Table1_Whole Transcriptome Mapping Identifies an Immune- and Metabolism-Related Non-coding RNA Landscape Remodeled by Mechanical Stress in IL-1β-Induced Rat OA-like Chondrocytes.DOCX

Background: Osteoarthritis (OA) is a common degenerative joint disease. The aims of this study are to explore the effects of mechanical stress on whole transcriptome landscape and to identify a non-coding transcriptome signature of mechanical stress. Methods: Next-generation RNA sequencing (RNA-seq) was performed on IL-1β-induced OA-like chondrocytes stimulated by mechanical stress. Integrated bioinformatics analysis was performed and further verified by experimental validations. Results: A total of 5,022 differentially expressed mRNAs (DEMs), 88 differentially expressed miRNAs (DEMIs), 1,259 differentially expressed lncRNAs (DELs), and 393 differentially expressed circRNAs (DECs) were identified as the transcriptome response to mechanical stress. The functional annotation of the DEMs revealed the effects of mechanical stress on chondrocyte biology, ranging from cell fate, metabolism, and motility to endocrine, immune response, and signaling transduction. Among the DELs, ∼92.6% were identified as the novel lncRNAs. According to the co-expressing DEMs potentially regulated by the responsive DELs, we found that these DELs were involved in the modification of immune and metabolism. Moreover, immune- and metabolism-relevant DELs exhibited a notable involvement in the competing endogenous RNA (ceRNA) regulation networks. Silencing lncRNA TCONS_00029778 attenuated cellular senescence induced by mechanical stress. Moreover, the expression of Cd80 was elevated by mechanical stress, which was rescued by silencing TCONS_00029778. Conclusion: The transcriptome landscape of IL-1β-induced OA-like chondrocytes was remarkably remodeled by mechanical stress. This study identified an immune- and metabolism-related ncRNA transcriptome signature responsive to mechanical stress and provides an insight of ncRNAs into chondrocyte biology and OA.背景：骨关节炎（Osteoarthritis, OA）是一种常见的退行性关节疾病。本研究旨在探索机械应力对全转录组图谱的影响，并鉴定出机械应力相关的非编码转录组特征。方法：对经机械应力刺激的白细胞介素-1β（Interleukin-1β, IL-1β）诱导的类骨关节炎软骨细胞开展下一代RNA测序（Next-generation RNA sequencing, RNA-seq）。通过整合生物信息学分析，并辅以实验验证进一步确认分析结果。结果：本研究共鉴定出5022个差异表达mRNA（differentially expressed mRNAs, DEMs）、88个差异表达miRNA（differentially expressed miRNAs, DEMIs）、1259个差异表达长链非编码RNA（differentially expressed long non-coding RNAs, DELs）以及393个差异表达环状RNA（differentially expressed circular RNAs, DECs），上述均为响应机械应力的转录组变化分子。对差异表达mRNA的功能注释结果显示，机械应力可影响软骨细胞生物学过程，涵盖细胞命运、代谢、运动能力，以及内分泌、免疫应答与信号转导等多个层面。在鉴定出的DELs中，约92.6%为新型长链非编码RNA。基于响应性DELs潜在调控的共表达差异mRNA分析发现，此类DELs参与免疫与代谢过程的调控修饰。此外，与免疫及代谢相关的DELs显著参与内源竞争RNA（competing endogenous RNA, ceRNA）调控网络。沉默长链非编码RNA TCONS_00029778可减轻机械应力诱导的细胞衰老。同时，机械应力可升高Cd80的表达水平，该效应可通过沉默TCONS_00029778得到逆转。结论：白细胞介素-1β诱导的类骨关节炎软骨细胞的转录组图谱可被机械应力显著重塑。本研究鉴定出了响应机械应力的免疫与代谢相关非编码RNA转录组特征，为非编码RNA在软骨细胞生物学及骨关节炎研究领域提供了新的理论视角。