Zhu Danxia, Fang Cheng, Li Xiaodong, Geng Yiting, Li Ruiqi, Wu Chen, Jiang Jingting, Wu Changping
Department of Oncology, The Third Affiliated Hospital of Soochow University, Changzhou 213003, China.
Department of Tumor Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou 213003, China.
Oncotarget. 2017 Apr 4;8(14):23228-23236. doi: 10.18632/oncotarget.15571.
Long non-coding RNAs (lncRNAs) are implicated in many tumors. To find novel targets for study of diffuse large B-cell lymphoma (DLBCL), our team performed genome-wide analyses of lncRNA expression in 5 DLBCL cell lines using the 4*180K Agilent lncRNA Chip system, and in normal B cells. Five lncRNAs were validated by quantitative reverse transcription polymerase chain reaction. The differentially expressed lncRNAs and mRNAs were identified via false discovery rate and fold-change filtering. Potential targets correlated with DLBCL were recognized via gene ontology and pathway analysis. Establishment of the co-expression network was done using Cytoscape. In total, 1053 lncRNAs and 4391 mRNAs were dysregulated in DLBCL cells, being comparing with normal B cells. The results suggested that the expressions of the 5 lncRNAs were consistent with the chip results. Several terms including the cell cycle, apoptosis, B cell receptor and NF-κB signaling pathways were important in the progression of DLBCL. The chromosome locations of a few lncRNAs and the associated coexpressed genes were demonstrated by cis-regulatory gene analyses. The results of trans-analyses showed that multiple transcription factors regulated lncRNA and gene expression. Those outstanding lncRNAs in each group were implicated in the regulation of the TF-lncRNA-target gene network. Our study identified a set of lncRNAs differentially expressed in DLBCL cells.
长链非编码RNA（lncRNAs）与多种肿瘤有关。为了寻找弥漫性大B细胞淋巴瘤（DLBCL）研究的新靶点，我们的团队使用4×180K安捷伦lncRNA芯片系统，对5种DLBCL细胞系以及正常B细胞中的lncRNA表达进行了全基因组分析。通过定量逆转录聚合酶链反应验证了5种lncRNAs。通过错误发现率和倍数变化筛选来鉴定差异表达的lncRNAs和mRNAs。通过基因本体论和通路分析识别与DLBCL相关的潜在靶点。使用Cytoscape建立共表达网络。与正常B细胞相比，DLBCL细胞中共有1053种lncRNAs和4391种mRNAs表达失调。结果表明，5种lncRNAs的表达与芯片结果一致。包括细胞周期、凋亡、B细胞受体和NF-κB信号通路在内的几个术语在DLBCL的进展中很重要。通过顺式调控基因分析证明了一些lncRNAs的染色体位置以及相关的共表达基因。反式分析结果表明，多种转录因子调节lncRNA和基因表达。每组中那些突出的lncRNAs参与了TF-lncRNA-靶基因网络的调控。我们的研究鉴定出一组在DLBCL细胞中差异表达的lncRNAs。
