Open AccessExpression profiling of long noncoding RNA identifies lnc‐ MMP 3‐1 as a prognostic biomarker in external auditory canal squamous cell carcinoma
Author(s) -
Liu Hong,
Dai Chunfu,
Wu Qianru,
Liu Hongyan,
Li Feitian
Publication year - 2017
Publication title -
cancer medicine
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.403
H-Index - 53
ISSN - 2045-7634
DOI - 10.1002/cam4.1213
Subject(s) - rna , transcriptome , biology , microrna , microarray , long non coding rna , gene expression , microarray analysis techniques , fold change , cancer research , gene expression profiling , dna microarray , gene , microbiology and biotechnology , genetics
Abstract Our previous studies suggested external auditory canal squamous cell carcinoma ( EACSCC ) is a rare malignancy with heterogeneous outcomes. This study aimed to identify lnc RNA profile of EACSCC and determine the clinical application. Differential expression genes ( DEG s) were investigated in EACSCC by whole transcriptome lnc RNA arrays ( GPL 23178). RT ‐ PCR was used to quantify the microarray data. Bioinformatics analyses were performed to evaluate DEG s regulations in gene ontology and cellular pathways. Fluorescence in situ hybridization ( FISH ) was utilized to validate lnc RNA expression. The overall survival was determined by Kaplan–Meier and log‐rank analyses. Our microarrays data had been submitted to Gene Expression Omnibus ( GSE 98912). We identified 5621 DEG s (3185 mRNA s, 2436 lnc RNA s) in EACSCC . Lnc‐ MMP 3‐1 was the top one upregulated lnc RNA in EACSCC with fold change of 237.2 ( P < 0.001). RT ‐ PCR results showed similar expression levels as microarrays data. Bioinformatics analyses indicated development of EACSCC was involved in aberrant alternations of multiple biological processes and cellular pathways. FSIH assays also found lnc‐ MMP 3‐1 was significantly differentially overexpressed in EACSCC ( P < 0.001). Tumor lnc‐ MMP 3‐1 levels were closely associated with differentiation degree ( P = 0.016), tumor invasion ( P = 0.015) and TNM stage ( P = 0.015). Moreover, lnc‐ MMP 3‐1 expression was a significant prognostic factor in EACSCC ( χ 2 = 4.276, P = 0.039). The study is the first screening and analysis of lnc RNA s profile in EACSCC and provides new insights into pathogenesis of this rare disease. Our findings offered convincing evidences that lnc‐ MMP 3‐1 is a novel survival predictor of EACSCC patients.