| Objective:Long noncoding RNA(lnc RNA) have received wide attention recently as key molecules that mediate a variety of physiological and pathological processes by regulating gene expression; however, the knowledge of lnc RNA in fibroblast-like synoviocytes(FLSs) from patients of rheumatoid arthritis(RA) is limited. Thus, we investigated the lnc RNA expression profiles in fibroblast-like synoviocytes(FLSs) from RA and trauma patients, and explored the function of abundantly expressed lnc RNAs.Methods:Lnc RNA and m RNA microarrays were performed to identify differentially expressed lnc RNAs in three pairs of specimens(RA, n=3; trauma patients, n=3)using FLSs from passage 3. Then gene ontology and pathway analyses of the differently expressed genes were carried out. Pathway analysis and Gene Ontology(GO) analysis were applied to explore the potential roles that the differentially expressed m RNAs play in a biological pathway or GO term. Quantitative polymerase chain reaction(q PCR) was used to validate the results. And correlation analysis was used to analyze the relationship between these aberrantly expressed lnc RNAs and clinical characteristics. A receiver operating characteristic(ROC) curve was constructed to evaluate the diagnostic value of the lnc RNAs identified. Gene co-expression networks were mbuilt according to differentially expressed lnc RNAs and m RNAs to predict biological functions and action mechanisms of these lnc RNAsResults:1. According to the gene expression profiles,135 lnc RNAs and 103 m RNAs were found to be differentially expressed between RA-FLSs and CON-FLSs. Of the 135 lnc RNAs identified, 62 lnc RNAs were up-regulated and 73 lnc RNAs were down-regulated in the RA-FLSs. Of the 103 m RNAs identified, 36 m RNAs were up-regulated and 67 m RNAs were down-regulated in the RA-FLSs.2. Real-time PCR confirmed that ENST00000483588 was overexpressed in the RA-FLSs, whereas the expression levels of ENST00000438399, uc004 afb.1 and ENST00000452247 were decreased, which showed similar trends with results of microarray.3. Moreover,the areas under the ROC curve were 0.85, 0.92, 0.97, and 0.92 for ENST00000483588, ENST00000438399, uc004 afb.1 and ENST00000452247, respectively, indicating that these lnc RNAs may have potential diagnostic value in RA. In addition, the expression level of ENST00000483588 was positively correlated with the level of C-reactive protein and Simple Disease Activity Index score, respectively.4. The result showed that ENST00000483588, ENST00000438399, uc004 afb.1 and ENST00000452247 were connected with 9, 9, 8 and 12 m RNAs, respectively.5. GO analysis revealed that the up-regulated m RNAs in RA-FLSs were related to 373 biological processes, 15 celluar components, 34 molecular functions; the down-regulated m RNAs were related to 129 biological processes, 17 celluar components, 20 molecular functions. Pathway analysis showed that the up-regulated m RNAs in RA-FLSs were involved in 9 pathways; the down-regulated m RNAs involved in 27 pathways.Conclusion: 1.The expression lnc RNA profile of RA-FLSs changes significantly compared with control group(CON-FLSs). ENST00000483588 was overexpressed and ENST00000438399, uc004 afb.1, and ENST00000452247 was underexpressed of these differentially expressed lnc RNAs. The expression level of ENST00000483588 was positively corrected with the level of CRP and the SDAI score indicating that this lnc RNA may have potential value for the diagnosis or assessment of disease activity of RA.2. The pathway analysis showed that the differentially expressed m RNAs in RA-FLSs were mainly related with m TOR, HIF-1, Ras, proteoglycans, and apoptosis signaling pathways. These m RNAs were further identified to be mainly involved in regulation of growth, vascular permeability, and leukocyte activation biological processes. The differentially expressed lnc RNAs in RA-FLSs may involved in the processes of cell proliferation and apoptosis and bone resorption. |
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