Analysis of the lncRNA-Associated Competing Endogenous RNA (ceRNA) Network for Tendinopathy
Background. We aimed to construct the lncRNA-associated competing endogenous RNA (ceRNA) network and distinguish feature lncRNAs associated with tendinopathy. Methods. We downloaded the gene profile of GSE26051 from the Gene Expression Omnibus (GEO), including 23 normal samples and 23 diseased tendo...
Saved in:
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Wiley
2022-01-01
|
| Series: | Genetics Research |
| Online Access: | http://dx.doi.org/10.1155/2022/9792913 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1832553467544076288 |
|---|---|
| author | Bing-Zhe Huang Yang Jing-Jing Xiao-Ming Dong null Zhuan Zhong null Xiao-Ning Liu |
| author_facet | Bing-Zhe Huang Yang Jing-Jing Xiao-Ming Dong null Zhuan Zhong null Xiao-Ning Liu |
| author_sort | Bing-Zhe Huang |
| collection | DOAJ |
| description | Background. We aimed to construct the lncRNA-associated competing endogenous RNA (ceRNA) network and distinguish feature lncRNAs associated with tendinopathy. Methods. We downloaded the gene profile of GSE26051 from the Gene Expression Omnibus (GEO), including 23 normal samples and 23 diseased tendons. Differentially expressed mRNAs (DEmRNAs) and differentially expressed lncRNAs (DElncRNAs) were identified, and functional and pathway enrichment analyses were performed. Protein-protein interaction (PPI) network was constructed and further analyzed by module mining. Moreover, a ceRNA regulatory network was constructed based on the identified lncRNA–mRNA coexpression relationship pairs and miRNA–mRNA regulation pairs. Results. We identified 1117 DEmRNAs and 57 DElncRNAs from the GEO data. The downregulated DEmRNAs were particularly associated with muscle contraction and muscle filament, while the upregulated ones were linked to extracellular matrix organization and cell adhesion. From the PPI network, 11 modules were extracted. Genes in MCODE 2 (such as TPM4) were significantly involved in cardiomyopathy, and genes in MCODE 4 (such as COL4A3 and COL4A4) were involved in focal adhesion, ECM-receptor interaction, and PI3K-Akt signaling pathway. The ceRNA network contained 7 lncRNAs (MIR133A1HG, LINC01405, PRKCQ-AS1, C10orf71-AS1, MBNL1-AS1, HOTAIRM1, and DNM3OS), 63 mRNAs, and 41 miRNAs. Downregulated lncRNA MIR133A1HG could competitively bind with hsa-miR-659-3p and hsa-miR-218-1-3p to regulate the TPM3. Meanwhile, MIR133A1HG could competitively bind with hsa-miR-1179 to regulate the COL4A3. Downregulated C10orf71-AS1 could competitively bind with hsa-miR-130a-5p to regulate the COL4A4. Conclusions. Seven important lncRNAs, particularly MIR133A1HG and C10orf71-AS1, were found associated with tendinopathy according to the lncRNA-associated ceRNA network. |
| format | Article |
| id | doaj-art-5e940ef7e392421692dd98130c6285e7 |
| institution | Kabale University |
| issn | 1469-5073 |
| language | English |
| publishDate | 2022-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Genetics Research |
| spelling | doaj-art-5e940ef7e392421692dd98130c6285e72025-02-03T05:53:51ZengWileyGenetics Research1469-50732022-01-01202210.1155/2022/9792913Analysis of the lncRNA-Associated Competing Endogenous RNA (ceRNA) Network for TendinopathyBing-Zhe Huang0Yang Jing-Jing1Xiao-Ming Dong2null Zhuan Zhong3null Xiao-Ning Liu4Orthopaedic Medical CenterOperation ServiceOrthopaedic Medical CenterOrthopaedic Medical CenterOrthopaedic Medical CenterBackground. We aimed to construct the lncRNA-associated competing endogenous RNA (ceRNA) network and distinguish feature lncRNAs associated with tendinopathy. Methods. We downloaded the gene profile of GSE26051 from the Gene Expression Omnibus (GEO), including 23 normal samples and 23 diseased tendons. Differentially expressed mRNAs (DEmRNAs) and differentially expressed lncRNAs (DElncRNAs) were identified, and functional and pathway enrichment analyses were performed. Protein-protein interaction (PPI) network was constructed and further analyzed by module mining. Moreover, a ceRNA regulatory network was constructed based on the identified lncRNA–mRNA coexpression relationship pairs and miRNA–mRNA regulation pairs. Results. We identified 1117 DEmRNAs and 57 DElncRNAs from the GEO data. The downregulated DEmRNAs were particularly associated with muscle contraction and muscle filament, while the upregulated ones were linked to extracellular matrix organization and cell adhesion. From the PPI network, 11 modules were extracted. Genes in MCODE 2 (such as TPM4) were significantly involved in cardiomyopathy, and genes in MCODE 4 (such as COL4A3 and COL4A4) were involved in focal adhesion, ECM-receptor interaction, and PI3K-Akt signaling pathway. The ceRNA network contained 7 lncRNAs (MIR133A1HG, LINC01405, PRKCQ-AS1, C10orf71-AS1, MBNL1-AS1, HOTAIRM1, and DNM3OS), 63 mRNAs, and 41 miRNAs. Downregulated lncRNA MIR133A1HG could competitively bind with hsa-miR-659-3p and hsa-miR-218-1-3p to regulate the TPM3. Meanwhile, MIR133A1HG could competitively bind with hsa-miR-1179 to regulate the COL4A3. Downregulated C10orf71-AS1 could competitively bind with hsa-miR-130a-5p to regulate the COL4A4. Conclusions. Seven important lncRNAs, particularly MIR133A1HG and C10orf71-AS1, were found associated with tendinopathy according to the lncRNA-associated ceRNA network.http://dx.doi.org/10.1155/2022/9792913 |
| spellingShingle | Bing-Zhe Huang Yang Jing-Jing Xiao-Ming Dong null Zhuan Zhong null Xiao-Ning Liu Analysis of the lncRNA-Associated Competing Endogenous RNA (ceRNA) Network for Tendinopathy Genetics Research |
| title | Analysis of the lncRNA-Associated Competing Endogenous RNA (ceRNA) Network for Tendinopathy |
| title_full | Analysis of the lncRNA-Associated Competing Endogenous RNA (ceRNA) Network for Tendinopathy |
| title_fullStr | Analysis of the lncRNA-Associated Competing Endogenous RNA (ceRNA) Network for Tendinopathy |
| title_full_unstemmed | Analysis of the lncRNA-Associated Competing Endogenous RNA (ceRNA) Network for Tendinopathy |
| title_short | Analysis of the lncRNA-Associated Competing Endogenous RNA (ceRNA) Network for Tendinopathy |
| title_sort | analysis of the lncrna associated competing endogenous rna cerna network for tendinopathy |
| url | http://dx.doi.org/10.1155/2022/9792913 |
| work_keys_str_mv | AT bingzhehuang analysisofthelncrnaassociatedcompetingendogenousrnacernanetworkfortendinopathy AT yangjingjing analysisofthelncrnaassociatedcompetingendogenousrnacernanetworkfortendinopathy AT xiaomingdong analysisofthelncrnaassociatedcompetingendogenousrnacernanetworkfortendinopathy AT nullzhuanzhong analysisofthelncrnaassociatedcompetingendogenousrnacernanetworkfortendinopathy AT nullxiaoningliu analysisofthelncrnaassociatedcompetingendogenousrnacernanetworkfortendinopathy |