| Literature DB >> 32016457 |
Ke Yao1, Yixian Yu1, Fei Li1, Peiming Jin1, Chaohua Deng1, Hong Zhang1.
Abstract
Long non‑coding RNAs (lncRNAs) are a group of non‑coding transcripts of >200 nucleotides. They can act as competing endogenous RNAs (ceRNAs) and suppress microRNA (miRNA) function by preventing them from binding to and interacting with target mRNAs. However, the specific role of the lncRNA‑associated ceRNA network in the pathogenesis of glaucoma has not yet been elucidated. To study this, data were downloaded from the Gene Expression Omnibus database (GSE126170), which contained three human trabecular meshwork cell (HTMC) samples treated with 300 µm hydrogen peroxide and three control samples treated with vehicle. Differentially expressed lncRNAs and mRNAs of HTMCs were obtained using the R package limma. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses of differentially expressed mRNAs were performed using the R package clusterProfiler. Finally, the ceRNA network was constructed using the mircode, miRDB, miRTarBase and TargetScan databases, and visualized using Cytoscape v3.6.1. The results showed that 70 lncRNAs and 558 mRNAs were identified to be significantly dysregulated (|log2FoldChange| >1 and adjusted P<0.05) in HTMCs under oxidative stress compared to those in HTMCs under control conditions. Moreover, 24 lncRNAs, 24 miRNAs and 40 mRNAs were closely connected, and were part of the ceRNA network. Among these, the expression levels of 19 lncRNAs were upregulated, and those of 5 lncRNAs were downregulated. To conclude, using bioinformatics analysis, the differential expression profiles of lncRNAs were reported and a lncRNA‑associated ceRNA network in HTMCs under oxidative stress was constructed. These results may bring to light a new pathological mechanism or a potential therapeutic target for glaucoma.Entities:
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Year: 2020 PMID: 32016457 PMCID: PMC7003033 DOI: 10.3892/mmr.2020.10955
Source DB: PubMed Journal: Mol Med Rep ISSN: 1791-2997 Impact factor: 2.952
Differentially expressed lncRNAs in the ceRNA network.
| lncRNA | Gene ID | Regulation | LogFC (T/N) | adj.P.Val |
|---|---|---|---|---|
| ACTN1-AS1 | 161159 | Up | 1.129092 | 0.016997 |
| AC005532 | – | Up | 1.406952 | 0.002765 |
| AC020594 | – | Up | 1.518925 | 0.026473 |
| AC024560 | – | Up | 1.922623 | 0.001163 |
| AC073072 | – | Up | 1.532428 | 0.013798 |
| AC096570 | – | Up | 1.747278 | 0.025237 |
| AF124730 | – | Up | 1.346528 | 0.042546 |
| AP000356 | – | Up | 1.720098 | 0.005243 |
| AP000695 | – | Up | 1.10531 | 0.004826 |
| AP006216 | – | Up | 1.004154 | 0.009124 |
| C21orf91-OT1 | 246312 | Up | 1.157345 | 0.013636 |
| DDX39B-AS1 | 106478957 | Up | 1.315506 | 0.001423 |
| ENO1-AS1 | 100505975 | Up | 1.829472 | 0.006297 |
| FARP1-AS1 | 100874080 | Up | 2.605723 | 0.003072 |
| GRTP1-AS1 | 100874068 | Up | 2.368667 | 0.003501 |
| PDZRN3-AS1 | 101927249 | Up | 1.152825 | 0.010978 |
| PEX5L-AS1 | 100874040 | Up | 1.606603 | 0.001311 |
| SNHG3 | 8420 | Up | 1.669148 | 0.00915 |
| SNRK-AS1 | 100873954 | Up | 1.375921 | 0.002028 |
| AC006026 | – | Down | −1.1049 | 0.031015 |
| AC025171 | – | Down | −1.13395 | 0.009238 |
| AF015720 | – | Down | −1.01988 | 0.041587 |
| NEAT1 | 283131 | Down | −1.47837 | 0.006227 |
| TTTY23 | 252955 | Down | −1.10446 | 0.021033 |
-, no corresponding gene ID in PubMed; T, human trabecular meshwork cells treated with 300 µM H2O2 for 2 h; N, human trabecular meshwork cells treated with vehicle; lncRNA, long non-coding RNA; AS, antisense; ceRNA, competing endogenous RNA; adj.P.Val, adjusted P-value; FC, fold change.
Figure 1.Differentially expressed genes and lncRNAs in human trabecular meshwork cells between the oxidative stress and control group. (A) Volcano map of differentially expressed genes; black dots represent non-differentially expressed genes. (B) Heatmap of differentially expressed lncRNAs; each column represents a sample and each row represents a specific lncRNA. |log2FC| >1 and adjusted P<0.05. Red indicates upregulation and green indicates downregulation of expression. Con, control; H2O2, hydrogen peroxide; lncRNA, long non-coding RNA; FC, fold change.
Figure 2.Heatmap of differentially expressed mRNAs. Red blocks indicate upregulation and green blocks indicate downregulation of expression levels. Con, control; H2O2, hydrogen peroxide.
Figure 3.Functional enrichment of differentially expressed mRNAs. (A) Enrichment of Gene Ontology analysis for differentially expressed mRNAs. (B) Enrichment of Kyoto Encyclopedia of Genes and Genomes pathway analysis for differentially expressed mRNAs. The size of the bubbles indicates the number of mRNAs; the larger the bubble, the greater the number of mRNAs. The color represents the adjusted P-value; the redder the bubble, the smaller the adjusted P-value.
lncRNAs and target miRNAs in the competing endogenous RNA network.
| Key lncRNAs | miRNAs |
|---|---|
| AC005532 | miR-125a-5p, miR-125b-5p, miR-139-5p, miR-17-5p, miR-20b-5p, miR-22-3p, miR-23b-3p |
| AC006026 | miR-129-5p, miR-1297, miR-135a-5p, miR-140-5p, miR-22-3p, miR-507 |
| AC020594 | miR-140-5p, miR-142-3p, miR-23b-3p, miR-27a-3p, miR-107 |
| AC024560 | miR-10a-5p, miR-1297, miR-137, miR-217, miR-22-3p, miR-23b-3p, miR-24-3p, miR-301b-3p, miR-363-3p, miR-429, miR-590-5p |
| AC025171 | miR-107, miR-10a-5p, miR-129-5p, miR-1297, miR-22-3p, miR-27a-3p, miR-507, miR-590-5p |
| AC073072 | miR-125a-5p, miR-125b-5p, miR-1297, miR-135a-5p, miR-140-5p, miR-23b-3p, miR-27a-3p, miR-301b-3p, miR-507 |
| AC096570 | miR-23b-3p, miR-24-3p |
| ACTN1-AS1 | miR-24-3p |
| AF015720 | miR-17-5p, miR-20b-5p |
| AF124730 | miR-139-5p |
| AP000356 | miR-129-5p, miR-17-5p, miR-20b-5p, miR-217 |
| AP000695 | miR-140-5p, miR-17-5p, miR-20b-5p, miR-24-3p, miR-27a-3p |
| AP006216 | miR-107, miR-129-5p, miR-22-3p, miR-23b-3p, miR-24-3p, miR-27a-3p |
| C21orf91-OT1 | miR-107, miR-125a-5p, miR-125b-5p, miR-129-5p, miR-22-3p, miR-27a-3p |
| DDX39B-AS1 | miR-212-3p, miR-24-3p, miR-363-3p |
| ENO1-AS1 | miR-217, miR-23b-3p |
| FARP1-AS1 | miR-129-5p, miR-27a-3p, miR-429, miR-507 |
| GRTP1-AS1 | miR-17-5p, miR-20b-5p, miR-301b-3p |
| NEAT1 | miR-107, miR-10a-5p, miR-125a-5p, miR-125b-5p, miR-129-5p, miR-1297, miR-135a-5p, miR-139-5p, miR-140-5p, miR-142-3p, miR-17-5p, miR-20b-5p, miR-212-3p, miR-217, miR-22-3p, miR-23b-3p, miR-24-3p, miR-27a-3p, miR-301b-3p, miR-429, miR-507 |
| PDZRN3-AS1 | miR-27a-3p |
| PEX5L-AS1 | miR-1297, miR-140-5p, miR-23b-3p |
| SNHG3 | miR-10a-5p, miR-129-5p, miR-135a-5p, miR-139-5p, miR-17-5p, miR-20b-5p, miR-24-3p |
| SNRK-AS1 | miR-10a-5p, miR-363-3p |
| TTTY23 | miR-10a-5p, miR-23b-3p |
lncRNA, long non-coding RNA; miR/miRNA, microRNA; AS, antisense.
Figure 4.Mutual mRNAs between differentially expressed and predicted mRNAs, and their GO analysis. (A) Venn diagram of differentially expressed mRNAs and predicted mRNAs. (B) GO enrichment analysis of the mRNAs involved in the competing endogenous RNA network. GO, Gene Ontology.
miRNAs and target mRNAs in the competing endogenous RNA network.
| miRNA | mRNA |
|---|---|
| miR-107 | ABL2, GPCPD1 |
| miR-10a-5p | H3F3B |
| miR-125a-5p | PRDM1, BMF, PRDM1, RYBP |
| miR-129-5p | PRDM1, RYBP, SOX4 |
| miR-1297 | CHAC1, PMAIP1 |
| miR-135a-5p | ARC |
| miR-137 | PTGS2 |
| miR-139-5p | FOS, JUN |
| miR-140-5p | PRDM1, YOD1 |
| miR-142-3p | CCNT2, SIK1 |
| miR-17-5p | CDKN1A, DNAJC27, KIAA1147, NAPEPLD, NPAS3, PARD6B, RRAGD, SIK1, SLC16A9, SOX4, YOD1 |
| miR-20b-5p | CDKN1A, DNAJC27, KIAA1147, PARD6B, RBM20, RRAGD, SIK1, SLC16A9, SOX4, YOD1 |
| miR-212-3p | BMPER |
| miR-217 | DACH1, PPM1D |
| miR-22-3p | CSF1R, H3F3B, PDIK1L |
| miR-23b-3p | SESN2 |
| miR-24-3p | MAGI1, MT1E, PER2, SESN1, YOD1, YRDC |
| miR-27a-3p | ABL2, DNAJC27, EIF5, ENDOU, FAM84B, H3F3B, MYT1, RYBP |
| miR-301b-3p | RBM20, RRAGD, SIK1, SOX4 |
| miR-363-3p | PER2, SOX4, TRIM36 |
| miR-429 | CCNT2, JUN, PARD6B, PMAIP1 |
| miR-507 | CCNT2 |
| miR-590-5p | PER2 |
miR/miRNA, microRNA.
Figure 5.Competing endogenous RNA network in human trabecular meshwork cells under oxidative stress. Pink rhombuses represent lncRNAs, green triangles represent miRNAs and blue dots are mRNAs. Grey lines indicate lncRNA-miRNA-mRNA interactions. lncRNA, long non-coding RNA; miR/miRNA, microRNA.