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Sindhu P, Magotra A, Sindhu V, Chaudhary P. Unravelling the impact of epigenetic mechanisms on offspring growth, production, reproduction and disease susceptibility. ZYGOTE 2024:1-17. [PMID: 39291610 DOI: 10.1017/s0967199424000224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2024]
Abstract
Epigenetic mechanisms, such as DNA methylation, histone modifications and non-coding RNA molecules, play a critical role in gene expression and regulation in livestock species, influencing development, reproduction and disease resistance. DNA methylation patterns silence gene expression by blocking transcription factor binding, while histone modifications alter chromatin structure and affect DNA accessibility. Livestock-specific histone modifications contribute to gene expression and genome stability. Non-coding RNAs, including miRNAs, piRNAs, siRNAs, snoRNAs, lncRNAs and circRNAs, regulate gene expression post-transcriptionally. Transgenerational epigenetic inheritance occurs in livestock, with environmental factors impacting epigenetic modifications and phenotypic traits across generations. Epigenetic regulation revealed significant effect on gene expression profiling that can be exploited for various targeted traits like muscle hypertrophy, puberty onset, growth, metabolism, disease resistance and milk production in livestock and poultry breeds. Epigenetic regulation of imprinted genes affects cattle growth and metabolism while epigenetic modifications play a role in disease resistance and mastitis in dairy cattle, as well as milk protein gene regulation during lactation. Nutri-epigenomics research also reveals the influence of maternal nutrition on offspring's epigenetic regulation of metabolic homeostasis in cattle, sheep, goat and poultry. Integrating cyto-genomics approaches enhances understanding of epigenetic mechanisms in livestock breeding, providing insights into chromosomal structure, rearrangements and their impact on gene regulation and phenotypic traits. This review presents potential research areas to enhance production potential and deepen our understanding of epigenetic changes in livestock, offering opportunities for genetic improvement, reproductive management, disease control and milk production in diverse livestock species.
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Affiliation(s)
- Pushpa Sindhu
- Department of Animal Genetics and Breeding, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Ankit Magotra
- Department of Animal Genetics and Breeding, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Vikas Sindhu
- Department of Animal Nutrition, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Pradeep Chaudhary
- Department of Animal Genetics and Breeding, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
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2
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Haimon MLJ, Estrada-Cortés E, Amaral TF, Martin H, Jeensuk S, Block J, Heredia D, Venturini M, Rojas CS, Gonella-Diaza AM, DiLorenzo N, Scheffler TL, Dufour P, Sirard MA, de Melo GD, Pohler KG, Hansen PJ. Provision of choline chloride to the bovine preimplantation embryo alters postnatal body size and DNA methylation†. Biol Reprod 2024; 111:567-579. [PMID: 38857381 DOI: 10.1093/biolre/ioae092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/18/2024] [Accepted: 06/08/2024] [Indexed: 06/12/2024] Open
Abstract
Choline is a vital micronutrient. In this study, we aimed to confirm, and expand on previous findings, how choline impacts embryos from the first 7 days of development to affect postnatal phenotype. Bos indicus embryos were cultured in a choline-free medium (termed vehicle) or medium supplemented with 1.8 mM choline. Blastocyst-stage embryos were transferred into crossbred recipients. Once born, calves were evaluated at birth, 94 days, 178 days, and at weaning (average age = 239 days). Following weaning, all calves were enrolled into a feed efficiency trial before being separated by sex, with males being slaughtered at ~580 days of age. Results confirm that exposure of 1.8 mM choline chloride during the first 7 days of development alters postnatal characteristics of the resultant calves. Calves of both sexes from choline-treated embryos were consistently heavier through weaning and males had heavier testes at 3 months of age. There were sex-dependent alterations in DNA methylation in whole blood caused by choline treatment. After weaning, feed efficiency was affected by an interaction with sex, with choline calves being more efficient for females and less efficient for males. Calves from choline-treated embryos were heavier, or tended to be heavier, than calves from vehicle embryos at all observations after weaning. Carcass weight was heavier for choline calves and the cross-sectional area of the longissimus thoracis muscle was increased by choline.
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Affiliation(s)
| | - Eliab Estrada-Cortés
- Department of Animal Sciences, University of Florida, Gainesville, FL, USA
- Campo Experimental Centro Altos de Jalisco, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Tepatitlán de Morelos, Jalisco, México
| | - Thiago F Amaral
- Department of Animal Sciences, University of Florida, Gainesville, FL, USA
| | - Hélène Martin
- Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle, Département des Sciences Animales, Faculté des Sciences de l'Agriculture et de l'Alimentation, Pavillon INAF, Université Laval, Québec, QC, Canada
| | - Surawich Jeensuk
- Department of Animal Sciences, University of Florida, Gainesville, FL, USA
- Department of Livestock Development, Bureau of Biotechnology in Livestock Production, Pathum Thani, Thailand
| | - Jeremy Block
- Department of Animal Science, University of Wyoming, Laramie, WY, USA
| | - Daniella Heredia
- North Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Marianna, FL, USA
| | - M Venturini
- North Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Marianna, FL, USA
| | - Camila Santos Rojas
- North Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Marianna, FL, USA
| | - Angela M Gonella-Diaza
- North Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Marianna, FL, USA
| | - Nicolas DiLorenzo
- North Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Marianna, FL, USA
| | - Tracy L Scheffler
- Department of Animal Sciences, University of Florida, Gainesville, FL, USA
| | - Pascal Dufour
- Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle, Département des Sciences Animales, Faculté des Sciences de l'Agriculture et de l'Alimentation, Pavillon INAF, Université Laval, Québec, QC, Canada
| | - Marc-André Sirard
- Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle, Département des Sciences Animales, Faculté des Sciences de l'Agriculture et de l'Alimentation, Pavillon INAF, Université Laval, Québec, QC, Canada
| | | | - Ky G Pohler
- Department of Animal Science, Texas A&M University, College Station, TX, USA
| | - Peter J Hansen
- Department of Animal Sciences, University of Florida, Gainesville, FL, USA
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Hansen PJ. Pressing needs and recent advances to enhance production of embryos in vitro in cattle. Anim Reprod 2024; 21:e20240036. [PMID: 39286365 PMCID: PMC11404885 DOI: 10.1590/1984-3143-ar2024-0036] [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: 03/20/2024] [Accepted: 06/07/2024] [Indexed: 09/19/2024] Open
Abstract
Embryo transfer in cattle is an increasingly important technique for cattle production. Full attainment of the benefits of the technology will depend on overcoming hurdles to optimal performance using embryos produced in vitro. Given its importance, embryo technology research should become a global research priority for animal reproduction science. Among the goals of that research should be developing methods to increase the proportion of oocytes becoming embryos through optimization of in vitro oocyte maturation and in vitro fertilization, producing an embryo competent to establish and maintain pregnancy after transfer, and increasing recipient fertility through selection, management and pharmacological manipulation. The embryo produced in vitro is susceptible to epigenetic reprogramming and methods should be found to minimize deleterious epigenetic change while altering the developmental program of the resultant calf to increase its health and productivity. There are widening opportunities to rethink the technological basis for much of the current practices for production and transfer of embryos because of explosive advances in fields of bioengineering such as microfluidics, three-dimensional printing of cell culture materials, organoid culture, live-cell imaging, and cryopreservation.
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Affiliation(s)
- Peter James Hansen
- D.H. Barron Reproductive and Perinatal Biology Research Program, Department of Animal Sciences, Genetics Institute, University of Florida, Gainesville, FL, United States
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Pedace L, Pizzi S, Abballe L, Vinci M, Antonacci C, Patrizi S, Nardini C, Del Bufalo F, Rossi S, Pericoli G, Gianno F, Besharat ZM, Tiberi L, Mastronuzzi A, Ferretti E, Tartaglia M, Locatelli F, Ciolfi A, Miele E. Evaluating cell culture reliability in pediatric brain tumor primary cells through DNA methylation profiling. NPJ Precis Oncol 2024; 8:92. [PMID: 38637626 PMCID: PMC11026496 DOI: 10.1038/s41698-024-00578-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 03/13/2024] [Indexed: 04/20/2024] Open
Abstract
In vitro models of pediatric brain tumors (pBT) are instrumental for better understanding the mechanisms contributing to oncogenesis and testing new therapies; thus, ideally, they should recapitulate the original tumor. We applied DNA methylation (DNAm) and copy number variation (CNV) profiling to characterize 241 pBT samples, including 155 tumors and 86 pBT-derived cell cultures, considering serum vs serum-free conditions, late vs early passages, and dimensionality (2D vs 3D cultures). We performed a t-SNE classification and identified differentially methylated regions in tumors compared to cell models. Early cell cultures recapitulate the original tumor, but serum media and 2D culturing were demonstrated to significantly contribute to the divergence of DNAm profiles from the parental ones. All divergent cells clustered together acquiring a common deregulated epigenetic signature suggesting a shared selective pressure. We identified a set of hypomethylated genes shared among unfaithful cells converging on response to growth factors and migration pathways, such as signaling cascade activation, tissue organization, and cellular migration. In conclusion, DNAm and CNV are informative tools that should be used to assess the recapitulation of pBT-cells from parental tumors.
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Affiliation(s)
- Lucia Pedace
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Simone Pizzi
- Molecular Genetics and Functional Genomics, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy
| | - Luana Abballe
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Maria Vinci
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Celeste Antonacci
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Sara Patrizi
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Claudia Nardini
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Francesca Del Bufalo
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Sabrina Rossi
- Pathology Unit, Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Giulia Pericoli
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Francesca Gianno
- Department of Radiological, Oncological and Anatomic Pathology, Sapienza University, Rome, Italy
| | | | - Luca Tiberi
- Armenise-Harvard Laboratory of Brain Disorders and Cancer, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Angela Mastronuzzi
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Elisabetta Ferretti
- Department of Experimental Medicine, "Sapienza" University, 00161, Rome, Italy
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy
| | - Franco Locatelli
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Andrea Ciolfi
- Molecular Genetics and Functional Genomics, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy.
| | - Evelina Miele
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
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Tutt DAR, Guven-Ates G, Kwong WY, Simmons R, Sang F, Silvestri G, Canedo-Ribeiro C, Handyside AH, Labrecque R, Sirard MA, Emes RD, Griffin DK, Sinclair KD. Developmental, cytogenetic and epigenetic consequences of removing complex proteins and adding melatonin during in vitro maturation of bovine oocytes. Front Endocrinol (Lausanne) 2023; 14:1280847. [PMID: 38027209 PMCID: PMC10647927 DOI: 10.3389/fendo.2023.1280847] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/02/2023] [Indexed: 12/01/2023] Open
Abstract
Background In vitro maturation (IVM) of germinal vesicle intact oocytes prior to in vitro fertilization (IVF) is practiced widely in animals. In human assisted reproduction it is generally reserved for fertility preservation or where ovarian stimulation is contraindicated. Standard practice incorporates complex proteins (CP), in the form of serum and/or albumin, into IVM media to mimic the ovarian follicle environment. However, the undefined nature of CP, together with batch variation and ethical concerns regarding their origin, necessitate the development of more defined formulations. A known component of follicular fluid, melatonin, has multifaceted roles including that of a metabolic regulator and antioxidant. In certain circumstances it can enhance oocyte maturation. At this stage in development, the germinal-vesicle intact oocyte is prone to aneuploidy and epigenetic dysregulation. Objectives To determine the developmental, cytogenetic and epigenetic consequences of removing CP and including melatonin during bovine IVM. Materials and methods The study comprised a 2 x 2 factorial arrangement comparing (i) the inclusion or exclusion of CP, and (ii) the addition (100 nM) or omission of melatonin, during IVM. Cumulus-oocyte complexes (COCs) were retrieved from stimulated cycles. Following IVM and IVF, putative zygotes were cultured to Day 8 in standard media. RNAseq was performed on isolated cumulus cells, cytogenetic analyses (SNP-based algorithms) on isolated trophectoderm cells, and DNA methylation analysis (reduced representation bisulfite sequencing) on isolated cells of the inner-cell mass. Results Removal of CP during IVM led to modest reductions in blastocyst development, whilst added melatonin was beneficial in the presence but detrimental in the absence of CP. The composition of IVM media did not affect the nature or incidence of chromosomal abnormalities but cumulus-cell transcript expression indicated altered metabolism (primarily lipid) in COCs. These effects preceded the establishment of distinct metabolic and epigenetic signatures several days later in expanded and hatching blastocysts. Conclusions These findings highlight the importance of lipid, particularly sterol, metabolism by the COC during IVM. They lay the foundation for future studies that seek to develop chemically defined systems of IVM for the generation of transferrable embryos that are both cytogenetically and epigenetically normal.
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Affiliation(s)
- Desmond A. R. Tutt
- School of Biosciences, University of Nottingham, Sutton Bonington, United Kingdom
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
| | - Gizem Guven-Ates
- School of Biosciences, University of Nottingham, Sutton Bonington, United Kingdom
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
| | - Wing Yee Kwong
- School of Biosciences, University of Nottingham, Sutton Bonington, United Kingdom
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
| | - Rob Simmons
- Paragon Veterinary Group, Carlisle, United Kingdom
| | - Fei Sang
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | | | | | - Alan H. Handyside
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | | | - Marc-André Sirard
- CRDSI, Département des Sciences Animales, Faculté des sciences de l’agriculture et de l’alimentation, Université Laval, Quebec City, QC, Canada
| | - Richard D. Emes
- School of Biosciences, University of Nottingham, Sutton Bonington, United Kingdom
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
| | - Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Kevin D. Sinclair
- School of Biosciences, University of Nottingham, Sutton Bonington, United Kingdom
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
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Hansen PJ. Review: Some challenges and unrealized opportunities toward widespread use of the in vitro-produced embryo in cattle production. Animal 2023; 17 Suppl 1:100745. [PMID: 37567654 PMCID: PMC10659117 DOI: 10.1016/j.animal.2023.100745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 02/05/2023] [Accepted: 02/06/2023] [Indexed: 08/13/2023] Open
Abstract
The embryo produced by in vitro oocyte maturation, fertilization, and embryonic development is an important resource for genetic improvement and has the potential to improve female fertility and to be programmed to produce offspring with superior ability for health and production. The cultured embryo is also an important component of several realized and potential technologies such as gene editing, somatic cell nuclear cloning, stem cell technologies and gamete generation in vitro. Full realization of the opportunities afforded by the in vitro-produced embryo will require overcoming some technical obstacles to cost-effective implementation of an embryo transfer program. Among the research goals for improving the penetration of embryo transfer in the cattle industry are development of methods to increase the supply of oocytes from genetically elite females, enhance the proportion of oocytes that become transferrable embryos, improve the fraction of embryos that establish pregnancy after transfer, reduce pregnancy wastage after pregnancy diagnosis, and identify culture conditions to optimize postnatal phenotype.
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Affiliation(s)
- Peter J Hansen
- Department of Animal Sciences, D.H. Barron Reproductive and Perinatal Biology Research Program, and Genetics Institute, University of Florida, Gainesville, FL 32611-0910, USA.
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Hufnagel A, Grant ID, Aiken CEM. Glucose and oxygen in the early intrauterine environment and their role in developmental abnormalities. Semin Cell Dev Biol 2022; 131:25-34. [PMID: 35410716 DOI: 10.1016/j.semcdb.2022.03.041] [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: 11/14/2021] [Revised: 03/02/2022] [Accepted: 03/31/2022] [Indexed: 12/14/2022]
Abstract
The early life environment can have profound impacts on the developing conceptus in terms of both growth and morphogenesis. These impacts can manifest in a variety of ways, including congenital fetal anomalies, placental dysfunction with subsequent effects on fetal growth, and adverse perinatal outcomes, or via effects on long-term health outcomes that may not be detected until later childhood or adulthood. Two key examples of environmental influences on early development are explored: maternal hyperglycaemia and gestational hypoxia. These are increasingly common pregnancy exposures worldwide, with potentially profound impacts on population health. We explore what is known regarding the mechanisms by which these environmental exposures can impact early intrauterine development and thus result in adverse outcomes in the immediate, short, and long term.
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Affiliation(s)
- Antonia Hufnagel
- University of Cambridge Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Imogen D Grant
- Department of Obstetrics and Gynaecology, University of Cambridge, Box 223, The Rosie Hospital and NIHR Cambridge Comprehensive Biomedical Research Centre, Cambridge CB2 0SW, UK
| | - Catherine E M Aiken
- Department of Obstetrics and Gynaecology, University of Cambridge, Box 223, The Rosie Hospital and NIHR Cambridge Comprehensive Biomedical Research Centre, Cambridge CB2 0SW, UK; University of Cambridge Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK.
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Coy P, Romar R, Romero-Aguirregomezcorta J. The embryo culture media in the era of epigenetics: is it time to go back to nature? Anim Reprod 2022; 19:e20210132. [PMID: 35493788 PMCID: PMC9037603 DOI: 10.1590/1984-3143-ar2021-0132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/21/2022] [Indexed: 02/04/2023] Open
Abstract
This review is intended to draw attention to the importance of the culture media composition on the health of the embryos, fetuses, newborns, and adults derived from assisted reproductive technologies (ART). Although current research and industry trends are to use chemically defined media because of their suitability for manufacturing, commercialization, and regulatory purposes, compelling evidence indicates that those media fail to adequately account for the biological demands of early embryogenesis. Here, we list the main undesirable consequences of the ART described in the literature and results we and others have obtained over the past decade exploring an alternative and more natural way to support embryo growth in vitro: inclusion of endogenous reproductive fluids as additives in the ART culture media for pigs, cows, and humans. This review systematically assesses the pros and cons of using reproductive fluid additives, as well as the requirements to implement this approach in the future.
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Affiliation(s)
- Pilar Coy
- Universidad de Murcia, Spain; Institute for Biomedical Research of Murcia, Spain
| | - Raquel Romar
- Universidad de Murcia, Spain; Institute for Biomedical Research of Murcia, Spain
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