A RNA-Sequencing approach for the identification of novel long non-coding RNA biomarkers in colorectal cancer

Long non-coding RNAs (lncRNAs) have been implicated in human pathology, however, their role in colorectal carcinogenesis have not been fully elucidated. In the current study, researchers from Baylor Scott & White Research Institute performed whole-transcriptome analysis in 3 pairs of colorectal cancer (CRC) and matched normal mucosa (NM) by RNA sequencing (RNA-seq). Followed by confirmation using the Cancer Genome Atlas (TCGA) dataset, the researchers identified 27 up-regulated and 22 down-regulated lncRNAs in CRC. Up-regulation of four lncRNAs, hereby named colorectal cancer associated lncRNA (CRCAL)-1 [AC021218.2], CRCAL-2 [LINC00858], CRCAL-3 [RP11-138J23.1] and CRCAL-4 [RP11-435O5.2], was further validated by real-time RT-PCR in 139 colorectal neoplasms and matched NM tissues. Knockdown of CRCAL-3 and CRCAL-4 in colon cancer cells reduced cell viability and colony formation ability, and induced cell cycle arrest. TCGA dataset supported the associations of CRCAL-3 and CRCAL-4 with cell cycle and revealed a co-expression network comprising dysregulated lncRNAs associated with protein-coding genes.

rna-seq

(a) Heatmap generated by RNA-seq data from our own sequencing (left) and TCGA (right) datasets showing the distinct expression pattern of lncRNAs in CRC and matched NM tissues. (b,c) Sequence information of RNA-seq data was visualized by IGV. Each row indicates paired colonic samples including CRC and matched NM from three patients. The vertical axis represents sequence reads at particular chromosomal position where the scale was large (0–1000) or small (0–5). While the reads for CRCAL-2 [LINC00858] (blue triangle) cannot be recognized with the large scale, nearby protein-coding genes, GHITM and C10orf99 (red triangles), showed abundant read counts (b). Although sequence reads for CRCAL-2 (blue arrow heads) was modest, its up-regulation was visible with the small scale (c).

RNA-seq identified numbers of novel lncRNAs dysregulated in CRC. In vitro experiments and GO term enrichment analysis indicated the functional relevance of CRCAL-3 and CRCAL-4 in association with cell cycle. These data highlight the capability of RNA-seq to discover novel lncRNAs involved in human carcinogenesis, which may serve as alternative biomarkers and/or molecular treatment targets.

Yamada A, Yu P, Lin W, Okugawa Y, Boland CR, Goel A. (2018) A RNA-Sequencing approach for the identification of novel long non-coding RNA biomarkers in colorectal cancer. Sci Rep 8(1):575. [article]

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