Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health Engineering, Key Lab for Space Biosciences and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, 710072, Xi'an, Shaanxi, China.
Research Center for Special Medicine and Health Systems Engineering, School of Life Sciences, Northwestern Polytechnical University, 710072, Xi'an, Shaanxi, China.
BMC Genomics. 2022 Oct 7;23(1):695. doi: 10.1186/s12864-022-08910-0.
Previous studies have shown that microtubule actin crosslinking factor 1 (MACF1) can regulate osteoblast proliferation and differentiation through non-coding RNA (ncRNA) in bone-forming osteoblasts. However, the role of MACF1 in targeting the competing endogenous RNA (ceRNA) network to regulate osteoblast differentiation remains poorly understood. Here, we profiled messenger RNA (mRNA), microRNA (miRNA), and long ncRNA (lncRNA) expression in MACF1 knockdown MC3TC‑E1 pre‑osteoblast cells.
In total, 547 lncRNAs, 107 miRNAs, and 376 mRNAs were differentially expressed. Significantly altered lncRNAs, miRNAs, and mRNAs were primarily found on chromosome 2. A lncRNA-miRNA-mRNA network was constructed using a bioinformatics computational approach. The network indicated that mir-7063 and mir-7646 were the most potent ncRNA regulators and mef2c was the most potent target gene. Pathway enrichment analysis showed that the fluid shear stress and atherosclerosis, p53 signaling, and focal adhesion pathways were highly enriched and contributed to osteoblast proliferation. Importantly, the fluid shear stress and atherosclerosis pathway was co-regulated by lncRNAs and miRNAs. In this pathway, Dusp1 was regulated by AK079370, while Arhgef2 was regulated by mir-5101. Furthermore, Map3k5 was regulated by AK154638 and mir-466q simultaneously. AK003142 and mir-3082-5p as well as Ak141402 and mir-446 m-3p were identified as interacting pairs that regulate target genes.
This study revealed the global expression profile of ceRNAs involved in the differentiation of MC3TC‑E1 osteoblasts induced by MACF1 deletion. These results indicate that loss of MACF1 activates a comprehensive ceRNA network to regulate osteoblast proliferation.
先前的研究表明，微管肌动蛋白交联因子 1（MACF1）可以通过成骨细胞中的非编码 RNA（ncRNA）调节成骨细胞的增殖和分化。然而，MACF1 如何通过靶向竞争内源性 RNA（ceRNA）网络来调节成骨细胞分化仍知之甚少。在此，我们对 MACF1 敲低 MC3TC-E1 前成骨细胞中的信使 RNA（mRNA）、微小 RNA（miRNA）和长非编码 RNA（lncRNA）表达进行了分析。
共检测到 547 个 lncRNA、107 个 miRNA 和 376 个 mRNA 表达发生改变。明显改变的 lncRNA、miRNA 和 mRNA 主要位于染色体 2 上。采用生物信息学计算方法构建了 lncRNA-miRNA-mRNA 网络。该网络表明 mir-7063 和 mir-7646 是最有效的 ncRNA 调节剂，mef2c 是最有效的靶基因。通路富集分析显示，流体切应力和动脉粥样硬化、p53 信号通路和黏着斑通路高度富集，对成骨细胞增殖有贡献。重要的是，流体切应力和动脉粥样硬化通路由 lncRNA 和 miRNA 共同调节。在该通路中，Dusp1 受 AK079370 调控，而 Arhgef2 受 mir-5101 调控。此外，Map3k5 同时受 AK154638 和 mir-466q 调控。AK003142 和 mir-3082-5p 以及 Ak141402 和 mir-446 m-3p 被鉴定为相互作用对，可调节靶基因。
本研究揭示了 MACF1 缺失诱导 MC3TC-E1 成骨细胞分化中涉及的 ceRNA 的全局表达谱。这些结果表明，MACF1 的缺失激活了一个全面的 ceRNA 网络来调节成骨细胞增殖。
