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Faulconnier Y, Pawlowski K, Chambon C, Durand D, Pires J, Leroux C. Liver transcriptome and proteome are modulated by nutrient restriction in early lactation cows challenged with intramammary lipopolysaccharide. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 52:101326. [PMID: 39303391 DOI: 10.1016/j.cbd.2024.101326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 09/06/2024] [Accepted: 09/09/2024] [Indexed: 09/22/2024]
Abstract
The objective was to evaluate the effects of nutrient restriction on liver function 24 h after an intramammary lipopolysaccharide (LPS) challenge in early lactation cows using transcriptomic and proteomic analyses. Multiparous Holstein cows were fed a lactation diet (CONT, n = 8) throughout the study or were switched to a diet diluted with barley straw (48 % DM) for 96 h (REST, n = 8) starting at 24 (18 to 30) days in milk. At 72 h, a healthy rear mammary quarter was infused with 50 μg of LPS in all cows. Blood and liver biopsies were collected at 96 h, corresponding to 24 h after LPS challenge. Liver transcriptome was analyzed with a 44 K bovine microarray and proteome by LC MS/MS. Transcriptomic and proteomic data were analyzed using GeneSpring (moderated t-test with Westfall-Young correction) and the "between subject design", respectively. Data mining was performed using Panther and Pathway Studio software. By design, the negative energy balance was -68 and -37 MJ/d in REST and CONT, respectively. Plasma non-esterified FAs, and β-hydroxybutyrate were significantly greater in REST compared to CONT, which is consistent with 96 h of nutrient restriction in REST and ketosis induction. We detected 77 and 91 differentially expressed genes at mRNA and protein levels, respectively, between CONT and REST. Genes involved in fatty acid synthesis (e.g.: ACAT, FASN, SCD) were downregulated in REST, whereas those involved in fatty acid oxidation, detoxification, cholesterol synthesis, lipoprotein lipid secretion, and gluconeogenesis (e.g.: ACAD, CPT1A, CPT1B, CPT2) were upregulated. Differentially abundant mRNAs and proteins were consistent with negative energy balance and plasma metabolite concentrations, and reflected a state of intense lipomobilization, glucose deficit and ketogenesis in REST cows. Nutrient restriction did not change in deep liver expression of genes directly involved in immune function 24 h after an intramammary LPS challenge.
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Affiliation(s)
- Yannick Faulconnier
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France
| | - Karol Pawlowski
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France; Warsaw University of Life Sciences, Faculty of Veterinary Medicine, Department of Pathology and Veterinary Diagnostics, Poland
| | - Christophe Chambon
- INRAE, Plateforme d'Exploration du Métabolisme, composante protéomique PFEMcp, F-63122 Saint-Genès Champanelle, France
| | - Denys Durand
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France
| | - José Pires
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France
| | - Christine Leroux
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France; Department of Food Science and Technology, University of California, Davis, CA, USA.
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Velayudhan SM, Alam S, Yin T, Brügemann K, Buerkert A, Sejian V, Bhatta R, Schlecht E, König S. Selective Sweeps in Cattle Genomes in Response to the Influence of Urbanization and Environmental Contamination. Genes (Basel) 2023; 14:2083. [PMID: 38003026 PMCID: PMC10671461 DOI: 10.3390/genes14112083] [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: 10/23/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
A genomic study was conducted to identify the effects of urbanization and environmental contaminants with heavy metals on selection footprints in dairy cattle populations reared in the megacity of Bengaluru, South India. Dairy cattle reared along the rural-urban interface of Bengaluru with/without access to roughage from public lakeshores were selected. The genotyped animals were subjected to the cross-population-extended haplotype homozygosity (XP-EHH) methodology to infer selection sweeps caused by urbanization (rural, mixed, and urban) and environmental contamination with cadmium and lead. We postulated that social-ecological challenges contribute to mechanisms of natural selection. A number of selection sweeps were identified when comparing the genomes of cattle located in rural, mixed, or urban regions. The largest effects were identified on BTA21, displaying pronounced peaks for selection sweeps for all three urbanization levels (urban_vs_rural, urban_vs_mixed and rural_vs_mixed). Selection sweeps are located in chromosomal segments in close proximity to the genes lrand rab interactor 3 (RIN3), solute carrier family 24 member 4 (SLC24A4), tetraspanin 3 (TSPAN3), and proline-serine-threonine phosphatase interacting protein 1 (PSTPIP1). Functional enrichment analyses of the selection sweeps for all three comparisons revealed a number of gene ontology (GO) and KEGG terms, which were associated with reproduction, metabolism, and cell signaling-related functional mechanisms. Likewise, a number of the chromosomal segments under selection were observed when creating cattle groups according to cadmium and lead contaminations. Stronger and more intense positive selection sweeps were observed for the cadmium contaminated group, i.e., signals of selection on BTA 16 and BTA19 in close proximity to genes regulating the somatotropic axis (growth factor receptor bound protein 2 (GRB2) and cell ion exchange (chloride voltage-gated channel 6 (CLCN6)). A few novel, so far uncharacterized genes, mostly with effects on immune physiology, were identified. The lead contaminated group revealed sweeps which were annotated with genes involved in carcass traits (TNNC2, SLC12A5, and GABRA4), milk yield (HTR1D, SLCO3A1, TEK, and OPCML), reproduction (GABRA4), hypoxia/stress response (OPRD1 and KDR), cell adhesion (PCDHGC3), inflammatory response (ADORA2A), and immune defense mechanism (ALCAM). Thus, the findings from this study provide a deeper insight into the genomic regions under selection under the effects of urbanization and environmental contamination.
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Affiliation(s)
| | - Shahin Alam
- Animal Husbandry in the Tropics and Subtropics, University of Kassel and Georg-August-Universität Göttingen, Steinstr. 19, 37213 Witzenhausen, Germany
| | - Tong Yin
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Ludwigstraße 21 b, 35390 Giessen, Germany
| | - Kerstin Brügemann
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Ludwigstraße 21 b, 35390 Giessen, Germany
| | - Andreas Buerkert
- Organic Plant Production and Agroecosystems Research in the Tropics and Subtropics, University of Kassel, 37213 Witzenhausen, Germany
| | - Veerasamy Sejian
- National Institute of Animal Nutrition and Physiology (NIANP), Hosur Rd, Chennakeshava Nagar, Adugodi, Bengaluru 560030, India
| | - Raghavendra Bhatta
- National Institute of Animal Nutrition and Physiology (NIANP), Hosur Rd, Chennakeshava Nagar, Adugodi, Bengaluru 560030, India
| | - Eva Schlecht
- Animal Husbandry in the Tropics and Subtropics, University of Kassel and Georg-August-Universität Göttingen, Steinstr. 19, 37213 Witzenhausen, Germany
| | - Sven König
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Ludwigstraße 21 b, 35390 Giessen, Germany
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Seregin AA, Smirnova LP, Dmitrieva EM, Zavialova MG, Simutkin GG, Ivanova SA. Differential Expression of Proteins Associated with Bipolar Disorder as Identified Using the PeptideShaker Software. Int J Mol Sci 2023; 24:15250. [PMID: 37894929 PMCID: PMC10607299 DOI: 10.3390/ijms242015250] [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: 07/28/2023] [Revised: 09/29/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023] Open
Abstract
The prevalence of bipolar disorder (BD) in modern society is growing rapidly, but due to the lack of paraclinical criteria, its differential diagnosis with other mental disorders is somewhat challenging. In this regard, the relevance of proteomic studies is increasing due to the development of methods for processing large data arrays; this contributes to the discovery of protein patterns of pathological processes and the creation of new methods of diagnosis and treatment. It seems promising to search for proteins involved in the pathogenesis of BD in an easily accessible material-blood serum. Sera from BD patients and healthy individuals were purified via affinity chromatography to isolate 14 major proteins and separated using 1D SDS-PAGE. After trypsinolysis, the proteins in the samples were identified via HPLC/mass spectrometry. Mass spectrometric data were processed using the OMSSA and X!Tandem search algorithms using the UniProtKB database, and the results were analyzed using PeptideShaker. Differences in proteomes were assessed via an unlabeled NSAF-based analysis using a two-tailed Bonferroni-adjusted t-test. When comparing the blood serum proteomes of BD patients and healthy individuals, 10 proteins showed significant differences in NSAF values. Of these, four proteins were predominantly present in BD patients with the maximum NSAF value: 14-3-3 protein zeta/delta; ectonucleoside triphosphate diphosphohydrolase 7; transforming growth factor-beta-induced protein ig-h3; and B-cell CLL/lymphoma 9 protein. Further exploration of the role of these proteins in BD is warranted; conducting such studies will help develop new paraclinical criteria and discover new targets for BD drug therapy.
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Affiliation(s)
- Alexander A. Seregin
- Mental Health Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk 634014, Russia; (A.A.S.)
| | - Liudmila P. Smirnova
- Mental Health Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk 634014, Russia; (A.A.S.)
| | - Elena M. Dmitrieva
- Mental Health Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk 634014, Russia; (A.A.S.)
| | | | - German G. Simutkin
- Mental Health Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk 634014, Russia; (A.A.S.)
| | - Svetlana A. Ivanova
- Mental Health Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk 634014, Russia; (A.A.S.)
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Muench MO, Fomin ME, Gutierrez AG, López-Terrada D, Gilfanova R, Nosworthy C, Beyer AI, Ostolaza G, Kats D, Matlock KL, Cairo S, Keller C. CD203c is expressed by human fetal hepatoblasts and distinguishes subsets of hepatoblastoma. Front Oncol 2023; 13:927852. [PMID: 36845728 PMCID: PMC9947649 DOI: 10.3389/fonc.2023.927852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 01/19/2023] [Indexed: 02/11/2023] Open
Abstract
Background & Aims Hepatocytic cells found during prenatal development have unique features compared to their adult counterparts, and are believed to be the precursors of pediatric hepatoblastoma. The cell-surface phenotype of hepatoblasts and hepatoblastoma cell lines was evaluated to discover new markers of these cells and gain insight into the development of hepatocytic cells and the phenotypes and origins of hepatoblastoma. Methods Human midgestation livers and four pediatric hepatoblastoma cell lines were screened using flow cytometry. Expression of over 300 antigens was evaluated on hepatoblasts defined by their expression of CD326 (EpCAM) and CD14. Also analyzed were hematopoietic cells, expressing CD45, and liver sinusoidal-endothelial cells (LSECs), expressing CD14 but lacking CD45 expression. Select antigens were further examined by fluorescence immunomicroscopy of fetal liver sections. Antigen expression was also confirmed on cultured cells by both methods. Gene expression analysis by liver cells, 6 hepatoblastoma cell lines, and hepatoblastoma cells was performed. Immunohistochemistry was used to evaluate CD203c, CD326, and cytokeratin-19 expression on three hepatoblastoma tumors. Results Antibody screening identified many cell surface markers commonly or divergently expressed by hematopoietic cells, LSECs, and hepatoblasts. Thirteen novel markers expressed on fetal hepatoblasts were identified including ectonucleotide pyrophosphatase/phosphodiesterase family member 3 (ENPP-3/CD203c), which was found to be expressed by hepatoblasts with widespread expression in the parenchyma of the fetal liver. In culture CD203c+CD326++ cells resembled hepatocytic cells with coexpression of albumin and cytokeratin-19 confirming a hepatoblast phenotype. CD203c expression declined rapidly in culture whereas the loss of CD326 was not as pronounced. CD203c and CD326 were co-expressed on a subset of hepatoblastoma cell lines and hepatoblastomas with an embryonal pattern. Conclusions CD203c is expressed on hepatoblasts and may play a role in purinergic signaling in the developing liver. Hepatoblastoma cell lines were found to consist of two broad phenotypes consisting of a cholangiocyte-like phenotype that expressed CD203c and CD326 and a hepatocyte-like phenotype with diminished expression of these markers. CD203c was expressed by some hepatoblastoma tumors and may represent a marker of a less differentiated embryonal component.
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Affiliation(s)
- Marcus O. Muench
- Vitalant Research Institute, San Francisco, CA, United States,Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, United States,*Correspondence: Marcus O. Muench,
| | - Marina E. Fomin
- Vitalant Research Institute, San Francisco, CA, United States
| | | | - Dolores López-Terrada
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States,Texas Children’s Cancer Center, Texas Children’s Hospital, Houston, TX, United States
| | | | | | - Ashley I. Beyer
- Vitalant Research Institute, San Francisco, CA, United States
| | | | - Dina Kats
- Pediatric Cancer Biology, Children’s Cancer Therapy Development Institute, Beaverton, OR, United States
| | | | - Stefano Cairo
- Research and Development Unit, XenTech, Evry, France
| | - Charles Keller
- Pediatric Cancer Biology, Children’s Cancer Therapy Development Institute, Beaverton, OR, United States
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Elolimy AA, Liang Y, Lopes MG, Loor JJ. Antioxidant networks and the microbiome as components of efficiency in dairy cattle. Livest Sci 2021. [DOI: 10.1016/j.livsci.2021.104656] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Milanesi M, Passamonti MM, Cappelli K, Minuti A, Palombo V, Sgorlon S, Capomaccio S, D’Andrea M, Trevisi E, Stefanon B, Williams JL, Ajmone-Marsan P. Genetic Regulation of Biomarkers as Stress Proxies in Dairy Cows. Genes (Basel) 2021; 12:genes12040534. [PMID: 33917627 PMCID: PMC8067459 DOI: 10.3390/genes12040534] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/31/2021] [Accepted: 04/02/2021] [Indexed: 01/02/2023] Open
Abstract
Stress in livestock reduces productivity and is a welfare concern. At a physiological level, stress is associated with the activation of inflammatory responses and increased levels of harmful reactive oxygen species. Biomarkers that are indicative of stress could facilitate the identification of more stress-resilient animals. We examined twenty-one metabolic, immune response, and liver function biomarkers that have been associated with stress in 416 Italian Simmental and 436 Italian Holstein cows which were genotyped for 150K SNPs. Single-SNP and haplotype-based genome-wide association studies were carried out to assess whether the variation in the levels in these biomarkers is under genetic control and to identify the genomic loci involved. Significant associations were found for the plasma levels of ceruloplasmin (Bos taurus chromosome 1-BTA1), paraoxonase (BTA4) and γ-glutamyl transferase (BTA17) in the individual breed analysis that coincided with the position of the genes coding for these proteins, suggesting that their expression is under cis-regulation. A meta-analysis of both breeds identified additional significant associations with paraoxonase on BTA 16 and 26. Finding genetic associations with variations in the levels of these biomarkers suggests that the selection for high or low levels of expression could be achieved rapidly. Whether the level of expression of the biomarkers correlates with the response to stressful situations has yet to be determined.
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Affiliation(s)
- Marco Milanesi
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (M.M.); (M.M.P.); (A.M.); (E.T.); (J.L.W.)
- Department for Innovation in Biological, Agro-Food and Forest Systems—DIBAF, Università della Tuscia, 01100 Viterbo, Italy
| | - Matilde Maria Passamonti
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (M.M.); (M.M.P.); (A.M.); (E.T.); (J.L.W.)
| | - Katia Cappelli
- Dipartimento di Medicina Veterinaria, Università degli Studi di Perugia, 06126 Perugia, Italy; (K.C.); (S.C.)
| | - Andrea Minuti
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (M.M.); (M.M.P.); (A.M.); (E.T.); (J.L.W.)
| | - Valentino Palombo
- Dipartimento Agricoltura Ambiente e Alimenti, Università del Molise, 86100 Campobasso, Italy; (V.P.); (M.D.)
| | - Sandy Sgorlon
- Dipartimento di Scienze Agroalimentari, Ambientali e Animali. Università degli Studi di Udine, 33100 Udine, Italy; (S.S.); (B.S.)
| | - Stefano Capomaccio
- Dipartimento di Medicina Veterinaria, Università degli Studi di Perugia, 06126 Perugia, Italy; (K.C.); (S.C.)
| | - Mariasilvia D’Andrea
- Dipartimento Agricoltura Ambiente e Alimenti, Università del Molise, 86100 Campobasso, Italy; (V.P.); (M.D.)
| | - Erminio Trevisi
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (M.M.); (M.M.P.); (A.M.); (E.T.); (J.L.W.)
| | - Bruno Stefanon
- Dipartimento di Scienze Agroalimentari, Ambientali e Animali. Università degli Studi di Udine, 33100 Udine, Italy; (S.S.); (B.S.)
| | - John Lewis Williams
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (M.M.); (M.M.P.); (A.M.); (E.T.); (J.L.W.)
- Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Adelaide, SA 5371, Australia
| | - Paolo Ajmone-Marsan
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (M.M.); (M.M.P.); (A.M.); (E.T.); (J.L.W.)
- Nutrigenomics and Proteomics Research Center-PRONUTRIGEN, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy
- Correspondence:
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Gessner DK, Brock C, Hof LM, Most E, Koch C, Eder K. Effects of supplementation of green tea extract on the milk performance of peripartal dairy cows and the expression of stress response genes in the liver. J Anim Sci Biotechnol 2020; 11:57. [PMID: 32518649 PMCID: PMC7273663 DOI: 10.1186/s40104-020-00465-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 04/24/2020] [Indexed: 11/23/2022] Open
Abstract
Background We hypothesised that supplementation of green tea extract (GTE) in dairy cows during the transition period can attenuate proinflammatory conditions and prevent endoplasmic reticulum (ER) stress in the liver of these cows. Thirty Holstein cows with an average parity of 3.06 (± 1.31, SD) were divided into a control group and a group that received a daily amount of 10 g of GTE from d 7 before the calving day and a daily amount of 20 g of GTE from the day of calving until d 7 of lactation. Results Cows supplemented with GTE did not show differences in energy intake or milk yield in weeks 2–7 of lactation. However, these cows had a lower milk fat concentration and a lower energy corrected milk yield than the control cows and showed a trend of improved energy balance. The relative mRNA concentrations of proinflammatory genes, genes involved in the acute phase reaction and antioxidant genes in the liver in weeks 1, 4 and 7 of lactation were not different between the two groups of cows. The concentrations of α-tocopherol and the Trolox equivalent antioxidant capacity in plasma were not different between the two groups. However, the group supplemented with GTE showed significant reductions of some genes of the unfolded protein response (UPR) in week 1 and a trend of lower liver triacylglycerol (TAG) concentrations in the liver compared to the control group. Conclusions This study shows that supplementation of GTE in dairy cows lowers the fat concentration in the milk but overall has no effect on the expression of inflammatory genes and the antioxidative status in dairy cows during early lactation. The finding of reduced mRNA levels of genes involved in the UPR at week 1, however, supports other results showing that supplementation of polyphenols could prevent the development of ER stress in the liver of cows during early lactation. The finding of a tendency towards a reduced TAG concentration in the liver of cows supplemented with GTE might be due to an improved energy balance in these cows.
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Affiliation(s)
- Denise K Gessner
- Institute of Animal Nutrition and Nutrition Physiology, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Corinna Brock
- Institute of Animal Nutrition and Nutrition Physiology, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Lena M Hof
- Institute of Animal Nutrition and Nutrition Physiology, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Erika Most
- Institute of Animal Nutrition and Nutrition Physiology, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Christian Koch
- Educational and Research Centre for Animal Husbandry, Hofgut Neumühle, 67728 Münchweiler an der Alsenz, Germany
| | - Klaus Eder
- Institute of Animal Nutrition and Nutrition Physiology, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
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Tong DL, Kempsell KE, Szakmany T, Ball G. Development of a Bioinformatics Framework for Identification and Validation of Genomic Biomarkers and Key Immunopathology Processes and Controllers in Infectious and Non-infectious Severe Inflammatory Response Syndrome. Front Immunol 2020; 11:380. [PMID: 32318053 PMCID: PMC7147506 DOI: 10.3389/fimmu.2020.00380] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 02/17/2020] [Indexed: 12/12/2022] Open
Abstract
Sepsis is defined as dysregulated host response caused by systemic infection, leading to organ failure. It is a life-threatening condition, often requiring admission to an intensive care unit (ICU). The causative agents and processes involved are multifactorial but are characterized by an overarching inflammatory response, sharing elements in common with severe inflammatory response syndrome (SIRS) of non-infectious origin. Sepsis presents with a range of pathophysiological and genetic features which make clinical differentiation from SIRS very challenging. This may reflect a poor understanding of the key gene inter-activities and/or pathway associations underlying these disease processes. Improved understanding is critical for early differential recognition of sepsis and SIRS and to improve patient management and clinical outcomes. Judicious selection of gene biomarkers suitable for development of diagnostic tests/testing could make differentiation of sepsis and SIRS feasible. Here we describe a methodologic framework for the identification and validation of biomarkers in SIRS, sepsis and septic shock patients, using a 2-tier gene screening, artificial neural network (ANN) data mining technique, using previously published gene expression datasets. Eight key hub markers have been identified which may delineate distinct, core disease processes and which show potential for informing underlying immunological and pathological processes and thus patient stratification and treatment. These do not show sufficient fold change differences between the different disease states to be useful as primary diagnostic biomarkers, but are instrumental in identifying candidate pathways and other associated biomarkers for further exploration.
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Affiliation(s)
- Dong Ling Tong
- Artificial Intelligence Laboratory, Faculty of Engineering and Computing, First City University College, Petaling Jaya, Malaysia.,School of Science and Technology, Nottingham Trent University, Nottingham, United Kingdom
| | - Karen E Kempsell
- Public Health England, National Infection Service, Porton Down, Salisbury, United Kingdom
| | - Tamas Szakmany
- Department of Anaesthesia Intensive Care and Pain Medicine, Division of Population Medicine, Cardiff University, Cardiff, United Kingdom
| | - Graham Ball
- School of Science and Technology, Nottingham Trent University, Nottingham, United Kingdom
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Benedet A, Ho PN, Xiang R, Bolormaa S, De Marchi M, Goddard ME, Pryce JE. The use of mid-infrared spectra to map genes affecting milk composition. J Dairy Sci 2019; 102:7189-7203. [PMID: 31178181 DOI: 10.3168/jds.2018-15890] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 04/12/2019] [Indexed: 12/20/2022]
Abstract
The aim of this study was to investigate the feasibility of using mid-infrared (MIR) spectroscopy analysis of milk samples to increase the power and precision of genome-wide association studies (GWAS) for milk composition and to better distinguish linked quantitative trait loci (QTL). To achieve this goal, we analyzed phenotypic data of milk composition traits, related MIR spectra, and genotypic data comprising 626,777 SNP on 5,202 Holstein, Jersey, and crossbred cows. We performed a conventional GWAS on protein, lactose, fat, and fatty acid concentrations in milk, a GWAS on individual MIR wavenumbers, and a partial least squares regression (PLS), which is equivalent to a multi-trait GWAS, exploiting MIR data simultaneously to predict SNP genotypes. The PLS detected most of the QTL identified using single-trait GWAS, usually with a higher significance value, as well as previously undetected QTL for milk composition. Each QTL tends to have a different pattern of effects across the MIR spectrum and this explains the increased power. Because SNP tracking different QTL tend to have different patterns of effect, it was possible to distinguish closely linked QTL. Overall, the results of this study suggest that using MIR data through either GWAS or PLS analysis applied to genomic data can provide a powerful tool to distinguish milk composition QTL.
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Affiliation(s)
- A Benedet
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Legnaro 35020, Padova, Italy
| | - P N Ho
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria 3083, Australia
| | - R Xiang
- Faculty of Veterinary & Agricultural Science, University of Melbourne, Victoria 3010, Australia
| | - S Bolormaa
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria 3083, Australia
| | - M De Marchi
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Legnaro 35020, Padova, Italy
| | - M E Goddard
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria 3083, Australia; Faculty of Veterinary & Agricultural Science, University of Melbourne, Victoria 3010, Australia
| | - J E Pryce
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria 3083, Australia; School of Applied Systems Biology, La Trobe University, Bundoora, Victoria 3083, Australia.
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Abstract
Inflammatory bowel disease is a chronic nonspecific inflammatory disease of the intestine. Its pathogenesis is not yet fully understood. It may be related to heredity, environmental triggers, infection, immune dysfunction and other factors. Purinergic receptor (P2X7R) ligand-gated ion channel is closely related to inflammation and widely expressed in intestinal cells. Previous studies have shown that ATP/P2X7R signal is involved in the pathogenesis of intestinal inflammation, but its specific mechanism needs further study. This article reviews the research progress of P2X7 receptor in inflammatory bowel disease.
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Affiliation(s)
- Yajun Liu
- a Department of Gastroenterology , Xiangya Hospital, Central South University , Changsha , China
| | - Xiaowei Liu
- a Department of Gastroenterology , Xiangya Hospital, Central South University , Changsha , China
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An Y, Cai H, Yang Y, Zhang Y, Liu S, Wu X, Duan Y, Sun D, Chen X. Identification of ENTPD8 and cytidine in pancreatic cancer by metabolomic and transcriptomic conjoint analysis. Cancer Sci 2018; 109:2811-2821. [PMID: 29987902 PMCID: PMC6125470 DOI: 10.1111/cas.13733] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 07/06/2018] [Accepted: 07/08/2018] [Indexed: 12/12/2022] Open
Abstract
To identify metabolic pathways that were perturbed in pancreatic cancer (PC), we investigated gene‐metabolite networks by integration of metabolomic and transcriptomic. In this research, we undertook the metabolomic study of 43 paired human PC samples, aiming to identify key metabolic alterations in PC. We also carried out in vitro experiments to validate that the key metabolite cytidine and its related gene ENTPD8 played an important role in PC cell proliferation. We screened out 13 metabolites differentially expressed in PC tissue (PCT) by liquid chromatography/mass spectrometry analysis on 34 metabolites, and the partial least square discrimination analysis results revealed that 9 metabolites among them were remarkably altered in PCT compared to adjacent noncancerous tissue (variable importance in projection >1, P < .05). Among the 9 metabolites, 7 might be potential biomarkers. The most significantly enriched metabolic pathway was pyrimidine metabolism. We analyzed 351 differentially expressed genes from The Cancer Genome Atlas and intersected them with Kyoto Encyclopedia of Genes and Genomes metabolic pathways. We found that ENTPD8 had a gene‐metabolite association with cytidine in the CTP dephosphorylation pathway. We verified by in vitro experiments that the CTP dephosphorylation pathway was changed in PCT compared with adjacent noncancerous tissue. ENTPD8 was downregulated in PCT, causing a reduction in cytidine formation and hence weakened CTP dephosphorylation in pyrimidine metabolism.
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Affiliation(s)
- Yong An
- Department of Hepato-Pancreato-Biliary Surgery, Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - Huihua Cai
- Department of Hepato-Pancreato-Biliary Surgery, Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - Yong Yang
- Department of Hepato-Pancreato-Biliary Surgery, Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - Yue Zhang
- Department of Hepato-Pancreato-Biliary Surgery, Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - Shengyong Liu
- Department of Hepato-Pancreato-Biliary Surgery, Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - Xinquan Wu
- Department of Hepato-Pancreato-Biliary Surgery, Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - Yunfei Duan
- Department of Hepato-Pancreato-Biliary Surgery, Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - Donglin Sun
- Department of Hepato-Pancreato-Biliary Surgery, Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - Xuemin Chen
- Department of Hepato-Pancreato-Biliary Surgery, Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
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Moran B, Cummins SB, Creevey CJ, Butler ST. Transcriptomics of liver and muscle in Holstein cows genetically divergent for fertility highlight differences in nutrient partitioning and inflammation processes. BMC Genomics 2016; 17:603. [PMID: 27514375 PMCID: PMC4982134 DOI: 10.1186/s12864-016-2938-1] [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: 02/18/2016] [Accepted: 07/14/2016] [Indexed: 01/01/2023] Open
Abstract
Background The transition between pregnancy and lactation is a major physiological change for dairy cows. Complex systemic and local processes involving regulation of energy balance, galactopoiesis, utilisation of body reserves, insulin resistance, resumption of oestrous cyclicity and involution of the uterus can affect animal productivity and hence farm profitability. Here we used an established Holstein dairy cow model of fertility that displayed genetic and phenotypic divergence in calving interval. Cows had similar genetic merit for milk production traits, but either very good genetic merit for fertility traits (‘Fert+’; n = 8) or very poor genetic merit for fertility traits (‘Fert-’; n = 8). We used RNA sequencing to investigate gene expression profiles in both liver and muscle tissue biopsies at three distinct time-points: late pregnancy, early lactation and mid lactation (-18, 1 and 147 days relative to parturition, respectively). Results We found 807 and 815 unique genes to be differentially expressed in at least one time-point in liver and muscle respectively, of which 79 % and 83 % were only found in a single time-point; 40 and 41 genes were found differentially expressed at every time-point indicating possible systemic or chronic dysregulation. Functional annotation of all differentially expressed genes highlighted two physiological processes that were impacted at every time-point in the study, These were immune and inflammation, and metabolic, lipid and carbohydrate-binding. Conclusion These pathways have previously been identified by other researchers. We show that several specific genes which are differentially regulated, including IGF-1, might impact dairy fertility. We postulate that an increased burden of reactive oxidation species, coupled with a chronic inflammatory state, might reduce dairy cow fertility in our model. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2938-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bruce Moran
- Teagasc, Animal & Grassland Research and Innovation Centre, Grange, Dunsany, Co. Meath, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Sean B Cummins
- Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Christopher J Creevey
- Teagasc, Animal & Grassland Research and Innovation Centre, Grange, Dunsany, Co. Meath, Ireland.,Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3FG, UK
| | - Stephen T Butler
- Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland.
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Khan MJ, Jacometo CB, Vailati Riboni M, Trevisi E, Graugnard DE, Corrêa MN, Loor JJ. Stress and inflammatory gene networks in bovine liver are altered by plane of dietary energy during late pregnancy. Funct Integr Genomics 2015; 15:563-76. [DOI: 10.1007/s10142-015-0443-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 04/07/2015] [Accepted: 04/20/2015] [Indexed: 01/26/2023]
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Bertoni G, Minuti A, Trevisi E. Immune system, inflammation and nutrition in dairy cattle. ANIMAL PRODUCTION SCIENCE 2015. [DOI: 10.1071/an14863] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Good health is essential for good performance and the welfare of dairy cows, and nutrition is an important component of good health. Health is influenced by the interaction between the innate adaptive components of the immune system and other factors, such as the local and systemic inflammatory response, which can sometimes be more harmful than useful. Therefore, for dairy cows, particularly those in the periparturient period, it is important to avoid, or reduce as much as possible, any kind of infectious, parasitic or metabolic disease and the associated inflammation. Such inflammation can impair cow performance by lowering milk yield, dry matter intake, fertility and energy efficiency, and can reduce liver function. Good nutrition is essential in maintaining a functional immune system, while also avoiding other causes of inflammation, such as tissue damage, and digestive and metabolic syndrome-related disorders. Provision of appropriate nutrients, such as antioxidants, omega-3 polyunsaturated fatty acids, conjugated linoleic acid and vitamin D can have anti-inflammatory effects. In the future, ways to reduce inflammation while maintaining a good immune defence must be developed and the susceptibility of the cow to diseases and inflammation evaluated. Ideally, we would be able to selectively breed for cows with a lower susceptibility to both diseases and inflammation.
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