Comprehensive characterization of cancer subtype associated long non-coding RNAs and their clinical implications

Abstract

Long non-coding RNAs (lncRNAs) are a kind of RNAs with regulation that participate fundamental cellular processes via diverse mechanisms. Despite the potential importance of lncRNAs in multiple kinds of cancer has been well studied, no comprehensive survey of cancer subtype associated lncRNAs. Here, we performed an array-based transcriptional survey of lncRNAs across 150 lung cancer samples comprising both adenocarcinoma and squamous cell carcinoma, and 306 breast cancer patients with clear clinical information. In lung cancer, 72 lncRNAs are identified to be associated with tumor subtypes and their functions as well as the associated proteins are predicted by constructing coding-non-coding co-expression network. The results suggest that they are mostly related with epidermis development, cell adhesion and response to stimulus. The validation results show the high concordance and confirmed the robust of the identification results. In breast cancer, we found 3 lncRNA genes are associated with estrogen receptor α (ER) positive and ER negative subtypes and tumor histologic grade. Survival (Kaplan-Meier) analysis results suggest that the expression pattern of the 3 lncRNAs is significantly correlated with clinical outcomes. The current study provides the first large-scale survey of lncRNAs within cancer subtypes, and may offer new targets for their diagnosis, therapy and prognosis.

Long Non-Coding RNAs and Their Roles in Non-Small-Cell Lung Cancer

“…For instance, patients with LAD and LSCC differ in clinical outcomes. Zhao et al identified 72 differentially-expressed (23 upregulated and 49 downregulated) lncRNAs in patients with LADs and LSCCs by using human Affymetrix microarrays (HGU133plus2.0) [90]. Likewise, White et al identified 27 lung cancer-associated lncRNAs, which could be used as novel biomarkers for stratifying LADs and LSCCs [91].…”

Co-expression network analysis of long noncoding RNAs (IncRNAs) and cancer genes revealsSFTA1P and CASC2abnormalities in lung squamous cell carcinoma

“…It was reported that SFTA1P was downregulated in NSCC and its main function was lying on epidermal growth, cell attachment and response to DNA damage. 25 The other IncRNA, CASC2, was reported to be inhibited by miR-21 in gliomas and, 26,27 which could be the ceRNA of other oncogenes.…”

Discovery and validation of immune-associated long non-coding RNA biomarkers associated with clinically molecular subtype and prognosis in diffuse large B cell lymphoma

“…There is growing evidence that cancer subtype could be characterized by differentiated lncRNA expression pattern, suggesting the potential of lncRNAs as potent biomarkers in cancer subtype. Several studies have observed subtype-specific lncRNA expression pattern between lung adenocarcinoma and squamous cell carcinoma [18, 19]. In breast cancer, the correlation between lncRNA expression and tumor subtype has also been investigated and some subtype-specific lncRNAs were identified [19–21].…”

“…Several studies have observed subtype-specific lncRNA expression pattern between lung adenocarcinoma and squamous cell carcinoma [18, 19]. In breast cancer, the correlation between lncRNA expression and tumor subtype has also been investigated and some subtype-specific lncRNAs were identified [19–21]. For example, a well-known lncRNA HOTAIR was up-regulated in the HER2-enriched subgroup [20].…”