Heterogeneous expression of long noncoding RNA RP11-109D20.2: Insights into regulatory gene expression roles in colon cancer.

OBJECTIVES

Colorectal cancer is one of the deadliest cancers worldwide, which can be prevented and even cured by early diagnosis and more efficient treatment modalities. Comprehensive transcriptional analysis has highlighted the importance of lncRNAs in CRC tumorigenesis. In this study, we identified co-expressed lncRNA networks based on public RNA sequencing data for biomarker prediction in CRC and then verified the best candidate experimentally.

MATERIALS AND METHODS

Publicly available RNA-sequencing data (BioProject PRJEB27536) of CRC samples and normal adjacent tissues were reanalyzed using the DESeq2 package in R to find differentially expressed lncRNAs. Pathway enrichment and gene network analysis were accomplished using GSEA and WGCNA to identify potential functions of lncRNAs with possible roles in tumorigenesis pathways. Subsequently, the expression of () was assessed in fresh/frozen tissues obtained from 46 CRC patients by quantitative RT-PCR.

RESULTS

A total of 17939 DElncRNAs were identified between CRC and normal tissues bioinformatics analyses. A significant up-regulation of (48%) was observed in CRC samples. Functional enrichment analysis showed that was mainly related to pathways like phosphoric ester hydrolase, oxidoreductase, phosphoric diester hydrolase, and cyclic-nucleotide phosphodiester activities. Moreover, elevated expression of in tumors with high levels of suggests a link between these genes.

CONCLUSION

Our data revealed that may have a considerable role in CRC progression. However, further functional analyses are essential to evaluate the probable role of as a potential diagnostic marker and its potential role in the dysregulation of cyclic nucleotide phosphodiesterase genes in CRC.