Genome-wide identification and characterization of long non-coding RNAs in MDCK cell lines with high and low tumorigenicities

Abstract

Madin-Darby canine kidney(MDCK) cells can be used to prepare cell-based influenza vaccines; however, little is known regarding the effect of lncRNA regulatorson tumorigenicity. In the present study, two cell lines with low tumorigenicity were screened from highly tumorigenic MDCK cell lines using monoclonal cell technology. Accordingly, three groups of lncRNAs were extracted from three cell lines and investigated using strand-specific Ribo-Zero RNA sequencing, detecting 1092 known and 619 novel lncRNAs. Moreover, in pairwise comparisons between the libraries of the nominally tumorigenic clones and the highly tumorigenic parent cell line, a total of 344 transcripts were expressed differentially, which were validated by qPCR using six randomly selected lncRNA genes. Furthermore, 63 target genes were identified in the upstream and downstream 100 kb of lncRNAs and their relative functions were analyzed. It was found that ten GO terms and twelve KEGG terms related to tumor by target genes and functional items. Five lncRNA transcripts and the corresponding differentially expressed target genes were used for co-expression network analysis. In addition, certain classical tumor pathways were also activated by target genes, among which, lncRNA MSTRG.1056.2 directly regulates ERBB3 to activate the PI3K-Akt pathway, contributing to tumorigenesis. Consequently, direct evidence was obtained that lncRNA regulates tumorigenesis, and a variety of target genes regulated by lncRNA were elucidated, which may be significant for non-tumorigenic MDCK cells lines acquisition.