Transcriptome profiling and co-expression network analysis of lncRNAs and mRNAs in colorectal cancer by RNA sequencing

• DOI: 10.1186/s12885-022-09878-6
• Publication Date: 2022-07-16T22:02:28Z
• Authors: Mingjie Li; Dandan Guo; Xijun Chen; Xinxin Lu; Xiaoli Huang; Yan’an Wu
• Keywords: Sequence Analysis, RNA; Research; Gene Expression Profiling; RNA-sequencing; Neoplasms. Tumors. Oncology. Including cancer and carcinogens; Colorectal cancer; Co-expression; 3. Good health; Gene Expression Regulation, Neoplastic; Phosphatidylinositol 3-Kinases; 03 medical and health sciences; lncRNA; 0302 clinical medicine; Humans; Gene Regulatory Networks; RNA, Long Noncoding; RNA, Messenger; Colorectal Neoplasms; Transcriptome; RC254-282

Long non-coding RNAs (lncRNAs) are widely involved in the pathogenesis of cancers. However, biological roles lncRNAs occurrence and progression colorectal cancer (CRC) remain unclear. The current study aimed to evaluate expression pattern messenger (mRNAs).RNA sequencing (RNA-Seq) CRC tissues adjacent normal from 6 patients was performed functional lncRNA-mRNA co-expression network constructed afterwards. Gene enrichment analysis demonstrated using DAVID 6.8 tool. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) used validate differentially expressed lncRNAs. Pearson correlation applied relationships between selected mRNAs.One thousand seven hundred sixteenth mRNAs 311 were screened out. Among these, 568 up-regulated while 1148 down-regulated, similarly 125 186 down-regulated. In addition, 1448 pairs out 940,905 candidate pairs. revealed that these lncRNA-related associated with cell adhesion, collagen differentiation, mainly enriched ECM-receptor interaction PI3K-Akt signaling pathways. Finally, RT-qPCR results verified lncRNAs, as well 60 tissues.In conclusion, RNA-seq bioinformatic strongly suggested dysregulation lncRNA is complicated process development, providing important insight regarding CRC.