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Rabel RAC, Marchioretto PV, Bangert EA, Wilson K, Milner DJ, Wheeler MB. Pre-Implantation Bovine Embryo Evaluation-From Optics to Omics and Beyond. Animals (Basel) 2023; 13:2102. [PMID: 37443900 DOI: 10.3390/ani13132102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/16/2023] [Accepted: 06/17/2023] [Indexed: 07/15/2023] Open
Abstract
Approximately 80% of the ~1.5 million bovine embryos transferred in 2021 were in vitro produced. However, only ~27% of the transferred IVP embryos will result in live births. The ~73% pregnancy failures are partly due to transferring poor-quality embryos, a result of erroneous stereomicroscopy-based morphological evaluation, the current method of choice for pre-transfer embryo evaluation. Numerous microscopic (e.g., differential interference contrast, electron, fluorescent, time-lapse, and artificial-intelligence-based microscopy) and non-microscopic (e.g., genomics, transcriptomics, epigenomics, proteomics, metabolomics, and nuclear magnetic resonance) methodologies have been tested to find an embryo evaluation technique that is superior to morphologic evaluation. Many of these research tools can accurately determine embryo quality/viability; however, most are invasive, expensive, laborious, technically sophisticated, and/or time-consuming, making them futile in the context of in-field embryo evaluation. However accurate they may be, using complex methods, such as RNA sequencing, SNP chips, mass spectrometry, and multiphoton microscopy, at thousands of embryo production/collection facilities is impractical. Therefore, future research is warranted to innovate field-friendly, simple benchtop tests using findings already available, particularly from omics-based research methodologies. Time-lapse monitoring and artificial-intelligence-based automated image analysis also have the potential for accurate embryo evaluation; however, further research is warranted to innovate economically feasible options for in-field applications.
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Affiliation(s)
- R A Chanaka Rabel
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Paula V Marchioretto
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Elizabeth A Bangert
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Kenneth Wilson
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Derek J Milner
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Matthew B Wheeler
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Biomedical and Translational Sciences, Carle-Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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2
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O'Donoghue S, Earley B, Johnston D, McCabe MS, Kim JW, Taylor JF, Duffy C, Lemon K, McMenamy M, Cosby SL, Morris DW, Waters SM. Whole blood transcriptome analysis in dairy calves experimentally challenged with bovine herpesvirus 1 (BoHV-1) and comparison to a bovine respiratory syncytial virus (BRSV) challenge. Front Genet 2023; 14:1092877. [PMID: 36873940 PMCID: PMC9981960 DOI: 10.3389/fgene.2023.1092877] [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: 11/08/2022] [Accepted: 01/25/2023] [Indexed: 02/19/2023] Open
Abstract
Bovine herpesvirus 1 (BoHV-1), is associated with several clinical syndromes in cattle, among which bovine respiratory disease (BRD) is of particular significance. Despite the importance of the disease, there is a lack of information on the molecular response to infection via experimental challenge with BoHV-1. The objective of this study was to investigate the whole-blood transcriptome of dairy calves experimentally challenged with BoHV-1. A secondary objective was to compare the gene expression results between two separate BRD pathogens using data from a similar challenge study with BRSV. Holstein-Friesian calves (mean age (SD) = 149.2 (23.8) days; mean weight (SD) = 174.6 (21.3) kg) were either administered BoHV-1 inoculate (1 × 107/mL × 8.5 mL) (n = 12) or were mock challenged with sterile phosphate buffered saline (n = 6). Clinical signs were recorded daily from day (d) -1 to d 6 (post-challenge), and whole blood was collected in Tempus RNA tubes on d six post-challenge for RNA-sequencing. There were 488 differentially expressed (DE) genes (p < 0.05, False Discovery rate (FDR) < 0.10, fold change ≥2) between the two treatments. Enriched KEGG pathways (p < 0.05, FDR <0.05); included Influenza A, Cytokine-cytokine receptor interaction and NOD-like receptor signalling. Significant gene ontology terms (p < 0.05, FDR <0.05) included defence response to virus and inflammatory response. Genes that are highly DE in key pathways are potential therapeutic targets for the treatment of BoHV-1 infection. A comparison to data from a similar study with BRSV identified both similarities and differences in the immune response to differing BRD pathogens.
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Affiliation(s)
- Stephanie O'Donoghue
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Meath, Ireland.,Discipline of Biochemistry, National University of Ireland, Galway, Ireland
| | - Bernadette Earley
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Meath, Ireland
| | - Dayle Johnston
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Meath, Ireland
| | - Matthew S McCabe
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Meath, Ireland
| | - Jae Woo Kim
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
| | - Jeremy F Taylor
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
| | - Catherine Duffy
- Veterinary Sciences Division, Agri-Food and Biosciences Institute, Stormont, Belfast, Northern Ireland
| | - Ken Lemon
- Veterinary Sciences Division, Agri-Food and Biosciences Institute, Stormont, Belfast, Northern Ireland
| | - Michael McMenamy
- Veterinary Sciences Division, Agri-Food and Biosciences Institute, Stormont, Belfast, Northern Ireland
| | - S Louise Cosby
- Veterinary Sciences Division, Agri-Food and Biosciences Institute, Stormont, Belfast, Northern Ireland
| | - Derek W Morris
- Discipline of Biochemistry, National University of Ireland, Galway, Ireland
| | - Sinéad M Waters
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Meath, Ireland
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3
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Banliat C, Mahé C, Lavigne R, Com E, Pineau C, Labas V, Guyonnet B, Mermillod P, Saint-Dizier M. The proteomic analysis of bovine embryos developed in vivo or in vitro reveals the contribution of the maternal environment to early embryo. BMC Genomics 2022; 23:839. [PMID: 36536309 PMCID: PMC9764490 DOI: 10.1186/s12864-022-09076-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Despite many improvements with in vitro culture systems, the quality and developmental ability of mammalian embryos produced in vitro are still lower than their in vivo counterparts. Though previous studies have evidenced differences in gene expression between in vivo- and in vitro-derived bovine embryos, there is no comparison at the protein expression level. RESULTS A total of 38 pools of grade-1 quality bovine embryos at the 4-6 cell, 8-12 cell, morula, compact morula, and blastocyst stages developed either in vivo or in vitro were analyzed by nano-liquid chromatography coupled with label-free quantitative mass spectrometry, allowing for the identification of 3,028 proteins. Multivariate analysis of quantified proteins showed a clear separation of embryo pools according to their in vivo or in vitro origin at all stages. Three clusters of differentially abundant proteins (DAPs) were evidenced according to embryo origin, including 463 proteins more abundant in vivo than in vitro across development and 314 and 222 proteins more abundant in vitro than in vivo before and after the morula stage, respectively. The functional analysis of proteins found more abundant in vivo showed an enrichment in carbohydrate metabolism and cytoplasmic cellular components. Proteins found more abundant in vitro before the morula stage were mostly localized in mitochondrial matrix and involved in ATP-dependent activity, while those overabundant after the morula stage were mostly localized in the ribonucleoprotein complex and involved in protein synthesis. Oviductin and other oviductal proteins, previously shown to interact with early embryos, were among the most overabundant proteins after in vivo development. CONCLUSIONS The maternal environment led to higher degradation of mitochondrial proteins at early developmental stages, lower abundance of proteins involved in protein synthesis at the time of embryonic genome activation, and a global upregulation of carbohydrate metabolic pathways compared to in vitro production. Furthermore, embryos developed in vivo internalized large amounts of oviductin and other proteins probably originated in the oviduct as soon as the 4-6 cell stage. These data provide new insight into the molecular contribution of the mother to the developmental ability of early embryos and will help design better in vitro culture systems.
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Affiliation(s)
- Charles Banliat
- grid.12366.300000 0001 2182 6141INRAE, CNRS, Tours University, IFCE, UMR PRC, Nouzilly, France ,Union Evolution, Rue Eric Tabarly, Noyal-Sur-Vilaine, France
| | - Coline Mahé
- grid.12366.300000 0001 2182 6141INRAE, CNRS, Tours University, IFCE, UMR PRC, Nouzilly, France
| | - Régis Lavigne
- grid.410368.80000 0001 2191 9284Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), UMR_S 1085, Rennes, France ,grid.410368.80000 0001 2191 9284Univ Rennes, CNRS, Inserm, Biosit UAR 3480 US_S 018, Protim Core Facility, Rennes, France
| | - Emmanuelle Com
- grid.410368.80000 0001 2191 9284Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), UMR_S 1085, Rennes, France ,grid.410368.80000 0001 2191 9284Univ Rennes, CNRS, Inserm, Biosit UAR 3480 US_S 018, Protim Core Facility, Rennes, France
| | - Charles Pineau
- grid.410368.80000 0001 2191 9284Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), UMR_S 1085, Rennes, France ,grid.410368.80000 0001 2191 9284Univ Rennes, CNRS, Inserm, Biosit UAR 3480 US_S 018, Protim Core Facility, Rennes, France
| | - Valérie Labas
- grid.12366.300000 0001 2182 6141INRAE, CNRS, Tours University, IFCE, UMR PRC, Nouzilly, France ,Pixanim, INRAE, Tours University, CHU of Tours, Nouzilly, France
| | - Benoit Guyonnet
- Union Evolution, Rue Eric Tabarly, Noyal-Sur-Vilaine, France
| | - Pascal Mermillod
- grid.12366.300000 0001 2182 6141INRAE, CNRS, Tours University, IFCE, UMR PRC, Nouzilly, France
| | - Marie Saint-Dizier
- grid.12366.300000 0001 2182 6141INRAE, CNRS, Tours University, IFCE, UMR PRC, Nouzilly, France
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4
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O’Callaghan E, Sánchez J, Rabaglino M, McDonald M, Liu H, Spencer T, Fair S, Kenny D, Lonergan P. Influence of sire fertility status on conceptus-induced transcriptomic response of the bovine endometrium. Front Cell Dev Biol 2022; 10:950443. [PMID: 36072344 PMCID: PMC9442353 DOI: 10.3389/fcell.2022.950443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
The aim was to examine the effect of sire fertility status on conceptus-induced changes in the bovine endometrial transcriptome. To generate elongated conceptuses, Day 7 blastocysts produced in vitro using frozen-thawed sperm from Holstein Friesian bulls (3 High fertility, HF and 3 Low fertility, LF) were transferred in groups of 5–10 into synchronized heifers (n = 7 heifers per bull) and recovered following slaughter on Day 15. Day 15 endometrial explants recovered from the uterine horn ipsilateral to the corpus luteum were recovered from synchronized cyclic heifers (n = 4). Explants from each heifer were co-cultured for 6 h in RPMI medium alone (Control) or with 100 ng/ml ovine recombinant interferon tau (IFNT) or with a single conceptus from each HF or LF bull. After 6 h, explants were snap frozen and stored at −80°C. Extracted mRNA was subjected to RNA-seq and the resulting data were analyzed with R software. The numbers of differentially expressed genes (DEG; FDR<0.05) were: HF vs. Control: 956; LF vs. Control: 1021; IFNT vs. Control: 1301; HF vs. LF: 2. Unsurprisingly, the majority of DEG (658) were common to all comparisons and were related to IFNT-induced changes in the endometrium. Prior to applying the adjusted p-value, there were 700 DEG between HF and LF, with 191 and 509 genes more expressed in HF or LF, respectively (p < 0.05). Overrepresentation analysis of KEGG pathways (FDR<0.05), revealed that DEG with higher expression in LF were involved in cell cycle and proteolysis, while those upregulated DEG by HF conceptuses were strongly associated with immune process pathways, such as TNF, NF-kappa B, cytokine-cytokine receptor interaction, and TLR signaling. These pathways were also enriched by DEG upregulated by IFNT compared to the Control. Furthermore, only the HF, and not the LF group, affected the expression of most genes in these pathways (p < 0.05) according to a negative binomial regression model. Finally, a weighted gene co-expression network analysis revealed two clusters of co-expressed genes associated with the HF conceptuses (p < 0.05), which were also enriched for the aforementioned pathways. In conclusion, HF conceptuses, similar to IFNT treatment, stimulated multiple pathways involved in immune response, which were apparently not affected by LF conceptuses.
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Affiliation(s)
- E. O’Callaghan
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - J.M. Sánchez
- Spanish National Research Council, National Institute for Agricultural and Food Research and Technology (CSIC-INIA), Madrid, Spain
| | - M.B. Rabaglino
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - M. McDonald
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - H. Liu
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
| | - T.E. Spencer
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
| | - S. Fair
- Laboratory of Animal Reproduction, School of Natural Sciences, Biomaterials Research Cluster, Bernal Institute, Faculty of Science and Engineering. University of Limerick, Limerick, Ireland
| | - D.A. Kenny
- Teagasc Animal and Grassland Research and Innovation Centre, Dunsany, Ireland
| | - P. Lonergan
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
- *Correspondence: P. Lonergan,
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5
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Banliat C, Mahé C, Lavigne R, Com E, Pineau C, Labas V, Guyonnet B, Mermillod P, Saint-Dizier M. Dynamic Changes in the Proteome of Early Bovine Embryos Developed In Vivo. Front Cell Dev Biol 2022; 10:863700. [PMID: 35386205 PMCID: PMC8979002 DOI: 10.3389/fcell.2022.863700] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/07/2022] [Indexed: 11/24/2022] Open
Abstract
Early embryo development is a dynamic process involving important molecular and structural changes leading to the embryonic genome activation (EGA) and early cell lineage differentiation. Our aim was to elucidate proteomic changes in bovine embryos developed in vivo. Eleven females were used as embryo donors and pools of embryos at the 4–6 cell, 8–12 cell, morula, compact morula and blastocyst stages were analyzed by nanoliquid chromatography coupled with label free quantitative mass spectrometry. A total of 2,757 proteins were identified, of which 1,950 were quantitatively analyzed. Principal component analysis of data showed a clear separation of embryo pools according to their developmental stage. The hierarchical clustering of differentially abundant proteins evidenced a first cluster of 626 proteins that increased in abundance during development and a second cluster of 400 proteins that decreased in abundance during development, with most significant changes at the time of EGA and blastocyst formation. The main pathways and processes overrepresented among upregulated proteins were RNA metabolism, protein translation and ribosome biogenesis, whereas Golgi vesicle transport and protein processing in endoplasmic reticulum were overrepresented among downregulated proteins. The pairwise comparison between stages allowed us to identify specific protein interaction networks and metabolic pathways at the time of EGA, morula compaction and blastocyst formation. This is the first comprehensive study of proteome dynamics in non-rodent mammalian embryos developed in vivo. These data provide a number of protein candidates that will be useful for further mechanistic and functional studies.
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Affiliation(s)
- Charles Banliat
- CNRS, INRAE, Université de Tours, IFCE, UMR PRC, Nouzilly, France.,Union Evolution, Noyal-sur-Vilaine, France
| | - Coline Mahé
- CNRS, INRAE, Université de Tours, IFCE, UMR PRC, Nouzilly, France
| | - Régis Lavigne
- Irset-UMRS 1085, Inserm, University of Rennes, Rennes, France.,Protim, Univ Rennes, Biosit-UMS 3480, US-S 018, Rennes, France
| | - Emmanuelle Com
- Irset-UMRS 1085, Inserm, University of Rennes, Rennes, France.,Protim, Univ Rennes, Biosit-UMS 3480, US-S 018, Rennes, France
| | - Charles Pineau
- Irset-UMRS 1085, Inserm, University of Rennes, Rennes, France.,Protim, Univ Rennes, Biosit-UMS 3480, US-S 018, Rennes, France
| | - Valérie Labas
- CNRS, INRAE, Université de Tours, IFCE, UMR PRC, Nouzilly, France.,Pixanim, INRAE, Université de Tours, CHU de Tours, Nouzilly, France
| | | | - Pascal Mermillod
- CNRS, INRAE, Université de Tours, IFCE, UMR PRC, Nouzilly, France
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