1
|
Terenina E, Iannuccelli N, Billon Y, Fève K, Gress L, Bazovkina D, Mormede P, Larzul C. Genetic determinism of cortisol levels in pig. Front Genet 2025; 16:1461385. [PMID: 40144889 PMCID: PMC11936974 DOI: 10.3389/fgene.2025.1461385] [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: 07/08/2024] [Accepted: 02/24/2025] [Indexed: 03/28/2025] Open
Abstract
In facing the challenge of sustainability, animal breeding provides the option to improve animal robustness. In the search for new selection criteria related to robustness, the hypothalamic-pituitary-adrenocortical (HPA) axis is studied as a major neuroendocrine system involved in metabolic regulations and adaptive responses. Indeed, HPA axis activity is strongly influenced by genetic factors acting at several levels of the axis. The adrenocorticotropic hormone (ACTH) stimulation test has long been used to analyze interindividual and genetic differences in HPA axis activity in several species, including pigs. To uncover the genetic determinism of HPA activity and its influence on functional traits and robustness, a divergent selection experiment was carried out for three generations in a Large White pig population based on plasma cortisol levels measured one hour after injection of ACTH. In the present study the response to selection was very strong (confirming our previous studies), with a heritability value of cortisol level after ACTH injections reaching 0.64 (±0.03). The difference between the two divergent lines was around five genetic standard deviations after three selection steps. A genome-wide association study pointed out the importance of the glucocorticoid receptor gene (NR3C1) in this response. The measurement of plasma corticosteroid-binding globulin (CBG) binding capacity excluded any significant role of CBG in this selection process. The phenotypic effect of selection on body weight and growth rate was modest and/or inconsistent across generations. The HPA axis, a major neuroendocrine system involved in adaptation processes is highly heritable and responsive to genetic selection. The present experiment confirms the importance of glucocorticoid receptor polymorphism in genetic variation of HPA axis activity-in addition to the previously demonstrated role of CBG gene polymorphism. Further studies will explore the effect of this divergent selection on production and robustness.
Collapse
Affiliation(s)
- Elena Terenina
- GenPhySE, INRAE, ENVT, Université de Toulouse, Castanet Tolosan, France
| | | | | | - Katia Fève
- GenPhySE, INRAE, ENVT, Université de Toulouse, Castanet Tolosan, France
| | - Laure Gress
- GenPhySE, INRAE, ENVT, Université de Toulouse, Castanet Tolosan, France
| | - Darya Bazovkina
- Federal Research Center Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Science, Novosibirsk, Russia
| | - Pierre Mormede
- GenPhySE, INRAE, ENVT, Université de Toulouse, Castanet Tolosan, France
| | - Catherine Larzul
- GenPhySE, INRAE, ENVT, Université de Toulouse, Castanet Tolosan, France
| |
Collapse
|
2
|
Mormede E, Mormede P. Genetic Variation of Hypothalamic-Pituitary-Adrenal Axis Activity in Farm Animals and Beyond. Neuroendocrinology 2024; 115:128-137. [PMID: 39626641 DOI: 10.1159/000542831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 11/14/2024] [Indexed: 01/21/2025]
Abstract
BACKGROUND Many experimental data in several species clearly demonstrate the important genetic contribution to variations in HPA axis activity. The influence of corticosteroid hormones on adaptive processes and on production traits such as growth rate, feed efficiency, carcass composition, and meat quality is a strong impetus to the search for the molecular bases of these differences for efficient genetic selection. SUMMARY Three main sources of genetic variability have been documented so far in farm animal species, the adrenal cortex sensitivity to ACTH-regulating corticosteroid hormone production, the bioavailability of corticosteroid hormones and especially corticosteroid-binding globulin capacity, and glucocorticoid receptor function. The effect of single mutations may be dependent on the genetic background, and genetic variation of cortisol levels may have different functional consequences depending on the molecular mechanisms responsible for this change. KEY MESSAGES Understanding the genetic basis of HPA axis activity allows the development of genomic tools and breeding technologies aimed at improving adaptive capacity and stress tolerance in farm animals and their use as valuable models for the genetic study of the HPA axis and the correlation with adaptation, metabolism, and other functions regulated by adrenal hormones, and associated pathologies (obesity, cardiovascular, etc.). The next step will be to explore HPA axis variability from a system genetics perspective including the multiple sources of variation and their interactions. This multifactorial approach is a prerequisite to the use of the HPA axis phenotypes in the genetic selection for more productive and robust animals, with a high level of production of quality products.
Collapse
Affiliation(s)
- Elena Mormede
- GenPhySE, Université de Toulouse, INRAE, INPT, ENVT, Toulouse, France
| | - Pierre Mormede
- GenPhySE, Université de Toulouse, INRAE, INPT, ENVT, Toulouse, France
| |
Collapse
|
3
|
Clarke BM, Kireta S, Johnston J, Christou C, Greenwood JE, Hurtado PR, Manavis J, Coates PT, Torpy DJ. In Vivo Formation of Adrenal Organoids in a Novel Porcine Model of Adrenocortical Cell Transplantation. Endocrinology 2024; 165:bqae086. [PMID: 39028678 DOI: 10.1210/endocr/bqae086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/25/2024] [Accepted: 07/12/2024] [Indexed: 07/21/2024]
Abstract
Recognizing the limitations of current therapies for Addison's disease, novel treatments that replicate dynamic physiologic corticosteroid secretion, under control of ACTH, are required. The aim of these experiments was to evaluate the feasibility of adrenocortical cell transplantation (ACT) in a large animal model, adapting methods successfully used for intracutaneous pancreatic islet cell transplantation, using a fully biodegradable temporizing matrix. Autologous porcine ACT was undertaken by bilateral adrenalectomy, cell isolation, culture, and intracutaneous injection into a skin site preprepared using a biodegradable temporizing matrix (BTM) foam. Hydrocortisone support was provided during adrenocortical cell engraftment and weaned as tolerated. Blood adrenocortical hormone concentrations were monitored, and the transplant site was examined at endpoint. Outcome measures included cellular histochemistry, systemic hormone production, and hydrocortisone independence. Transplanted adrenocortical cells showed a capability to survive and proliferate within the intracutaneous site and an ability to self-organize into discrete tissue organoids with features of the normal adrenal histologic architecture. Interpretation of systemic hormone levels was confounded by the identification of accessory adrenals and regenerative cortical tissue within the adrenal bed postmortem. Corticosteroids were unable to be completely ceased. ACT in a large animal model has not previously been attempted, yet it is an important step toward clinical translation. These results demonstrate rhe potential for ACT based on the development of adrenal organoids at the BTM site. However, the inability to achieve clinically relevant systemic hormone production suggests insufficient function, likely attributable to insufficient cells through delivered dose and subsequent proliferation.
Collapse
Affiliation(s)
- Brigette Marie Clarke
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide 5005, Australia
- Endocrine and Metabolic Unit, Royal Adelaide Hospital, Adelaide 5000, Australia
- Endocrine and Diabetes Services, The Queen Elizabeth Hospital, Adelaide 5011, Australia
| | - Svjetlana Kireta
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide 5005, Australia
- Central Northern Adelaide Renal and Transplantation Service, Royal Adelaide Hospital, Adelaide 5000, Australia
| | - Julie Johnston
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide 5005, Australia
- Central Northern Adelaide Renal and Transplantation Service, Royal Adelaide Hospital, Adelaide 5000, Australia
| | - Chris Christou
- Preclinical Imaging Research Laboratories, South Australian Health and Medical Research Institute, Gilles Plains 5086, Australia
| | | | - Plinio R Hurtado
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide 5005, Australia
- Central Northern Adelaide Renal and Transplantation Service, Royal Adelaide Hospital, Adelaide 5000, Australia
| | - Jim Manavis
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide 5005, Australia
| | - Patrick Toby Coates
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide 5005, Australia
- Central Northern Adelaide Renal and Transplantation Service, Royal Adelaide Hospital, Adelaide 5000, Australia
| | - David J Torpy
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide 5005, Australia
- Endocrine and Metabolic Unit, Royal Adelaide Hospital, Adelaide 5000, Australia
| |
Collapse
|
4
|
Rode F, Bundgaard C, Areberg J, Madsen LB, Taavoniku I, Hansen L, Weisser J, Olsen LR, Elgaard HT, Eneberg E, Didriksen M. Stress-free blood sampling in minipigs: A novel method for assessing 24-h cortisol profiles and drug effects on diurnal and ultradian rhythms. J Pharmacol Toxicol Methods 2024; 127:107504. [PMID: 38678804 DOI: 10.1016/j.vascn.2024.107504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/02/2024] [Accepted: 04/07/2024] [Indexed: 05/01/2024]
Abstract
We developed a novel, stress-free blood sampling method for minipigs, allowing continuous cortisol monitoring over 24 h. Baseline cortisol levels exhibited both ultradian and diurnal rhythms. During nighttime, smaller ultradian rhythms overlaid a lower baseline cortisol, which increased in sleeping pigs before lights were turned on. Additionally, we developed an analytical tool based on the R package "pracma" to quantify ultradian peak and circadian components of the cortisol profiles. To validate our model, we investigated the effects of Verucerfont, a CRH receptor antagonist, and Venlafaxine, a serotonin-norepinephrine reuptake inhibitor. Verucerfont reduced cortisol levels during the first 9 h without affecting diurnal rhythm. Cortisol peak parameters decreased, with a 31% reduction in overall area under the curve (AUC) and a 38% reduction in ultradian average AUC. Ultradian peaks decreased from 7 to 4.5, with 34% lower amplitude. Venlafaxine maintained plasma concentrations within the targeted human effective range. This method enables us to enhance our understanding of cortisol regulation and provide valuable insights for the impact of investigation drugs on the diurnal and ultradian rhythms of cortisol.
Collapse
|
5
|
Comparative Transcriptomic Analysis of mRNAs, miRNAs and lncRNAs in the Longissimus dorsi Muscles between Fat-Type and Lean-Type Pigs. Biomolecules 2022; 12:biom12091294. [PMID: 36139132 PMCID: PMC9496231 DOI: 10.3390/biom12091294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 09/05/2022] [Accepted: 09/09/2022] [Indexed: 11/24/2022] Open
Abstract
In pigs, meat quality and production are two important traits affecting the pig industry and human health. Compared to lean-type pigs, fat-type pigs contain higher intramuscular fat (IMF) contents, better taste and nutritional value. To uncover genetic factors controlling differences related to IMF in pig muscle, we performed RNA-seq analysis on the transcriptomes of the Longissimus dorsi (LD) muscle of Laiwu pigs (LW, fat-type pigs) and commercial Duroc × Landrace × Yorkshire pigs (DLY, lean-type pigs) at 150 d to compare the expression profiles of mRNA, miRNA and lncRNA. A total of 225 mRNAs, 12 miRNAs and 57 lncRNAs were found to be differentially expressed at the criteria of |log2(foldchange)| > 1 and q < 0.05. The mRNA expression of LDHB was significantly higher in the LD muscle of LW compared to DLY pigs with log2(foldchange) being 9.66. Using protein interaction prediction method, we identified more interactions of estrogen-related receptor alpha (ESRRA) associated with upregulated mRNAs, whereas versican (VCAN) and proenkephalin (PENK) were associated with downregulated mRNAs in LW pigs. Integrated analysis on differentially expressed (DE) mRNAs and miRNAs in the LD muscle between LW and DLY pigs revealed two network modules: between five upregulated mRNA genes (GALNT15, FKBP5, PPARGC1A, LOC110258214 and LOC110258215) and six downregulated miRNA genes (ssc-let-7a, ssc-miR190-3p, ssc-miR356-5p, ssc-miR573-5p, ssc-miR204-5p and ssc-miR-10383), and between three downregulated DE mRNA genes (IFRD1, LOC110258600 and LOC102158401) and six upregulated DE miRNA genes (ssc-miR1379-3p, ssc-miR1379-5p, ssc-miR397-5p, ssc-miR1358-5p, ssc-miR299-5p and ssc-miR1156-5p) in LW pigs. Based on the mRNA and ncRNA binding site targeting database, we constructed a regulatory network with miRNA as the center and mRNA and lncRNA as the target genes, including GALNT15/ssc-let-7a/LOC100523888, IFRD1/ssc-miR1379-5p/CD99, etc., forming a ceRNA network in the LD muscles that are differentially expressed between LW and DLY pigs. Collectively, these data may provide resources for further investigation of molecular mechanisms underlying differences in meat traits between lean- and fat-type pigs.
Collapse
|
6
|
Zhao F, Wei QW, Li BJ, Weng QN, Jiang Y, Ning CB, Liu KQ, Wu WJ, Liu HL. Impact of adrenocorticotropin hormone administration on the endocrinology, estrus onset, and ovarian function of weaned sows. Endocr J 2022; 69:23-33. [PMID: 34456194 DOI: 10.1507/endocrj.ej21-0184] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Chronic stress affects the reproductive health of mammals; however, the impact of adrenocorticotropin hormone (ACTH) level elevation during chronic stress on the reproduction of weaned sows remains unclear. In this study, nine weaned sows with the same parturition date were randomly divided into control group (n = 4) and ACTH group (n = 5). Each group received intravenous administration of ACTH three times daily for 7 days. Blood samples were collected every 3 h after injection. A radioimmunoassay was used to measure the concentrations of cortisol, luteinizing hormone (LH), follicle-stimulating hormone (FSH), progesterone (P4) and estradiol-17β (E2) in the blood. Estrus was determined according to changes in the vulva and the boar contact test. The mRNA expressions of glucocorticoid receptor, FSH receptor, LH receptor (LHR) in the corpus luteum (CL) were detected by qRT-PCR. The results showed that ACTH administration substantially delayed the initiation of estrus and the pre-ovulatory LH peak. The sows of control group ovulated within 10 days and the ovulation rate was 100%, while it was 60% in the ACTH group. Two sows of ACTH group showed pseudo-estrus. The E2 concentrations significantly decreased in the ACTH group at 36 h, 42 h and 66 h of the experimental period. The P4 concentrations in the ACTH group significantly decreased at 132, 138, and 147 h of the experimental period. ACTH significantly reduced the LHR mRNA expression in CLs. In conclusion, long-term repeated ACTH administration affects the endocrinology, estrus onset, and ovarian function of weaned sows.
Collapse
Affiliation(s)
- Fang Zhao
- Institute of Animal Science, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
- Key Laboratory of Crop and Animal Integrated Farming, Ministry of Agriculture and Rural Affairs, Nanjing, 210014, China
| | - Quan-Wei Wei
- Laboratory of Animal Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Bo-Jiang Li
- Laboratory of Animal Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qian-Nan Weng
- Laboratory of Animal Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yi Jiang
- Laboratory of Animal Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Cai-Bo Ning
- Laboratory of Animal Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kai-Qing Liu
- Laboratory of Animal Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wang-Jun Wu
- Laboratory of Animal Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hong-Lin Liu
- Laboratory of Animal Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| |
Collapse
|
7
|
Srikanth K, Park JE, Ji SY, Kim KH, Lee YK, Kumar H, Kim M, Baek YC, Kim H, Jang GW, Choi BH, Lee SD. Genome-Wide Transcriptome and Metabolome Analyses Provide Novel Insights and Suggest a Sex-Specific Response to Heat Stress in Pigs. Genes (Basel) 2020; 11:genes11050540. [PMID: 32403423 PMCID: PMC7291089 DOI: 10.3390/genes11050540] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/06/2020] [Accepted: 05/06/2020] [Indexed: 12/16/2022] Open
Abstract
Heat stress (HS) negatively impacts pig production and swine health. Therefore, to understand the genetic and metabolic responses of pigs to HS, we used RNA-Seq and high resolution magic angle spinning (HR-MAS) NMR analyses to compare the transcriptomes and metabolomes of Duroc pigs (n = 6, 3 barrows and 3 gilts) exposed to heat stress (33 °C and 60% RH) with a control group (25 °C and 60% RH). HS resulted in the differential expression of 552 (236 up, 316 down) and 879 (540 up, 339 down) genes and significant enrichment of 30 and 31 plasma metabolites in female and male pigs, respectively. Apoptosis, response to heat, Toll-like receptor signaling and oxidative stress were enriched among the up-regulated genes, while negative regulation of the immune response, ATP synthesis and the ribosomal pathway were enriched among down-regulated genes. Twelve and ten metabolic pathways were found to be enriched (among them, four metabolic pathways, including arginine and proline metabolism, and three metabolic pathways, including pantothenate and CoA biosynthesis), overlapping between the transcriptome and metabolome analyses in the female and male group respectively. The limited overlap between pathways enriched with differentially expressed genes and enriched plasma metabolites between the sexes suggests a sex-specific response to HS in pigs.
Collapse
Affiliation(s)
- Krishnamoorthy Srikanth
- Amimal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea; (K.S.); (J.-E.P.); (H.K.); (H.K.); (G.-W.J.); (B.-H.C.)
| | - Jong-Eun Park
- Amimal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea; (K.S.); (J.-E.P.); (H.K.); (H.K.); (G.-W.J.); (B.-H.C.)
| | - Sang Yun Ji
- Animal Nutrition and Physiology Team, National Institute of Animal Science, RDA, Wanju 55365, Korea; (S.Y.J.); (K.H.K.); (Y.K.L.); (M.K.); (Y.C.B.)
| | - Ki Hyun Kim
- Animal Nutrition and Physiology Team, National Institute of Animal Science, RDA, Wanju 55365, Korea; (S.Y.J.); (K.H.K.); (Y.K.L.); (M.K.); (Y.C.B.)
| | - Yoo Kyung Lee
- Animal Nutrition and Physiology Team, National Institute of Animal Science, RDA, Wanju 55365, Korea; (S.Y.J.); (K.H.K.); (Y.K.L.); (M.K.); (Y.C.B.)
| | - Himansu Kumar
- Amimal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea; (K.S.); (J.-E.P.); (H.K.); (H.K.); (G.-W.J.); (B.-H.C.)
| | - Minji Kim
- Animal Nutrition and Physiology Team, National Institute of Animal Science, RDA, Wanju 55365, Korea; (S.Y.J.); (K.H.K.); (Y.K.L.); (M.K.); (Y.C.B.)
| | - Youl Chang Baek
- Animal Nutrition and Physiology Team, National Institute of Animal Science, RDA, Wanju 55365, Korea; (S.Y.J.); (K.H.K.); (Y.K.L.); (M.K.); (Y.C.B.)
| | - Hana Kim
- Amimal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea; (K.S.); (J.-E.P.); (H.K.); (H.K.); (G.-W.J.); (B.-H.C.)
| | - Gul-Won Jang
- Amimal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea; (K.S.); (J.-E.P.); (H.K.); (H.K.); (G.-W.J.); (B.-H.C.)
| | - Bong-Hwan Choi
- Amimal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea; (K.S.); (J.-E.P.); (H.K.); (H.K.); (G.-W.J.); (B.-H.C.)
| | - Sung Dae Lee
- Animal Nutrition and Physiology Team, National Institute of Animal Science, RDA, Wanju 55365, Korea; (S.Y.J.); (K.H.K.); (Y.K.L.); (M.K.); (Y.C.B.)
- Correspondence: ; Tel.: +82-63-238-7454; Fax: +82-63-238-7497
| |
Collapse
|
8
|
Comparison of cortisol concentrations in plasma and saliva in dairy cattle following ACTH stimulation. J DAIRY RES 2019; 86:406-409. [PMID: 31722772 DOI: 10.1017/s0022029919000669] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The experiments described in this research communication compared cortisol concentrations in plasma and saliva samples collected from dairy cattle before and after an adrenocorticotropic hormone (ACTH) application. For that purpose, blood and saliva samples were collected from five dairy cows at determined time intervals before (490 min and down to 0 min) and after (10 min and up to 500 min) an ACTH application. Mean baseline cortisol concentrations were greater in plasma compared to saliva. The relative increases and decreases in plasma and salivary cortisol concentrations following ACTH were similar. After ACTH, we observed an increase in cortisol concentrations in plasma after 10 min and in saliva after 20 min. The time of peak concentrations after ACTH were reached at 70 and 80 min for plasma and saliva, respectively. After peak concentrations, values steadily declined and returned to baseline values at 169 ± 15 min in plasma and 170 ± 14 min in saliva. Ratios between salivary and plasma cortisol concentrations were on average 0.09 and did not change substantially during the ACTH challenge. There was a strong positive relationship between salivary and plasma cortisol concentrations. These results indicate that salivary cortisol concentrations can be a good indicator of ACTH-induced plasma cortisol concentrations in dairy cattle.
Collapse
|
9
|
Messad F, Louveau I, Koffi B, Gilbert H, Gondret F. Investigation of muscle transcriptomes using gradient boosting machine learning identifies molecular predictors of feed efficiency in growing pigs. BMC Genomics 2019; 20:659. [PMID: 31419934 PMCID: PMC6697907 DOI: 10.1186/s12864-019-6010-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 07/30/2019] [Indexed: 01/09/2023] Open
Abstract
Background Improving feed efficiency (FE) is a major challenge in pig production. This complex trait is characterized by a high variability. Therefore, the identification of predictors of FE may be a relevant strategy to reduce phenotyping efforts in breeding and selection programs. The aim of this study was to investigate the suitability of expressed muscle genes in prediction of FE traits in growing pigs. The approach considered different transcriptomics experiments to cover a large range of FE values and identify reliable predictors. Results Microarrays data were obtained from longissimus muscles of two lines divergently selected for residual feed intake (RFI). Pigs (n = 71) from three experiments belonged to generations 6 to 8 of selection, were fed either a diet with a standard composition or a diet rich in fiber and lipids, received feed ad libitum or at restricted level, and weighed between 80 and 115 kg at slaughter. For each pig, breeding value for RFI was estimated (RFI-BV), and feed conversion ratio (FCR) and energy-based feed conversion ratio (FCRe) were calculated during the test periods. Gradient boosting algorithms were used on the merged muscle transcriptomes to identify very important predictors of FE traits. About 20,405 annotated molecular probes were commonly expressed in longissimus muscle across experiments. Six to 267 expressed muscle genes covering a variety of biological processes were found as important predictors for RFI-BV (R2 = 0.63–0.65), FCR (R2 = 0.61–0.70) and FCRe (R2 = 0.49–0.52). The error of prediction was less than 8% for FCR. Altogether, 56 predictors were common to RFI-BV and FCR. Expression levels of 24 target genes were further measured by qPCR. Linear regression confirmed the good accuracy of combining mRNA levels of these genes to fit FE traits (RFI-BV: R2 = 0.73, FRC: R2 = 0.76; FCRe: R2 = 0.75). Stepwise regression procedure highlighted 10 genes (FKBP5, MUM1, AKAP12, FYN, TMED3, PHKB, TGF, SOCS6, ILR4, and FRAS1) in a linear combination predicting FCR and FCRe. In addition, FKBP5 and expression levels of five other genes (IGF2, SERINC3, CSRNP3, EZR and RPL16) significantly contributed to RFI-BV. Conclusion It was possible to identify few genes expressed in muscle that might be reliable predictors of feed efficiency. Electronic supplementary material The online version of this article (10.1186/s12864-019-6010-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Farouk Messad
- Pegase, INRA, Agrocampus Ouest, 35590, Saint-Gilles, France
| | | | - Basile Koffi
- Pegase, INRA, Agrocampus Ouest, 35590, Saint-Gilles, France
| | | | | |
Collapse
|
10
|
Zhao X, Niu L, Clerici C, Russo R, Byrd M, Setchell KD. Data analysis of MS-based clinical lipidomics studies with crossover design: A tutorial mini-review of statistical methods. CLINICAL MASS SPECTROMETRY (DEL MAR, CALIF.) 2019; 13:5-17. [PMID: 34841080 PMCID: PMC8620525 DOI: 10.1016/j.clinms.2019.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 05/15/2019] [Accepted: 05/15/2019] [Indexed: 11/28/2022]
Abstract
Clinical lipidomics using mass spectrometry (MS) is important to support discovery of biomarkers for diagnosis and understanding the pathophysiology of diseases. Frequently, lipidomics data from clinical studies have large variations among individuals because the human metabolome/lipidome is strongly influenced by genotype, daily activity, diet and gut flora. This inter-personal variability makes data analysis more complex and normally requires a large cohort for robust statistical analysis. Crossover designed experiments treat each subject as his or her own control, thereby reducing the between-subject variability, such that the effects of exposure/treatment are more likely to be identified when using a relatively small number of subjects. This design repeatedly samples an individual when crossing over from one treatment/exposure to another during the course of the study. The acquired datasets have a distinct data structure resulting from repeated longitudinal measurements. A variety of statistical methods are used in published crossover studies, but many appear to ignore the data structure inherent in the experimental design. An appropriate data analysis approach is critical to discovering robust clinical biomarkers. Hereby, we summarize the statistical methodologies suitable for clinical lipidomics studies using crossover design. To help understand and apply these methods to practical cases, we focused on the general concepts of statistical models in the context of analysis of metabolomics data without spending too much effort on mathematical details. Importantly, we aim to evaluate these methods and provide suggestions for data analysis and biomarker discovery. We applied the discussed methods on a MS-based lipidomics dataset from a double-blind random crossover designed clinical dietary intervention study. The strength and potential pitfalls of each method are briefly discussed and a suggestion for analytic workflow proposed.
Collapse
Affiliation(s)
- Xueheng Zhao
- Division of Pathology and Laboratory Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Liang Niu
- Division of Biostatistics and Bioinformatics, Department of Environmental Health, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Carlo Clerici
- Clinica Di Gastroenterologia – Endoscopia – Epatologia, Policlinico, S. Maria Della Misericordia Azienda Ospedaliera Di Perugia, Italy
| | - Roberta Russo
- Clinica Di Gastroenterologia – Endoscopia – Epatologia, Policlinico, S. Maria Della Misericordia Azienda Ospedaliera Di Perugia, Italy
| | - Melissa Byrd
- Division of Pathology and Laboratory Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Kenneth D.R. Setchell
- Division of Pathology and Laboratory Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| |
Collapse
|
11
|
Yu CH, Chen CY, Chang CC. The immediate effects of weaning stress on the hypothalamus-pituitary-adrenal alteration of newly weaned piglets. J Anim Physiol Anim Nutr (Berl) 2019; 103:1218-1223. [PMID: 30994220 DOI: 10.1111/jpn.13104] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 02/04/2019] [Accepted: 03/28/2019] [Indexed: 01/06/2023]
Abstract
This study was conducted to examine the effects of weaning stress on gene expression of specific markers in hypothalamus-pituitary-adrenal (HPA) axis and neuronal activity in the newly weaned piglets. Twelve 28-days-old, newly weaned crossbred (Landrace × Yorkshire × Duroc) male piglets from 6 l (2 piglets/l) were randomly categorized into two groups: (a) weaning stress: piglets were separated from their dams, relocated and mixed with the unacquainted domestic piglets for 2 hr (stress, n = 6); (b) no-stress: piglets stayed with their dams in the farrowing house (NS; n = 6). After weaning stress, all piglets were electrically euthanized and the blood samples/HPA tissues were collected for subsequent analysis, including plasma cortisol and mRNA expression of c-fos, c-jun, corticotropin-releasing hormone (CRH), CRH receptor 1 (CRHR-1) and adrenocorticotropin hormone receptor (MC2R). Results: Weaning stress significantly (p < 0.05) increased the plasma cortisol level and suppressed the expression of c-fos and CRH in hypothalamus. In addition, weaning stress enhanced the mRNA abundance of c-jun and CRHR-1 in the pituitary gland. No significant differences in the gene expression of MC2R and CRHR-1 were observed in the adrenal gland between treatment groups. Taken together, HPA involved in weaning stress and CRHR-1 and c-jun could be potential markers to evaluate the activation of HPA axis.
Collapse
Affiliation(s)
- Chien-Ho Yu
- Department of Veterinary Medicine, National Chiayi University, Chiayi, Taiwan
| | - Ching-Yi Chen
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Chih-Cheng Chang
- Department of Veterinary Medicine, National Chiayi University, Chiayi, Taiwan
| |
Collapse
|
12
|
Boschetti E, Hernández-Castellano LE, Righetti PG. Progress in farm animal proteomics: The contribution of combinatorial peptide ligand libraries. J Proteomics 2019; 197:1-13. [DOI: 10.1016/j.jprot.2019.02.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 01/17/2019] [Accepted: 02/07/2019] [Indexed: 02/08/2023]
|
13
|
Li Z, Kanitz E, Tuchscherer M, Tuchscherer A, Metges CC, Trakooljul N, Wimmers K, Murani E. Kinetics of Physiological and Behavioural Responses in Endotoxemic Pigs with or without Dexamethasone Treatment. Int J Mol Sci 2019; 20:ijms20061393. [PMID: 30897706 PMCID: PMC6471452 DOI: 10.3390/ijms20061393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/17/2019] [Accepted: 03/19/2019] [Indexed: 12/15/2022] Open
Abstract
Although dexamethasone (DEX) is a widely used immunoregulatory agent, knowledge about its pharmacological properties in farm animals, especially pigs, is insufficient. Previous studies suggest that compared to other species, pigs are less sensitive to the immunosuppression conferred by DEX and more sensitive to the threat of bacterial endotoxins. However, there is a paucity of studies examining DEX immunomodulation in endotoxemia in this species. In this study, a porcine endotoxemia model was established by lipopolysaccharide (LPS) and the effect of DEX-pretreatment on the magnitude and kinetics of neuroendocrine, metabolic, hematologic, inflammatory, and behavioural responses were examined. DEX decreased cortisol, adrenocorticotropic hormone (ACTH), red blood cell, hemoglobin, hematocrit, and lymphocyte whereas glucose concentration was increased under both normal and endotoxemic conditions. By contrast, DEX decreased triglyceride, lactate, and IL-6 concentrations and increased platelet count only under an endotoxemic condition. DEX also reduced the frequency of sickness behaviour following LPS challenge. PCA showed that glucose and triglyceride metabolism together with red blood cell count mainly contributed to the separation of clusters during DEX treatment. Our study demonstrates that DEX protects pigs from inflammation and morbidity in endotoxemia, in spite of their less sensitivity to DEX. Moreover, its considerable role in the regulation of the metabolic and hematologic responses in endotoxemic pigs is revealed for the first time.
Collapse
Affiliation(s)
- Zhiwei Li
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany.
| | - Ellen Kanitz
- Institute of Behavioural Physiology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany.
| | - Margret Tuchscherer
- Institute of Behavioural Physiology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany.
| | - Armin Tuchscherer
- Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany.
| | - Cornelia C Metges
- Institute of Nutritional Physiology "Oskar Kellner", Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany.
| | - Nares Trakooljul
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany.
| | - Klaus Wimmers
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany.
| | - Eduard Murani
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany.
| |
Collapse
|
14
|
Hervé J, Terenina E, Haurogné K, Bacou E, Kulikova E, Allard M, Billon Y, Bach JM, Mormède P, Lieubeau B. Effects of divergent selection upon adrenocortical activity on immune traits in pig. BMC Vet Res 2019; 15:71. [PMID: 30832653 PMCID: PMC6398250 DOI: 10.1186/s12917-019-1809-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 02/19/2019] [Indexed: 01/22/2023] Open
Abstract
Background The sustainability of farming and animal welfare requires the reconsideration of current selection schemes. In particular, implementation of new selection criteria related to animal health and welfare should help to produce more robust animals and to reduce anti-microbial use. The hypothalamo-pituitary-adrenocortical (HPA) axis plays a major role in metabolic regulation and adaptation processes and its activity is strongly influenced by genetic factors. A positive association between HPA axis activity and robustness was recently described. To explore whether selecting pigs upon HPA axis activity could increase their robustness, a divergent selection experiment was carried out in the Large White pig breed. This allowed the generation of low (HPAlo) and high (HPAhi) responders to adrenocorticotropic hormone administration. Results In this study, we compared 23 hematologic and immune parameters of 6-week-old, HPAlo and HPAhi piglets and analysed their response to a low dose of lipopolysaccharide (LPS) two weeks later. At six weeks of age, HPAhi piglets displayed greater red blood cell and leucocyte number including CD8α+ γδ cells, cytotoxic T lymphocytes, naive T helper (Th) cells and B lymphocytes as compared to HPAlo individuals. The ability of blood cells to secrete TNFα in response to LPS ex vivo was higher for HPAhi pigs. At week eight, the inflammatory response to the LPS in vivo challenge was poorly affected by the HPA axis activity. Conclusions Divergent selection upon HPA axis activity modulated hematologic and immune parameters in 6-week-old pigs, which may confer an advantage to HPAhi pigs at weaning. However, HPAlo and HPAhi piglets did not exhibit major differences in the parameters analysed two weeks later, i. e. in 8-week-old pigs. In conclusion, chronic exposure to high cortisol levels in HPAhi pigs does not negatively impact immunity. Electronic supplementary material The online version of this article (10.1186/s12917-019-1809-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Julie Hervé
- IECM, INRA, Oniris, La Chantrerie, CS 40706, F-44307, Nantes Cedex 3, France.
| | - Elena Terenina
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, F-31326, Castanet-Tolosan, France.
| | - Karine Haurogné
- IECM, INRA, Oniris, La Chantrerie, CS 40706, F-44307, Nantes Cedex 3, France
| | - Elodie Bacou
- IECM, INRA, Oniris, La Chantrerie, CS 40706, F-44307, Nantes Cedex 3, France
| | - Elizaveta Kulikova
- Federal Research Center, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russian Federation, 630090
| | - Marie Allard
- IECM, INRA, Oniris, La Chantrerie, CS 40706, F-44307, Nantes Cedex 3, France
| | - Yvon Billon
- GenESI, INRA, Le Magneraud, F-17700, Saint-Pierre-d'Amilly, France
| | - Jean-Marie Bach
- IECM, INRA, Oniris, La Chantrerie, CS 40706, F-44307, Nantes Cedex 3, France
| | - Pierre Mormède
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, F-31326, Castanet-Tolosan, France
| | - Blandine Lieubeau
- IECM, INRA, Oniris, La Chantrerie, CS 40706, F-44307, Nantes Cedex 3, France
| |
Collapse
|
15
|
Terenina E, Sautron V, Ydier C, Bazovkina D, Sevin-Pujol A, Gress L, Lippi Y, Naylies C, Billon Y, Liaubet L, Mormede P, Villa-Vialaneix N. Time course study of the response to LPS targeting the pig immune gene networks. BMC Genomics 2017; 18:988. [PMID: 29273011 PMCID: PMC5741867 DOI: 10.1186/s12864-017-4363-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 12/01/2017] [Indexed: 12/23/2022] Open
Abstract
Background Stress is a generic term used to describe non-specific responses of the body to all kinds of challenges. A very large variability in the response can be observed across individuals, depending on numerous conditioning factors like genetics, early influences and life history. As a result, there is a wide range of individual vulnerability and resilience to stress, also called robustness. The importance of robustness-related traits in breeding strategies is increasing progressively towards the production of animals with a high level of production under a wide range of climatic conditions and management systems, together with a lower environmental impact and a high level of animal welfare. The present study aims at describing blood transcriptomic, hormonal, and metabolic responses of pigs to a systemic challenge using lipopolysaccharide (LPS). The objective is to analyze the individual variation of the biological responses in relation to the activity of the HPA axis measured by the levels of plasma cortisol after LPS and ACTH in 120 juvenile Large White (LW) pigs. The kinetics of the response was measured with biological variables and whole blood gene expression at 4 time points. A multilevel statistical analysis was used to take into account the longitudinal aspect of the data. Results Cortisol level reaches its peak 4 h after LPS injection. The characteristic changes of white blood cell count to LPS were observed, with a decrease of total count, maximal at t=+4 h, and the mirror changes in the respective proportions of lymphocytes and granulocytes. The lymphocytes / granulocytes ratio was maximal at t=+1 h. An integrative statistical approach was used and provided a set of candidate genes for kinetic studies and ongoing complementary studies focused on the LPS-stimulated inflammatory response. Conclusions The present study demonstrates the specific biomarkers indicative of an inflammation in swine. Furthermore, these stress responses persist for prolonged periods of time and at significant expression levels, making them good candidate markers for evaluating the efficacy of anti-inflammatory drugs. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4363-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Elena Terenina
- INRA, UMR 1388 GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet-Tolosan, F-31326, France.
| | - Valérie Sautron
- INRA, UMR 1388 GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet-Tolosan, F-31326, France
| | - Caroline Ydier
- INRA, UMR 1388 GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet-Tolosan, F-31326, France
| | - Darya Bazovkina
- Department of Behavioral Neurogenomics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Amélie Sevin-Pujol
- INRA, UMR 1388 GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet-Tolosan, F-31326, France
| | - Laure Gress
- INRA, UMR 1388 GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet-Tolosan, F-31326, France
| | - Yannick Lippi
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, F-31027, France
| | - Claire Naylies
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, F-31027, France
| | - Yvon Billon
- INRA, UE 1372 GenESI, Surgeres, F-17700, France
| | - Laurence Liaubet
- INRA, UMR 1388 GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet-Tolosan, F-31326, France
| | - Pierre Mormede
- INRA, UMR 1388 GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet-Tolosan, F-31326, France
| | | |
Collapse
|
16
|
Rauw WM, Johnson AK, Gomez-Raya L, Dekkers JCM. A Hypothesis and Review of the Relationship between Selection for Improved Production Efficiency, Coping Behavior, and Domestication. Front Genet 2017; 8:134. [PMID: 29033975 PMCID: PMC5624995 DOI: 10.3389/fgene.2017.00134] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 09/12/2017] [Indexed: 01/11/2023] Open
Abstract
Coping styles in response to stressors have been described both in humans and in other animal species. Because coping styles are directly related to individual fitness they are part of the life history strategy. Behavioral styles trade off with other life-history traits through the acquisition and allocation of resources. Domestication and subsequent artificial selection for production traits specifically focused on selection of individuals with energy sparing mechanisms for non-production traits. Domestication resulted in animals with low levels of aggression and activity, and a low hypothalamic-pituitary-adrenal (HPA) axis reactivity. In the present work, we propose that, vice versa, selection for improved production efficiency may to some extent continue to favor docile domesticated phenotypes. It is hypothesized that both domestication and selection for improved production efficiency may result in the selection of reactive style animals. Both domesticated and reactive style animals are characterized by low levels of aggression and activity, and increased serotonin neurotransmitter levels. However, whereas domestication quite consistently results in a decrease in the functional state of the HPA axis, the reactive coping style is often found to be dominated by a high HPA response. This may suggest that fearfulness and coping behavior are two independent underlying dimensions to the coping response. Although it is generally proposed that animal welfare improves with selection for calmer animals that are less fearful and reactive to novelty, animals bred to be less sensitive with fewer desires may be undesirable from an ethical point of view.
Collapse
Affiliation(s)
- Wendy M Rauw
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain.,Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Anna K Johnson
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Luis Gomez-Raya
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain.,Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Jack C M Dekkers
- Department of Animal Science, Iowa State University, Ames, IA, United States
| |
Collapse
|
17
|
The multiple adrenocorticotropic hormone injections significantly alters hepatic proteome in growing pigs. Livest Sci 2017. [DOI: 10.1016/j.livsci.2017.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
18
|
Han TL, Yang Y, Zhang H, Law KP. Analytical challenges of untargeted GC-MS-based metabolomics and the critical issues in selecting the data processing strategy. F1000Res 2017; 6:967. [PMID: 28868138 PMCID: PMC5553085 DOI: 10.12688/f1000research.11823.1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/12/2017] [Indexed: 12/16/2022] Open
Abstract
Background: A challenge of metabolomics is data processing the enormous amount of information generated by sophisticated analytical techniques. The raw data of an untargeted metabolomic experiment are composited with unwanted biological and technical variations that confound the biological variations of interest. The art of data normalisation to offset these variations and/or eliminate experimental or biological biases has made significant progress recently. However, published comparative studies are often biased or have omissions.
Methods: We investigated the issues with our own data set, using five different representative methods of internal standard-based, model-based, and pooled quality control-based approaches, and examined the performance of these methods against each other in an epidemiological study of gestational diabetes using plasma.
Results: Our results demonstrated that the quality control-based approaches gave the highest data precision in all methods tested, and would be the method of choice for controlled experimental conditions. But for our epidemiological study, the model-based approaches were able to classify the clinical groups more effectively than the quality control-based approaches because of their ability to minimise not only technical variations, but also biological biases from the raw data.
Conclusions: We suggest that metabolomic researchers should optimise and justify the method they have chosen for their experimental condition in order to obtain an optimal biological outcome.
Collapse
Affiliation(s)
- Ting-Li Han
- Mass Spectrometry Centre, China-Canada-New Zealand Joint Laboratory of Maternal and Foetal Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Yang Yang
- Mass Spectrometry Centre, China-Canada-New Zealand Joint Laboratory of Maternal and Foetal Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Hua Zhang
- Mass Spectrometry Centre, China-Canada-New Zealand Joint Laboratory of Maternal and Foetal Medicine, Chongqing Medical University, Chongqing, 400016, China.,Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Kai P Law
- Mass Spectrometry Centre, China-Canada-New Zealand Joint Laboratory of Maternal and Foetal Medicine, Chongqing Medical University, Chongqing, 400016, China
| |
Collapse
|
19
|
Ahlberg V, Hjertner B, Wallgren P, Hellman S, Lövgren Bengtsson K, Fossum C. Innate immune responses induced by the saponin adjuvant Matrix-M in specific pathogen free pigs. Vet Res 2017; 48:30. [PMID: 28532492 PMCID: PMC5441066 DOI: 10.1186/s13567-017-0437-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 04/27/2017] [Indexed: 12/05/2022] Open
Abstract
Saponin-based adjuvants have been widely used to enhance humoral and cellular immune responses in many species, but their mode of action is not fully understood. A characterization of the porcine transcriptional response to Matrix-M was performed in vitro using lymphocytes, monocytes or monocyte-derived dendritic cells (MoDCs) and in vivo. The effect of Matrix-M was also evaluated in specific pathogen free (SPF) pigs exposed to conventionally reared pigs. The pro-inflammatory cytokine genes IL1B and CXCL8 were up-regulated in monocytes and lymphocytes after Matrix-M exposure. Matrix-M also induced IL12B, IL17A and IFNG in lymphocytes and IFN-α gene expression in MoDCs. Several genes were indicated as up-regulated by Matrix-M in blood 18 h after injection, of which the genes for IFN-α and TLR2 could be statistically confirmed. Respiratory disease developed in all SPF pigs mixed with conventional pigs within 1–3 days. Two out of four SPF pigs injected with saline prior to contact exposure displayed systemic symptoms that was not recorded for the four pigs administered Matrix-M. Granulocyte counts, serum amyloid A levels and transcription of IL18 and TLR2 coincided with disease progression in the pigs. These results support further evaluation of Matrix-M as a possible enhancer of innate immune responses during critical moments in pig management.
Collapse
Affiliation(s)
- Viktor Ahlberg
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, SLU, Uppsala, Sweden
| | - Bernt Hjertner
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, SLU, Uppsala, Sweden
| | - Per Wallgren
- National Veterinary Institute, SVA, Uppsala, Sweden
| | - Stina Hellman
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, SLU, Uppsala, Sweden
| | | | - Caroline Fossum
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, SLU, Uppsala, Sweden.
| |
Collapse
|
20
|
Law KP, Zhang H. The pathogenesis and pathophysiology of gestational diabetes mellitus: Deductions from a three-part longitudinal metabolomics study in China. Clin Chim Acta 2017; 468:60-70. [DOI: 10.1016/j.cca.2017.02.008] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 02/06/2017] [Accepted: 02/12/2017] [Indexed: 01/19/2023]
|
21
|
Law KP, Mao X, Han TL, Zhang H. Unsaturated plasma phospholipids are consistently lower in the patients diagnosed with gestational diabetes mellitus throughout pregnancy: A longitudinal metabolomics study of Chinese pregnant women part 1. Clin Chim Acta 2017; 465:53-71. [DOI: 10.1016/j.cca.2016.12.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 11/28/2016] [Accepted: 12/12/2016] [Indexed: 12/12/2022]
|
22
|
Bacou E, Haurogné K, Mignot G, Allard M, De Beaurepaire L, Marchand J, Terenina E, Billon Y, Jacques J, Bach JM, Mormède P, Hervé J, Lieubeau B. Acute social stress-induced immunomodulation in pigs high and low responders to ACTH. Physiol Behav 2016; 169:1-8. [PMID: 27867043 DOI: 10.1016/j.physbeh.2016.11.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 11/07/2016] [Accepted: 11/08/2016] [Indexed: 01/11/2023]
Abstract
Pig husbandry is known as an intensive breeding system, piglets being submitted to multiple stressful events such as early weaning, successive mixing, crowding and shipping. These stressors are thought to impair immune defences and might contribute, at least partly, to the prophylactic use of antibiotics. Robustness was recently defined as the ability of an individual to express a high-production potential in a wide variety of environmental conditions. Increasing robustness thus appears as a valuable option to improve resilience to stressors and could be obtained by selecting piglets upon their adrenocortical activity. In this study, we aimed at depicting the consequences of an acute social stress on the immune capacity of piglets genetically selected upon divergent hypothalamic-pituitary-adrenocortical (HPA) axis activity. For this purpose, we monitored neuroendocrine and immune parameters, in high- (HPAhi) and low- (HPAlo) responders to ACTH, just before and immediately after a one-hour mixing with unfamiliar conspecifics. As expected, stressed piglets displayed higher levels of circulating cortisol and norepinephrine. Blood cell count analysis combined to flow cytometry revealed a stress-induced leukocyte mobilization in the bloodstream with a specific recruitment of CD8α+ lymphocytes. Besides, one-hour mixing decreased LPS-induced IL-8 and TNFα secretions in whole-blood assays (WBA) and reduced mononuclear cell phagocytosis. Altogether, our data demonstrate that acute social stress alters immune competence of piglets from both groups, and bring new insights in favour of good farming practices. While for most parameters high- and low-responders to ACTH behaved similarly, HPAhi piglets displayed higher number of CD4+ CD8α- T cells, as well as increased cytokine production in WBA (LPS-induced TNFα and PIL-induced IL-8), which could confer them increased resistance to pathogens. Finally, a principal component analysis including all parameters highlighted that overall stress effects were less pronounced on piglets with a strong HPA axis. Thus, selection upon adrenocortical axis activity seems to reduce the magnitude of response to stress and appears as a good tool to increase piglet robustness.
Collapse
Affiliation(s)
- Elodie Bacou
- IECM, INRA, Oniris, Université de Nantes, LUNAM, La Chantrerie, CS 40706, F-44307 Nantes Cedex 3, France
| | - Karine Haurogné
- IECM, INRA, Oniris, Université de Nantes, LUNAM, La Chantrerie, CS 40706, F-44307 Nantes Cedex 3, France
| | - Grégoire Mignot
- IECM, INRA, Oniris, Université de Nantes, LUNAM, La Chantrerie, CS 40706, F-44307 Nantes Cedex 3, France
| | - Marie Allard
- IECM, INRA, Oniris, Université de Nantes, LUNAM, La Chantrerie, CS 40706, F-44307 Nantes Cedex 3, France
| | - Laurence De Beaurepaire
- IECM, INRA, Oniris, Université de Nantes, LUNAM, La Chantrerie, CS 40706, F-44307 Nantes Cedex 3, France
| | - Jordan Marchand
- IECM, INRA, Oniris, Université de Nantes, LUNAM, La Chantrerie, CS 40706, F-44307 Nantes Cedex 3, France
| | - Elena Terenina
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, F-31326 Castanet-Tolosan, France
| | - Yvon Billon
- GenESI, INRA, Le Magneraud, F-17700 Saint-Pierre-d'Amilly, France
| | | | - Jean-Marie Bach
- IECM, INRA, Oniris, Université de Nantes, LUNAM, La Chantrerie, CS 40706, F-44307 Nantes Cedex 3, France
| | - Pierre Mormède
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, F-31326 Castanet-Tolosan, France
| | - Julie Hervé
- IECM, INRA, Oniris, Université de Nantes, LUNAM, La Chantrerie, CS 40706, F-44307 Nantes Cedex 3, France.
| | - Blandine Lieubeau
- IECM, INRA, Oniris, Université de Nantes, LUNAM, La Chantrerie, CS 40706, F-44307 Nantes Cedex 3, France.
| |
Collapse
|