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Zhou C, Wang Y, He S, Lin S, Cheng J, Hu Q, Meng F, Gu T, Cai G, Li Z, Wu Z, Hong L. DIA-based quantitative proteomic analysis of porcine endometrium in the peri-implantation phase. J Proteomics 2024; 293:105065. [PMID: 38158016 DOI: 10.1016/j.jprot.2023.105065] [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: 07/18/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024]
Abstract
The 12th day of gestation is a critical period for embryo loss and the beginning of imminent implantation in sows. Data independent acquisition (DIA) technology is one of the high-throughput, high-resolution and reproducible proteomics technologies for large-scale digital qualitative and quantitative research. The aim of this study was to identify and characterize the protein abundance landscape of Yorkshire pig endometrium on the 12th day of pregnancy (P12) and estrous cycle (C12) using DIA proteomics. A total of 1251 differentially abundant proteins (DAPs) were identified, of which 882 were up-regulated and 369 were down-regulated at P12. Functional enrichment analysis showed that the identified proteins were related to metabolism, biosynthesis and signaling pathways. Three proteins were selected for Western blot (WB) validation and the results were consistent with the DIA data. Further combined with transcriptome data, fibrinogen like 2 (FGL2) and S100 calcium binding protein A8 (S100A8) were verified to be highly abundant in the P12 endometrial epithelium. In summary, there were significantly different abundance of proteome profiles in C12 and P12 endometrium, suggesting that DAPs are associated with changes in endometrial receptivity, which laid the foundation for further research on related regulatory mechanisms. SIGNIFICANCE: The 12th day of gestation is an important point in the peri-implantation period of pigs, when the endometrium presents a receptive state under the stimulation of estrogen. DIA proteomics technology is an emerging protein identification technology in recent years, which can obtain protein information through comprehensive and unbiased scanning. In this study, DIA technology was used to characterize endometrial proteins in pigs during the peri-implantation period. The results showed that higher protein abundance was detected using the DIA technique, and some of these DAPs may be involved in regulating embryo implantation. This study will help to better reveal the related proteins involved in embryo implantation, and lay a foundation for further research on the mechanism of endometrial regulation of embryo implantation. SIGNIFICANCE OF THE STUDY: The 12th day of gestation is an important point in the peri-implantation period of pigs, when the endometrium presents a receptive state under the stimulation of estrogen. DIA proteomics technology is an emerging protein identification technology in recent years, which can obtain protein information through comprehensive and unbiased scanning. In this study, DIA technology was used to characterize endometrial proteins in pigs during the peri-implantation period. The results showed that higher protein abundance was detected using the DIA technique, and some of these DAPs may be involved in regulating embryo implantation. This study will help to better reveal the related proteins involved in embryo implantation, and lay a foundation for further research on the mechanism of endometrial regulation of embryo implantation.
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Affiliation(s)
- Chen Zhou
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; National Engineering Research Center for Breeding Swine Industry, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Yongzhong Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; National Engineering Research Center for Breeding Swine Industry, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Simin He
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; National Engineering Research Center for Breeding Swine Industry, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Shifei Lin
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; National Engineering Research Center for Breeding Swine Industry, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Jie Cheng
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; National Engineering Research Center for Breeding Swine Industry, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Qun Hu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; National Engineering Research Center for Breeding Swine Industry, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Fanming Meng
- Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Ting Gu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; National Engineering Research Center for Breeding Swine Industry, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Gengyuan Cai
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; National Engineering Research Center for Breeding Swine Industry, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Zicong Li
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; National Engineering Research Center for Breeding Swine Industry, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Zhenfang Wu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; National Engineering Research Center for Breeding Swine Industry, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China; Yunfu Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu, China; Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Guangzhou, China.
| | - Linjun Hong
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; National Engineering Research Center for Breeding Swine Industry, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China; Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Guangzhou, China.
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Kopij G, Kiezun M, Dobrzyn K, Zaobidna E, Zarzecka B, Rak A, Kaminski T, Kaminska B, Smolinska N. Visfatin Affects the Transcriptome of Porcine Luteal Cells during Early Pregnancy. Int J Mol Sci 2024; 25:2339. [PMID: 38397019 PMCID: PMC10889815 DOI: 10.3390/ijms25042339] [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: 01/19/2024] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 02/25/2024] Open
Abstract
Visfatin/NAMPT (VIS), the hormone exerting a pleiotropic effect, is also perceived as an important factor in the regulation of reproductive processes and pregnancy maintenance. Previous studies confirmed its involvement in the control of porcine pituitary and ovary function. In this study, we hypothesized that VIS may affect the global transcriptome of luteal cells and thus regulate the functioning of the ovaries. Illumina's NovaSeq 6000 RNA sequencing was performed to investigate the differentially expressed genes (DEGs) and long non-coding RNAs (DELs) as well as the occurrence of differential alternative splicing events (DASs) in the porcine luteal cells exposed to VIS (100 ng/mL) during the implantation period. The obtained results revealed 170 DEGs (99 up- and 71 downregulated) assigned to 45 functional annotations. Moreover, we revealed 40 DELs, of which 3 were known and 37 were described for the first time. We identified 169 DASs events. The obtained results confirmed a significant effect of VIS on the transcriptome and spliceosome of luteal cells, including the genes involved in the processes crucial for successful implantation and pregnancy maintenance as angiogenesis, steroidogenesis, inflammation, cell development, migration, and proliferation.
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Affiliation(s)
- Grzegorz Kopij
- Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland; (G.K.); (M.K.); (K.D.); (E.Z.); (B.Z.); (T.K.); (B.K.)
| | - Marta Kiezun
- Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland; (G.K.); (M.K.); (K.D.); (E.Z.); (B.Z.); (T.K.); (B.K.)
| | - Kamil Dobrzyn
- Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland; (G.K.); (M.K.); (K.D.); (E.Z.); (B.Z.); (T.K.); (B.K.)
| | - Ewa Zaobidna
- Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland; (G.K.); (M.K.); (K.D.); (E.Z.); (B.Z.); (T.K.); (B.K.)
| | - Barbara Zarzecka
- Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland; (G.K.); (M.K.); (K.D.); (E.Z.); (B.Z.); (T.K.); (B.K.)
| | - Agnieszka Rak
- Institute of Zoology and Biomedical Research, Jagiellonian University in Krakow, Gronostajowa 9, 30-387 Krakow, Poland;
| | - Tadeusz Kaminski
- Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland; (G.K.); (M.K.); (K.D.); (E.Z.); (B.Z.); (T.K.); (B.K.)
| | - Barbara Kaminska
- Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland; (G.K.); (M.K.); (K.D.); (E.Z.); (B.Z.); (T.K.); (B.K.)
| | - Nina Smolinska
- Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland; (G.K.); (M.K.); (K.D.); (E.Z.); (B.Z.); (T.K.); (B.K.)
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Jastrzebski JP, Pascarella S, Lipka A, Dorocki S. IncRna: The R Package for Optimizing lncRNA Identification Processes. J Comput Biol 2023; 30:1322-1326. [PMID: 37878344 DOI: 10.1089/cmb.2023.0091] [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] [Indexed: 10/26/2023] Open
Abstract
In silico identification of long noncoding RNAs (lncRNAs) is a multistage process including filtering of transcripts according to their physical characteristics (e.g., length, exon-intron structure) and determination of the coding potential of the sequence. A common issue within this process is the choice of the most suitable method of coding potential analysis for the conducted research. Selection of tools on the sole basis of their single performance may not provide the most effective choice for a specific problem. To overcome these limitations, we developed the R library lncRna, which provides functions to easily carry out the entire lncRNA identification process. For example, the package prepares the data files for coding potential analysis to perform error analysis. Moreover, the package gives the opportunity to analyze the effectiveness of various combinations of the lncRNA prediction methods to select the optimal configuration of the entire process.
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Affiliation(s)
- Jan Pawel Jastrzebski
- Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Stefano Pascarella
- Department of Biochemical Sciences "A. Rossi Fanelli" Sapienza University of Rome, Rome, Italy
| | - Aleksandra Lipka
- Institute of Oral Biology, Faculty of Dentistry University of Oslo, Oslo, Norway
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