RNA-Seq profiling of circular RNA in human lung adenocarcinoma and squamous cell carcinoma

Abstract

Emerging evidences demonstrate that circular RNAs (circRNAs) are abnormally expressed in tumors and could serve as prognostic markers for cancers. However, the expression patterns and clinical implications of circRNAs in non-small cell lung cancer (NSCLC) remain obscure. In this study, we profiled circRNA expressions in 10 pairs of lung adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC) after ribosomal RNA-depletion and RNase R digestion to enrich circRNAs. Combining five circRNA computational programs, we found that LUAD and LUSC not only share common expression patterns, but also exhibit distinct circRNA expression signatures. Moreover, the Receiver Operating Characteristic (ROC) curve analysis indicated that hsa_circ_0077837 and hsa_circ_0001821 could serve as potential biomarkers for both LUAD and LUSC, while hsa_circ_0001073 and hsa_circ_0001495 could be diagnostic/subtyping marker for LUAD and LUSC, respectively. Therefore, our findings highlight the important diagnostic potential of circRNAs in NSCLC.

Keywords: Circular RNAs; Lung adenocarcinoma; Lung squamous carcinoma; circRNA sequencing.

Fig. 1

Characterization of circRNAs identified in lung tumors and their adjacent normal tissues. a The number of circRNAs and back-spliced reads identified in lung tumors and normal tissues. b The chromosome distribution of total identified circRNAs in lung tissues. c Number of circRNAs produced from one gene. d Exon numbers of identified circRNAs. e The length distribution of identified circRNAs. f Comparison of circRNAs identified in this study and circBase

Fig. 2

Identification and validation of differentially expressed circRNAs in LUAD and LUSC. a Hierarchical clustering heatmap of dysregulated circRNAs between LUAD or LUSC and their adjacent normal tissues. b Comparison of differentially expressed circRNAs identified in LUAD and LUSC tissues. c, g Schematic diagram of hsa_circ_0001821(c) and hsa_circ_0077837(g). d, h Agarose gel electrophoresis and Sanger sequencing of RT-PCR products of hsa_circ_0001821(d) and hsa_circ_0077837(h). e-f, i-j Relative expression of hsa_circ_0001821 (e, f) and hsa_circ_0077837 (i, j) in LUAD and LUSC tissues for circRNA sequencing and in another independent cohort of NSCLC patients’ samples

Fig. 3

ROC analyses of differentially expressed circRNAs in LUAD and LUSC. a-d ROC curve analyses of hsa_circ_0077837 (a), hsa_circ_0001821 (b), hsa_circ_0001073 (c) and hsa_circ_0001495 (d) for NSCLC, LUAD or LUSC diagnosis