| Literature DB >> 32792959 |
Jing Ye1, Bingbing Xu1, Baoshi Fan2, Jiying Zhang1, Fuzhen Yuan1, Yourong Chen1, Zewen Sun1, Xin Yan1, Yifan Song1, Shitang Song1, Meng Yang2, Jia-Kuo Yu1.
Abstract
BACKGROUND: Unlike bone tissue, little progress has been made regarding cartilage regeneration, and many challenges remain. Furthermore, the key roles of cartilage lesion caused by traumas, focal lesion, or articular overstress remain unclear. Traumatic injuries to the meniscus as well as its degeneration are important risk factors for long-term joint dysfunction, degenerative joint lesions, and knee osteoarthritis (OA) a chronic joint disease characterized by degeneration of articular cartilage and hyperosteogeny. Nearly 50% of the individuals with meniscus injuries develop OA over time. Due to the limited inherent self-repair capacity of cartilage lesion, the Biomaterial drug-nanomedicine is considered to be a promising alternative. Therefore, it is important to elucidate the gene potential regeneration mechanisms and discover novel precise medication, which are identified through this study to investigate their function and role in pathogenesis.Entities:
Keywords: biomaterial drug; cartilage; clinical translation; immune response; nanomedicine; text mining
Year: 2020 PMID: 32792959 PMCID: PMC7394085 DOI: 10.3389/fphar.2020.01138
Source DB: PubMed Journal: Front Pharmacol ISSN: 1663-9812 Impact factor: 5.810
Figure 1General text mining approach. The data mining was expanded to distinguish genes connected with osteoarthritis (OA) and patients without osteoarthritis (marked control) (N-OA), using the Gene Expression Omnibus. The obtained genes were investigated for their function and gene pathway using GO and KEGG. The enrichment was attained by PPI with STRING. The final enriched gene list was identified using the DGIdb.
Figure 2Work flow of statistics mining. (A) Text mining: on the pursuit concepts osteoarthritis (OA) and patients without osteoarthritis (N-OA), text digging was accomplished with GEO, and 62,976 genes were established. (B) Gene enrichment: gene enrichment analysis was accomplished with GO and KEGG to enrich 66 genes. Meanwhile, by uploading Search Tool for the STRING, 66 hub genes were enriched, and among them eight significant genes were targetable by drugs using DGIdb. (C) Drug-gene interaction: these eight genes were established in DGIdb and the inhibitor Selenocysteine drugs were recognized as having a prospective impact on cartilage regeneration.
Sixty-six DEG were recognized in GSE117999.
| DEGs | Gene symbol |
|---|---|
| Upregulated |
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| Downregulated |
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The DEGs are sorted in adjusted p-value ascending order.
Figure 3Volcano Plot image displaying the 66 genes that were significantly up-regulated or down-regulated (P-value < 0.05) in OA cartilage, compared to normal controls.
Figure 4GO and KEGG pathways of DEGs meaningfully enriched in OA.
The GO and KEGG Enrichment Analysis of DEGs.
| Category | Term | Count | p Value |
|---|---|---|---|
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| GO:0030520~intracellular estrogen receptor signaling pathway |
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| GO:0002227~innate immune response in mucosa |
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| GO:0019731~antibacterial humoral response |
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| GO:0050830~defense response to Gram-positive bacterium |
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| GO:0005887~integral component of plasma membrane |
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| GO:0003700~transcription factor activity, sequence-specific DNA binding |
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| GO:0002504~antigen processing and presentation of peptide or polysaccharide antigen via MHC class II |
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| GO:0019882~antigen processing and presentation |
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| GO:0060333~interferon-gamma-mediated signaling pathway |
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| GO:0031295~T cell costimulation |
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| GO:0019886~antigen processing and presentation of exogenous peptide antigen via MHC class II |
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| GO:0042613~MHC class II protein complex |
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| GO:0071556~integral component of lumenal side of endoplasmic reticulum membrane |
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| GO:0016604~nuclear body |
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| GO:0030658~transport vesicle membrane |
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| GO:0030669~clathrin-coated endocytic vesicle membrane |
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| GO:0012507~ER to Golgi transport vesicle membrane |
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| GO:0016021~integral component of membrane |
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| GO:0030666~endocytic vesicle membrane |
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| GO:0032588~trans-Golgi network membrane |
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| GO:0032395~MHC class II receptor activity |
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| hsa05310: Asthma |
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| hsa05332: Graft-versus-host disease |
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| hsa05330: Allograft rejection |
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| hsa04940: Type I diabetes mellitus |
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| hsa04672: Intestinal immune network for IgA production |
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| hsa05320: Autoimmune thyroid disease |
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| hsa05150: Staphylococcus aureus infection |
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| hsa05416: Viral myocarditis |
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| hsa05321: Inflammatory bowel disease (IBD) |
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| hsa05140: Leishmaniosis |
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| hsa04612: Antigen processing and presentation |
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| hsa05323: Rheumatoid arthritis |
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| hsa05145: Toxoplasmosis |
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| hsa05169: Epstein-Barr virus infection |
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| hsa05322: Systemic lupus erythematosus |
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| hsa04514: Cell adhesion molecules (CAMs) |
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Figure 5PPI networks of DEGs. Sixty-six genes were clarified into the PPI network using the STRING databank. ↑ indicates up-Genes; ↓ indicates down-Genes.
Figure 6The functional enrichment analysis of eight applicant cartilage regeneration - associated genes (green shows that the gene is enhanced in the related pathway, black shows not on the contrary).
Figure 7The schematic structure of Selenocysteine.
Figure 8The expression of CAMP transcripts differentially expressed between normal and osteoarthritis was validated by real-time PCR. The data is presented as mean with standard error of the mean.