Li Yue, Liu Xueru, Zhang Wenyue, Song Xuefei, Zhang Leilei, Xiao Caiwen
Department of Ophthalmology, School of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, Shanghai, China.
Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China.
Front Genet. 2022 Feb 28;13:834111. doi: 10.3389/fgene.2022.834111. eCollection 2022.
This study was designed to identify differently expressed circular RNAs (circRNAs) and investigate their potential roles in lacrimal sacs from patients with chronic dacryocystitis. The lacrimal sac samples of three chronic dacryocystitis patients and three control subjects were collected for RNA sequencing after ribosomal RNA was depleted. Differently expressed circRNAs and messenger RNAs (mRNAs) were used for co-expression analysis. CircRNA-microRNA (miRNA)-mRNA interaction network were also established by miRanda software. Meanwhile, pathway and functional enrichment analysis were conducted for the down- and up-regulated mRNAs in the circRNA-mRNA co-expression network. The expression levels of circRNAs and mRNAs in chronic dacryocystitis and control samples were validated by quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR). In all the 3,909 circRNAs predicted through RNA sequencing, 25 circRNAs (20 up-regulated and 5 down-regulated) expressed differently in chronic dacryocystitis samples. Besides, there identified 1,486 differentially expressed mRNAs. Of these differently expressed circRNAs and mRNAs, eight were validated by qRT-PCR, including MYH2, DSP, CD27, CCL5, FN1, has_circ_0004792, has_circ_0001062, and has_circ_0115476. Gene Ontology (GO) analysis indicated that the majority of altered mRNAs in this co-expression network were involved in immune system processes and meanwhile Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that these altered expressed mRNAs were also amplified in bacterial invasion of epithelial cells, both of which were thought to be involved in the pathogenesis of chronic dacryocystitis. In the circRNA-miRNA-mRNA interaction network, six circRNAs were found to be related to Th1 and Th2 cell differentiation, which was closely associated with the development of chronic dacryocystitis. This study identified statistically significant differences between circRNAs and mRNAs of lacrimal sac samples of chronic dacryocystitis patients and control individuals and provides novel insight into the regulatory mechanism of circRNAs, miRNAs, and mRNAs in the pathogenesis of chronic dacryocystitis.
本研究旨在鉴定差异表达的环状RNA（circRNA），并探讨其在慢性泪囊炎患者泪囊中潜在的作用。收集3例慢性泪囊炎患者和3例对照者的泪囊样本，去除核糖体RNA后进行RNA测序。对差异表达的circRNA和信使RNA（mRNA）进行共表达分析。同时利用miRanda软件构建circRNA-微小RNA（miRNA）-mRNA相互作用网络。对circRNA-mRNA共表达网络中下调和上调的mRNA进行通路和功能富集分析。采用定量实时逆转录聚合酶链反应（qRT-PCR）验证慢性泪囊炎和对照样本中circRNA和mRNA的表达水平。通过RNA测序预测的3909个circRNA中，有25个circRNA（20个上调和5个下调）在慢性泪囊炎样本中差异表达。此外，鉴定出1486个差异表达的mRNA。在这些差异表达的circRNA和mRNA中，8个通过qRT-PCR得到验证，包括MYH2、DSP、CD27、CCL5、FN1、has_circ_0004792、has_circ_0001062和has_circ_0115476。基因本体（GO）分析表明，该共表达网络中大多数变化的mRNA参与免疫系统过程，同时京都基因与基因组百科全书（KEGG）分析显示，这些变化表达mRNA在细菌侵袭上皮细胞中也被富集，这两者都被认为与慢性泪囊炎的发病机制有关。在circRNA-miRNA-mRNA相互作用网络中，发现6个circRNA与Th1和Th2细胞分化相关，这与慢性泪囊炎的发展密切相关。本研究确定了慢性泪囊炎患者和对照个体泪囊样本中circRNA和mRNA的统计学显著差异，并为circRNA、miRNA和mRNA在慢性泪囊炎发病机制中的调控机制提供了新的见解。
