RNA-Seq profiling of leukocytes reveals a sex-dependent global circular RNA upregulation in multiple sclerosis and 6 candidate biomarkers

Abstract

Background Multiple sclerosis (MS) is a chronic autoimmune disease of the central nervous system, with higher prevalence in women, that leads to neurological disability. The disease course and clinical phenotype are highly variable and therefore, biomarkers for the diagnosis, classification, monitoring of the disease and treatment assessment are needed. Studies have shown a dysregulation in the coding and non-coding RNAs and proposed some as biomarkers. However, still none of them have reached the clinical practice. Recently, circular RNAs (circRNAs) have emerged as new players in the transcriptome that hold a great potential as biomarkers in several diseases. Methods Leukocytes from 50 MS patients and 20 healthy controls (HC) were RNA-sequenced to study the linear and circular transcriptome. Differential expression analysis was performed by DESeq and circRNA candidates were studied in a second cohort (70MS and 46HC) by RT-qPCR and in paired samples drawn during the relapse and remission phases (20 patients). Results Among the differentially expressed circRNAs, the 96.1% are upregulated in patients compared to controls, but similar circRNA profiles are found between MS types. The same upregulation trend was observed in females but not in males or in the linear transcriptome. The upregulation of 6 circRNAs was validated and a change in their expression was found between relapse and remission. The 6 circRNAs showed a good performance to discriminate patients from HC with a combined AUC of 0.852. Conclusion There is global, specific and sex dependent increase of circRNA expression in MS and 6 circRNAs are proposed as potential biomarkers.

Profiling of plasma extracellular vesicle transcriptome reveals that circRNAs are prevalent and differ between multiple sclerosis patients and healthy controls

“…Anyway, both circular and linear transcripts differentially expressed between MS patients and healthy controls as well as transcripts that are unique to the diseased conditions could potentially be used as minimally invasive biomarkers of the disease. In fact it is worth noting that one of the circRNAs found to be altered in RR-MS patients' EVs when compared to controls' EVs (circNEIL3) has previously been suggested as a biomarker candidate in leukocytes from RR-MS patients [38]. In contrast, in leukocytes, a very small proportion of the circRNA pro le was different between RR-MS and SP-MS patients, and consequently, no potential biomarkers of conversion could be found [38].…”

“…Interestingly, highly structured circRNAs have been described to be able to regulate the innate immune response in Systemic Lupus Erythematosus patients by binding and inhibiting the activation of the PKR [28]. Therefore, it is tempting to think that although they could be packaged into EVs more easily, highly structured circRNAs are preferentially accumulated in leukocytes in order to regulate the aberrant activation of the immune system particularly in MS patients where they have been found to be upregulated [38]. Similarly, in case circRNAs could be functional miRNA sponges, this functionality could in uence their release into EVs.…”

“…After calculating the miRNA BS density, the miRNA sponging potential appears to be negligible among the circRNAs in leukocytes and in EVs, thus it is unlikely to in uence the circRNA loading into EVs. [38].…”

“…In order to know whether this distribution of RNA types is EV speci c or not, we compared the transcriptomic pro le described for EVs in the present work to the transcriptomic pro le found for leukocyte samples of RR-MS, SP-MS and HCs following the same sequencing and analysis protocol previously published by our group [38].…”

CircRNA FUT10 regulates the regenerative potential of aged skeletal muscle stem cells by targeting HOXA9

“…Recently, the regulatory potential of circRNAs and their role in the development and progression of muscle diseases have been reported [ 15 , 25 , 26 ]. Studies have also suggested that circRNA is involved in cellular aging [ 27 – 29 ]. One recent study reported that circLMO7 regulates myoblast differentiation and survival via miR-378a-3p [ 30 ].…”