The long-non coding RNA HOTAIR shapes the inflammatory response in joints of the lower extremity

Various forms of chronic arthritis like osteoarthritis (OA) or rheumatoid arthritis (RA) are major causes of disability and represent a global burden on health care systems. Inter- and intraindividual differences in the phenotype of arthritis often prevent early diagnosis and effective treatment. Previously, we suggested that site-specific differences in the joint stroma influence the development and the outcome of arthritis and showed that the long non-coding RNA HOTAIR is expressed exclusively in synovial fibroblasts (SF) of lower joints. Here, we further analysed the function of HOTAIR in SF and in arthritis development. We show that joint-specific HOTAIR expression in SF is stronlgy imprinted in the chromatin landscape of SF by epigenetic mechanisms. Nevertheless, HOTAIR expression in knee SF was downregulated by inflammatory cytokines. Accordingly, HOTAIR was more expressed in OA tissues than in RA tissues. Downregulation of HOTAIR regulated relevant arthritis pathways by epigenetic and transcriptional mechanisms and modified the migratory function of SF, decreased SF mediated osteoclastogenesis, and increased the attraction of B cells by SF. We propose that HOTAIR downregulation in inflammation epigenetically regulates important pathways and functions in SF, and thus modulates the phenotype of arthritis in lower extremity joints. Total RNA was extracted from three human knee synovial fibroblasts silenced for HOTAIR and control synovial fibroblasts 48h after transfection. Synovial fibroblasts were transfected with 50 nM antisense LNA HOTAIR GapmeR (Exiqon, Sequence: 5′-AGGCTTCTAAATCCGT-3′) using Lipofectamine 2000 (Invitrogen). Antisense LNA GapmeR Negative Control A (Cat No 300610) was used as transfection control. Chromatin immunoprecipitation sequencing (ChIPseq) H3K27me3 histone analysis in synovial fibroblasts invalidated for HOTAIR compared to control synovial fibroblasts. Single cell RNAseq data from cultured synovial fibroblasts transfected with either control or HOTAIR targeting GapmeR.