Profiling of Plasma Extracellular Vesicle Transcriptome Reveals That circRNAs Are Prevalent and Differ between Multiple Sclerosis Patients and Healthy Controls

Abstract

(1) Background: Extracellular vesicles (EVs) are released by most cell types and are implicated in several biological and pathological processes, including multiple sclerosis (MS). Differences in the number and cargo of plasma-derived EVs have been described in MS. In this work, we have characterised the EV RNA cargo of MS patients, with particular attention to circular RNAs (circRNAs), which have attracted increasing attention for their roles in physiology and disease and their biomarker potential. (2) Methods: Plasma-derived EVs were isolated by differential centrifugation (20 patients, 8 controls), and RNA-Sequencing was used to identify differentially expressed linear and circRNAs. (3) Results: We found differences in the RNA type distribution, circRNAs being enriched in EVs vs. leucocytes. We found a number of (corrected p-value < 0.05) circRNA significantly DE between the groups. Nevertheless, highly structured circRNAs are preferentially retained in leukocytes. Differential expression analysis reports significant differences in circRNA and linear RNA expression between MS patients and controls, as well as between different MS types. (4) Conclusions: Plasma derived EV RNA cargo is not a representation of leukocytes’ cytoplasm but a message worth studying. Moreover, our results reveal the interest of circRNAs as part of this message, highlighting the importance of further understanding RNA regulation in MS.

A Comprehensive Exploration of the Transcriptomic Landscape in Multiple Sclerosis: A Systematic Review

“…Thus, from a comparison of the profile of non-coding RNAs observed in vesicles against the one in the cytoplasm of leukocytes, there was no linear correspondence, not even for circRNAs. Also, the circRNAs in vesicles were smaller and more poorly structured than the leukocyte ones [ 56 ].…”

Emerging Biomarkers of Multiple Sclerosis in the Blood and the CSF: A Focus on Neurofilaments and Therapeutic Considerations

“…The circRNA profile of an individual might not just be an excellent biomarker to monitor relapse activity, but based on recent research, it may be used to differentiate between MS subtypes. Iparraguirre et al [ 444 ] have found that healthy controls and patients with SP and RR MS have fundamentally different circRNA profiles. They also demonstrated that miRNA "sponging” might not be circRNAs primary function in extracellular vesicles and leukocytes despite prior knowledge.…”

Multi-Omics Integrative Approach of Extracellular Vesicles: A Future Challenging Milestone

“…Nonetheless, several studies have been demonstrating that miRNAs represent just a minority of the total RNAs contained in EVs, throwing light on the classes of non-coding RNAs [ 82 ]. Recently, Iparraguirre et al investigated the RNA cargo in plasma-derived EVs of multiple sclerosis (MS) patients, reporting a particular enrichment of circRNAs in EVs of MS patients and significant differences in circRNA and linear RNA expression between MS types as well [ 83 ]; Magaña et al evaluated the small ncRNA pattern in EVs released from medulloblastoma (MB) and diffuse infiltrative pontine glioma (DIPG) patient-derived cell lines, identifying novel miRNAs not previously associated to the pathogenesis of the diseases and demonstrating an enrichment of Y-RNAs in the released EVs [ 84 ], and Peng et al evaluated piRNAs in urinary EVs as non-invasive biomarkers for prostate cancer diagnosis [ 85 ]. Although scientific community has been giving great attention to the EVs RNA profiling in order to explore their gene-regulatory activities and their potentiality in paving a new direction in therapeutic targeting, the state-of-the-art of EVs transcriptomics is to provide a clear picture of the EVs content, however many improvements are needed to better understand the message mediated by these structures [ 86 ].…”