Heterogeneous expression of long noncoding RNA RP۱۱-۱۰۹D۲۰.۲: Insights into regulatory gene expression roles in colon cancer

Objective(s): 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 PRJEB۲۷۵۳۶) of CRC samples and normal adjacent tissues were reanalyzed using the DESeq۲ 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 RP۱۱-۱۰۹D۲۰.۲ (lnc-Duox۲-۱:۱) was assessed in fresh/frozen tissues obtained from ۴۶ CRC patients by quantitative RT-PCR. Results: A total of ۱۷۹۳۹ DElncRNAs were identified between CRC and normal tissues via bioinformatics analyses. A significant up-regulation of RP۱۱-۱۰۹D۲۰.۲ (۴۸%) was observed in CRC samples. Functional enrichment analysis showed that RP۱۱-۱۰۹D۲۰.۲ was mainly related to pathways like phosphoric ester hydrolase, oxidoreductase, phosphoric diester hydrolase, and cyclic-nucleotide phosphodiester activities. Moreover, elevated expression of DUOX۲ in tumors with high levels of RP۱۱-۱۰۹D۲۰.۲ suggests a link between these genes.Conclusion: Our data revealed that RP۱۱-۱۰۹D۲۰.۲ may have a considerable role in CRC progression. However, further functional analyses are essential to evaluate the probable role of RP۱۱-۱۰۹D۲۰.۲ as a potential diagnostic marker and its potential role in the dysregulation of cyclic nucleotide phosphodiesterase genes in CRC.

Keywords:

Biomarker , Colorectal cancer , Gene expression profiling , Long noncoding RNA RP۱۱-۱۰۹D۲۰.۲ , RNA sequencing analysis