Circular RNA Landscape in Extracellular Vesicles from Human Biofluids

Overview

Journal Genome Med

Publisher Biomed Central

Specialty Genetics

Date 2024 Nov 1

PMID 39482783

Authors

Jingjing Zhao

Qiaojuan Li

Jia Hu

Hongwu Yu

Youmin Shen

Hongyan Lai

Qin Li

Hena Zhang

Yan Li

Zhuting Fang

Shenglin Huang

Affiliations

Soon will be listed here.

Abstract

Background: Circular RNAs (circRNAs) have emerged as a prominent class of covalently closed single-stranded RNA molecules that exhibit tissue-specific expression and potential as biomarkers in extracellular vesicles (EVs) derived from liquid biopsies. Still, their characteristics and applications in EVs remain to be unveiled.

Methods: We performed a comprehensive analysis of EV-derived circRNAs (EV-circRNAs) using transcriptomics data obtained from 1082 human body fluids, including plasma, urine, cerebrospinal fluid (CSF), and bile. Our validation strategy utilized RT-qPCR and RNA immunoprecipitation assays, complemented by computational techniques for analyzing EV-circRNA features and RNA-binding protein interactions.

Results: We identified 136,327 EV-circRNAs from various human body fluids. Significantly, a considerable amount of circRNAs with a high back-splicing ratio are highly enriched in EVs compared to linear RNAs. Additionally, we discovered brain-specific circRNAs enriched in plasma EVs and cancer-associated EV-circRNAs linked to clinical outcomes. Moreover, we demonstrated that EV-circRNAs have the potential to serve as biomarkers for evaluating immunotherapy efficacy in non-small cell lung cancer (NSCLC). Importantly, we identified the involvement of RBPs, particularly YBX1, in the sorting mechanism of circRNAs into EVs.

Conclusions: This study unveils the extensive repertoire of EV-circRNAs across human biofluids, offering insights into their potential as disease biomarkers and their mechanistic roles within EVs. The identification of specific circRNAs and the elucidation of RBP-mediated sorting mechanisms open new avenues for the clinical application of EV-circRNAs in disease diagnostics and therapeutics.

Citing Articles

Current Insights into the Roles of LncRNAs and CircRNAs in Pulpitis: A Narrative Review.

Fuchen-Ramos D, Leija-Montoya A, Gonzalez-Ramirez J, Isiordia-Espinoza M, Garcia-Arevalo F, Pitones-Rubio V Int J Mol Sci. 2025; 25(24.

PMID: 39769365 PMC: 11677139. DOI: 10.3390/ijms252413603.

References

Van Nostrand E, Freese P, Pratt G, Wang X, Wei X, Xiao R . A large-scale binding and functional map of human RNA-binding proteins. Nature. 2020; 583(7818):711-719. PMC: 7410833. DOI: 10.1038/s41586-020-2077-3. View

Liu C, Chen L . Circular RNAs: Characterization, cellular roles, and applications. Cell. 2022; 185(12):2016-2034. DOI: 10.1016/j.cell.2022.04.021. View

Ngo L, Bert A, Dredge B, Williams T, Murphy V, Li W . Nuclear export of circular RNA. Nature. 2024; 627(8002):212-220. DOI: 10.1038/s41586-024-07060-5. View

Zhang F, Jiang J, Qian H, Yan Y, Xu W . Exosomal circRNA: emerging insights into cancer progression and clinical application potential. J Hematol Oncol. 2023; 16(1):67. PMC: 10294326. DOI: 10.1186/s13045-023-01452-2. View

Garcia-Martin R, Wang G, Brandao B, Zanotto T, Shah S, Patel S . MicroRNA sequence codes for small extracellular vesicle release and cellular retention. Nature. 2021; 601(7893):446-451. PMC: 9035265. DOI: 10.1038/s41586-021-04234-3. View

Asao T, Tobias G, Lucotti S, Jones D, Matei I, Lyden D . Extracellular vesicles and particles as mediators of long-range communication in cancer: connecting biological function to clinical applications. Extracell Vesicles Circ Nucl Acids. 2024; 4(3):461-485. PMC: 11067132. DOI: 10.20517/evcna.2023.37. View

. The Genotype-Tissue Expression (GTEx) project. Nat Genet. 2013; 45(6):580-5. PMC: 4010069. DOI: 10.1038/ng.2653. View

Stranska R, Gysbrechts L, Wouters J, Vermeersch P, Bloch K, Dierickx D . Comparison of membrane affinity-based method with size-exclusion chromatography for isolation of exosome-like vesicles from human plasma. J Transl Med. 2018; 16(1):1. PMC: 5761138. DOI: 10.1186/s12967-017-1374-6. View

Dobin A, Davis C, Schlesinger F, Drenkow J, Zaleski C, Jha S . STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2012; 29(1):15-21. PMC: 3530905. DOI: 10.1093/bioinformatics/bts635. View

10.

Li Z, Zhu X, Huang S . Extracellular vesicle long non-coding RNAs and circular RNAs: Biology, functions and applications in cancer. Cancer Lett. 2020; 489:111-120. DOI: 10.1016/j.canlet.2020.06.006. View

11.

Yang S, Wang D, Zhong S, Chen W, Wang F, Zhang J . Tumor-derived exosomal circPSMA1 facilitates the tumorigenesis, metastasis, and migration in triple-negative breast cancer (TNBC) through miR-637/Akt1/β-catenin (cyclin D1) axis. Cell Death Dis. 2021; 12(5):420. PMC: 8080849. DOI: 10.1038/s41419-021-03680-1. View

12.

Li Y, Hu J, Wang M, Yuan Y, Zhou F, Zhao H . Exosomal circPABPC1 promotes colorectal cancer liver metastases by regulating HMGA2 in the nucleus and BMP4/ADAM19 in the cytoplasm. Cell Death Discov. 2022; 8(1):335. PMC: 9308786. DOI: 10.1038/s41420-022-01124-z. View

13.

Shetgaonkar G, Marques S, DCruz C, Vibhavari R, Kumar L, Shirodkar R . Exosomes as cell-derivative carriers in the diagnosis and treatment of central nervous system diseases. Drug Deliv Transl Res. 2021; 12(5):1047-1079. PMC: 8942947. DOI: 10.1007/s13346-021-01026-0. View

14.

Kristensen L, Jakobsen T, Hager H, Kjems J . The emerging roles of circRNAs in cancer and oncology. Nat Rev Clin Oncol. 2021; 19(3):188-206. DOI: 10.1038/s41571-021-00585-y. View

15.

Maas S, Breakefield X, Weaver A . Extracellular Vesicles: Unique Intercellular Delivery Vehicles. Trends Cell Biol. 2016; 27(3):172-188. PMC: 5318253. DOI: 10.1016/j.tcb.2016.11.003. View

16.

Chen X, Li A, Sun B, Yang Y, Han Y, Yuan X . 5-methylcytosine promotes pathogenesis of bladder cancer through stabilizing mRNAs. Nat Cell Biol. 2019; 21(8):978-990. DOI: 10.1038/s41556-019-0361-y. View

17.

Younas N, Fernandez Flores L, Hopfner F, Hoglinger G, Zerr I . A new paradigm for diagnosis of neurodegenerative diseases: peripheral exosomes of brain origin. Transl Neurodegener. 2022; 11(1):28. PMC: 9082915. DOI: 10.1186/s40035-022-00301-5. View

18.

Glazar P, Papavasileiou P, Rajewsky N . circBase: a database for circular RNAs. RNA. 2014; 20(11):1666-70. PMC: 4201819. DOI: 10.1261/rna.043687.113. View

19.

Sherman B, Hao M, Qiu J, Jiao X, Baseler M, Lane H . DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update). Nucleic Acids Res. 2022; 50(W1):W216-W221. PMC: 9252805. DOI: 10.1093/nar/gkac194. View

20.

Li Y, Zheng Q, Bao C, Li S, Guo W, Zhao J . Circular RNA is enriched and stable in exosomes: a promising biomarker for cancer diagnosis. Cell Res. 2015; 25(8):981-4. PMC: 4528056. DOI: 10.1038/cr.2015.82. View