Transcriptional analysis of long non-coding RNAs in facet joint osteoarthritis

Abstract

It is recognized that facet joint osteoarthritis (FJOA) is commonly induced by the degeneration of articular cartilage of the facet joint. However, the specific pathological mechanisms underlying facet joint osteoarthritis has not yet been elucidated. To obtain the differential expression patterns and putative functions of long noncoding RNAs (lncRNAs) in FJOA, in the current study, we detected the expression levels of lncRNAs in patients with varying degrees of facet cartilage degeneration (control group: normal or mild facet cartilage degeneration; FJOA: moderate to severe facet cartilage degeneration) by RNA deep sequencing. Differentially expressed lncRNAs were screened and the accuracy of sequencing data was further validated by using quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Target genes of differentially expressed lncRNAs were predicted by antisense and/or cis-regulatory module prediction. Predicted target genes were further analyzed by Gene Ontology (GO) and Kyoto Enrichment of Genes and Genomes pathway analysis (KEGG) to discover enriched cellular component, molecular function, biological process, and signaling pathways. Our results provided a general view of the expression changes of lncRNAs in FJOA and thus might facilitate the illumination of the underlying mechanisms of FJOA.

Fig. 1. Schematic of the experimental protocols of deep sequencing and bioinformatic analysis.

Fig. 2. The percentage of lncRNA classification. The percentages of antisense, intergenic, intronic, and sense overlapping, were listed.

Fig. 3. The volcano plot of differentially expressed lncRNAs. Up-regulated lncRNAs were labeled in red and down-regulated lncRNAs were labeled in green.

Fig. 4. Validation of lncRNA expressions by qRT-PCR. qRT-PCR was used to determine the expression levels of lncRNAs lncRNA MIR22HG, lncRNA RERG-AS1, lncRNA HECTD2-AS1, XLOC_091678, linc01783 and XLOC_091845 in the control group and in the FJOA group.

Fig. 5. (A) GO cellular component, molecular function, and biological process of antisense predicted target genes. (B) Top enriched KEGG pathways of antisense predicted target genes.

Fig. 6. (A) GO cellular component, molecular function, and biological process of cis-regulatory module predicted target genes. (B) Top enriched KEGG pathways of cis-regulatory module predicted target genes.