Genome‐wide analysis of long noncoding RNA (lncRNA) expression in colorectal cancer tissues from patients with liver metastasis

Abstract

The liver is the most frequent site of metastasis in colorectal cancer (CRC), in which long noncoding RNAs (lncRNAs) may play a crucial role. In this study, we performed a genome‐wide analysis of lncRNA expression to identify novel targets for the further study of liver metastasis in CRC. Samples obtained from CRC patients were analyzed using Arraystar human 8 × 60K lncRNA/mRNA v3.0 microarrays chips to find differentially expressed lncRNAs and mRNAs. The results were confirmed by quantitative reverse transcription‐polymerase chain reaction (qRT‐PCR). The differentially expressed lncRNAs and mRNAs were identified through fold change filtering. Gene ontology (GO) and pathway analyses were performed using standard enrichment computational methods. In the CRC tissues from patients with liver metastasis, 2636 lncRNAs were differentially expressed, including 1600 up‐regulated and 1036 down‐regulated over two‐fold compared with the CRC tissues without metastasis. Among the 1584 differentially expressed mRNAs, 548 were up‐regulated and 1036 down‐regulated. GO and pathway analysis of the up‐regulated and down‐regulated mRNAs yielded different results. The up‐regulated mRNAs were associated with single‐organism process (biological process), membrane part (cellular component), and transporter activity (molecular function), whereas the down‐regulated mRNAs were associated with cellular process, membrane, and binding, respectively. In the pathway analysis, 27 gene pathways associated with the up‐regulated mRNAs and 51 gene pathways associated with the down‐regulated mRNAs were targeted. The significant changes in NQO2 (NM_000904) mRNA and six associated lncRNAs were selected for validation by qRT‐PCR. Aberrantly expressed lncRNAs may play an important role in the liver metastasis of CRC. The further study can provide useful insights into the biology and, ultimately, the prevention of liver metastasis.

Transcriptome analysis in primary colorectal cancer tissues from patients with and without liver metastases using next‐generation sequencing

“…Advanced bioinformatics tool could help us to understand the roles of these DEGs. In terms of Gene Ontology, one of the top terms associated with biological process is single‐organism process, which agrees with a previous study by Chen and colleagues , whereas in the molecular function analysis, binding is another term shared between this study and the previous study . This consistency not only suggests that most DEGs contribute to these two common processes, but also enhanced the credibility of both studies.…”

“…This consistency not only suggests that most DEGs contribute to these two common processes, but also enhanced the credibility of both studies. For the KEGG pathways, cytokine‐cytokine receptor interaction, CAMs, PI3K‐Akt signaling pathway, Leishmaniasis, and rheumatoid arthritis were also identified in the previous study . Among these, the PI3K‐Akt pathway is recognized as a carcinogenesis‐related pathway, which is also the pathway shared by two validated DEGs, OSM and SPP1, suggesting that the PI3K‐Akt pathway is very significant .…”

Meta-signature LncRNAs serve as novel biomarkers for colorectal cancer: integrated bioinformatics analysis, experimental validation and diagnostic evaluation

“…This may attribute to the limitations of data mining algorithm and different test methods mentioned in many related reports5556. The qRT-PCR results of cell lines basically corresponded to microarray data.…”

LINC00312 represses proliferation and metastasis of colorectal cancer cells by regulation of miR‐21

“…Zhu et al reported that LINC00312 inhibits cell proliferation and promotes apoptosis via HOXA5 in non‐small cell lung cancer . A recent study has shown that LINC00312 is down‐regulated in CRC tissues with metastasis compared with CRC tissues without metastasis by miRNA microarray analysis, suggesting that LINC00312 may be involved in CRC progression. Here, our results show that LINC00312 is significantly down‐regulated in CRC tissues and cell lines.…”