| Objective:To detected the expressions of long non-coding RNAs(lncRNAs)and messenger RNAs(mRNAs)in vitreous humor(VH)of proliferative diabetic retinopathy(PDR)patients and idiopathic macular hole(IMH)patients;in the meantime,to evaluated the effects of anti-vascular endothelial growth factor(anti-VEGF)treatment on the expressions of lncRNAs and mRNAs in the VH of PDR patients.Methods:1.The expressions of lncRNAs and mRNAs both in the VH of PDR patients(Group C)and IMH patients(group A)were detected by gene microarray(where the sample size were 3 cases in each group).In addition,the effects of anti-VEGF treatment(Group B)on the expressions of lncRNAs and mRNAs in the VH of PDR patients were evaluated by gene microarray.2.Ten differentially expressed lncRNAs in the gene microarray results were chosen for quantitative real-time polymerase chain reaction(q RT-PCR).3.Bioinformatics analysis was done for further investigation of the differentially expressed lncRNAs and mRNAs.Results:1.Group C compared with Group AIn total,1067 transcripts of lncRNAs were identified with differential expressions.Among these transcripts of lncRNAs,526 were significantly upregulated and 541 were significantly downregulated.TC1000007367.hg.1 was the most significant upregulated lncRNA(Fold-change =4.6)and TC0800006500.hg.1 was the most significantly downregulated lncRNA(Fold-change =-6.98).Five chosen lncRNAs were validated by q RT-PCR.The result showed that RP11-573J24.1,RP11-787B4.2,RP11-654G14.1,LINC01210,RP11-502I4.3 were decreased expressions which were consistent with the trend of gene microarray.In the Gene ontology(GO)enrichment analysis showed that 113 terms corresponded to upregulated transcripts,that 148 terms corresponded to downregulated transcripts.Upregulated transcripts were highly enriched for G protein-coupled receptor activity,transmembrane signaling receptor activity,signaling receptor activity,and so on.Downregulated transcripts were highly enriched for protein kinase C inhibitor activity,G protein-coupled receptor activity,Wnt-activated receptor activity,and so on.Kyoto encyclopedia of genes and genomes(KEGG)pathway analysis showed that a pathway corresponded to upregulated transcripts and that the enriched pathway was Olfactory transduction.With respect to downregulated transcripts,there were five pathways corresponded and enriched pathways included Aldosterone-regulated sodium reabsorption,Alzheimer disease,Proteasome,Olfactory transduction,and Basal cell carcinoma.We constructed the coding-noncoding gene co-expression network to find the potential core genes,and to find target genes of lncRNAs by the analysis of nearby genes.2.Group B compared with Group CIn total,835 transcripts of lncRNAs were identified with differential expressions.Among these transcripts of lncRNAs,455 were significantly upregulated and 380 were significantly downregulated.TC0600012915.hg.1 was the most significant upregulated lncRNA(Fold-change =3.92)and TC1400006820.hg.1 was the most significantly downregulated lncRNA(Fold-change =-3.6).A chosen lncRNA was validated by q RT-PCR.The result showed that RP4-631H13.2 was increased expression which was consistent with the trend of gene microarray.However,there were no significant differences in expression levels of RP11-407H12.8、CTD-2532K18.1、RP11-116N8.4、RP11-370P15.2.In the GO enrichment analysis showed that 109 terms corresponded to upregulated transcripts that 27 terms corresponded to downregulated transcripts.Upregulated transcripts were highly enriched for transforming growth factor beta receptor binding,DNA-dependent ATPase activity,ubiquitin hydrolase activity,and so on.Downregulated transcripts were highly enriched for G protein-coupled receptor activity,transmembrane signaling receptor activity,signaling receptor activity,and so on.KEGG pathway analysis showed that a pathway corresponded to upregulated transcripts and that the enriched pathway was Homologous recombination.With respect to downregulated transcripts,there is a pathway corresponded and enriched pathway was Olfactory transduction.We constructed the coding-noncoding gene co-expression network to find the potential core genes,and to find target genes of lncRNAs by the analysis of nearby genes.Conclusion:1.There had been the systemic expression differences in the VH from PDR patients and in the control from subjects with IMH patients at the microarray level.There had been the systemic expression differences after anti-VEGF treatment in the VH from patients with PDR.2.Compared with IMH patients,RP11-573J24.1,RP11-787B4.2,RP11-654G14.1,LINC01210,RP11-502I4.3 in VH of PDR patients were decreased expressions.After anti-VEGF treatment,RP4-631H13.2 in the VH of PDR patients was increased expression.However,there were no significant differences in expression levels of RP11-407H12.8、CTD-2532K18.1、RP11-116N8.4、RP11-370P15.2.3.Bioinformatics analysis could be used for investigation of the role of the differentially expressed lncRNAs and mRNAs in the pathogenesis of PDR. |
