Single-Nucleus RNA Sequencing Reveals Cellular Transcriptome Features at Different Growth Stages in Porcine Skeletal Muscle
Porcine latissimus dorsi muscle (LDM) is a crucial source of pork products. Meat quality indicators, such as the proportion of muscle fibers and intramuscular fat (IMF) deposition, vary during the growth and development of pigs. Numerous studies have highlighted the heterogeneous nature of skeletal...
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2025-01-01
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| author | Ziyu Chen Xiaoqian Wu Dongbin Zheng Yuling Wang Jie Chai Tinghuan Zhang Pingxian Wu Minghong Wei Ting Zhou Keren Long Mingzhou Li Long Jin Li Chen |
| author_facet | Ziyu Chen Xiaoqian Wu Dongbin Zheng Yuling Wang Jie Chai Tinghuan Zhang Pingxian Wu Minghong Wei Ting Zhou Keren Long Mingzhou Li Long Jin Li Chen |
| author_sort | Ziyu Chen |
| collection | DOAJ |
| description | Porcine latissimus dorsi muscle (LDM) is a crucial source of pork products. Meat quality indicators, such as the proportion of muscle fibers and intramuscular fat (IMF) deposition, vary during the growth and development of pigs. Numerous studies have highlighted the heterogeneous nature of skeletal muscle, with phenotypic differences reflecting variations in cellular composition and transcriptional profiles. This study investigates the cellular-level transcriptional characteristics of LDM in large white pigs at two growth stages (170 days vs. 245 days) using single-nucleus RNA sequencing (snRNA-seq). We identified 56,072 cells across 12 clusters, including myofibers, fibro/adipogenic progenitor (FAP) cells, muscle satellite cells (MUSCs), and other resident cell types. The same cell types were present in the LDM at both growth stages, but their proportions and states differed. A higher proportion of FAPs was observed in the skeletal muscle of 245-day-old pigs. Additionally, these cells exhibited more active communication with other cell types compared to 170-day-old pigs. For instance, more interactions were found between FAPs and pericytes or endothelial cells in 245-day-old pigs, including collagen and integrin family signaling. Three subclasses of FAPs was identified, comprising FAPs_<i>COL3A1</i><sup>+</sup>, FAPs_<i>PDE4D</i><sup>+</sup>, and FAPs_<i>EBF1</i><sup>+</sup>, while adipocytes were categorized into Ad_<i>PDE4D</i><sup>+</sup> and Ad_<i>DGAT2</i><sup>+</sup> subclasses. The proportions of these subclasses differed between the two age groups. We also constructed differentiation trajectories for FAPs and adipocytes, revealing that FAPs in 245-day-old pigs differentiated more toward fibrosis, a characteristic reminiscent of the high prevalence of skeletal muscle fibrosis in aging humans. Furthermore, the Ad_<i>PDE4D</i><sup>+</sup> adipocyte subclass, predominant in 245-day-old pigs, originated from FAPs_<i>PDE4D</i><sup>+</sup> expressing the same gene, while the Ad_<i>DGAT2</i><sup>+</sup> subclass stemmed from FAPs_<i>EBF1</i><sup>+</sup>. In conclusion, our study elucidates transcriptional differences in skeletal muscle between two growth stages of pigs and provides insights into mechanisms relevant to pork meat quality and skeletal muscle diseases. |
| format | Article |
| id | doaj-art-fd83f226302b4a2186d5fa38f6b6b7e2 |
| institution | Kabale University |
| issn | 2073-4409 |
| language | English |
| publishDate | 2025-01-01 |
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| spelling | doaj-art-fd83f226302b4a2186d5fa38f6b6b7e22025-01-10T13:16:19ZengMDPI AGCells2073-44092025-01-011413710.3390/cells14010037Single-Nucleus RNA Sequencing Reveals Cellular Transcriptome Features at Different Growth Stages in Porcine Skeletal MuscleZiyu Chen0Xiaoqian Wu1Dongbin Zheng2Yuling Wang3Jie Chai4Tinghuan Zhang5Pingxian Wu6Minghong Wei7Ting Zhou8Keren Long9Mingzhou Li10Long Jin11Li Chen12Chongqing Academy of Animal Science, Chongqing 402460, ChinaChongqing Academy of Animal Science, Chongqing 402460, ChinaState Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 625041, ChinaState Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 625041, ChinaChongqing Academy of Animal Science, Chongqing 402460, ChinaChongqing Academy of Animal Science, Chongqing 402460, ChinaChongqing Academy of Animal Science, Chongqing 402460, ChinaNational Center of Technology Innovation for Pigs, Chongqing 402460, ChinaSichuan Litian Animal Husbandry Co., Ltd., Dazhou 635711, ChinaState Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 625041, ChinaState Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 625041, ChinaState Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 625041, ChinaChongqing Academy of Animal Science, Chongqing 402460, ChinaPorcine latissimus dorsi muscle (LDM) is a crucial source of pork products. Meat quality indicators, such as the proportion of muscle fibers and intramuscular fat (IMF) deposition, vary during the growth and development of pigs. Numerous studies have highlighted the heterogeneous nature of skeletal muscle, with phenotypic differences reflecting variations in cellular composition and transcriptional profiles. This study investigates the cellular-level transcriptional characteristics of LDM in large white pigs at two growth stages (170 days vs. 245 days) using single-nucleus RNA sequencing (snRNA-seq). We identified 56,072 cells across 12 clusters, including myofibers, fibro/adipogenic progenitor (FAP) cells, muscle satellite cells (MUSCs), and other resident cell types. The same cell types were present in the LDM at both growth stages, but their proportions and states differed. A higher proportion of FAPs was observed in the skeletal muscle of 245-day-old pigs. Additionally, these cells exhibited more active communication with other cell types compared to 170-day-old pigs. For instance, more interactions were found between FAPs and pericytes or endothelial cells in 245-day-old pigs, including collagen and integrin family signaling. Three subclasses of FAPs was identified, comprising FAPs_<i>COL3A1</i><sup>+</sup>, FAPs_<i>PDE4D</i><sup>+</sup>, and FAPs_<i>EBF1</i><sup>+</sup>, while adipocytes were categorized into Ad_<i>PDE4D</i><sup>+</sup> and Ad_<i>DGAT2</i><sup>+</sup> subclasses. The proportions of these subclasses differed between the two age groups. We also constructed differentiation trajectories for FAPs and adipocytes, revealing that FAPs in 245-day-old pigs differentiated more toward fibrosis, a characteristic reminiscent of the high prevalence of skeletal muscle fibrosis in aging humans. Furthermore, the Ad_<i>PDE4D</i><sup>+</sup> adipocyte subclass, predominant in 245-day-old pigs, originated from FAPs_<i>PDE4D</i><sup>+</sup> expressing the same gene, while the Ad_<i>DGAT2</i><sup>+</sup> subclass stemmed from FAPs_<i>EBF1</i><sup>+</sup>. In conclusion, our study elucidates transcriptional differences in skeletal muscle between two growth stages of pigs and provides insights into mechanisms relevant to pork meat quality and skeletal muscle diseases.https://www.mdpi.com/2073-4409/14/1/37skeletal musclepigsingle-nucleus RNA sequencingdevelopmentIMF |
| spellingShingle | Ziyu Chen Xiaoqian Wu Dongbin Zheng Yuling Wang Jie Chai Tinghuan Zhang Pingxian Wu Minghong Wei Ting Zhou Keren Long Mingzhou Li Long Jin Li Chen Single-Nucleus RNA Sequencing Reveals Cellular Transcriptome Features at Different Growth Stages in Porcine Skeletal Muscle Cells skeletal muscle pig single-nucleus RNA sequencing development IMF |
| title | Single-Nucleus RNA Sequencing Reveals Cellular Transcriptome Features at Different Growth Stages in Porcine Skeletal Muscle |
| title_full | Single-Nucleus RNA Sequencing Reveals Cellular Transcriptome Features at Different Growth Stages in Porcine Skeletal Muscle |
| title_fullStr | Single-Nucleus RNA Sequencing Reveals Cellular Transcriptome Features at Different Growth Stages in Porcine Skeletal Muscle |
| title_full_unstemmed | Single-Nucleus RNA Sequencing Reveals Cellular Transcriptome Features at Different Growth Stages in Porcine Skeletal Muscle |
| title_short | Single-Nucleus RNA Sequencing Reveals Cellular Transcriptome Features at Different Growth Stages in Porcine Skeletal Muscle |
| title_sort | single nucleus rna sequencing reveals cellular transcriptome features at different growth stages in porcine skeletal muscle |
| topic | skeletal muscle pig single-nucleus RNA sequencing development IMF |
| url | https://www.mdpi.com/2073-4409/14/1/37 |
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