Yang Yujuan, Sun Qi, Guo Jing, Liu Zhen, Wang Jianwei, Yao Yao, Yu Pengyi, Cao Jiayu, Zhang Yu, Song Xicheng
Department of Otorhinolaryngology, Head and Neck Surgery, Yantai Yuhuangding Hospital, Qingdao University, Yantai, China.
Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases, Yantai, China.
Front Genet. 2022 May 31;13:811679. doi: 10.3389/fgene.2022.811679. eCollection 2022.
LncRNA-miRNA-mRNA competing endogenous RNA (ceRNA) networks are thought to be involved in regulating the development of various inflammatory diseases. Up to now, the mechanism of such a network in allergic rhinitis (AR) remains unclear. In the study, we investigated the differential expression of lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) by performing a microarray analysis of peripheral blood obtained from AR patients and healthy control subjects. StarBase 2.0 was used to predict miRNAs that might interact with various DElncRNAs and DEmRNAs. We constructed a ceRNA network based on potential lncRNA-miRNA-mRNA interactions. The Cluster Profiler R package was used to perform a functional enrichment analysis of the hub-ceRNA, and Molecular Complex Detection (MCODE) was used for further identification of the hub-ceRNA network. The expression levels of genes contained in the hub-ceRNA network were validated by RT-PCR. In total, 247 DEmRNAs and 18 DelncRNAs were aberrantly expressed in the PBMCs of AR patients. A ceRNA network consisting of 3 lncRNAs, 45 miRNAs, and 75 mRNAs was constructed. A GO analysis showed that negative regulation of immune response, response to interferon-beta, and response to interferon-alpha were important terms. A KEGG pathway analysis showed that 75 mRNAs were significantly enriched in "NOD-like receptor signaling pathway" and "tryptophan metabolism". Ultimately, a hub-ceRNA network was constructed based on 1 lncRNA (AC011511.5), 5 miRNAs (hsa-miR-576-5p, hsa-miR-520c-5p, hsa-miR-519b-5p, hsa-miR-519c-5p, and hsa-miR-518d-5p), and 2 mRNAs (ZFP36L1 and SNX27). Following further verification, we found that overexpression of lncRNA AC011511.5 or inhibitor of miR-576-5p upregulated SNX27 expression. The expression of SNX27 in the lncRNA AC011511.5 overexpression & miR-576-5p inhibitor group was not different from that in the miR-576-5p inhibitor group or lncRNA AC011511.5 overexpression group, indicating that overexpression of lncRNA AC011511.5 could not further upregulate the expression of SNX27 in miR-576-5p inhibitor Jurkat cells. This network may provide new insights to search for biomarkers that can be used for the diagnosis and clinical treatment of AR.
长链非编码RNA-微小RNA-信使RNA竞争性内源RNA（ceRNA）网络被认为参与调节各种炎症性疾病的发展。迄今为止，这种网络在变应性鼻炎（AR）中的机制仍不清楚。在本研究中，我们通过对AR患者和健康对照者外周血进行微阵列分析，研究了长链非编码RNA（DElncRNAs）和信使RNA（DEmRNAs）的差异表达。使用StarBase 2.0预测可能与各种DElncRNAs和DEmRNAs相互作用的微小RNA。我们基于潜在的长链非编码RNA-微小RNA-信使RNA相互作用构建了一个ceRNA网络。使用Cluster Profiler R包对中心ceRNA进行功能富集分析，并使用分子复合物检测（MCODE）进一步鉴定中心ceRNA网络。通过逆转录聚合酶链反应验证中心ceRNA网络中所含基因的表达水平。总共，247种DEmRNAs和18种DelncRNAs在AR患者的外周血单核细胞中异常表达。构建了一个由3种长链非编码RNA、45种微小RNA和75种信使RNA组成的ceRNA网络。基因本体（GO）分析表明，免疫反应的负调控、对β干扰素的反应和对α干扰素的反应是重要的条目。京都基因与基因组百科全书（KEGG）通路分析表明，75种信使RNA在“NOD样受体信号通路”和“色氨酸代谢”中显著富集。最终，基于1种长链非编码RNA（AC011511.5）、5种微小RNA（hsa-miR-576-5p、hsa-miR-520c-5p、hsa-miR-519b-5p、hsa-miR-519c-5p和hsa-miR-518d-5p）和2种信使RNA（ZFP36L1和SNX27）构建了一个中心ceRNA网络。进一步验证后，我们发现长链非编码RNA AC011511.5的过表达或miR-576-5p的抑制剂上调了SNX27的表达。长链非编码RNA AC011511.5过表达&miR-576-5p抑制剂组中SNX27的表达与miR-576-5p抑制剂组或长链非编码RNA AC011511.5过表达组中的表达无差异，表明长链非编码RNA AC011511.5的过表达不能进一步上调miR-576-5p抑制剂Jurkat细胞中SNX27的表达。该网络可能为寻找可用于AR诊断和临床治疗的生物标志物提供新的见解。
