Related Experiment Video
Updated: Jul 29, 2025
TRAP-rc, Translating Ribosome Affinity Purification from Rare Cell Populations of Drosophila Embryos
Published on: September 10, 2015
Decoding the transcriptome of muscular dystrophy due to Ptrf deficiency using single-nucleus RNA sequencing
Xiaokai Li1, Zhining Zhong1, Ruowei Zhang1
1Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.
Abstract:
Lacking PTRF (polymerase I and transcript release factor), an essential caveolae component, causes a secondary deficiency of caveolins resulting in muscular dystrophy. The transcriptome responses of different types of muscle fibers and mononuclear cells in skeletal muscle to muscular dystrophy caused by Ptrf deletion have not been explored. Here, we created muscular dystrophy mice by Ptrf knockout and applied single-nucleus RNA sequencing (snRNA-seq) to unveil the transcriptional changes of the skeletal muscle at single-nucleus resolution. 11 613 muscle nuclei (WT, 5838; Ptrf KO, 5775) were classified into 12 clusters corresponding to 11 nuclear types. Trajectory analysis revealed the potential transition between type IIb_1 and IIb_2 myonuclei upon muscular dystrophy. Functional enrichment analysis indicated that apoptotic signaling and enzyme-linked receptor protein signaling pathway were significantly enriched in type IIb_1 and IIb_2 myonuclei of Ptrf KO, respectively. The muscle structure development and the PI3K-AKT signaling pathway were significantly enriched in type IIa and IIx myonuclei of Ptrf KO. Meanwhile, metabolic pathway analysis showed a decrease in overall metabolic pathway activity of myonuclei subtypes upon muscular dystrophy, with the most decrease in type IIb_1 myonuclei. Gene regulatory network analysis found that the activity of Mef2c, Mef2d, Myf5, and Pax3 regulons was enhanced in type II myonuclei of Ptrf KO, especially in type IIb_2 myonuclei. In addition, we investigated the transcriptome changes in adipocytes and found that muscular dystrophy enhanced the lipid metabolic capacity of adipocytes. Our findings provide a valuable resource for exploring the molecular mechanism of muscular dystrophy due to Ptrf deficiency.
Insights
Polymerase I and transcript release factor (PTRF) deficiency causes muscular dystrophy. Single-nucleus RNA sequencing revealed altered gene expression and metabolic pathways in muscle fibers and adipocytes, offering insights into disease mechanisms.
Area of Science:
- Molecular Biology
- Genetics
- Cell Biology
Background:
- Polymerase I and transcript release factor (PTRF) is crucial for caveolae formation.
- PTRF deficiency leads to secondary caveolin loss and muscular dystrophy.
- Transcriptome responses in skeletal muscle subtypes during PTRF-deficient muscular dystrophy are largely unexplored.
Purpose of the Study:
- To investigate the transcriptional landscape of skeletal muscle at single-nucleus resolution in a mouse model of PTRF-deficient muscular dystrophy.
- To identify specific changes in different muscle fiber types and associated cells.
- To elucidate molecular pathways affected by PTRF deficiency.
Main Methods:
- Creation of a Ptrf knockout mouse model for muscular dystrophy.
- Application of single-nucleus RNA sequencing (snRNA-seq) on skeletal muscle.
- Bioinformatic analysis including nucleus classification, trajectory analysis, functional enrichment, metabolic pathway analysis, and gene regulatory network analysis.
Main Results:
- 11,613 muscle nuclei were classified into 12 clusters representing 11 nuclear types.
- Trajectory analysis suggested transitions between type IIb_1 and IIb_2 myonuclei.
- Ptrf knockout induced apoptotic signaling, altered receptor signaling, impacted muscle structure development, and affected the PI3K-AKT pathway.
- Overall metabolic activity decreased in myonuclei, particularly in type IIb_1.
- Mef2c, Mef2d, Myf5, and Pax3 regulon activity increased in type II myonuclei.
- Adipocytes showed enhanced lipid metabolic capacity.
Conclusions:
- Ptrf deficiency profoundly alters skeletal muscle transcriptome, affecting specific myonuclei subtypes and metabolic pathways.
- The study provides a high-resolution molecular map of muscular dystrophy induced by Ptrf deficiency.
- Findings offer insights into the complex cellular and molecular mechanisms underlying this condition and identify potential therapeutic targets.
