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. 2021 Nov 16:2021:2866475.
doi: 10.1155/2021/2866475. eCollection 2021.

Identification of miRNA Regulatory Networks and Candidate Markers for Fracture Healing in Mice

Xianglu Li  1 , Zhaohua Zhong  2 , Enguang Ma  3 , Xiaowei Wu  1
Affiliations

Identification of miRNA Regulatory Networks and Candidate Markers for Fracture Healing in Mice

Xianglu Li et al. Comput Math Methods Med. .

Abstract

Background: It is important to improve the understanding of the fracture healing process at the molecular levels, then to discover potential miRNA regulatory mechanisms and candidate markers.

Methods: Expression profiles of mRNA and miRNA were obtained from the Gene Expression Omnibus database. We performed differential analysis, enrichment analysis, protein-protein interaction (PPI) network analysis. The miRNA-mRNA network analysis was also performed.

Results: We identified 499 differentially expressed mRNAs (DEmRs) that were upregulated and 534 downregulated DEmRs during fracture healing. They were mainly enriched in collagen fibril organization and immune response. Using the PPI network, we screened 10 hub genes that were upregulated and 10 hub genes downregulated with the largest connectivity. We further constructed the miRNA regulatory network for hub genes and identified 13 differentially expressed miRNAs (DEmiRs) regulators. Cd19 and Col6a1 were identified as key candidate mRNAs with the largest fold change, and their DEmiR regulators were key candidate regulators.

Conclusion: Cd19 and Col6a1 might serve as candidate markers for fracture healing in subsequent studies. Their expression is regulated by miRNAs and is involved in collagen fibril organization and immune responses.

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Conflict of interest statement

The authors declare that they have no conflict of interest.

Figures

Figure 1
Figure 1
Differentially expressed genes in mice after fracture. (a) Principal component analysis of fracture samples from mice at different time points. (b) Heatmap of mRNA expression in samples at different time points. Red represents upregulation and blue represents downregulation. Differentially expressed mRNAs between different time points after fracture and 0 day. Intersection mRNAs that were upregulated (c) and downregulated (d) simultaneously in the three groups of differences.
Figure 2
Figure 2
Enrichment results of mRNAs with altered expression during fracture repair. (a) The top ten biological processes of common upregulated mRNAs. (b) KEGG pathway of common upregulated mRNAs. (c) The top ten biological processes of common downregulated mRNAs. (d) KEGG pathway of common downregulated mRNAs.
Figure 3
Figure 3
PPI network of common upregulated or downregulated mRNAs. (a) The top 10 degree in the PPI network of the common upregulated mRNAs. (b) The top 10 degree in the PPI network of the common downregulated mRNAs. The redder the color, the greater the degree of connectivity in the PPI network.
Figure 4
Figure 4
miRNA regulation of hub genes. (a) Differentially expressed miRNAs between mice at different time points after fracture and controls. Intersection genes were considered as core miRNAs. (b) Expression heatmap of core miRNAs in different groups. (c) Intersection between upregulated hub genes predicted miRNA regulators and downregulated DEmiRs. (d) Intersection between downregulated hub genes predicted miRNA regulators and upregulated DEmiRs.
Figure 5
Figure 5
Identification of key regulatory pairs in the regulatory network of miRNA targeted mRNAs. (a) Targeted regulatory relationship between DEmiRs and hub genes. (b) DEmiRs participated in the KEGG signaling pathway by targeting hub genes. (c) Expression levels of key DEmiR regulators and mRNAs at different time points after fracture in mice.
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