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

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.