The cox-filter method identifies respective subtype-specific lncRNA prognostic signatures for two human cancers

Abstract

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 subtypethe Cox-filter methodto 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.

Model construction and risk analysis of the lncRNA genes associated with the prognosis of esophageal adenocarcinoma with immune infiltration

“…In North America and Europe, including the United States, Canada and the United Kingdom, the incidence of EAC is high (16). However, in recent years, the morbidity and mortality of EAC in China has shown an increasing trend, which has aroused widespread concern (17)(18)(19). Despite continued advances in its diagnosis and treatment, the prognosis of EAC patients remains poor (20).…”

Identification of long non-coding RNA signatures for squamous cell carcinomas and adenocarcinomas

“…PVT1 is a well-known oncogene and correlated with a variety of cancers according to both the lncRNADisease 2.0 knowledgebase and the GeneCards database [ 121 ]. In our previous study [ 122 ], PVT1 was identified as a subtype-specific prognostic gene for esophageal adenocarcinoma using a feature selection algorithm called the Cox-filter method [ 123 ]. In this study, it was identified as a pan AC discriminative gene, which leads us to anticipate that PVT1 may be more relevant to the AC type than the SCC type, even though PVT1 has also been verified in the literature to associate with the SCC cancer type such as esophageal squamous cell carcinoma [ 124 ].…”

“…Of the pan-AC prognostic lncRNAs, MALAT1 is a well-known oncogene and has been linked to a variety of cancers so far, including non-small cell lung cancer, cervical cancer, tongue squamous cell carcinomas and gastric cancer. In our previous study [ 122 ], it was identified as a subtype-specific prognostic gene for laryngeal squamous cell carcinoma using the Cox-filter method [ 123 ], further implying its possibility of being a pan-cancer lncRNA.…”

Integrative analysis of Mendelian randomization and gene expression profiles reveals a null causal relationship between adiponectin and diabetic retinopathy

“…The examination of transcriptomic data, such as mRNA molecules, has the potential to elucidate the involvement of specific genes in complex diseases [ 11 ], such as heart disease [ 12 ], lung cancer [ 13 , 14 ], and diabetes [ 15 ]. To date, numerous studies have been conducted to identify relevant gene signatures associated with DR, utilizing transcriptomic data and bioinformatics methods [ 16–19 ].…”