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

Kang Ren,Guoshuai An,Yingyuan Wang,Qianqian Jin,Liangliang Wang,Jie Cao,Junhong Sun,Yingjie Tian,Qiuxiang Du,Lihong Dang,Na Li,Liang Wang

doi:10.3389/fgene.2021.650874

Kang Ren, Guoshuai An + Show 10 more

Open Access

https://doi.org/10.3389/fgene.2021.650874

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Abstract

Following skeletal muscle injury (SMI), from post-injury reaction to repair consists of a complex series of dynamic changes. However, there is a paucity of research on detailed transcriptional dynamics and time-dependent marker gene expression in the early stages after SMI. In this study, skeletal muscle tissue in rats was taken at 4 to 48 h after injury for next-generation sequencing. We examined the transcriptional kinetics characteristics during above time periods after injury. STEM and maSigPro were used to screen time-correlated genes. Integrating 188 time-correlated genes with 161 genes in each time-related gene module by WGCNA, we finally identified 18 network-node regulatory genes after SMI. Histological staining analyses confirmed the mechanisms underlying changes in the tissue damage to repair process. Our research linked a variety of dynamic biological processes with specific time periods and provided insight into the characteristics of transcriptional dynamics, as well as screened time-related biological indicators with biological significance in the early stages after SMI.

Highlights

Skeletal muscle injury (SMI), which has many possible etiologies, is commonly observed in daily life and trauma surgery practice (Zhu et al, 2007; Huard et al, 2016)
According to the above principles, we focused on several phases of pathological changes in the early period after skeletal muscle injury (SMI), Based on this, the Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways screened are shown in Supplementary Figure 6
Having analyzed the highly correlated (HCr) modules identified by weighted gene co-expression network analysis (WGCNA) and expanded on the transcriptional dynamics of the gene expression profiles in all time periods covering the early stages of the SMI repair process, we focused on the time-dependent variation in gene expression

Summary

Introduction

Skeletal muscle injury (SMI), which has many possible etiologies, is commonly observed in daily life and trauma surgery practice (Zhu et al, 2007; Huard et al, 2016). Among many factors that may induce SMI, mechanical trauma- and sports-related injuries are common in both clinical and forensic practice (Best and Hunter, 2000). In clinical settings as well as in many cases of intentional injuries, traffic accidents, insurance claims, and other emergencies, mechanical trauma-induced SMI can result in physical dysfunction. This has adverse effects on the activities of daily living and work capabilities of the injured parties and is related to wound age estimation in some criminal or civil cases (Grellner and Madea, 2007). Detailed analyses of the pathological processes occurring after SMI, gene expression changes, and damage repair mechanisms have far-reaching significance for clinical sports medicine and forensics

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