Investigating Transcriptional Dynamics Changes and Time-Dependent Marker Gene Expression in the Early Period After Skeletal Muscle Injury in Rats

Ren, Kangning; Wang, Liangliang; Wang, Liang; Du, Qiu-xiang; Cao, Jie; Jin, Qianqian; An, Guo-shuai; Li, Na; Dang, Li-hong; Tian, Yingjie; Wang, Ying-Yuan; Sun, Jun-hong

doi:10.3389/fgene.2021.650874

Cited by 12 publications

(20 citation statements)

References 86 publications

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“…At P0 but not P3, we see overlap with a botulinum toxin rat model of atrophy one week after treatment, and with a rat skeletal muscle injury model (Mukund et al, 2014; Ren et al, 2021). Injection of BT was used to inhibit motor neuron activity, thus mimicking conditions of muscle inactivity often seen in multiple neuromuscular disorders or bed-ridden patients (Mukund et al, 2014).…”

Section: Resultsmentioning

confidence: 85%

Gene expression differences associated with intrinsic hindfoot muscle loss in the jerboa,Jaculus jaculus

Tran,

Ochoa Reyes,

Weitzel

et al. 2024

Preprint

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Vertebrate animals that run or jump across sparsely vegetated habitats, such as horses and jerboas, have reduced the number of distal limb bones, and many have lost most or all distal limb muscle. We previously showed that nascent muscles are present in the jerboa hindfoot at birth and that these myofibers are rapidly and completely lost soon after by a process that shares features with pathological skeletal muscle atrophy. Here, we apply an intra- and inter-species approach, comparing jerboa and mouse muscles, to identify gene expression differences associated with the initiation and progression of jerboa hindfoot muscle loss. We show evidence for reduced Hepatocyte Growth Factor (HGF) and Fibroblast Growth Factor (FGF) signaling and an imbalance in nitric oxide signaling; all are pathways that are necessary for skeletal muscle development and regeneration. We also find evidence for phagosome formation, which hints at how myofibers may be removed by autophagy or by non-professional phagocytes without evidence for cell death or immune cell activation. Last, we show significant overlap between genes associated with jerboa hindfoot muscle loss and genes that are differentially expressed in a variety of human muscle pathologies and rodent models of muscle loss disorders. All together, these data provide molecular insight into the mechanism of evolutionary and developmental muscle loss in jerboa hindfeet.

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Section: Resultsmentioning

confidence: 85%

Gene expression differences associated with intrinsic hindfoot muscle loss in the jerboa,Jaculus jaculus

Tran,

Ochoa Reyes,

Weitzel

et al. 2024

Preprint

View full text Add to dashboard Cite

show abstract

Section: Resultsmentioning

confidence: 99%

“…The mRNA levels of Cd155 significantly increased at 3, 7, and 14 dpi and showed a decreasing trend from 3 to 14 dpi (Figure 1A). To further prove the relationship between Cd155 levels and regeneration, we analyzed the Cd155 mRNA levels of muscular tissue before and after injury through the Gene Expression Omnibus (GEO) dataset GSE171243, 21 and a slightly increasing trend 4 hours post-injury was observed in the muscular tissue, but with no statistical significance (p = .0765; Figure 1B). Additionally, since effective muscle regeneration mainly depends on SC number and function, the difference in CD155 expression between quiescent and proliferative SCs freshly isolated from skeletal muscle was analyzed in the dataset of GSE175501.…”

Section: Cd155 Is Upregulated During Skeletal Muscle Regenerationmentioning

confidence: 99%

CD155 is essential for skeletal muscle regeneration by regulating satellite cell proliferation and differentiation

Li,

Zhang,

Liu

et al. 2024

The FASEB Journal

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CD155, a member of the immunoglobulin superfamily, is closely related to cell proliferation, adhesion, and migration. CD155 is overexpressed on the surface of cancer cells to promote cell proliferation and is upregulated in damaged tissues as a stress‐induced molecule. The process of skeletal muscle regeneration after injury is complex and involves injurious stimulation and subsequent satellite cell proliferation. However, the role of CD155 in this process remains unelucidated. This study aimed to explore the role of CD155 in injured skeletal muscle regeneration and to clarify its effect on satellite cell proliferation and differentiation. Here, quantitative real‐time polymerase chain reaction (RT‐qPCR) and immunofluorescence results indicated that CD155 expression in satellite cells increased after skeletal muscle injury. CD155 knockout in mice impaired the regeneration of skeletal muscle. A bone marrow transplantation mouse model was constructed and revealed that CD155 on skeletal muscle tissues, not immune cells, affected muscle regeneration. In vitro, CD155 knockdown in myoblasts inhibited their proliferation and differentiation. The transcriptomic analysis also indicated that CD155 absence can impair the biological proliferation and differentiation process of myoblasts. Our research demonstrates that CD155 directly promotes injured muscle regeneration by regulating satellite cell proliferation and differentiation, which may be a potential therapeutic molecule for skeletal muscle injury.

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“…Compared to focusing only on differentially expressed genes, WGCNA is able to use genome-wide information to obtain our gene sets of interest, which not only narrows the screening scope but also makes the analysis more accurate. This technique has been applied extensively to plants, humans, mice, poultry, and livestock (36)(37)(38)(39)(40)(41).…”

Section: Discussionmentioning

confidence: 99%

Integration of RNA-seq and ATAC-seq identifies muscle-regulated hub genes in cattle

Wang

Yang

et al. 2022

Front. Vet. Sci.

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As the main product of livestock, muscle itself plays an irreplaceable role in maintaining animal body movement and regulating metabolism. Therefore, it is of great significance to explore its growth, development and regeneration to improve the meat yield and quality of livestock. In this study, we attempted to use RNA-seq and ATAC-seq techniques to identify differentially expressed genes (DEGs) specifically expressed in bovine skeletal muscle as potential candidates for studying the regulatory mechanisms of muscle development. Microarray data from 8 tissue samples were selected from the GEO database for analysis. First, we obtained gene modules related to each tissue through WGCNA analysis. Through Gene Ontology (GO) functional annotation, the module of lightyellow (MElightyellow) was closely related to muscle development, and 213 hub genes were screened as follow-up research targets. Further, the difference analysis showed that, except for PREB, all other candidate hub genes were up-regulated (muscle group vs. other-group). ATAC-seq analysis showed that muscle-specific accessible chromatin regions were mainly located in promoter of genes related to muscle structure development (GO:0061061), muscle cell development (GO:0055001) and muscle system process (GO:0003012), which were involved in cAMP, CGMP-PKG, MAPK, and other signaling pathways. Next, we integrated the results of RNA-seq and ATAC-seq analysis, and 54 of the 212 candidate hub genes were identified as key regulatory genes in skeletal muscle development. Finally, through motif analysis, 22 of the 54 key genes were found to be potential target genes of transcription factor MEF2C. Including CAPN3, ACTN2, MB, MYOM3, SRL, CKM, ALPK3, MAP3K20, UBE2G1, NEURL2, CAND2, DOT1L, HRC, MAMSTR, FSD2, LRRC2, LSMEM1, SLC29A2, FHL3, KLHL41, ATXN7L2, and PDRG1. This provides a potential reference for studying the molecular mechanism of skeletal muscle development in mammals.

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Investigating Transcriptional Dynamics Changes and Time-Dependent Marker Gene Expression in the Early Period After Skeletal Muscle Injury in Rats

Cited by 12 publications

References 86 publications

Gene expression differences associated with intrinsic hindfoot muscle loss in the jerboa,Jaculus jaculus

Gene expression differences associated with intrinsic hindfoot muscle loss in the jerboa,Jaculus jaculus

CD155 is essential for skeletal muscle regeneration by regulating satellite cell proliferation and differentiation

Integration of RNA-seq and ATAC-seq identifies muscle-regulated hub genes in cattle

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