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Zhu JH, Guan XC, Yi LL, Xu H, Li QY, Cheng WJ, Xie YX, Li WZ, Zhao HY, Wei HJ, Zhao SM. Single-nucleus transcriptome sequencing reveals hepatic cell atlas in pigs. BMC Genomics 2023; 24:770. [PMID: 38087243 PMCID: PMC10717992 DOI: 10.1186/s12864-023-09765-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 10/24/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND As the largest substantive organ of animals, the liver plays an essential role in the physiological processes of digestive metabolism and immune defense. However, the cellular composition of the pig liver remains poorly understood. This investigation used single-nucleus RNA sequencing technology to identify cell types from liver tissues of pigs, providing a theoretical basis for further investigating liver cell types in pigs. RESULTS The analysis revealed 13 cells clusters which were further identified 7 cell types including endothelial cells, T cells, hepatocytes, Kupffer cells, stellate cells, B cells, and cholangiocytes. The dominant cell types were endothelial cells, T cells and hepatocytes in the liver tissue of Dahe pigs and Dahe black pigs, which accounts for about 85.76% and 82.74%, respectively. The number of endothelial cells was higher in the liver tissue of Dahe pigs compared to Dahe black pigs, while the opposite tendency was observed for T cells. Moreover, functional enrichment analysis demonstrated that the differentially expressed genes in pig hepatic endothelial cells were significantly enriched in the protein processing in endoplasmic reticulum, MAPK signaling pathway, and FoxO signaling pathway. Functional enrichment analysis demonstrated that the differentially expressed genes in pig hepatic T cells were significantly enriched in the thyroid hormone signaling pathway, B cell receptor signaling pathway, and focal adhesion. Functional enrichment analysis demonstrated that the differentially expressed genes in pig hepatic hepatocytes were significantly enriched in the metabolic pathways. CONCLUSIONS In summary, this study provides a comprehensive cell atlas of porcine hepatic tissue. The number, gene expression level and functional characteristics of each cell type in pig liver tissue varied between breeds.
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Affiliation(s)
- Jun-Hong Zhu
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, 650201, China
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China
| | - Xuan-Cheng Guan
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, 650201, China
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China
| | - Lan-Lan Yi
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, 650201, China
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China
| | - Hong Xu
- School of Public Finance and Economics, Yunnan University of Finance and Economics, Kunming, 650221, China
| | - Qiu-Yan Li
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, 650201, China
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China
| | - Wen-Jie Cheng
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, 650201, China
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China
| | - Yu-Xiao Xie
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, 650201, China
- College of Biology and Agriculture, Zunyi Normal University, Zunyi, 563006, China
| | - Wei-Zhen Li
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201, China
| | - Hong-Ye Zhao
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201, China
| | - Hong-Jiang Wei
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China.
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201, China.
| | - Su-Mei Zhao
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, 650201, China.
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China.
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Li Q, Zheng Y, Sun Y, Xu G. Resveratrol attenuated fatty acid synthesis through MAPK-PPAR pathway in red tilapia. Comp Biochem Physiol C Toxicol Pharmacol 2023; 268:109598. [PMID: 36898469 DOI: 10.1016/j.cbpc.2023.109598] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/22/2023] [Accepted: 03/01/2023] [Indexed: 03/11/2023]
Abstract
High-fat (HF) diets have been shown to cause hepatic impairment in fish species, but the mode of action, especially the pathways involved, has not yet been determined. In this study, the effects of resveratrol (RES) supplementation on the hepatic structure and fat metabolism of red tilapia (Oreochromis niloticus) were determined. Based on transcriptome and proteomics results, RES was found to promote fatty acid β-oxidation in the blood, liver, and liver cells associated with apoptosis and the MAPK/PPAR signaling pathway. RES supplementation was found to alter the expression of genes related to apoptosis and fatty acid pathways like blood itga6a and armc5 which were upregulated and downregulated respectively by high-fat feeding while ggh and ensonig00000008711 increased and decreased, respectively, with RES addition. Relative to the PPAR signaling pathway, fabp10a and acbd7 showed a reverse U-shaped tendency, both in different treatments and at different times. Proteomics results demonstrated that MAPK/PPAR, carbon/glyoxylate, dicarboxylate/glycine serine, and threonine/drug-other enzymes/beta-alanine metabolism pathways in the RES group were significantly affected, and Fasn and Acox1 decreased and increased, respectively, with RES addition. Seven subgroups were obtained using scRNA-seq, and enrichment analysis showed that the PPAR signaling pathway was upregulated with RES supplementation. RES significantly increased the expression of the marked genes (pck1) ensonig00000037711, fbp10a, granulin, hbe1, and zgc:136461, which are liver cell-specific genes. In conclusion, RES resulted in significantly enriched DGEs associated with fat metabolism and synthesis via the MAPK-PPAR signaling pathway.
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Affiliation(s)
- Quanjie Li
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center (FFRC), Chinese Academy of Fishery Sciences (CAFS), Wuxi, Jiangsu 214081, China
| | - Yao Zheng
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center (FFRC), Chinese Academy of Fishery Sciences (CAFS), Wuxi, Jiangsu 214081, China
| | - Yi Sun
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center (FFRC), Chinese Academy of Fishery Sciences (CAFS), Wuxi, Jiangsu 214081, China
| | - Gangchun Xu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center (FFRC), Chinese Academy of Fishery Sciences (CAFS), Wuxi, Jiangsu 214081, China.
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