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Screening of gene signatures for rheumatoid arthritis and osteoarthritis based on bioinformatics analysis.

He P, Zhang Z, Liao W, Xu D, Fu M, Kang Y - Mol Med Rep (2016)

Bottom Line: The significant DEGs in module 1, including collagen, type I, α 1 (COL1A1), COL3A1, COL4A1 and COL11A1, were predominantly enriched in the extracellular matrix (ECM)‑receptor interaction and focal adhesion pathways.Additionally, significant DEGs in module 2, including radical S‑adenosyl methionine domain containing 2 (RSAD2), 2'‑5'‑oligoadenylate synthetase 2 (OAS2), myxovirus (influenza virus) resistance 1 (MX1) and ISG15 ubiquitin‑like modifier (ISG15), were predominantly associated with immune function pathways.In conclusion, the present study indicated that RSAD2, OAS2, MX1 and ISG15 may be notable gene signatures in RA development via regulation of the immune response.

View Article: PubMed Central - PubMed

Affiliation: Department of Joint Surgery, The First Affiliated Hospital of Sun Yat‑sen University, Guangzhou, Guangdong 510080, P.R. China.

ABSTRACT
The current study aimed to identify gene signatures during rheumatoid arthritis (RA) and osteoarthritis (OA), and used these to elucidate the underlying modular mechanisms. Using the Gene Expression Omnibus database, the present study obtained the GSE7669 mRNA expression microarray data from RA and OA synovial fibroblasts (n=6 each). The differentially expressed genes (DEGs) in RA synovial samples compared with OA samples were identified using the Linear Models for Microarray Analysis package. The Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed using the Database for Annotation Visualization and Integrated Discovery. A protein‑protein interaction network was constructed and the modules were further analyzed using the Molecular Complex Detection plugin of Cytoscape. A total of 181 DEGs were identified by comparing RA and OA synovial samples (96 up‑ and 85 downregulated genes). The significant DEGs in module 1, including collagen, type I, α 1 (COL1A1), COL3A1, COL4A1 and COL11A1, were predominantly enriched in the extracellular matrix (ECM)‑receptor interaction and focal adhesion pathways. Additionally, significant DEGs in module 2, including radical S‑adenosyl methionine domain containing 2 (RSAD2), 2'‑5'‑oligoadenylate synthetase 2 (OAS2), myxovirus (influenza virus) resistance 1 (MX1) and ISG15 ubiquitin‑like modifier (ISG15), were predominantly associated with immune function pathways. In conclusion, the present study indicated that RSAD2, OAS2, MX1 and ISG15 may be notable gene signatures in RA development via regulation of the immune response. COL3A1, COL4A1, COL1A1 and COL11A1 may be important gene signatures in OA development via involvement in the pathways of ECM-receptor interactions and focal adhesions.

No MeSH data available.


Related in: MedlinePlus

Protein-protein interaction network of DEGs. Red nodes represent upregulated genes in RA samples (downregulated in OA samples). Green nodes represent downregulated genes in RA samples. Color depth represents level of significance, with deeper colors indicating greater significance. DEG, differentially expressed gene; RA, rheumatoid arthritis; OA, osteoarthritis.
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f1-mmr-14-02-1587: Protein-protein interaction network of DEGs. Red nodes represent upregulated genes in RA samples (downregulated in OA samples). Green nodes represent downregulated genes in RA samples. Color depth represents level of significance, with deeper colors indicating greater significance. DEG, differentially expressed gene; RA, rheumatoid arthritis; OA, osteoarthritis.

Mentions: Based on the information of the STRING database, a total of 343 protein interactions with combined scores >0.4 were included in the PPI network (Fig. 1). The top 20 hub proteins were identified according to connectivity degree (Table III), including collagen type I α 1 (COL1A1), COL1A2, COL3A1, COL4A2, integrin α 1, COL4A1, biglycan and COL11A1. Notably, in addition to interferon-induced protein with tetratricopeptide repeats 3, these hub nodes were upregulated and the majority of them are collagen proteins.


Screening of gene signatures for rheumatoid arthritis and osteoarthritis based on bioinformatics analysis.

He P, Zhang Z, Liao W, Xu D, Fu M, Kang Y - Mol Med Rep (2016)

Protein-protein interaction network of DEGs. Red nodes represent upregulated genes in RA samples (downregulated in OA samples). Green nodes represent downregulated genes in RA samples. Color depth represents level of significance, with deeper colors indicating greater significance. DEG, differentially expressed gene; RA, rheumatoid arthritis; OA, osteoarthritis.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4940106&req=5

f1-mmr-14-02-1587: Protein-protein interaction network of DEGs. Red nodes represent upregulated genes in RA samples (downregulated in OA samples). Green nodes represent downregulated genes in RA samples. Color depth represents level of significance, with deeper colors indicating greater significance. DEG, differentially expressed gene; RA, rheumatoid arthritis; OA, osteoarthritis.
Mentions: Based on the information of the STRING database, a total of 343 protein interactions with combined scores >0.4 were included in the PPI network (Fig. 1). The top 20 hub proteins were identified according to connectivity degree (Table III), including collagen type I α 1 (COL1A1), COL1A2, COL3A1, COL4A2, integrin α 1, COL4A1, biglycan and COL11A1. Notably, in addition to interferon-induced protein with tetratricopeptide repeats 3, these hub nodes were upregulated and the majority of them are collagen proteins.

Bottom Line: The significant DEGs in module 1, including collagen, type I, α 1 (COL1A1), COL3A1, COL4A1 and COL11A1, were predominantly enriched in the extracellular matrix (ECM)‑receptor interaction and focal adhesion pathways.Additionally, significant DEGs in module 2, including radical S‑adenosyl methionine domain containing 2 (RSAD2), 2'‑5'‑oligoadenylate synthetase 2 (OAS2), myxovirus (influenza virus) resistance 1 (MX1) and ISG15 ubiquitin‑like modifier (ISG15), were predominantly associated with immune function pathways.In conclusion, the present study indicated that RSAD2, OAS2, MX1 and ISG15 may be notable gene signatures in RA development via regulation of the immune response.

View Article: PubMed Central - PubMed

Affiliation: Department of Joint Surgery, The First Affiliated Hospital of Sun Yat‑sen University, Guangzhou, Guangdong 510080, P.R. China.

ABSTRACT
The current study aimed to identify gene signatures during rheumatoid arthritis (RA) and osteoarthritis (OA), and used these to elucidate the underlying modular mechanisms. Using the Gene Expression Omnibus database, the present study obtained the GSE7669 mRNA expression microarray data from RA and OA synovial fibroblasts (n=6 each). The differentially expressed genes (DEGs) in RA synovial samples compared with OA samples were identified using the Linear Models for Microarray Analysis package. The Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed using the Database for Annotation Visualization and Integrated Discovery. A protein‑protein interaction network was constructed and the modules were further analyzed using the Molecular Complex Detection plugin of Cytoscape. A total of 181 DEGs were identified by comparing RA and OA synovial samples (96 up‑ and 85 downregulated genes). The significant DEGs in module 1, including collagen, type I, α 1 (COL1A1), COL3A1, COL4A1 and COL11A1, were predominantly enriched in the extracellular matrix (ECM)‑receptor interaction and focal adhesion pathways. Additionally, significant DEGs in module 2, including radical S‑adenosyl methionine domain containing 2 (RSAD2), 2'‑5'‑oligoadenylate synthetase 2 (OAS2), myxovirus (influenza virus) resistance 1 (MX1) and ISG15 ubiquitin‑like modifier (ISG15), were predominantly associated with immune function pathways. In conclusion, the present study indicated that RSAD2, OAS2, MX1 and ISG15 may be notable gene signatures in RA development via regulation of the immune response. COL3A1, COL4A1, COL1A1 and COL11A1 may be important gene signatures in OA development via involvement in the pathways of ECM-receptor interactions and focal adhesions.

No MeSH data available.


Related in: MedlinePlus