Construction of lncRNA-miRNA-mRNA network based on ceRNA mechanism reveals the function of lncRNA in the pathogenesis of gout

Abstract

Objective: To identify differentially expressed lncRNA, miRNA, and mRNA during the pathogenesis of gout, explore the ceRNA network regulatory mechanism of gout, and seek potential therapeutic targets.

Method: First, gout-related chips were retrieved by GEO database. Then, the analysis of differentially expressed lncRNAs and mRNAs was conducted by R language and other software. Besides, miRNA and its regulated mRNA were predicted based on public databases, the intersection of differentially expressed mRNA and predicated mRNA was taken, and the lncRNA-miRNA-mRNA regulatory relationships were obtained to construct the ceRNA regulatory network. Subsequently, hub genes were screened by the STRING database and Cytoscape software. Then the DAVID database was used to illustrate the gene functions and related pathways of hub genes and to mine key ceRNA networks.

Results: Three hundred and eighty-eight lncRNAs and 758 mRNAs were identified with significant differential expression in gout patient, which regulates hub genes in the ceRNA network, such as JUN, FOS, PTGS2, NR4A2, and TNFAIP3. In the ceRNA network, lncRNA competes with mRNA for miRNA, thus affecting the IL-17 signaling pathway, TNF signaling pathway, Oxytocin signaling pathway, and NF-κB signaling pathway through regulating the cell's response to chemical stress. The research indicates that five miRNAs (miR-429, miR-137, miR-139-5p, miR-217, miR-23b-3p) and five lncRNAs (SNHG1, FAM182A, SPAG5-AS1, HNF1A-AS1, UCA1) play an important role in the formation and development of gout.

Conclusion: The interaction in the ceRNA network can affect the formation and development of gout by regulating the body's inflammatory response as well as proliferation, differentiation, and apoptosis of chondrocytes and osteoclasts. The identification of potential therapeutic targets and signaling pathways through ceRNA network can provide a reference for further research on the pathogenesis of gout.

Keywords: GEO database; LncRNA; bioinformatics; competitive endogenous RNA; gout.

FIGURE 1

Expression levels of differentially expressed lncRNAs in different samples. Note: The left vertical axis represents the cluster analysis of differentially expressed lncRNAs, and the right vertical axis represents the name of differentially expressed lncRNAs. Red represents high relative expression, and brighter red represents more significant high relative expression. Green represents low relative expression, and brighter green represents more significant low relative expression. Black represents no significant difference in relative expression. At the top, blue represents peripheral blood samples of healthy control and red represents that of gout patients

FIGURE 2

ceRNA regulatory network. Note: Red circle represent lncRNA, green diamond represents mRNA, blue rectangle represents miRNA, and lines between nodes represent the regulatory relationship.

FIGURE 3

Protein interaction network. Note: Red node represents up‐regulated mRNA, green node represents down‐regulated mRNA, and the line between nodes represents interaction relationship. The larger the node and the darker the color, the greater the degree value. Thickness of the edge reflects the connection score. The thicker the edge, the closer the interaction between mRNAs

FIGURE 4

GO enrichment analysis of hub genes bubble diagram (A) and chord diagram (B). Note: (A) The vertical axis represents the name of GO enrichment analysis, and the horizontal axis represents the proportion of enriched genes in total human genes. Redder bubble indicates more significant enrichment and larger bubble indicates more enriched genes in the item. (B) The relationship between the top five GO items and hub genes is represented by chord graph, and the colors of nodes are displayed according to the value of logFC

FIGURE 5

The KEGG enrichment analysis of hub genes bubble diagram (A) and chord diagram (B). Note: (A) The vertical axis represents the pathway name, and the horizontal axis represents the proportion of enriched genes in total human genes. Redder bubble indicates more significant enrichment and larger bubble indicates more enriched genes in the item. (B) The relationship between the top five pathways and hub genes is represented by chord graph, and the colors of nodes are displayed according to the value of logFC

FIGURE 6

The key ceRNA network that up‐regulates mRNA. Note: Red circle represents lncRNA, green diamond represents mRNA, blue rectangle represents miRNA, and the line between nodes represents the regulatory relationship

FIGURE 7

Mechanistic map of hub genes and their enrichment pathways. NOTE: TNF receptor signaling complex (TNF‐RSC) is formed when TNF binds with TNF receptor (TNFR). The receptor‐interacting protein 1 (RIP1) and inhibitor of nuclear factor kappa‐B kinase (IKKα, β, γ) can be recruited and ubiquitinated by TNF‐RSC through linear ubiquitin chain assembly complex (LUBAC). (1) TAK1 is activated by ubiquitination of RIP1, which could further activate IKK, JNK, and p38. Then, NF‐κB and AP‐1 are respectively upregulated by IKK, JNK, and p38. AP‐1 is a transcription gene which is related to chondrocyte degradation, OC differentiation, macrophages, and Th17 cells secrete inflammation factors (IL‐17, IL‐23, etc). (2) NF‐κB binding protein (IKB) can be phosphorylated and cleaved by IKK kinase, which enables NF‐κB to transfer from cytoplasm to nucleus. This process can trigger the transactivation of PTGS2, which can promote the release of ROS‐dependent IL‐1β. The secretion of inflammatory factors in macrophages and TH17 can be promoted by IL‐1β