Small RNA signatures of the anterior cruciate ligament from patients with knee joint osteoarthritis

The anterior cruciate ligaments are susceptible to degeneration, resulting in pain, reduced mobility and development of the degenerative joint disease osteoarthritis. There is currently a paucity of knowledge on how anterior cruciate ligament degeneration and disease can lead to osteoarthritis. Small non-coding RNAs (sncRNAs), such as microRNAs, and small nucleolar RNA, are important regulators of gene expression. We aimed to identify sncRNA profiles of human anterior cruciate ligaments to provide novel insights into their roles in osteoarthritis. RNA was extracted from the anterior cruciate ligaments of non-osteoarthritic knee joints (control) and end-stage osteoarthritis knee joints, used for small RNA sequencing and significantly differentially expressed sncRNAs defined. Bioinformatic analysis was undertaken on the differentially expressed miRNAs and their putative target mRNAs to investigate pathways and biological processes affected. Our analysis identified 184 sncRNA that were differentially expressed between control ACLs derived from osteoarthritic joints with a false discovery adjusted p value<0.05; 68 small nucleolar RNAs, 26 small nuclear RNAs and 90 microRNAs. We identified both novel and previously identified (miR-206, -101, -365 and -29b and -29c) osteoarthritis-related microRNAs and other sncRNAs (including SNORD74, SNORD114, SNORD72) differentially expressed in ligaments derived from osteoarthritic joints. Significant cellular functions deduced by the differentially small nuclear RNAs and 90 microRNAs. We identified expressed miRNAs included differentiation of muscle (P<0.001), inflammation (P<1.42E-10), proliferation of chondrocytes (P<0.03), fibrosis (P<0.001) and cell viability (P<0.03). Putative mRNAs were associated with the canonical pathways Hepatic Fibrosis Signalling (P<3.7E-32), and Osteoarthritis (P<2.2E-23). Biological processes included apoptosis (P<1.7E-85), fibrosis (P<1.2E-79), inflammation (P<3.4E-88), necrosis (P<7.2E-88) and angiogenesis (P<5.7E-101). SncRNAs are important regulators of anterior cruciate disease during osteoarthritis and may be used as therapeutic targets to prevent and manage anterior cruciate ligament disease and the resultant osteoarthritis.