Comprehensive analysis of long non-coding RNA and mRNA expression profiles in rheumatoid arthritis

Abnormal expression of long non-coding RNA (lncRNA) has been demonstrated to be involved in a variety of human diseases. However, the role of lncRNA remains largely unknown in rheumatoid arthritis (RA). The present study aimed to investigate whether lncRNA are differentially expressed in RA. Differentially expressed lncRNA and mRNA in peripheral blood mononuclear cells from individuals with RA and healthy controls were detected using a human lncRNA microarray containing 30,586 lncRNA and 26,109 coding transcripts. Several candidate lncRNA and mRNA in 24 paired samples were verified by reverse transcription-quantitative polymerase chain reaction analysis. Bioinformatics analyses (Gene Ontology and Kyoto Encyclopedia of Genes and Genomes) were used to evaluate signaling pathways and biological functions influenced by the differentially expressed mRNA. A total of 5,045 lncRNA (upregulated, 2,410; downregulated, 2,635) and 3,289 mRNA (upregulated, 1,403; downregulated, 1,886) were differentially expressed in patients with RA (fold change >2; P<0.05). The majority of abnormal lncRNA were from intergenic spacer regions (42%), natural antisense (19%) and intronic antisense (15%) to protein-coding loci. lncRNA target prediction indicated the presence of 135 potential lncRNA-mRNA target pairs for the 85 aberrant lncRNA and 109 aberrant mRNA. Significantly enriched (P<0.05) signaling pathways based on deregulated mRNA were mostly implicated in bile secretion, T cell receptor signaling pathway and systemic lupus erythematosus. In summary, to the best of our knowledge, the present study executed global expression profiling of lncRNA and mRNA involved in RA for the first time. These results may provide important insights regarding lncRNA in RA pathogenesis and provide potential therapeutic targets.