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Ren Z, Zhang S, Shi L, Zhou A, Lin X, Zhang J, Zhu X, Huang L, Li K. Integrated ATAC-seq and RNA-seq Analysis of In Vitro Cultured Skeletal Muscle Satellite Cells to Understand Changes in Cell Proliferation. Cells 2024; 13:1031. [PMID: 38920660 PMCID: PMC11201436 DOI: 10.3390/cells13121031] [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: 05/25/2024] [Revised: 06/06/2024] [Accepted: 06/07/2024] [Indexed: 06/27/2024] Open
Abstract
Skeletal muscle satellite cells, the resident stem cells in pig skeletal muscle, undergo proliferation and differentiation to enable muscle tissue repair. The proliferative and differentiative abilities of these cells gradually decrease during in vitro cultivation as the cell passage number increases. Despite extensive research, the precise molecular mechanisms that regulate this process are not fully understood. To bridge this knowledge gap, we conducted transcriptomic analysis of skeletal muscle satellite cells during in vitro cultivation to quantify passage number-dependent changes in the expression of genes associated with proliferation. Additionally, we explored the relationships between gene transcriptional activity and chromatin accessibility using transposase-accessible chromatin sequencing. This revealed the closure of numerous open chromatin regions, which were primarily located in intergenic regions, as the cell passage number increased. Integrated analysis of the transcriptomic and epigenomic data demonstrated a weak correlation between gene transcriptional activity and chromatin openness in expressed genic regions; although some genes (e.g., GNB4 and FGD5) showed consistent relationships between gene expression and chromatin openness, a substantial number of differentially expressed genes had no clear association with chromatin openness in expressed genic regions. The p53-p21-RB signaling pathway may play a critical regulatory role in cell proliferation processes. The combined transcriptomic and epigenomic approach taken here provided key insights into changes in gene expression and chromatin openness during in vitro cultivation of skeletal muscle satellite cells. These findings enhance our understanding of the intricate mechanisms underlying the decline in cellular proliferation capacity in cultured cells.
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Affiliation(s)
- Zeyu Ren
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Laboratory of Genetic Breeding, Reproduction and Precision Livestock Farming, Hubei Provincial Center of Technology Innovation for Domestic Animal Breeding, Wuhan Polytechnic University, Wuhan 430023, China; (Z.R.); (S.Z.); (L.S.); (A.Z.)
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China;
| | - Siyi Zhang
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Laboratory of Genetic Breeding, Reproduction and Precision Livestock Farming, Hubei Provincial Center of Technology Innovation for Domestic Animal Breeding, Wuhan Polytechnic University, Wuhan 430023, China; (Z.R.); (S.Z.); (L.S.); (A.Z.)
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China;
| | - Liangyu Shi
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Laboratory of Genetic Breeding, Reproduction and Precision Livestock Farming, Hubei Provincial Center of Technology Innovation for Domestic Animal Breeding, Wuhan Polytechnic University, Wuhan 430023, China; (Z.R.); (S.Z.); (L.S.); (A.Z.)
| | - Ao Zhou
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Laboratory of Genetic Breeding, Reproduction and Precision Livestock Farming, Hubei Provincial Center of Technology Innovation for Domestic Animal Breeding, Wuhan Polytechnic University, Wuhan 430023, China; (Z.R.); (S.Z.); (L.S.); (A.Z.)
| | - Xin Lin
- College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin 300392, China;
| | - Jing Zhang
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Laboratory of Genetic Breeding, Reproduction and Precision Livestock Farming, Hubei Provincial Center of Technology Innovation for Domestic Animal Breeding, Wuhan Polytechnic University, Wuhan 430023, China; (Z.R.); (S.Z.); (L.S.); (A.Z.)
| | - Xiusheng Zhu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China;
| | - Lei Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China;
| | - Kui Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China;
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Zhao F, Fan Z, Jia R, Liu Q, Wang M, Sui J, Liu H. Mesenchymal Stem Cells Accelerate Recovery of Acetic Acid-Induced Chronic Gastric Ulcer by Regulating Ekt/Akt/TRIM29 Axis. Stem Cells Int 2024; 2024:6202123. [PMID: 38213743 PMCID: PMC10781525 DOI: 10.1155/2024/6202123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 11/08/2023] [Accepted: 12/07/2023] [Indexed: 01/13/2024] Open
Abstract
Chronic gastric ulcer (CGU), a prevalent digestive disease, has a high incidence and is seriously harmful to human health. Mesenchymal stem cells (MSCs) have been proven to have beneficial therapeutic effects in many human diseases. Here, a CGU model induced by acetic acid in mice was used to evaluate the repair effects and potential mechanism of human umbilical cord-derived MSCs (hUC-MSCs) and hUC-MSCs derived conditioned medium (hUC-MSC-CM). We found that hUC-MSCs and hUC-MSC-CM treatment significantly repaired morphological characteristics of CGU, improved proliferation and decreased apoptosis of gastric cells, and promoted the generation of new blood vessels in granulation tissues. In addition, we could detect the homing of MSCs in gastric tissue, and MSCs may differentiate into Lgr5-positive cells. As well as this, in vitro experiments showed that hUC-MSC-CM could promote cell proliferation, stimulate cell cycle progression, and reduce the incidence of apoptosis. The transcriptome of cells and the iTRAQ proteome of gastric tissues suggest that MSCs may play a therapeutic role by increasing the expression of TRIM29. Additionally, it was found that knocking down TRIM29 significantly decreased the ameliorative effects of hUC-MSC-CM on cell apoptosis. As a result of further molecular experiments, it was found that TRIM29 is capable of phosphorylating Erk/Akt in specific cell type. As a whole, it appears that hUC-MSCs can be an effective therapeutic approach for promoting gastric ulcer healing and may exert therapeutic effects in the form of paracrine and differentiation into gastric cells.
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Affiliation(s)
- Feiyue Zhao
- Handan Pharmaceutical Co. Ltd., Handan, Hebei Province, China
- Key Laboratory of Chinese Medicine for Gastric Medicine, Handan, Hebei Province, China
| | - Zhibin Fan
- Handan Pharmaceutical Co. Ltd., Handan, Hebei Province, China
| | - Ruikang Jia
- Handan Pharmaceutical Co. Ltd., Handan, Hebei Province, China
| | - Qichao Liu
- Handan Pharmaceutical Co. Ltd., Handan, Hebei Province, China
| | - Menglei Wang
- Key Laboratory of Chinese Medicine for Gastric Medicine, Handan, Hebei Province, China
| | - Jianliang Sui
- School of Life Science and Food Engineering, Hebei University of Engineering, Handan, Hebei Province, China
| | - Huiyun Liu
- Handan Pharmaceutical Co. Ltd., Handan, Hebei Province, China
- Key Laboratory of Chinese Medicine for Gastric Medicine, Handan, Hebei Province, China
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He X, Wu R, Yun Y, Qin X, Huang Y, Chen L, Han Y, Wu J, Sha L, Borjigin G. MicroRNA and circular RNA profiling in the deposited fat tissue of Sunite sheep. Front Vet Sci 2022; 9:954882. [DOI: 10.3389/fvets.2022.954882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022] Open
Abstract
As the most typical deposited fat, tail fat is an important energy reservoir for sheep adapted to harsh environments and plays an important role as a raw material in daily life. However, the regulatory mechanisms of microRNA (miRNA) and circular RNA (circRNA) in tail fat development remain unclear. In this study, we characterized the miRNA and circRNA expression profiles in the tail fat of sheep at the ages of 6, 18, and 30 months. We identified 219 differentially expressed (DE) miRNAs (including 12 novel miRNAs), which exhibited a major tendency to be downregulated, and 198 DE circRNAs, which exhibited a tendency to be upregulated. Target gene prediction analysis was performed for the DE miRNAs. Functional analysis revealed that their target genes were mainly involved in cellular interactions, while the host genes of DE circRNAs were implicated in lipid and fatty acid metabolism. Subsequently, we established a competing endogenous RNA (ceRNA) network based on the negative regulatory relationship between miRNAs and target genes. The network revealed that upregulated miRNAs play a leading role in the development of tail fat. Finally, the ceRNA relationship network with oar-miR-27a_R-1 and oar-miR-29a as the core was validated, suggesting possible involvement of these interactions in tail fat development. In summary, DE miRNAs were negatively correlated with DE circRNAs during sheep tail fat development. The multiple ceRNA regulatory network dominated by upregulated DE miRNAs may play a key role in this developmental process.
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