LncRNA profile study reveals a three-lncRNA signature associated with the survival of patients with oesophageal squamous cell carcinoma

Abstract

BackgroundOesophageal cancer is one of the most deadly forms of cancer worldwide. Long non-coding RNAs (lncRNAs) are often found to have important regulatory roles.ObjectiveTo assess the lncRNA expression profile of oesophageal squamous cell carcinoma (OSCC) and identify prognosis-related lncRNAs.MethodLncRNA expression profiles were studied by microarray in paired tumour and normal tissues from 119 patients with OSCC and validated by qRT-PCR. The 119 patients were divided randomly into training (n=60) and test (n=59) groups. A prognostic signature was developed from the training group using a random Forest supervised classification algorithm and a nearest shrunken centroid algorithm, then validated in a test group and further, in an independent cohort (n=60). The independence of the signature in survival prediction was evaluated by multivariable Cox regression analysis.ResultsLncRNAs showed significantly altered expression in OSCC tissues. From the training group, we identified a three-lncRNA signature (including the lncRNAs ENST00000435885.1, XLOC_013014 and ENST00000547963.1) which classified the patients into two groups with significantly different overall survival (median survival 19.2 months vs >60 months, p<0.0001). The signature was applied to the test group (median survival 21.5 months vs >60 months, p=0.0030) and independent cohort (median survival 25.8 months vs >48 months, p=0.0187) and showed similar prognostic values in both. Multivariable Cox regression analysis showed that the signature was an independent prognostic factor for patients with OSCC. Stratified analysis suggested that the signature was prognostic within clinical stages.ConclusionsOur results suggest that the three-lncRNA signature is a new biomarker for the prognosis of patients with OSCC, enabling more accurate prediction of survival.

A genome‐wide analysis of long noncoding RNA profile identifies differentially expressed lncRNAs associated with Esophageal cancer

“…Four public esophageal cancer microarray profiling datasets (GSE45670,23 GSE53622,12 GSE89102, GSE92396) were downloaded from the Gene Expression Omnibus (GEO). lncRNAs profiling of GEO microarray datasets was annotated and analyzed based on the Affymetrix Human Genome U133 Plus 2.0 Array and U133A Array, Agilent‐038314 CBC Homo sapiens lncRNA + mRNA microarray V2.0, Agilent‐045997 Arraystar human lncRNA microarray V3, and Affymetrix Human Gene 1.0 ST Array platforms.…”

“…To date, increasing evidence have demonstrated that lncRNAs are widely expressed in most of organ tissues, and participate in various cellular biological process, including X chromatin imprinting, muscle cells differentiation, immune response, cell fate decision, tumor cell proliferation, and drug resistance 10, 11. Importantly, RNA sequencing and microarray analyses of tumor and normal tissues in diverse types of human cancers revealed that thousands of lncRNAs are dysregulated in cancer tissues, and part of these lncRNAs are emerging as key molecules during carcinogenesis 12, 13. lncRNAs involve in the tumorigenesis by functioning as oncogenes or tumor suppressors through chromatin remodeling, histone modification, acting as sponge for microRNAs, and affecting RNA stability 14, 15.…”

Upregulated GAPLINC predicts a poor prognosis in bladder cancer patients and promotes tumor proliferation and invasion

“…An increasing amount of evidence has demonstrated that lncRNAs exhibit crucial regulatory roles in the biological processes of cancer, including genomic imprinting, chromatin modification and post-transcriptional processing (7)(8)(9)(10). Increasingly, studies have indicated that lncRNAs may be used as potential prognostic biomarkers and therapeutic targets (11,12). Gastric adenocarcinoma-associated, positive CD44 regulator, long intergenic noncoding RNA (GAPLINC) has been demonstrated to be aberrantly expressed in gastric and colorectal cancer (13,14).…”

lncRNA uc009yby.1 promotes renal cell proliferation and is associated with poor survival in patients with clear cell renal cell carcinomas

“…Furthermore, the function of uc009yby.1 in renal cells was investigated using two siRNAs to inhibit uc009yby.1 expression, revealing that this lncRNA could enhance renal cell proliferation; this suggests that uc009yby.1 may be a novel therapeutic target for ccRCC. Numerous studies have indicated that certain lncRNAs have aberrant expression profiles in various kinds of tumors, such as gastric (15)(16)(17), colon (18,19), esophageal (20)(21)(22) and liver (23) cancers. Yu et al (12) recently reported on a class of lncRNAs that are aberrantly expressed in ccRCC cells, in which multiple lncRNAs were upregulated.…”