RNA-Seq Profiling of Circular RNAs of Exosomes in Cerebrospinal Fluid of Patients With Meningeal Carcinomatosis

Abstract

The onset of meningeal carcinomatosis (MC) is concealed and early diagnosis is difficult. Recognition of new biomarkers is essential. Exosomes are cell-derived membrane vesicles, contents of which are steady and could be transported into receiver cells to exert their biological roles. Circular RNAs (circRNA) are special noncoding RNAs. They can regulate target gene messenger RNA expression and play important roles in many biological processes. CircRNAs are enriched and stable in exosomes. However, the expression profile and function of exosomal circRNAs in human MC have not been reported. In this study, secondary sequencing was used to profile circRNA expression of exosomes in cerebrospinal fluid (CSF) samples from three MC patients and three healthy controls. A separate set (n = 15) of CSF samples of MCs and healthy controls were subjected to RT‐PCR for validation of circRNAs expression profile. Gene Ontology (GO) functional analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and circRNA‐miRNA network analysis were also performed to predict the function of circRNA in MC. The current study is the first to systematically characterize and annotate exosomal circRNA expression in MC. A total of 12 503 circRNAs were identified and annotated, most of the circRNAs were novel (n = 8940). Statistical analysis revealed 39 differentially expressed (DE) exosomal circRNAs between MC and control samples. Then, we analyzed the functions and signaling of the differentially expressed genes' pathways to reveal the putative mechanism of how these exosomal circRNAs work in MC. Moreover, we verified some candidates in another 15 MC and control samples by qRT-PCR, and the networks of circRNA-miRNA base on these circRNAs were constructed respectively. Finally, we demonstrated that four of them (hsa_circ_0001451, hsa_circ_0001769, hsa_circ_0000198, and hsa_circ_000118) had the potential for diagnosing MC. Funding Information: The study was supported by the fund of Special scientific research project of health young medical science and technology talents in Autonomous Region (WJWY202210), the Key Research and Development Program of Shandong Province (2017GSF218046), the National Natural Science Foundation of China (81901106, 81973630), the Natural Science Foundation of Shandong Province (ZR2020QH289, ZR2020QH331, ZR2020QH122, ZR2020QH097), Shandong University Multidisciplinary Research and Innovation Team of Young Scholars (2020QNQT019), Rongxiang Regenerative Medicine Foundation of Shandong University (No.2019SDRX-09). Declaration of Interests: The authors declare that they have no competing interests. Ethics Approval Statement: The study was approved by the Ethics Committee of the Second Hospital of Shandong University. All subjects signed informed consent.