Head and neck squamous cell carcinoma (
HNSCC) is an aggressive epithelial
malignancy characterized by frequent mutations and
metastasis. Long noncoding RNAs (lncRNAs) have been implicated in
tumorigenesis and serve as novel prognostic
biomarkers in different
cancers. To enhance our understanding of lncRNAs that may have
biological significance in
HNSCC and may serve as prognostic
biomarkers, we globally profiled lncRNAs in
HNSCC by analyzing the
RNA-seq data from The Atlas of Noncoding RNAs in
Cancer (TANRIC) database. Of 3576 lncRNAs, we identified 926 (higher-688, lower-238) lncRNAs with a 2-fold abundance difference among the forty
HNSCC and paired adjacent normal tissue. We investigated differential abundance of lncRNAs based on TP53 mutation and p16 status. We found 133 lncRNAs to have differential abundance by 2-fold among the mutant vs wild-type TP53 samples, whereas among p16-negative vs positive samples, we identified 710 lncRNAs with the same criteria. Meanwhile, analysis of the 15 most abundant lncRNAs in the
tumor samples identified five lncRNAs whose higher abundance was associated with poor overall patient survival. Among these five, higher abundance of LINC00460 associated with poor patient survival in an independent cohort of 82
HNSCC patients. To further evaluate the potential function of LINC00460, we performed
lncRNA-mRNAs co-expression analysis and found that higher abundance of LINC00460 associated with
cancer-related
biological pathways including EMT and other inflammatory response pathways. In summary, we report LINC00460 is more abundant in
tumors compared to adjacent normal tissue and that it may serve as a potential prognostic
biomarker in
HNSCC.