Tian Suyan, Wang Chi, Zhang Jing, Yu Dan
Division of Clinical Research, The First Hospital of Jilin University, 1Xinmin Street, Changchun, Jilin, 130021, People's Republic of China.
Department of Biostatistics, College of Public Health, University of Kentucky, 800 Rose St, Lexington, KY, 40536, USA.
BMC Med Genomics. 2020 Feb 5;13(1):18. doi: 10.1186/s12920-020-0691-4.
The most common histological subtypes of esophageal cancer are squamous cell carcinoma (ESCC) and adenocarcinoma (EAC). It has been demonstrated that non-marginal differences in gene expression and somatic alternation exist between these two subtypes; consequently, biomarkers that have prognostic values for them are expected to be distinct. In contrast, laryngeal squamous cell cancer (LSCC) has a better prognosis than hypopharyngeal squamous cell carcinoma (HSCC). Likewise, subtype-specific prognostic signatures may exist for LSCC and HSCC. Long non-coding RNAs (lncRNAs) hold promise for identifying prognostic signatures for a variety of cancers including esophageal cancer and head and neck squamous cell carcinoma (HNSCC).
In this study, we applied a novel feature selection method capable of identifying specific prognostic signatures uniquely for each subtype - the Cox-filter method - to The Cancer Genome Atlas esophageal cancer and HSNCC RNA-Seq data, with the objectives of constructing subtype-specific prognostic lncRNA expression signatures for esophageal cancer and HNSCC.
By incorporating biological relevancy information, the lncRNA lists identified by the Cox-filter method were further refined. The resulting signatures include genes that are highly related to cancer, such as H19 and NEAT1, which possess perfect prognostic values for esophageal cancer and HNSCC, respectively.
The Cox-filter method is indeed a handy tool to identify subtype-specific prognostic lncRNA signatures. We anticipate the method will gain wider applications.
食管癌最常见的组织学亚型是鳞状细胞癌（ESCC）和腺癌（EAC）。已经证明，这两种亚型之间在基因表达和体细胞改变方面存在非边缘差异；因此，预计对它们具有预后价值的生物标志物会有所不同。相比之下，喉鳞状细胞癌（LSCC）的预后比下咽鳞状细胞癌（HSCC）好。同样，LSCC和HSCC可能存在亚型特异性的预后特征。长链非编码RNA（lncRNA）有望为包括食管癌和头颈部鳞状细胞癌（HNSCC）在内的多种癌症识别预后特征。
在本研究中，我们将一种能够为每个亚型独特地识别特定预后特征的新型特征选择方法——Cox过滤法——应用于癌症基因组图谱食管癌和HSNCC的RNA测序数据，目的是构建食管癌和HNSCC的亚型特异性预后lncRNA表达特征。
通过纳入生物学相关性信息，对Cox过滤法识别出的lncRNA列表进行了进一步细化。所得特征包括与癌症高度相关的基因，如H19和NEAT1，它们分别对食管癌和HNSCC具有完美的预后价值。
Cox过滤法确实是一种识别亚型特异性预后lncRNA特征的便捷工具。我们预计该方法将得到更广泛的应用。
