Oncotarget

Research Papers:

Predictive analysis of long non-coding RNA expression profiles in diffuse large B-cell lymphoma

Danxia Zhu, Cheng Fang, Xiaodong Li, Yiting Geng, Ruiqi Li, Chen Wu, Jingting Jiang and Changping Wu _

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Oncotarget. 2017; 8:23228-23236. https://doi.org/10.18632/oncotarget.15571

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Abstract

Danxia Zhu1,*, Cheng Fang1,*, Xiaodong Li1,*, Yiting Geng1, Ruiqi Li1, Chen Wu1, Jingting Jiang2, Changping Wu1,2

1Department of Oncology, The Third Affiliated Hospital of Soochow University, Changzhou 213003, China

2Department of Tumor Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou 213003, China

*These authors contributed equally to this work

Correspondence to:

Jingting Jiang, email: jiangjingting@suda.edu.cn

Changping Wu, email: wcpjjt@163.com

Keywords: diffuse large B cell lymphoma, long noncoding RNAs, microarray

Received: August 15, 2016     Accepted: February 12, 2017     Published: February 21, 2017

ABSTRACT

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.


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