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Shivaani M, Madan P. Application of imaging and spectroscopy techniques for grading of bovine embryos - a review. Front Vet Sci 2024; 11:1364570. [PMID: 38774909 PMCID: PMC11107339 DOI: 10.3389/fvets.2024.1364570] [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: 01/08/2024] [Accepted: 04/18/2024] [Indexed: 05/24/2024] Open
Abstract
Although embryo transfers have grown considerably in the cattle industry, the selection of embryos required for successful pregnancies remains a challenging task. Visual inspection of 7th-day embryos using a stereomicroscope, followed by classification based on morphological features is the most commonly practiced procedure. However, there are inaccuracies and inconsistencies in the manual grading of bovine embryos. The objective of this review was to evaluate the potential of imaging and spectroscopic techniques in the selection of bovine embryos. Digital analysis of microscopic images through extracting visual features in the embryo region, and classification using machine learning methods have yielded about 88-96% success in pregnancies. The Raman spectral pattern provides valuable information regarding developmental stages and quality of the embryo. The Raman spectroscopy approach has also been successfully used to determine various parameters of bovine oocytes. Besides, Fourier Transform Infrared (FTIR) spectroscopy has the ability to assess embryo quality through analyzing embryo composition, including nucleic acid and amides present. Hyperspectral Imaging has also been used to characterize metabolite production during embryo growth. Although the time-lapse imaging approach is beneficial for morphokinetics evaluation of embryo development, optimized protocols are required for successful implementation in bovine embryo transfers. Most imaging and spectroscopic findings are still only at an experimental stage. Further research is warranted to improve the repeatability and practicality to implement in commercial facilities.
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Affiliation(s)
| | - Pavneesh Madan
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
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2
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da Fonseca Junior AM, Ispada J, Dos Santos EC, de Lima CB, da Silva JVA, Paulson E, Goszczynski DE, Goissis MD, Ross PJ, Milazzotto MP. Adaptative response to changes in pyruvate metabolism on the epigenetic landscapes and transcriptomics of bovine embryos. Sci Rep 2023; 13:11504. [PMID: 37460590 DOI: 10.1038/s41598-023-38686-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 07/12/2023] [Indexed: 07/20/2023] Open
Abstract
The epigenetic reprogramming that occurs during the earliest stages of embryonic development has been described as crucial for the initial events of cell specification and differentiation. Recently, the metabolic status of the embryo has gained attention as one of the main factors coordinating epigenetic events. In this work, we investigate the link between pyruvate metabolism and epigenetic regulation by culturing bovine embryos from day 5 in the presence of dichloroacetate (DCA), a pyruvate analog that increases the pyruvate to acetyl-CoA conversion, and iodoacetate (IA), which inhibits the glyceraldehyde-3-phosphate dehydrogenase (GAPDH), leading to glycolysis inhibition. After 8 h of incubation, both DCA and IA-derived embryos presented higher mitochondrial membrane potential. Nevertheless, in both cases, lower levels of acetyl-CoA, ATP-citrate lyase and mitochondrial membrane potential were found in blastocysts, suggesting an adaptative metabolic response, especially in the DCA group. The metabolic alteration found in blastocysts led to changes in the global pattern of H3K9 and H3K27 acetylation and H3K27 trimethylation. Transcriptome analysis revealed that such alterations resulted in molecular differences mainly associated to metabolic processes, establishment of epigenetic marks, control of gene expression and cell cycle. The latter was further confirmed by the alteration of total cell number and cell differentiation in both groups when compared to the control. These results corroborate previous evidence of the relationship between the energy metabolism and the epigenetic reprogramming in preimplantation bovine embryos, reinforcing that the culture system is decisive for precise epigenetic reprogramming, with consequences for the molecular control and differentiation of cells.
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Affiliation(s)
- Aldcejam Martins da Fonseca Junior
- Federal University of ABC - Center for Natural and Human Sciences, Av. Dos Estados, 5001, Bairro Santa Terezinha, Bloco A, Lab 504-3, Santo André, SP, CEP: 09210-580, Brazil
| | - Jessica Ispada
- Federal University of ABC - Center for Natural and Human Sciences, Av. Dos Estados, 5001, Bairro Santa Terezinha, Bloco A, Lab 504-3, Santo André, SP, CEP: 09210-580, Brazil
| | - Erika Cristina Dos Santos
- Federal University of ABC - Center for Natural and Human Sciences, Av. Dos Estados, 5001, Bairro Santa Terezinha, Bloco A, Lab 504-3, Santo André, SP, CEP: 09210-580, Brazil
| | | | - João Vitor Alcantara da Silva
- Federal University of ABC - Center for Natural and Human Sciences, Av. Dos Estados, 5001, Bairro Santa Terezinha, Bloco A, Lab 504-3, Santo André, SP, CEP: 09210-580, Brazil
| | - Erika Paulson
- Department of Animal Science, University of California, UC - Davis, Davis, USA
| | | | | | - Pablo Juan Ross
- Department of Animal Science, University of California, UC - Davis, Davis, USA
| | - Marcella Pecora Milazzotto
- Federal University of ABC - Center for Natural and Human Sciences, Av. Dos Estados, 5001, Bairro Santa Terezinha, Bloco A, Lab 504-3, Santo André, SP, CEP: 09210-580, Brazil.
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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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Ispada J, Milazzotto MP. Silencing mark H3K27me3 is differently reprogrammed in bovine embryos with distinct kinetics of development. Reprod Domest Anim 2021; 57:333-336. [PMID: 34854135 DOI: 10.1111/rda.14060] [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: 07/15/2021] [Accepted: 11/28/2021] [Indexed: 11/30/2022]
Abstract
The kinetics of the first cleavages is a predictor of blastocyst development and implantation. For bovine embryos, this attribute was previously related to distinct metabolic, molecular and epigenetic profiles, including DNA and histone modifications. In the present work, we described the dynamics of trimethylation of lysine 27 on histone H3 (H3K27me3) in fast and slow developing embryos and verified if this epigenetic mark was also influenced by the speed of the first cleavages. In vitro-produced bovine embryos were classified as fast (4 or more cells) or slow (2 cells) at 40 hr post fertilization (hpf) and either collected or cultured until 96 hpf or 186 hpf. Immunofluorescence analysis was performed in these three time points and showed that although both groups presented the same levels of H3K27me3 at 40 hpf, slow embryos presented a pronounced increase in this mark at 186 hpf when compared to fast embryos, resulting in blastocysts with remarkable differences in H3K27me3 levels. In conclusion, the increased levels of this repressive histone post-translation modification (PTM) might be an attempt of slow embryos to promote gene expression control and chromatin integrity, since it was already reported that these embryos present reduced levels of other epigenetic repressive marks as DNA methylation and trimethylation of lysine 9 on histone H3 (H3K9me3).
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Affiliation(s)
- Jessica Ispada
- Laboratory of Cellular and Molecular Biology, Center of Natural and Human Science, Federal University of ABC, Santo Andre, Brazil.,Institute of Biomedical Sciences, University of Sao Paulo, Butanta, Brazil
| | - Marcella Pecora Milazzotto
- Laboratory of Cellular and Molecular Biology, Center of Natural and Human Science, Federal University of ABC, Santo Andre, Brazil.,Institute of Biomedical Sciences, University of Sao Paulo, Butanta, Brazil
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Martínez-Periñán E, García-Mendiola T, Enebral-Romero E, Del Caño R, Vera-Hidalgo M, Vázquez Sulleiro M, Navío C, Pariente F, Pérez EM, Lorenzo E. A MoS 2 platform and thionine-carbon nanodots for sensitive and selective detection of pathogens. Biosens Bioelectron 2021; 189:113375. [PMID: 34087724 DOI: 10.1016/j.bios.2021.113375] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/16/2021] [Accepted: 05/17/2021] [Indexed: 12/20/2022]
Abstract
This work focuses on the combination of molybdenum disulfide (MoS2) and à la carte functionalized carbon nanodots (CNDs) for the development of DNA biosensors for selective and sensitive detection of pathogens. MoS2 flakes prepared through liquid-phase exfoliation, serves as platform for thiolated DNA probe immobilization, while thionine functionalized carbon nanodots (Thi-CNDs) are used as electrochemical indicator of the hybridization event. Spectroscopic and electrochemical studies confirmed the interaction of Thi-CNDs with DNA. As an illustration of the pathogen biosensor functioning, DNA sequences from InIA gen of Listeria monocytogenes bacteria and open reading frame sequence (ORF1ab) of SARS-CoV-2 virus were detected and quantified with a detection limit of 67.0 fM and 1.01 pM, respectively. Given the paradigmatic selectivity of the DNA hybridization, this approach allows pathogen detection in the presence of other pathogens, demonstrated by the detection of Listeria monocytogenes in presence of Escherichia coli. We note that this design is in principle amenable to any pathogen for which the DNA has been sequenced, including other viruses and bacteria. As example of the application of the method in real samples it has been used to directly detect Listeria monocytogenes in cultures without any DNA Polymerase Chain Reaction (PCR) amplification process.
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Affiliation(s)
| | - Tania García-Mendiola
- Departamento de Química Analítica. Universidad Autónoma de Madrid, 28049, Madrid, Spain; Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Ciudad Universitaria de Cantoblanco, 28049, Madrid, Spain.
| | | | - Rafael Del Caño
- Departamento de Química Analítica. Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | | | | | - Cristina Navío
- IMDEA-Nanociencia, Ciudad Universitaria de Cantoblanco, 28049, Madrid, Spain
| | - Félix Pariente
- Departamento de Química Analítica. Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Emilio M Pérez
- IMDEA-Nanociencia, Ciudad Universitaria de Cantoblanco, 28049, Madrid, Spain
| | - Encarnación Lorenzo
- Departamento de Química Analítica. Universidad Autónoma de Madrid, 28049, Madrid, Spain; Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Ciudad Universitaria de Cantoblanco, 28049, Madrid, Spain; IMDEA-Nanociencia, Ciudad Universitaria de Cantoblanco, 28049, Madrid, Spain.
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Metabolites Secreted by Bovine Embryos In Vitro Predict Pregnancies That the Recipient Plasma Metabolome Cannot, and Vice Versa. Metabolites 2021; 11:metabo11030162. [PMID: 33799889 PMCID: PMC7999939 DOI: 10.3390/metabo11030162] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/02/2021] [Accepted: 03/08/2021] [Indexed: 12/23/2022] Open
Abstract
This work describes the use of mass spectrometry-based metabolomics as a non-invasive approach to accurately predict birth prior to embryo transfer (ET) starting from embryo culture media and plasma recipient. Metabolomics was used here as a predictive platform. Day-6 in vitro produced embryos developed singly in modified synthetic oviduct fluid culture medium (CM) drops for 24 h were vitrified as Day-7 blastocysts and transferred to recipients. Day-0 and Day-7 recipient plasma (N = 36 × 2) and CM (N = 36) were analyzed by gas chromatography coupled to the quadrupole time of flight mass spectrometry (GC-qTOF). Metabolites quantified in CM and plasma were analyzed as a function to predict pregnancy at Day-40, Day-62, and birth (univariate and multivariate statistics). Subsequently, a Boolean matrix (F1 score) was constructed with metabolite pairs (one from the embryo, and one from the recipient) to combine the predictive power of embryos and recipients. Validation was performed in independent cohorts of ETs analyzed. Embryos that did not reach birth released more stearic acid, capric acid, palmitic acid, and glyceryl monostearate in CM (i.e., (p < 0.05, FDR < 0.05, Receiver Operator Characteristic—area under curve (ROC-AUC) > 0.669)). Within Holstein recipients, hydrocinnamic acid, alanine, and lysine predicted birth (ROC-AUC > 0.778). Asturiana de los Valles recipients that reached birth showed lower concentrations of 6-methyl-5-hepten-2-one, stearic acid, palmitic acid, and hippuric acid (ROC-AUC > 0.832). Embryonal capric acid and glyceryl-monostearate formed F1 scores generally >0.900, with metabolites found both to differ (e.g., hippuric acid, hydrocinnamic acid) or not (e.g., heptadecanoic acid, citric acid) with pregnancy in plasmas, as hypothesized. Efficient lipid metabolism in the embryo and the recipient can allow pregnancy to proceed. Changes in phenolics from plasma suggest that microbiota and liver metabolism influence the pregnancy establishment in cattle.
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Milazzotto MP, de Lima CB, da Fonseca AM, dos Santos EC, Ispada J. Erasing gametes to write blastocysts: metabolism as the new player in epigenetic reprogramming. Anim Reprod 2020; 17:e20200015. [PMID: 33029209 PMCID: PMC7534565 DOI: 10.1590/1984-3143-ar2020-0015] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/23/2020] [Indexed: 12/13/2022] Open
Abstract
Understanding preimplantation embryonic development is crucial for the improvement of assisted reproductive technologies and animal production. To achieve this goal, it is important to consider that gametes and embryos are highly susceptible to environmental changes. Beyond the metabolic adaptation, the dynamic status imposed during follicular growth and early embryogenesis may create marks that will guide the molecular regulation during prenatal development, and consequently impact the offspring phenotype. In this context, metaboloepigenetics has gained attention, as it investigates the crosstalk between metabolism and molecular control, i.e., how substrates generated by metabolic pathways may also act as players of epigenetic modifications. In this review, we present the main metabolic and epigenetic events of pre-implantation development, and how these systems connect to open possibilities for targeted manipulation of reproductive technologies and animal production systems.
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Affiliation(s)
- Marcella Pecora Milazzotto
- Laboratório de Epigenética e Metabolismo Embrionário, Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, Brasil
- Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Camila Bruna de Lima
- Laboratório de Epigenética e Metabolismo Embrionário, Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, Brasil
- Département des Sciences Animales, Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle, Faculté des Sciences de l’Agriculture et de l’Alimentation, Université Laval, Quebec, Canada
| | - Aldcejam Martins da Fonseca
- Laboratório de Epigenética e Metabolismo Embrionário, Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, Brasil
| | - Erika Cristina dos Santos
- Laboratório de Epigenética e Metabolismo Embrionário, Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, Brasil
| | - Jessica Ispada
- Laboratório de Epigenética e Metabolismo Embrionário, Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, Brasil
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Liang B, Gao Y, Xu J, Song Y, Xuan L, Shi T, Wang N, Hou Z, Zhao YL, Huang WE, Chen ZJ. Raman profiling of embryo culture medium to identify aneuploid and euploid embryos. Fertil Steril 2019; 111:753-762.e1. [PMID: 30683589 DOI: 10.1016/j.fertnstert.2018.11.036] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 11/26/2018] [Accepted: 11/26/2018] [Indexed: 10/27/2022]
Abstract
OBJECTIVE To develop and validate Raman metabolic footprint analysis to determine chromosome euploidy and aneuploidy in embryos fertilized in vitro. DESIGN Retrospective study. SETTING Academic hospital. PATIENT(S) Unselected assisted reproductive technology population. INTERVENTION(S) To establish the analysis protocol, spent embryo culture medium samples with known genetic outcomes from 87 human embryos were collected and measured with the use of Raman spectroscopy. Individual Raman spectra were analyzed to find biologic components contributing to either euploidy or aneuploidy. To validate the protocol via machine-learning algorithms, additional 1,107 Raman spectra from 123 embryo culture media (61 euploidy and 62 aneuploidy) were analyzed. MAIN OUTCOME MEASURE(S) Raman-based footprint profiling of spent culture media and preimplantation genetic testing for aneuploidy (PGT-A). RESULT(S) Mean-centered Raman spectra and principal component analysis showed differences in the footprints of euploid and aneuploid embryos growing in culture medium. Significant differences in Raman bands associated with small RNAs and lipids were also observed. Stacking classification based on k-nearest-neighbor, random forests, and extreme-gradient-boosting algorithms achieved an overall accuracy of 95.9% in correctly assigning either euploidy or aneuploidy based on Raman spectra, which was validated by PGT-A sequencing results. CONCLUSION(S) This study suggests that chromosomal abnormalities in embryos should lead to changes of metabolic footprints in embryo growth medium that can be detected by Raman spectroscopy. The ploidy status of embryos was analyzed by means of Raman-based footprint profiling of spent culture media and was consistent with PGT-A testing performed by next-generation sequencing.
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Affiliation(s)
- Bo Liang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yuan Gao
- Center for Reproductive Medicine, Provincial Hospital Affiliated with Shandong University, Jinan, Shandong, China; Key Laboratory for Reproductive Endocrinology of Ministry of Education, Jinan, Shandong, China
| | - Jiabao Xu
- Department of Engineering Science, University of Oxford, Oxford, United Kingdom
| | - Yizhi Song
- Department of Engineering Science, University of Oxford, Oxford, United Kingdom
| | - Liming Xuan
- Basecare Medical Device Co., Suzhou, Jiangsu, China
| | - Ting Shi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ning Wang
- Mathematical Institute, University of Oxford, Oxford, United Kingdom
| | - Zhaoxu Hou
- Mathematical Institute, University of Oxford, Oxford, United Kingdom
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Wei E Huang
- Department of Engineering Science, University of Oxford, Oxford, United Kingdom
| | - Zi-Jiang Chen
- Center for Reproductive Medicine, Provincial Hospital Affiliated with Shandong University, Jinan, Shandong, China; Key Laboratory for Reproductive Endocrinology of Ministry of Education, Jinan, Shandong, China
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Li XX, Cao PH, Han WX, Xu YK, Wu H, Yu XL, Chen JY, Zhang F, Li YH. Non-invasive metabolomic profiling of culture media of ICSI- and IVF-derived early developmental cattle embryos via Raman spectroscopy. Anim Reprod Sci 2018; 196:99-110. [DOI: 10.1016/j.anireprosci.2018.07.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 06/18/2018] [Accepted: 07/02/2018] [Indexed: 10/28/2022]
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Ispada J, de Lima CB, Sirard MA, Fontes PK, Nogueira MFG, Annes K, Milazzotto MP. Genome-wide screening of DNA methylation in bovine blastocysts with different kinetics of development. Epigenetics Chromatin 2018; 11:1. [PMID: 29310712 PMCID: PMC5757301 DOI: 10.1186/s13072-017-0171-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 12/14/2017] [Indexed: 01/01/2023] Open
Abstract
Background The timing of the first cell divisions may predict the developmental potential of an embryo, including its ability to establish pregnancy. Besides differences related to metabolism, stress, and survival, embryos with different speeds of development present distinct patterns of gene expression, mainly related to energy and lipid metabolism. As gene expression is regulated by epigenetic factors, and that includes DNA methylation patterns, in this study we compared the global DNA methylation profile of embryos with different kinetics of development in order to identify general pathways and regions that are most influenced by this phenotype. For this purpose, bovine embryos were in vitro produced using sexed semen (female), classified as fast (four or more cells) or slow (two cells) at 40 hpi and cultured until blastocyst stage, when they were analyzed. Results Genome-wide DNA methylation analysis identified 11,584 differently methylated regions (DMRs) (7976 hypermethylated regions in fast and 3608 hypermethylated regions in slow embryos). Fast embryos presented more regions classified as hypermethylated distributed throughout the genome, as in introns, exons, promoters, and repeat elements while in slow embryos, hypermethylated regions were more present in CpG islands. DMRs were clustered by means of biological processes, and the most affected pathways were related to cell survival/differentiation and energy/lipid metabolism. Transcripts profiles from DM genes connected with these pathways were also assessed, and the most part disclosed changes in relative quantitation. Conclusion The kinetics of the first cleavages influences the DNA methylation and expression profiles of genes related to metabolism and differentiation pathways and may affect embryo viability. Electronic supplementary material The online version of this article (10.1186/s13072-017-0171-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jessica Ispada
- Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil. .,Laboratório de Biologia Celular e Molecular - Bloco A - 502-3, Center of Natural and Human Sciences, Universidade Federal do ABC, Av dos Estados, 5001, Bangu, Santo André, São Paulo, Brazil.
| | - Camila Bruna de Lima
- Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil.,Laboratório de Biologia Celular e Molecular - Bloco A - 502-3, Center of Natural and Human Sciences, Universidade Federal do ABC, Av dos Estados, 5001, Bangu, Santo André, São Paulo, Brazil
| | - Marc-André Sirard
- Centre de Recherche en Biologie de la Reproduction, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Quebec, Canada
| | - Patrícia Kubo Fontes
- Departament of Pharmacology, Institute of Biosciences, Universidade Estadual Paulista (UNESP), Campus Botucatu, Botucatu, São Paulo, Brazil
| | - Marcelo Fábio Gouveia Nogueira
- Departament of Biological Sciences, School of Sciences and Languages, Universidade Estadual Paulista (UNESP), Campus Assis, Assis, São Paulo, Brazil
| | - Kelly Annes
- Laboratório de Biologia Celular e Molecular - Bloco A - 502-3, Center of Natural and Human Sciences, Universidade Federal do ABC, Av dos Estados, 5001, Bangu, Santo André, São Paulo, Brazil
| | - Marcella Pecora Milazzotto
- Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil. .,Laboratório de Biologia Celular e Molecular - Bloco A - 502-3, Center of Natural and Human Sciences, Universidade Federal do ABC, Av dos Estados, 5001, Bangu, Santo André, São Paulo, Brazil.
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