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Zhao X, Wu S, Yun Y, Du Z, Liu S, Bo C, Gao Y, Yang L, Song L, Bai C, Su G, Li G. Integrating Transcriptomics, Proteomics, and Metabolomics to Investigate the Mechanism of Fetal Placental Overgrowth in Somatic Cell Nuclear Transfer Cattle. Int J Mol Sci 2024; 25:9388. [PMID: 39273344 PMCID: PMC11395630 DOI: 10.3390/ijms25179388] [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: 07/30/2024] [Revised: 08/28/2024] [Accepted: 08/28/2024] [Indexed: 09/15/2024] Open
Abstract
A major factor limiting the development of somatic cell nuclear transfer (SCNT) technology is the low success rate of pregnancy, mainly due to placental abnormalities disrupting the maternal-fetal balance during pregnancy. Although there has been some progress in research on the abnormal enlargement of cloned bovine placenta, there are still few reports on the direct regulatory mechanisms of enlarged cloned bovine placenta tissue. In this study, we conducted sequencing and analysis of transcriptomics, proteomics, and metabolomics of placental tissues from SCNT cattle (n = 3) and control (CON) cattle (n = 3). The omics analysis results indicate abnormalities in biological functions such as protein digestion and absorption, glycolysis/gluconeogenesis, the regulation of lipid breakdown, as well as glycerolipid metabolism, and arginine and proline metabolism in the placenta of SCNT cattle. Integrating these analyses highlights critical metabolic pathways affecting SCNT cattle placenta, including choline metabolism and unsaturated fatty acid biosynthesis. These findings suggest that aberrant expressions of genes, proteins, and metabolites in SCNT placentas affect key pathways in protein digestion, growth hormone function, and energy metabolism. Our results suggest that abnormal protein synthesis, growth hormone function, and energy metabolism in SCNT bovine placental tissues contribute to placental hypertrophy. These findings offer valuable insights for further investigation into the mechanisms underlying SCNT bovine placental abnormalities.
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Affiliation(s)
- Xiaoyu Zhao
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
- College of Life Sciences, Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
| | - Shanshan Wu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Yuan Yun
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
- College of Life Sciences, Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
| | - Zhiwen Du
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
- College of Life Sciences, Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
| | - Shuqin Liu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
- College of Life Sciences, Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
| | - Chunjie Bo
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
- College of Life Sciences, Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
| | - Yuxin Gao
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
- College of Life Sciences, Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
| | - Lei Yang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
- College of Life Sciences, Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
| | - Lishuang Song
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
- College of Life Sciences, Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
| | - Chunling Bai
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
- College of Life Sciences, Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
| | - Guanghua Su
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
- College of Life Sciences, Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
| | - Guangpeng Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
- College of Life Sciences, Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
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Malpotra S, Goel P, Shyam S, Singh MK, Palta P. Global DNA methylation profiles of buffalo (Bubalus bubalis) preimplantation embryos produced by handmade cloning and in vitro fertilization. Sci Rep 2022; 12:5161. [PMID: 35338228 PMCID: PMC8956680 DOI: 10.1038/s41598-022-09207-8] [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: 05/22/2021] [Accepted: 12/06/2021] [Indexed: 12/26/2022] Open
Abstract
Somatic cell nuclear transfer technique (SCNT) has proved to be an outstanding method of multiplication of elite animals but accompanied with low efficiency and live birth rate of cloned animals. Epigenetic alterations of DNA has been one of the culprits behind this issue. Cloned embryos are found to deviate slightly from regular pattern of demethylation and re-methylation at the time of nuclear reprogramming and embryonic development when compared with embryos produced by in vitro fertilization (IVF). Thus, the present study was aimed at evaluating global DNA methylation profiles of cloned embryos at 2-cell, 8-cell and blastocyst stages and compare it with corresponding stages of embryos produced by IVF by using MeDIP-Sequencing on Illumina-based platform. We found out that cloned embryos exhibited significantly different DNA methylation pattern as compared to IVF embryos with respect to distribution of differentially methylated regions in different components of genome, CpG islands distribution and methylation status, gene ontological profiles and pathways affected throughout the developmental stages. The data generated from MeDIP-Seq was validated at blastocyst stage cloned and IVF embryos by bisulfite-sequencing PCR on five randomly selected gene regions.
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Affiliation(s)
- Shivani Malpotra
- Embryo Biotechnology Lab, Animal Biotechnology Centre, ICAR-National Dairy Research Institute (Deemed University), Karnal, Haryana, 132001, India.
| | - Pallavi Goel
- Embryo Biotechnology Lab, Animal Biotechnology Centre, ICAR-National Dairy Research Institute (Deemed University), Karnal, Haryana, 132001, India
| | - Songyukta Shyam
- Embryo Biotechnology Lab, Animal Biotechnology Centre, ICAR-National Dairy Research Institute (Deemed University), Karnal, Haryana, 132001, India
| | - Manoj Kumar Singh
- Embryo Biotechnology Lab, Animal Biotechnology Centre, ICAR-National Dairy Research Institute (Deemed University), Karnal, Haryana, 132001, India
| | - Prabhat Palta
- Embryo Biotechnology Lab, Animal Biotechnology Centre, ICAR-National Dairy Research Institute (Deemed University), Karnal, Haryana, 132001, India
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Kim HR, Lee JE, Oqani RK, Kim SY, Wakayama T, Li C, Sa SJ, Woo JS, Jin DI. Aberrant Expression of TIMP-2 and PBEF Genes in the Placentae of Cloned Mice Due to Epigenetic Reprogramming Error. PLoS One 2016; 11:e0166241. [PMID: 27855185 PMCID: PMC5113924 DOI: 10.1371/journal.pone.0166241] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 10/25/2016] [Indexed: 11/19/2022] Open
Abstract
Cloned mice derived from somatic or ES cells show placental overgrowth (placentomegaly) at term. We had previously analyzed cloned and normal mouse placentae by using two-dimensional gel electrophoresis and mass spectrometry to identify differential protein expression patterns. Cloned placentae showed upregulation of tissue inhibitor of metalloproteinase-2 (TIMP-2), which is involved in extracellular matrix degradation and tissue remodeling, and downregulation of pre-B cell colony enhancing factor 1 (PBEF), which inhibits apoptosis and induces spontaneous labor. Here, we used Western blotting to further analyze the protein expression levels of TIMP-2 and PBEF in cloned placentae derived from cumulus cells, TSA-treated cumulus cells, intracytoplasmic sperm injection (ICSI), and natural mating (NM control). Cloned and TSA-treated cloned placentae had higher expression levels of TIMP-2 compared with NM control and ICSI-derived placentae, and there was a positive association between TIMP-2 expression and the placental weight of cloned mouse concepti. Conversely, PBEF protein expression was significantly lower in cloned and ICSI placentae compared to NM controls. To examine whether the observed differences were due to abnormal gene expression caused by faulty epigenetic reprogramming in clones, we investigated DNA methylation and histone modification in the promoter regions of the genes encoding TIMP-2 and PBEF. Sodium bisulfite sequencing did not reveal any difference in DNA methylation between cloned and NM control placentae. However, ChIP assays revealed that the level of H3-K9/K14 acetylation at the TIMP-2 locus was higher in cloned placentae than in NM controls, whereas acetylation of the PBEF promoter was lower in cloned and ICSI placenta versus NM controls. These results suggest that cloned placentae appear to suffer from failure of histone modification-based reprogramming in these (and potentially other) developmentally important genes, leading to aberrant expression of their protein products. These changes are likely to be involved in generating the abnormalities seen in cloned mouse placentae, including enlargement and/or a lack of proper placental function.
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Affiliation(s)
- Hong Rye Kim
- Department of Animal Science & Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Jae Eun Lee
- Department of Animal Science & Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Reza Kheirkhahi Oqani
- Department of Animal Science & Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - So Yeon Kim
- Department of Animal Science & Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Teruhiko Wakayama
- Faculty of Life and Environmental Science, University of Yamanashi, Yamanashi, Japan
| | - Chong Li
- School of Medicine, Tongi University, Shanghai, China
| | - Su Jin Sa
- Department of Animal Resource Development, National Institute of Animal Science, Cheonan, Republic of Korea
| | - Je Seok Woo
- Department of Animal Resource Development, National Institute of Animal Science, Cheonan, Republic of Korea
| | - Dong Il Jin
- Department of Animal Science & Biotechnology, Chungnam National University, Daejeon, Republic of Korea
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Kim HR, Han RX, Diao YF, Park CS, Jin DI. Epigenetic characterization of the PBEF and TIMP-2 genes in the developing placentae of normal mice. BMB Rep 2011; 44:535-40. [PMID: 21871178 DOI: 10.5483/bmbrep.2011.44.8.535] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Reprogramming errors, which appear frequently in cloned animals, are reflected by aberrant gene expression. We previously reported the aberrant expression of TIMP-2 and PBEF in cloned placenta and differential expression of PBEF genes during pregnancy. To examine the epigenetic modifications that regulate dynamic gene expression in developing placentae, we herein analyzed the mRNA and protein expression levels of PBEF and TIMP-2 in the placentae of normal mice during pregnancy and then examined potential correlations with epigenetic modifications. DNA methylation pattern analysis revealed no difference, but ChIP assays using antibodies against H3-K9/K14 and H4-K5 histone acetylation revealed that the H3-K9/K14 acetylation levels, but not the H4-K5 acetylation levels, of the TIMP-2 and PBEF loci were significantly correlated with their gene expression levels during placentation in normal mice. These results suggest that epigenetic changes may regulate gene expression level in the developing placentae of normal mice and that inappropriate epigenetic reprogramming might be one cause of the abnormal placentae seen in cloned animals.
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Affiliation(s)
- Hong-Rye Kim
- Department of Animal Science & Biotechnology, Research Center for Transgenic Cloned Pig, Chungnam National University, Deajeon, Korea
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Yang B, Wang J, Tang B, Liu Y, Guo C, Yang P, Yu T, Li R, Zhao J, Zhang L, Dai Y, Li N. Characterization of bioactive recombinant human lysozyme expressed in milk of cloned transgenic cattle. PLoS One 2011; 6:e17593. [PMID: 21436886 PMCID: PMC3059212 DOI: 10.1371/journal.pone.0017593] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Accepted: 01/27/2011] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND There is great potential for using transgenic technology to improve the quality of cow milk and to produce biopharmaceuticals within the mammary gland. Lysozyme, a bactericidal protein that protects human infants from microbial infections, is highly expressed in human milk but is found in only trace amounts in cow milk. METHODOLOGY/PRINCIPAL FINDINGS We have produced 17 healthy cloned cattle expressing recombinant human lysozyme using somatic cell nuclear transfer. In this study, we just focus on four transgenic cattle which were natural lactation. The expression level of the recombinant lysozyme was up to 25.96 mg/L, as measured by radioimmunoassay. Purified recombinant human lysozyme showed the same physicochemical properties, such as molecular mass and bacterial lysis, as its natural counterpart. Moreover, both recombinant and natural lysozyme had similar conditions for reactivity as well as for pH and temperature stability during in vitro simulations. The gross composition of transgenic and non-transgenic milk, including levels of lactose, total protein, total fat, and total solids were not found significant differences. CONCLUSIONS/SIGNIFICANCE Thus, our study not only describes transgenic cattle whose milk offers the similar nutritional benefits as human milk but also reports techniques that could be further refined for production of active human lysozyme on a large scale.
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Affiliation(s)
- Bin Yang
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, People's Republic of China
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