Co-expression network analysis of lncRNAs and mRNAs in OPTN-silenced cells

The aim of the present study was to reveal the role of long noncoding RNAs (lncRNAs) in the regulation of the pathogenesis of optineurin (OPTN)-silenced cells. The microarray data set GSE12452 was re-annotated using the non-coding RNA function annotation server to identify differentially expressed lncRNAs. Weighted correlation network analysis was used to construct an lncRNA-lncRNA co-expression network and identify co-expression modules. Three OPTN small interfering RNAs (siRNAs) were transiently transfected into HeLa cells. Reverse transcription‑quantitative polymerase chain reaction (RT-qPCR) and western blot analysis were used to detect OPTN expression and select the most effective OPTN siRNA to construct stably transfected cells. RT-qPCR was used to quantify the identified lncRNAs in the OPTN-silenced cells. The potential functions of these modules were explored by the functional enrichment of the corresponding co-expressed genes. A total of 3,495 lncRNAs were re-annotated. Of these, matrix metalloprotease 12 and RP11-169D4.1 were upregulated, and RP1-212P9.2 was downregulated. The results of the RT-qPCR analysis of RP1-212P9.2 and RP11‑169D4.1 were consistent with the re-annotated data in the OPTN‑silenced cells. Gene Ontology analyses indicated that the biological functions of the mRNAs co-expressed with these lncRNAs were associated with gene product regulation, and neuronal migration, polarity and differentiation. In addition, Kyoto Encyclopedia of Genes and Genomes analysis indicated that the two validated lncRNAs were associated with the transforming growth factor-β signaling pathway and the apoptosis pathway, respectively. In conclusion, the abnormal lncRNAs identified in OPTN-silenced cells indicate that lncRNAs may contribute to the molecular pathogenesis of OPTN-associated diseases.