TRNA-derived fragment TRF365 regulates the metabolism of anterior cruciate ligament cells by targeting IKBKB

Dianbo Long,Guping Mao,Zengfa Deng,Ruobing Xin,Zhiwen Li,Baoxi Yu,Ziji Zhang,Zhi Yang,Yiyang Xu,Zhijian Yang,Yan Kang,Aishan He,Hongyi Liao

doi:10.1038/s41420-021-00806-4

Abstract

tRNA-derived fragments (tRFs) are new noncoding RNAs, and recent studies have shown that tRNAs and tRFs have important functions in cell metabolism via posttranscriptional regulation of gene expression. However, whether tRFs regulate cellular metabolism of the anterior cruciate ligament (ACL) remains elusive. The aim of this study was to investigate the role and action mechanism of tRFs in ACL cell metabolism. A tRF array was used to determine tRF expression profiles in different human ACL cells, and quantitative real-time polymerase chain reaction and fluorescence in situ hybridisation were used to determine TRF365 expression. ACL cells were transfected with a TRF365 mimic or a TRF365 inhibitor to determine whether TRF365 regulates IKBKB expression. A rescue experiment and dual-luciferase reporter assay were conducted to determine whether the 3′-untranslated region (UTR) of IKBKB has a TRF365-binding site. TRF365 was weakly expressed in osteoarthritis (OA) ACL and interleukin-1β-treated ACL cells. IKBKB was highly expressed in OA ACL and interleukin-1β-treated ACL cells; transfection with the TRF365 mimic suppressed IKBKB expression, whereas transfection with the TRF365 inhibitor had the opposite effect. A dual-luciferase reporter assay showed that TRF365 silenced the expression of IKBKB by binding to its 3′-UTR. Thus, TRF365 regulates the metabolism of ACL cells by targeting IKBKB. In summary, TRF365 may provide a new direction for the study of ACL degeneration and on the pathophysiological process of OA.

Highlights

Osteoarthritis (OA) is the most common degenerative joint disease, and its incidence has increased in recent years [1]
Among the transfer RNAs (tRNAs)-derived fragments (tRFs) that were consistently differentially expressed in all three paired samples, 29 were down-regulated in OA, and IL-1β-treated anterior cruciate ligament (ACL) cells (Fig. 2B)
Six tRFs were selected, and their expression was verified by quantitative real-time polymerase chain reaction, which showed low expression of tRF-3008B, tRF-3030B, TRF365, tRF-5008C, tRF-5009A, and tRF-5020B in OA and IL-1β ACL cells (Fig. 2D)

Summary

Introduction

Osteoarthritis (OA) is the most common degenerative joint disease, and its incidence has increased in recent years [1]. The anterior cruciate ligament (ACL) is an intra-articular ligament that maintains the stability of the knee joint and plays an important role in the occurrence and development of OA. Recent studies have shown that there is an interrelation between ACL inflammation and degeneration, cartilage degradation, and dysbalanced subchondral bone remodelling [3,4,5]. Noncoding RNAs (ncRNAs) have been a focus of research in the last decade and have been extensively studied in OA progression [6]; the role of ncRNAs in ACL cell metabolism has not been sufficiently investigated. Transfer RNAs (tRNAs) and tRNA-derived small RNAs have been found to play important roles in the posttranscriptional control of gene expression [8]. A new function of tRNAs has been discovered; that is, they can give rise to tRFs, which have their own functions [8,9,10]

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