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Santana PDPB, Pinheiro KDC, Pereira LCDS, Andrade SS, Aburjaile FF, Ramos PDCDA, de Souza EB, da Costa NN, Cordeiro MDS, Santos SDSD, Miranda MDS, Ramos RTJ, da Silva ALDC. RNA sequencing and gene co-expression network of in vitro matured oocytes and blastocysts of buffalo. Anim Reprod 2024; 21:e20230131. [PMID: 38912163 PMCID: PMC11192227 DOI: 10.1590/1984-3143-ar2023-0131] [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: 09/27/2023] [Accepted: 04/24/2024] [Indexed: 06/25/2024] Open
Abstract
In reproductive technologies, uncovering the molecular aspects of oocyte and embryo competence under different conditions is crucial for refining protocols and enhancing efficiency. RNA-seq generates high-throughput data and provides transcriptomes that can undergo additional computational analyses. This study presented the transcriptomic profiles of in vitro matured oocytes and blastocysts produced in vitro from buffalo crossbred (Bubalus bubalis), coupled with gene co-expression and module preservation analysis. Cumulus Oophorus Complexes, obtained from slaughterhouse-derived ovaries, were subjected to in vitro maturation to yield metaphase II oocytes (616) or followed in vitro fertilization and culture to yield blastocysts for sequencing (526). Oocyte maturation (72%, ±3.34 sd) and embryo development (21.3%, ±4.18 sd) rates were obtained from three in vitro embryo production routines following standard protocols. Sequencing of 410 metaphase II oocytes and 70 hatched blastocysts (grade 1 and 2) identified a total of 13,976 genes, with 62% being ubiquitously expressed (8,649). Among them, the differentially expressed genes (4,153) and the strongly variable genes with the higher expression (fold-change above 11) were highlighted in oocytes (BMP15, UCHL1, WEE1, NLRPs, KPNA7, ZP2, and ZP4) and blastocysts (APOA1, KRT18, ANXA2, S100A14, SLC34A2, PRSS8 and ANXA2) as representative indicators of molecular quality. Additionally, genes exclusively found in oocytes (224) and blastocysts (2,200) with specific biological functions were identified. Gene co-expression network and module preservation analysis revealed strong preservation of functional modules related to exosome components, steroid metabolism, cell proliferation, and morphogenesis. However, cell cycle and amino acid transport modules exhibited weak preservation, which may reflect differences in embryo development kinetics and the activation of cell signaling pathways between buffalo and bovine. This comprehensive transcriptomic profile serves as a valuable resource for assessing the molecular quality of buffalo oocytes and embryos in future in vitro embryo production assays.
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Affiliation(s)
| | | | | | - Soraya Silva Andrade
- Laboratório de Genômica e Bioinformática, Universidade Federal do Pará, Belém, PA, Brasil
| | | | | | - Eduardo Baia de Souza
- Laboratório de Fertilização In Vitro, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brasil
| | - Nathalia Nogueira da Costa
- Laboratório de Fertilização In Vitro, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brasil
| | | | | | - Moysés dos Santos Miranda
- Laboratório de Fertilização In Vitro, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brasil
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Jia B, Xiang D, Yang H, Liang J, Lv C, Yang Q, Huang X, Quan G, Wu G. Transcriptome analysis of porcine embryos derived from oocytes vitrified at the germinal vesicle stage. Theriogenology 2024; 218:99-110. [PMID: 38316086 DOI: 10.1016/j.theriogenology.2024.01.032] [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: 10/03/2023] [Revised: 01/24/2024] [Accepted: 01/24/2024] [Indexed: 02/07/2024]
Abstract
Vitrification of porcine immature oocytes at the germinal vesicle (GV) stage reduces subsequent embryo yield and changes at the molecular level may occur during embryonic development. Therefore, the present study used porcine parthenogenetic embryos as a model to investigate the effect of GV oocyte vitrification on the transcriptional profiles of the resultant embryos at the 4-cell and blastocyst stages using the Smart-seq2 RNA-seq technique. We identified 743 (420 up-regulated and 323 down-regulated) and 994 (554 up-regulated and 440 down-regulated) differentially expressed genes (DEGs) from 4-cell embryos and blastocysts derived from vitrified GV oocytes, respectively. Functional enrichment analysis of DEGs in 4-cell embryos showed that vitrification of GV oocytes influenced regulatory mechanisms related to transcription regulation, apoptotic process, metabolism and key pathways such as the MAPK signaling pathway. Moreover, DEGs in blastocysts produced from vitrified GV oocytes were enriched in critical biological functions including cell adhesion, cell migration, AMPK signaling pathway, GnRH signaling pathway and so on. In addition, the transcriptomic analysis and quantitative real-time PCR results were consistent. In summary, the present study revealed that the vitrification of porcine GV oocytes could alter gene expression patterns during subsequent embryonic developmental stages, potentially affecting their developmental competence.
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Affiliation(s)
- Baoyu Jia
- Key Laboratory for Porcine Gene Editing and Xenotransplantation in Yunnan Province, College of Veterinary Medicine, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Decai Xiang
- National Regional Genebank (Yunnan) of Livestock and Poultry Genetic Resources, Yunnan Provincial Engineering Laboratory of Animal Genetic Resource Conservation and Germplasm Enhancement, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan, 650224, China
| | - Han Yang
- Key Laboratory for Porcine Gene Editing and Xenotransplantation in Yunnan Province, College of Veterinary Medicine, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Jiachong Liang
- National Regional Genebank (Yunnan) of Livestock and Poultry Genetic Resources, Yunnan Provincial Engineering Laboratory of Animal Genetic Resource Conservation and Germplasm Enhancement, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan, 650224, China
| | - Chunrong Lv
- National Regional Genebank (Yunnan) of Livestock and Poultry Genetic Resources, Yunnan Provincial Engineering Laboratory of Animal Genetic Resource Conservation and Germplasm Enhancement, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan, 650224, China
| | - Qige Yang
- Key Laboratory for Porcine Gene Editing and Xenotransplantation in Yunnan Province, College of Veterinary Medicine, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Xinyu Huang
- Key Laboratory for Porcine Gene Editing and Xenotransplantation in Yunnan Province, College of Veterinary Medicine, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Guobo Quan
- National Regional Genebank (Yunnan) of Livestock and Poultry Genetic Resources, Yunnan Provincial Engineering Laboratory of Animal Genetic Resource Conservation and Germplasm Enhancement, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan, 650224, China.
| | - Guoquan Wu
- National Regional Genebank (Yunnan) of Livestock and Poultry Genetic Resources, Yunnan Provincial Engineering Laboratory of Animal Genetic Resource Conservation and Germplasm Enhancement, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan, 650224, China.
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Sananmuang T, Puthier D, Nguyen C, Chokeshaiusaha K. Differential transcript usage across mammalian oocytes at the germinal vesicle and metaphase II stages. Theriogenology 2024; 215:1-9. [PMID: 37995439 DOI: 10.1016/j.theriogenology.2023.11.016] [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: 08/22/2023] [Revised: 11/11/2023] [Accepted: 11/13/2023] [Indexed: 11/25/2023]
Abstract
Ongoing progress in mRNA-Sequencing technologies has significantly contributed to the refinement of assisted reproductive technologies. However, the prior investigations have predominantly concentrated on alterations in overall gene expression levels, thereby leaving a considerable gap in our understanding of the influence of transcript isoform expression on fundamental cellular mechanisms of oocytes. Given the efficacy of differential transcript usage (DTU) analysis to address such knowledge, we conducted comprehensive DTU analysis utilizing mRNA-Seq datasets of germinal vesicle (GV) and metaphase II (MII) oocytes across six mammalian species from the SRA database, including cow, donkey, horse, human, mouse, and pig. To further illuminate the roles of these genes, we also conducted a rigorous Gene Ontology (GO) term enrichment analysis. While the DTU analysis of each species exhibited several genes with alterations in their transcript isoform usage, referred to as DTU genes, this study focused on only ten cross-species DTU genes sharing among a minimum of five distinct species (FDR≤0.05). These cross-species DTU genes were as follows: ABCF1, CDC6, CFAP36, CNOT10, DNM3, IWS1, NBN, NDEL1, RAD50 and ZCCHC17. GO term enrichment analysis unveiled the alignment of these cross-species DTU gene functions with RNA and cell-cycle control mechanisms across diverse mammalian species, thereby suggesting their vital roles during oocyte maturation. Further exploration of the transcript isoforms of these genes hence bore the potential to uncover novel transcript isoform markers for future reproductive technologies in both human and animal contexts.
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Affiliation(s)
- Thanida Sananmuang
- Rajamangala University of Technology Tawan-OK, Faculty of Veterinary Medicine, Chonburi, Thailand
| | - Denis Puthier
- Aix-Marseille Université, INSERM UMR 1090, TAGC, Marseille, France
| | - Catherine Nguyen
- Aix-Marseille Université, INSERM UMR 1090, TAGC, Marseille, France
| | - Kaj Chokeshaiusaha
- Rajamangala University of Technology Tawan-OK, Faculty of Veterinary Medicine, Chonburi, Thailand.
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