Yonsei Med J.  2018 Aug;59(6):760-768. 10.3349/ymj.2018.59.6.760.

Exploring the Key Genes and Pathways of Osteoarthritis in Knee Cartilage in a Rat Model Using Gene Expression Profiling

• Ren YM
• Zhao X
• Yang T
• Duan YH
• Sun YB
• Zhao WJ
• Tian MQ

• KMID: 2415535
• DOI: http://doi.org/10.3349/ymj.2018.59.6.760

Abstract

PURPOSE
To compare differentially expressed genes (DEGs) mediating osteoarthritis (OA) in knee cartilage and in normal knee cartilage in a rat model of OA and to identify their impact on molecular pathways associated with OA.
MATERIALS AND METHODS
A gene expression profile was downloaded from the Gene Expression Omnibus database. Analysis of DEGs was carried out using GEO2R. Enrichment analyses were performed on the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway using the Search Tool for the Retrieval of Interacting Genes database (http://www.string-db.org/). Subsequently, the regulatory interaction network of OA-associated genes was visualized using Cytoscape software (version 3.4.0; www.cytoscape.org).
RESULTS
In the gene expression profile GSE103416, a total of 99 DEGs were identified. Among them, 76 DEGs (76.77%) were overexpressed, and the remaining 23 DEGs (23.23%) were underexpressed. GO and pathway enrichment analyses of target genes were performed. Using gene-gene interaction network analysis, relevant core genes, including MET, UBB, GNAI3, and GNA13, were shown to hold a potential relationship with the development of OA in cartilage. Using quantitative real-time PCR, the Gna13/cGMP-PKG signaling pathway was identified as a potential research target for therapy and for further understanding the development of OA.
CONCLUSION
The results of the present study provide a comprehensive understanding of the roles of DEGs in knee cartilage in relation to the development of OA.

Keyword

Bioinformatics analysis; cartilage; differentially expressed genes; osteoarthritis

MeSH Terms

Animals
Cartilage*
Gene Expression Profiling*
Gene Expression*
Gene Ontology
Genes, vif
Genome
Knee*
Models, Animal*
Negotiating
Osteoarthritis*
Rats*
Real-Time Polymerase Chain Reaction
Transcriptome

Figure

• 

  Fig. 1 Box plot for the sample data after normalization.

• 

  Fig. 2 The volcano plot of DEGs. The abscissa indicates log2 FC, and the ordinates are −log10 (p-value). Each point represents a gene. The green dots represent the downregulated DEGs, red dots represent the upregulated DEGs, and black dots represent non-DEGs. DEG, differentially expressed gene; FC, fold change.

• 

  Fig. 3 Gene Ontology-enrichment analysis of biological processes (A), molecular functions (B), and cellular components (C). OA, osteoarthritis.

• 

  Fig. 4 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of differentially expressed genes (DEGs). The different node colors mean different pathways, and the closer the colors are, the closer the function clustering of pathways are.

• 

  Fig. 5 The distribution of core genes in the interaction network. The black node means the core gene. The red line means the fitted line, and the blue line means the power law. The correlation between the data points and corresponding points on the line is approximately 0.893. The R-squared value is 0.887, giving a relatively high confidence that the underlying model is indeed linear.

• 

  Fig. 6 The top three modules from the gene-gene interaction network. The squares represent the differentially expressed genes (DEGs) in modules, and the lines show the interaction between the DEGs.

• 

  Fig. 7 Validation of the differential expression of mRNA of corresponding genes identified in the OA knee cartilage groups, compared with NC groups, by qRT-PCR. Data indicate relative expression following normalization. Values are means±standard error (*p<0.05). Figures (A–C) show that three mRNAs of differentially expressed genes (Gnai3, Gna13, PKGII) were downregulated in OA knee cartilage groups compared with normal knee cartilage groups. Figures (D–F) showed that three mRNAs of genes (Met, Ubb, Sox9) were upregulated in OA knee cartilage groups, compared with normal knee cartilage groups. OA, osteoarthritis; NC, normal control.

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