIONS REPs calculated from thyroid and cytochrome P450 endpoints realistically reflect human exposure scenarios because they are based on human chronic and low-dose exposures. While the CYP 1A1 seems more suitable for toxicity evaluation of PCDD/Fs, the CYP 1B1 is more apt for PCDFs and PCBs and reflects different pathways.
Collapse
Affiliation(s)
- Soňa Wimmerová
- Slovak Medical University, Limbová 14, 83303 Bratislava, Slovakia.
| | - Martin van den Berg
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, P.O. Box 80.176, 3508, TD, Utrecht, The Netherlands.
| | - Jana Chovancová
- Slovak Medical University, Limbová 14, 83303 Bratislava, Slovakia.
| | | | - Todd A Jusko
- Departments of Public Health Sciences and Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.
| | - Majorie B M van Duursen
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, P.O. Box 80.176, 3508, TD, Utrecht, The Netherlands.
| | | | - Rocio F Canton
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, P.O. Box 80.176, 3508, TD, Utrecht, The Netherlands.
| | - Karin I van Ede
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, P.O. Box 80.176, 3508, TD, Utrecht, The Netherlands.
| | - Tomáš Trnovec
- Slovak Medical University, Limbová 14, 83303 Bratislava, Slovakia.
| |
Collapse
|
7
|
Girolami F, Spalenza V, Manzini L, Carletti M, Nebbia C. Constitutive expression of the AHR signaling pathway in a bovine mammary epithelial cell line and modulation by dioxin-like PCB and other AHR ligands. Toxicol Lett 2015; 232:98-105. [DOI: 10.1016/j.toxlet.2014.09.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 09/15/2014] [Accepted: 09/16/2014] [Indexed: 12/20/2022]
|