Temporal expression of wound healing–related genes inform wound age estimation in rats after a skeletal muscle contusion: a multivariate statistical model analysis

Du, Qiu-xiang; Li, Na; Dang, Li-hong; Dong, Ta-na; Lu, H L; Shi, Fu-xia; Jin, Qianqian; Cao, Jie; Sun, Junhong

doi:10.1007/s00414-018-01990-2

Cited by 16 publications

(15 citation statements)

References 28 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…For another part, during the damage-repair process post-SMI, the dynamic changes based on transcriptional kinetics and data on the time-specific and time-related gene screening obtained via the application of time-related algorithms have high reference value, especially for forensic research on wound age estimation. Additionally, we have information on methods for the examination of initial tissue morphology (Yagi et al, 2016), the quantitative analysis of labeled proteins (Zhao et al, 2009), combined PCR analysis of multiple indicators (Du et al, 2013), and more recently, combining multiple indicators and multiple statistical analysis approaches (Du et al, 2020). In this study, instead of a theoretical algorithm, we developed a method for selecting time-dependent indexes using omics data.…”

Section: Discussionmentioning

confidence: 99%

“…Wound response and healing are dynamic processes with degeneration, inflammation, regeneration, and fibrosis occurring sequentially (Li and Luo, 2019). To clarify the detailed pathological changes, biological processes, and possible mechanisms of the SMI repair process, there have been a number of studies at the levels of tissue morphology, cells (proliferation, apoptosis, and autophagy), proteins, nucleic acids, and molecular biology (Zhu et al, 2007;Zhao et al, 2009;Rybalko et al, 2015;Du et al, 2020;Sugasawa et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

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

Ren

Wang

et al. 2021

Front. Genet.

Self Cite

View full text Add to dashboard Cite

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.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Ren

Wang

et al. 2021

Front. Genet.

Self Cite

View full text Add to dashboard Cite

show abstract

“…Skeletal muscle injury is one of the most common injuries in forensic science [15]. After acute skeletal muscle injury, the injury site experiences damage, degeneration, and necrosis of the muscle fiber structure, after which inflammatory cells and factors infiltrate the injury site [16][17][18][19][20].…”

Section: Discussionmentioning

confidence: 99%

Analysis of sensitivity and specificity: precise recognition of neutrophils during regeneration of contused skeletal muscle in rats

Niu

et al. 2020

Forensic Sciences Research

Self Cite

View full text Add to dashboard Cite

2020): Analysis of sensitivity and specificity: precise recognition of neutrophils during regeneration of contused skeletal muscle in rats, Forensic Sciences Research, ABSTRACT In this report, we applied the TissueFAXS 200 digital pathological analysis system to rapidly and accurately identify neutrophils during regeneration of contused skeletal muscle, and to provide information for follow-up studies on neutrophils to estimate wound age. Rat injury model was established, and skeletal muscle samples were obtained from the control group and contusion groups at 1, 1.5, 2, 3, 4, and 6 h, as well as at 1, 3, 5, and 15 d post-injury (n ¼ 5 per group). The expression of nuclei and neutrophils was detected by hematoxylin and eosin (HE) staining and immunohistochemical (IHC) staining. A total of 20 injury site areas of 0.25 mm 2 (0.5 mm Â 0.5 mm) were then randomly selected at all time points. A TissueFAXS 200 digital pathological analysis system was used to identify the positive and negative numbers. Knowledge of five professional medical workers were considered the gold standard to measure the false positive rate (FPR), false negative rate (FNR), sensitivity, specificity, and area under the curve (AUC) of receiver operating characteristic (ROC) curves. As a result, with a staining area of neutrophils from 8 mm 2 to 15 mm 2 , the FPR was 4.28%-12.14%, the FNR was 12.42%-64.08%, the sensitivity was 35.92%-87.58%, the specificity was 87.86%-95.72%, the Youden index was 0.316-0.754, accuracy was 82.80%-88.30%, and the AUC was 0.771-0.826. The AUC was largest when the cut-off value of the staining area was 12 mm 2 . Our results show that this software-based method is more accurate than the human eye in evaluating neutrophil infiltration. Based on the sensitivity and specificity, neutrophils can be accurately identified during regeneration of contused skeletal muscle. The TissueFAXS 200 digital pathological analysis system can also be used to optimize conditions for different cell types under various injury conditions to determine the optimal cut-off value of the staining area and provide optimal conditions for further study. Furthermore, it will provide evidence for forensic pathology cases. ARTICLE HISTORY

show abstract

“…Barington et al and Yu et al showed that the infiltration of inflammatory cells [12][13][14] and expression levels of regulatory mediators (cytokines, growth factors etc.) [15,16] show a time-dependent response after injury, and could be useful for wound age estimation.…”

Section: Introductionmentioning

confidence: 99%

Insight into molecular profile changes after skeletal muscle contusion using microarray and bioinformatics analyses

Bai

et al. 2021

Bioscience Reports

Self Cite

View full text Add to dashboard Cite

Muscle trauma frequently occurs in daily life. However, the molecular mechanisms of muscle healing, which partly depend on the extent of the damage, are not well understood. The present study aimed to investigate gene expression profiles following mild and severe muscle contusion, and to provide more information about the molecular mechanisms underlying the repair process. A total of 33 rats were divided randomly into control (n=3), mild contusion (n=15), and severe contusion (n=15) groups; the contusion groups were further divided into five subgroups (1, 3, 24, 48, and 168 h post-injury; n=3 per subgroup). A total of 2844 and 2298 differentially expressed genes (DEGs) were identified using microarray analyses in the mild and severe contusions, respectively. From the analysis of the 1620 coexpressed genes in mildly and severely contused muscle, we discovered that the gene profiles in functional modules and temporal clusters were similar between the mild and severe contusion groups; moreover, the genes showed time-dependent patterns of expression, which allowed us to identify useful markers of wound age. The functional analyses of genes in the functional modules and temporal clusters were performed, and the hub genes in each module–cluster pair were identified. Interestingly, we found that genes down-regulated at 24-48 h were largely associated with metabolic processes, especially of the oxidative phosphorylation (OXPHOS), which has been rarely reported. These results improve our understanding of the molecular mechanisms underlying muscle repair, and provide a basis for further studies of wound age estimation.

show abstract

Temporal expression of wound healing–related genes inform wound age estimation in rats after a skeletal muscle contusion: a multivariate statistical model analysis

Cited by 16 publications

References 28 publications

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

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

Analysis of sensitivity and specificity: precise recognition of neutrophils during regeneration of contused skeletal muscle in rats

Insight into molecular profile changes after skeletal muscle contusion using microarray and bioinformatics analyses

Contact Info

Product

Resources

About