Integrative analysis reveals clinical phenotypes and oncogenic potentials of long non-coding RNAs across 15 cancer types.

Long non-coding RNAs (lncRNAs) have been shown to contribute to tumorigenesis. However, surprisingly little is known about the comprehensive clinical and genomic characterization of lncRNAs across human cancer.

In this study, researchers at Sun Yat-sen University conducted comprehensive analyses for the expression profile, clinical outcomes, somatic copy number alterations (SCNAs) profile of lncRNAs in ~7000 clinical samples from 15 different cancer types. They identified significantly differentially expressed lncRNAs between tumor and normal tissues from each cancer. Notably, they characterized 47 lncRNAs which were extensively dysregulated in at least 10 cancer types, suggesting a conserved function in cancer development. the researchers also analyzed the associations between lncRNA expressions and patient survival, and identified sets of lncRNAs that possessed significant prognostic values in specific cancer types. The combined analysis of SCNA data and expression data uncovered 116 dysregulated lncRNAs are strikingly genomic altered across 15 cancer types, indicating their oncogenic potentials. This study may lay the groundwork for future functional studies of lncRNAs and help facilitate the discovery of novel clinical biomarkers.

Somatic copy number analysis of lncRNAs

A. The bar plot shows the number of SCNA-containing lncRNAs with positive correlation between expression and copy number in each cancer type. The dark color represents amplified lncRNAs whereas the light color represents deleted lncRNAs. B. The Circos plot shows the distribution of 102 SCNA-containing lncRNAs with positive correlation between expression and copy number within the genome and across multiple cancer types (≥3 cancer types). The outermost track represents chromosomes. Histograms located in the innermost track represent the number of cancer types associated with the lncRNAs. Red represents amplification, and blue represents deletion. The distance between any two curves represents one cancer type. C. The heatmap shows 116 dysregulated lncRNAs are strikingly genomic altered across 15 cancer types. Yellow represents values that are not significant; light green represents deletion and down-regulation; orange represents amplification and up-regulation.