circRNA expression analysis in lung adenocarcinoma: comparison of paired fresh frozen and formalin-fixed paraffin-embedded specimens

Abstract

Circular RNA (circRNAs) is a novel class of endogenous non-coding RNAs which is widely involved in carcinogenesis. Archived formalin-fixed paraffin-embedded (FFPE) specimens represent valuable resources for cancer research. Currently there is a lack of systematic analysis on the feasibility of circRNAs expression analysis using FFPE samples. Here, we reported the first comparison study of circRNA expression from paired fresh frozen and FFPE specimens of lung adenocarcinoma. circRNAs expression of paired lung adenocarcinoma and adjacent normal samples, starting from either fresh frozen or FFPE materials, were analyzed via a high-throughput circRNA microarray. Hierarchical clustering was performed on samples. qRT-PCR was used to confirm the differentially expressed circRNAs. The circRNA regulation networks were built by bioinformatics tools for several candidate circRNAs. Our results demonstrated that there was a good correlation in circRNAs expression analysis utilizing fresh frozen or FFPE tissues. Tumors and adjacent normal tissues can be clustered correctly by the differentially expressed circRNAs in fresh frozen or FFPE groups. Furthermore, three differentially expressed circRNAs, hsa_circRNA_100421, hsa_circRNA_104329 and hsa_circRNA_101969 were verified by qRT-PCR assay. Bioinformatics analysis was also applied to predict the circRNA-miRNA-protein coding gene interaction network for each of above circRNAs. To the best of our knowledge, this is the first report demonstrating that the circRNAs microarray analysis, starting from FFPE specimens, is comparable with that based on fresh frozen samples. Therefore FFPE specimen represents a good substitute for fresh frozen tissue, especially when fresh frozen specimen is limited.

Keywords: FFPE specimens; Lung adenocarcinoma; circRNA microarray.