Comparative Analysis of Pan-cancer and Normal Tissues Reveals Cancer Tissue-enriched CircRNAs Associated with Cancer Mutations as Potential Exosomal Biomarkers

Abstract Background: A growing body of evidence has shown that circular RNAs (circRNAs) are promising exosomal cancer biomarker candidates. However, global alterations of circRNAs in cancer and the driving force of circRNA biogenesis remain under investigation. Studies on these factors are needed to identify ideal circRNA biomarkers for cancer.Methods: We comparatively analyzed the circRNA landscape in pan-cancer and normal tissues to investigate their biologically significant characteristics and identify circRNAs enriched in pan-cancer. We used co-expression analysis, LASSO regularization, and support vector machine to analyze 265 pan-cancer and 319 normal tissues to identify circRNAs with the highest ability to distinguish cancer tissues from normal tissues which showed high expression in plasma exosomes from patients with cancer (e.g., hepatocellular carcinoma, HCC) and were associated with cancer mutations. Results: Expression of circRNAs was reduced in cancer tissues and plasma exosomes from patients with cancer than in normal tissues and exosomes from healthy controls. The circRNAs with the strongest ability to distinguish between cancer and normal tissues were among the top 10% of stably expressed circRNAs. Compared with normal-tissue-enriched circRNAs, cancer-tissue‒enriched circRNAs exhibited a more prominent association with cancer mutations and higher levels in plasma exosomes from patients with HCC. Particularly, we identified dynein axonemal heavy chain 14 (DNAH14), which serves as the host gene of three cancer tissue-enriched circRNAs, as one of the top back-spliced genes exclusive to cancer tissues. Among these three circRNAs, chr1_224952669_224968874_+ was significantly elevated in plasma exosomes from patients with HCC and was associated with the cancer mutation chr1:224952669: G>A, a splice acceptor variant that is potentially a driving force of circRNA biogenesis.Conclusions: Our bioinformatic analyses provide insights into the characteristics of the circRNA landscape in cancer and the potential of cancer mutation-associated and cancer tissue-enriched RNAs as plasma exosomal cancer biomarkers. Moreover, our results highlight DNAH14 as a host gene that should be further examined in studies of circRNA in cancer.