Integrated Analysis of lncRNA and mRNA Expression Profiles Indicates Age-Related Changes in Meniscus

Li-Ya Ai; Ming-Ze Du; You-Rong Chen; Peng-Yan Xia; Ji-Ying Zhang; Dong Jiang

doi:10.3389/fcell.2022.844555

Integrated Analysis of lncRNA and mRNA Expression Profiles Indicates Age-Related Changes in Meniscus

Front Cell Dev Biol. 2022 Mar 10:10:844555. doi: 10.3389/fcell.2022.844555. eCollection 2022.

Authors

Li-Ya Ai^{1

2}, Ming-Ze Du^{1

2}, You-Rong Chen^{1

2}, Peng-Yan Xia^{3

4}, Ji-Ying Zhang^{1

2}, Dong Jiang^{1

2}

Affiliations

¹ Department of Sports Medicine, Peking University Third Hospital, Beijing, China.
² Institute of Sports Medicine of Peking University, Beijing, China.
³ Department of Immunology, NHC Key Laboratory of Medical Immunology, School of Basic Medical Sciences, Peking University, Beijing, China.
⁴ Key Laboratory of Molecular Immunology, Chinese Academy of Medical Sciences, Beijing, China.

Abstract

Little has been known about the role of long non-coding RNA (lncRNA) involves in change of aged meniscus. Microarray analyses were performed to identify lncRNAs and mRNAs expression profiles of meniscus in young and aging adults and apple bioinformatics methods to analyse their potential roles. The differentially expressed (DE) lncRNAs and mRNAs were confirmed by qRT-PCR. A total of 1608 DE lncRNAs and 1809 DE mRNAs were identified. Functional and pathway enrichment analyses of all DE mRNAs showed that DE mRNAs were mainly involved in the TGF-beta, Wnt, Hippo, PI3K-Akt signaling pathway. The expressions of TNFRSF11B and BMP2 were significantly upregulated in aging group. LASSO logistic regression analysis of the DE lncRNAs revealed four lncRNAs (AC124312.5, HCG11, POC1B-AS1, and AP001011.1) that were associated with meniscus degradation. CNC analysis demonstrated that AP001011 inhibited the expression of TNFRSF11B and AC1243125 upregulated the expression of TNFRSF11B. CeRNA analysis suggested that POC1B-AS1 regulates the expression of BMP2 by sponging miR 130a-3p, miR136-5p, miR 18a-3p, and miR 608. Furthermore, subcellular localization and m⁶A modification sites prediction analysis of these four lncRNAs was performed. These data lay a foundation for extensive studies on the role of lncRNAs in change of aged meniscus.

Keywords: aging; bioinformatics; long non coding RNA; mRNA; meniscus.