Systematic Analysis and Identification of Dysregulated Panel lncRNAs Contributing to Poor Prognosis in Head-Neck Cancer

Abstract

Head and neck cancer (HNC) is one of the most prevalent cancers worldwide, accounting for approximately 5% of all cancers. While the underlying molecules and their pathogenetic mechanisms in HNC have yet to be well elucidated, recent studies have shown that dysregulation of lncRNAs may disrupt the homeostasis of various biological pathways. However, the understanding of lncRNAs in HNC is still limited by the lack of expression profiling. In the present study, we employed a systematic strategy to identify a panel of lncRNA associated with HNC. A cancer-related lncRNA profile PCR array was screened to explore potential molecules specific for HNC. A total of 55 lncRNAs were found to be dysregulated in HNC cells when compared to normal keratinocytes. Further analysis of the prognostic significance using The Cancer Genome Atlas (TCGA) database revealed 15 lncRNAs highly correlated with overall survival in HNC patients. Additionally, clinical sample expression analysis of the TCGA-HNSC cohort revealed 16 highly dysregulated lncRNAs in HNC, resulting in a combined 31-lncRNA signature panel that could predict prognosis. Validation of these molecules confirmed the considerable level of altered expressions in HNC cells, with XIST, HOXA11-AS, TSIX, MALAT1, WT1-AS, and IPW being the most prominently dysregulated. We further selected a molecule from our panel (XIST) to confirm the validity of these lncRNAs in the regulation of cancer aggressiveness. Gene ontology (GO) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analyses demonstrated that XIST participated in various cancer-related functions, including cell proliferation and metastasis. XIST silencing with the RNAi technique substantially reduced invasion and migration in several HNC cell lines. Thus, our study defined a 31-lncRNA panel as prognostic signatures in HNC. These perspective results provide a knowledge foundation for further application of these molecules in precision medicine.

Molecular Signature of Long Non-Coding RNA Associated with Areca Nut-Induced Head and Neck Cancer

“…However, these arrays allow sensitive, specific, and rapid data analysis. Previous studies have reported the use of PCR arrays to analyze genes in specific diseases, such as cancers [ 33 ]. In this study, we employed a PCR-based array to analyze 84 cancer-associated lncRNAs in areca nut-treated HNC cells.…”

“…The Human Cancer PathwayFinder RT2 PCR array system consisting of 84 cancer-related lncRNA assays was used for lncRNA screening (QIAGEN GmbH, Hilden, Germany). The lncRNA PCR array was performed according to the manufacturer’s protocol as previously described [ 33 ]. Briefly, cell pellets were harvested, washed with PBS, and subjected to RNA isolation using TRIzol reagent (Life Technologies, Carlsbad, CA, USA).…”

“…The expression level of each lncRNA was analyzed by the RT-qPCR as previously described [ 33 ]. Briefly, total RNA was extracted using the TRIzol reagent (Life Technologies).…”

“…Based on this dataset, several lncRNA profiles associated with specific carcinogenic attributes were constructed. These include the effects of alcohol consumption [ 26 ], human papillomavirus infection [ 27 ], immunity or tumor microenvironment [ 28 , 29 ], and their association with prognosis [ 29 , 30 , 31 , 32 , 33 ]. However, most studies solely analyzed big data without further experimental validation, which may limit the pathological insight of candidate molecules.…”

An Axis between the Long Non-Coding RNA HOXA11-AS and NQOs Enhances Metastatic Ability in Oral Squamous Cell Carcinoma

“…Oncogenic lncRNAs, which are upregulated in cancer, are expected to be diagnostic markers, prognostic factors, and even novel therapeutic molecular targets [43]. HOXA11AS is one of the 16 most dysregulated lncRNAs in head and neck cancer and has attracted attention as a therapeutic target [44]. Attempts to apply lncRNA targeting to therapy have included the use of antisense oligonucleotides and small molecules to block the functional interactions between lncRNAs and proteins, and inactivation of lncRNA-encoding genes and the transcripts based on the CRISPR-Cas system are under development [45].…”