Analysis of long non-coding RNA expression profiles in gastric cancer

Abstract

AIM:To investigate the expression patterns of long non-coding RNAs (lncRNAs) in gastric cancer. METHODS:Two publicly available human exon arrays for gastric cancer and data for the corresponding normal tissue were downloaded from the Gene Expression Omnibus (GEO). We re-annotated the probes of the human exon arrays and retained the probes uniquely mapping to lncRNAs at the gene level. LncRNA expression profiles were generated by using robust multi-array average method in affymetrix power tools. The normalized data were then analyzed with a Bioconductor package linear models for microarray data and genes with adjusted P -values below 0.01 were considered differentially expressed. An independent data set was used to validate the results. RESULTS:With the computational pipeline established to re-annotate over 6.5 million probes of the Affymetrix Human Exon 1.0 ST array, we identified 136053 probes uniquely mapping to lncRNAs at the gene level. These probes correspond to 9294 lncRNAs, covering nearly 76% of the GENCODE lncRNA data set. By analyzing GSE27342 consisting of 80 paired gastric cancer and normal adjacent tissue samples, we identified 88 lncRNAs that were differentially expressed in gastric cancer, some of which have been reported to play a role in cancer, such as LINC00152, taurine upregulated 1, urothelial cancer associated 1, Pvt1 oncogene, small nucleolar RNA host gene 1 and LINC00261. In the validation data set GSE33335, 59% of these differentially expressed lncRNAs showed significant expression changes (adjusted P -value < 0.01) with the same direction. CONCLUSION:We identified a set of lncRNAs differentially expressed in gastric cancer, providing useful information for discovery of new biomarkers and therapeutic targets in gastric cancer. © 2013 Baishideng. All rights reserved.Key words: Long non-coding RNA; Gastric cancer; Microarray analysis; Data mining Core tip: Long non-coding RNAs (lncRNAs) have risen to prominence with important roles in a broad range of biological processes. LncRNA expression patterns and their biological functions in gastric cancer still remain unknown. We re-annotated the probes from an Affymetrix Human Exon 1.0 ST array and identified probes uniquely mapping to lncRNAs at the gene level. These probes correspond to 9294 lncRNAs, covering nearly 76% of the GENCODE lncRNA data set. We identified a set of lncRNAs that were differentially expressed in gastric cancer. In an independent data set, 59% of these differentially expressed lncRNAs showed significant expression changes with the same direction.

Long Noncoding RNA GAPLINC Regulates CD44-Dependent Cell Invasiveness and Associates with Poor Prognosis of Gastric Cancer

“…Despite the above findings, our current knowledge about the expression patterns and functional roles of lncRNAs in gastric cancer is still limited. In previous studies, efforts have been made to reannotate the probes of Affymetrix microarrays that match lncRNA sequences in several cancers, including gastric cancer (25). However, this method covers less than 65% of lncRNA genes, and thus should not be considered as unbiased analysis.…”

Transcriptome sequencing reveals altered long intergenic non-coding RNAs in lung cancer

“…However, for the first time we were able to identify solid tumorassociated lncRNAs not previously implicated in lung cancer as well as uncharacterized lncRNAs altered in lung cancer. For example, linc-UBC1 (LCAL6) was discovered in bladder cancer [32]; UCA1 (LCAL52) in bladder [33], ovarian [46] and breast cancer [47]; LINC00261 (LCAL62) in gastric cancer [31]; ESCCAL-1 (LCAL80) [30] and ENST00000547963 (LCAL84) [34] in esophageal squamous cell carcinoma; CCAT1 (LCAL85) in colon cancer [29]; and PART1 (LCAL92) in prostate cancer [35] and glioblastoma multiforme [48]. Overall, these findings emphasize the importance of unbiased sequencing approaches to better understand the non-coding RNA landscape of cancer.…”

“…The 111 LCALs include a lncRNA known to play a role in lung cancer (SCAL1 [16]), cancer-associated lncRNAs not previously implicated in lung cancer (CCAT1 [29], ESC-CAL-1 [30], LINC00261 [31], linc-UBC1 [32], UCA1 [33], ENST00000547963 [34], and PART-1 [35]), a lncRNA implicated in a lethal lung developmental disorder (FENDRR [36]), and three previously unannotated lncRNAs. Interestingly, the remaining 99 lncRNAs were previously annotated in normal human tissues but not implicated in human disease.…”

TM4SF5-CTD-2354A18.1-miR-4697-3P may play a key role in the pathogenesis of gastric cancer

“…More and more evidence has proved lncRNAs and mRNAs, which may be the most important factors, to result in gastric cancer (10,27,28). Therefore, we evaluated the lncRNAs and mRNAs expression profiles in gastric cancer tissue and corresponding non-tumorous tissues in patients, which was to reveal the potential role of lncRNAs and mRNAs in the pathogenesis of gastric cancer.…”

“…Ji-hang Yuan et al (9) observed that the lncRNA-activated by TGF-β (lncRNA-ATB) was up-regulated in hepatocellular carcinoma (HCC) metastases and associated with poor prognosis. Wei-Jun Cao et al (10) identifi ed a set of lncRNAs differentially expressed in gastric cancer by microarray. Qianqian Pang et al (11) showed that the expression level of LINC00152 in gastric carcinoma was signifi cantly increased, compared with matched normal tissue and normal mucosa from healthy controls.…”