Open AccessGenome‐wide analysis of long noncoding RNA (lnc RNA ) expression in colorectal cancer tissues from patients with liver metastasis
Author(s) -
Chen Dong,
Sun Qiang,
Cheng Xiaofei,
Zhang Lufei,
Song Wei,
Zhou Dongkai,
Lin Jianjiang,
Wang Weilin
Publication year - 2016
Publication title -
cancer medicine
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.403
H-Index - 53
ISSN - 2045-7634
DOI - 10.1002/cam4.738
Subject(s) - biology , messenger rna , rna , long non coding rna , gene expression , metastasis , dna microarray , gene , microarray analysis techniques , microbiology and biotechnology , cancer research , cancer , genetics
The liver is the most frequent site of metastasis in colorectal cancer ( CRC ), in which long noncoding RNA s (lnc RNA s) may play a crucial role. In this study, we performed a genome‐wide analysis of lnc RNA 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 lnc RNA / mRNA v3.0 microarrays chips to find differentially expressed lnc RNA s and mRNA s. The results were confirmed by quantitative reverse transcription‐polymerase chain reaction ( qRT ‐ PCR ). The differentially expressed lnc RNA s and mRNA s 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 lnc RNA s 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 mRNA s, 548 were up‐regulated and 1036 down‐regulated. GO and pathway analysis of the up‐regulated and down‐regulated mRNA s yielded different results. The up‐regulated mRNA s were associated with single‐organism process (biological process), membrane part (cellular component), and transporter activity (molecular function), whereas the down‐regulated mRNA s were associated with cellular process, membrane, and binding, respectively. In the pathway analysis, 27 gene pathways associated with the up‐regulated mRNA s and 51 gene pathways associated with the down‐regulated mRNA s were targeted. The significant changes in NQO 2 ( NM _000904) mRNA and six associated lnc RNA s were selected for validation by qRT ‐ PCR . Aberrantly expressed lnc RNA s 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.