Abstract
BackgroundFew diagnostic and prognostic biomarkers are available for head-and-neck squamous cell carcinoma (HNSCC). Long non-coding RNAs (lncRNAs) have shown promise as biomarkers in other cancer types and in some cases functionally contribute to tumor development and progression. Here, we searched for lncRNAs useful as biomarkers in HNSCC.MethodsPublic datasets were mined for lncRNA candidates. Two independent HNSCC tissue sets and a bladder cancer tissue set were analyzed by RT-qPCR. Effects of lncRNA overexpression or downregulation on cell proliferation, clonogenicity, migration and chemosensitivity were studied in HNSCC cell lines.ResultsData mining revealed prominently CASC9, a lncRNA significantly overexpressed in HNSCC tumor tissues according to the TCGA RNAseq data. Overexpression was confirmed by RT-qPCR analyses of patient tissues from two independent cohorts. CASC9 expression discriminated tumors from normal tissues with even higher specificity than HOTAIR, a lncRNA previously suggested as an HNSCC biomarker. Specificity of HNSCC detection by CASC9 was further improved by combination with HOTAIR. Analysis of TCGA pan-cancer data revealed significant overexpression of CASC9 across different other entities including bladder, liver, lung and stomach cancers and especially in squamous cell carcinoma (SCC) of the lung. By RT-qPCR analysis we furthermore detected stronger CASC9 overexpression in pure SCC of the urinary bladder and mixed urothelial carcinoma with squamous differentiation than in pure urothelial carcinomas. Thus, CASC9 might represent a general diagnostic biomarker and particularly for SCCs. Unexpectedly, up- or downregulation of CASC9 expression in HNSCC cell lines with low or high CASC9 expression, respectively, did not result in significant changes of cell viability, clonogenicity, migration or chemosensitivity.ConclusionsCASC9 is a promising biomarker for HNSCC detection. While regularly overexpressed, however, this lncRNA does not seem to act as a major driver of development or progression in this tumor.
Highlights
Few diagnostic and prognostic biomarkers are available for head-and-neck squamous cell carcinoma (HNSCC)
Prominent examples of such Long non-coding RNA (lncRNA) are TINCR, which contributes to keratinocyte differentiation [4], and HOTAIR, which is overexpressed in different cancer types, including head- and -neck squamous cell carcinoma (HNSCC) [5], and is typically associated with increased proliferation and migration of tumor cells
To identify lncRNAs deregulated in HNSCC, we interrogated data published by Zou et al [9] and public data from the TCGA consortium via the TANRIC database
Summary
Few diagnostic and prognostic biomarkers are available for head-and-neck squamous cell carcinoma (HNSCC). Long non-coding RNAs (lncRNAs) have shown promise as biomarkers in other cancer types and in some cases functionally contribute to tumor development and progression. Long non-coding RNAs (lncRNAs) have moved into the focus of cancer research as good candidates for tumor biomarkers and as regulators of various neoplastic cell properties. Dysregulation of lncRNA expression has been reported for different cancer types and may contribute to tumor development and progression [2, 3] Prominent examples of such lncRNAs are TINCR, which contributes to keratinocyte differentiation [4], and HOTAIR, which is overexpressed in different cancer types, including head- and -neck squamous cell carcinoma (HNSCC) [5], and is typically associated with increased proliferation and migration of tumor cells
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