School of Life Sciences, University of Science and Technology of China, Hefei 230026, China.
College of Liren, Yanshan University, Qinhuangdao 066004, China.
J Zhejiang Univ Sci B. 2018;19(9):674-688. doi: 10.1631/jzus.B1700319.
In this study, we aimed to expand current knowledge of head and neck squamous cell carcinoma (HNSCC)-associated long noncoding RNAs (lncRNAs), and to discover potential lncRNA prognostic biomarkers for HNSCC based on next-generation RNA-seq.
RNA-seq data of 546 samples from patients with HNSCC were downloaded from The Cancer Genome Atlas (TCGA), including 43 paired samples of tumor tissue and adjacent normal tissue. An integrated analysis incorporating differential expression, weighted gene co-expression networks, functional enrichment, clinical parameters, and survival analysis was conducted to discover HNSCC-associated lncRNAs. The function of CYTOR was verified by cell-based experiments. To further identify lncRNAs with prognostic significance, a multivariate Cox proportional hazard regression analysis was performed. The identified lncRNAs were validated with an independent cohort using clinical feature relevance analysis and multivariate Cox regression analysis.
We identified nine HNSCC-relevant lncRNAs likely to play pivotal roles in HNSCC onset and development. By functional enrichment analysis, we revealed that CYTOR might participate in the multistep pathological processes of cancer, such as ribosome biogenesis and maintenance of genomic stability. CYTOR was identified to be positively correlated with lymph node metastasis, and significantly negatively correlated with overall survival (OS) and disease free survival (DFS) of HNSCC patients. Moreover, CYTOR inhibited cell apoptosis following treatment with the chemotherapeutic drug diamminedichloroplatinum (DDP). HCG22, the most dramatically down-regulated lncRNA in tumor tissue, may function in epidermis differentiation. It was also significantly associated with several clinical features of patients with HNSCC, and positively correlated with patient survival. CYTOR and HCG22 maintained their prognostic values independent of several clinical features in multivariate Cox hazards analysis. Notably, validation either based on an independent HNSCC cohort or by laboratory experiments confirmed these findings.
Our transcriptomic analysis suggested that dysregulation of these HNSCC-associated lncRNAs might be involved in HNSCC oncogenesis and progression. Moreover, CYTOR and HCG22 were confirmed as two independent prognostic factors for HNSCC patient survival, providing new insights into the roles of these lncRNAs in HNSCC as well as clinical applications.
本研究旨在通过下一代 RNA 测序，扩展对头颈鳞状细胞癌（HNSCC）相关长链非编码 RNA（lncRNA）的认识，并发现潜在的 HNSCC 预后 lncRNA 生物标志物。
从癌症基因组图谱（TCGA）下载了 546 例 HNSCC 患者的 RNA-seq 数据，包括 43 对肿瘤组织和相邻正常组织样本。通过差异表达、加权基因共表达网络、功能富集、临床参数和生存分析的综合分析，发现与 HNSCC 相关的 lncRNA。通过细胞实验验证 CYTOR 的功能。为了进一步鉴定具有预后意义的 lncRNA，进行了多变量 Cox 比例风险回归分析。通过临床特征相关性分析和多变量 Cox 回归分析，在独立队列中验证了鉴定出的 lncRNA。
我们发现了九个可能在 HNSCC 发生和发展中发挥关键作用的 HNSCC 相关 lncRNA。通过功能富集分析，我们揭示了 CYTOR 可能参与癌症的多步病理过程，如核糖体生物发生和基因组稳定性的维持。CYTOR 被确定为与淋巴结转移呈正相关，与 HNSCC 患者的总生存（OS）和无病生存（DFS）显著负相关。此外，在使用化疗药物顺铂（DDP）处理后，CYTOR 抑制细胞凋亡。在肿瘤组织中下调最显著的 lncRNA HCG22，可能在表皮分化中发挥作用。它还与 HNSCC 患者的多个临床特征显著相关，与患者生存呈正相关。在多变量 Cox 危害分析中，CYTOR 和 HCG22 独立于多个临床特征保持其预后价值。值得注意的是，无论是基于独立的 HNSCC 队列的验证还是通过实验室实验均证实了这些发现。
我们的转录组分析表明，这些与 HNSCC 相关的 lncRNA 的失调可能参与 HNSCC 的发生和发展。此外，CYTOR 和 HCG22 被确认为 HNSCC 患者生存的两个独立预后因素，为这些 lncRNA 在 HNSCC 中的作用以及临床应用提供了新的见解。
