BACKGROUND 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). METHODS 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. RESULTS 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. CONCLUSIONS The Cox-filter method is indeed a handy tool to identify subtype-specific prognostic lncRNA signatures. We anticipate the method will gain wider applications.

中文翻译：

---

cox-filter 方法可识别两种人类癌症各自亚型特异性的 lncRNA 预后特征。

背景技术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，这两种亚型之间存在基因表达和体细胞交替的非边际差异；因此，对他们具有预后价值的生物标志物预计是不同的。相比之下，喉鳞状细胞癌（LSCC）的预后优于下咽鳞状细胞癌（HSCC）。同样，LSCC 和 HSCC 可能存在亚型特异性预后特征。长非编码 RNA (lncRNA) 有望识别多种癌症的预后特征，包括食管癌和头颈鳞状细胞癌 (HNSCC)。方法在这项研究中，我们将一种新颖的特征选择方法应用于癌症基因组图谱食管癌和 HSNCC RNA-Seq 数据，该方法能够识别每种亚型独特的特定预后特征 - Cox 过滤方法，目的是构建亚型 -食管癌和 HNSCC 的特异性预后 lncRNA 表达特征。结果通过整合生物相关性信息，Cox-filter方法识别的lncRNA列表得到进一步细化。由此产生的特征包括与癌症高度相关的基因，例如 H19 和 NEAT1，它们分别对食管癌和 HNSCC 具有完美的预后价值。结论 Cox-filter 方法确实是识别亚型特异性预后 lncRNA 特征的便捷工具。我们预计该方法将获得更广泛的应用。