Extensive downregulation of immune gene expression by microRNA-140-3p 5′ isomiR in an in vitro model of osteoarthritis

OBJECTIVE: MicroRNA-140-3p is the most prevalent form of canonical miR-140 in native chondrocytes. IsomiRs are sequence variants of microRNAs with potentially distinct functionalities. Here we present functional studies of canonical microRNA-140-3p and two of its most prevalent isomiRs, a 5′ isomiR and a 3′ isomiR, in an inflammation-induced model of osteoarthritis (OA). METHOD: Canonical miR-140-3p, the 5′ isomiR and the 3′ isomiR were overexpressed separately in chondrocytes from three donors and subsequently subjected to an inflammatory milieu mediated by interleukin 1 beta and tumor necrosis factor alpha. RNA sequencing was performed on the cells to investigate the altered transcriptomes, RT-qPCR was performed to validate important observations, and western blot analysis was carried out to further study key inflammatory molecules. RESULTS: The three microRNAs downregulated many of the same genes. However, the 5′ isomiR showed a much greater target spectrum compared to the other two miRNAs, and downregulated cascades of genes downstream of interferon beta, interferon gamma and interleukin 1 beta as well as genes involved in several other inflammatory and antiviral pathways. In addition the 5′ isomiR downregulated practically all HLA class II and class I genes. CONCLUSION: Introduction of the 5′ isomiR led to downregulation of genes essential for some of the most important inflammation cascades and virtual silencing of genes responsible for antigen presentation. These observations may indicate a very promising therapeutic potential for the 5′ isomiR for OA and several inflammatory conditions, particularly HLA associated immune conditions including many arthritic diseases.