Competing endogenous RNA network mediated by circ_3205 in SARS-CoV-2 infected cells

Abstract

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a new member of the Betacoronaviridae family, responsible for the recent pandemic outbreak of COVID-19. To start exploring the molecular events that follow host cell infection, we queried VirusCircBase and identified a circular RNA (circRNA) predicted to be synthesized by SARS-CoV-2, circ_3205, which we used to probe: (i) a training cohort comprised of two pools of cells from three nasopharyngeal swabs of SARS-CoV-2 infected (positive) or uninfected (negative, UCs) individuals; (ii) a validation cohort made up of 12 positive and 3 negative samples. The expression of circRNAs, miRNAs and miRNA targets was assayed through real-time PCR. CircRNA–miRNA interactions were predicted by TarpMiR, Analysis of Common Targets for circular RNAs (ACT), and STarMir tools. Enrichment of the biological processes and the list of predicted miRNA targets were retrieved from DIANA miRPath v3.0. Our results showed that the predicted SARS-CoV-2 circ_3205 was expressed only in positive samples and its amount positively correlated with that of SARS-CoV-2 Spike (S) mRNA and the viral load (r values = 0.80952 and 0.84867, Spearman’s correlation test, respectively). Human (hsa) miR-298 was predicted to interact with circ_3205 by all three predictive tools. KCNMB4 and PRKCE were predicted as hsa-miR-298 targets. Interestingly, the function of both is correlated with blood coagulation and immune response. KCNMB4 and PRKCE mRNAs were upregulated in positive samples as compared to UCs (6 and 8.1-fold, p values = 0.049 and 0.02, Student’s t test, respectively) and their expression positively correlated with that of circ_3205 (r values = 0.6 and 0.25, Spearman’s correlation test, respectively). We propose that our results convincingly suggest that circ_3205 is a circRNA synthesized by SARS-CoV-2 upon host cell infection and that it may behave as a competitive endogenous RNA (ceRNA), sponging hsa-miR-298 and contributing to the upregulation of KCNMB4 and PRKCE mRNAs.

Identification of circulating microRNA profiles associated with pulmonary function and radiologic features in survivors of SARS-CoV-2-induced ARDS

“…Furthermore, the deregulation in individual expression programmes may not explain the complexity of the disease. For instance, Barbagallo et al [ 35 ] have recently demonstrated a profound perturbation in competitive endogenous RNA networks due to SARS-CoV-2 infection which ultimately impacts on disease progression. Advanced statistical tools seem fundamental to describe the interaction between miRNAs and the phenotype and identify nonlinear associations between miRNA levels and the outcome.…”

circSMARCA5 Is an Upstream Regulator of the Expression of miR-126-3p, miR-515-5p, and Their mRNA Targets, Insulin-like Growth Factor Binding Protein 2 (IGFBP2) and NRAS Proto-Oncogene, GTPase (NRAS) in Glioblastoma

“…Numerous RBPs play a crucial role in the post-transcriptional processing of pri-miRNAs and pre-miRNAs [ 68 ]: among them, the splicing factor SRSF1 has been demonstrated to regulate the expression of several mature miRNAs by a cross-talk with the enzymes involved in the processing of their precursors, through mechanisms that have been only partially explained to date [ 69 ]. The interplay between circRNAs and miRNAs has been mainly described as a ceRNA network, in which circRNAs, including circSMARCA5, act as sponges for miRNAs [ 24 , 25 , 26 , 27 , 70 , 71 , 72 , 73 , 74 ]; however, circRNAs have not been yet reported as upstream regulators of miRNA expression, to the best of our knowledge. Because of their role as decoys for several RBPs, here we hypothesize that circRNAs may act as upstream epigenetic regulators of the miRNAome inside cells.…”

New insights on circular RNAs and their potential applications as biomarkers, therapeutic agents, and preventive vaccines in viral infections: with a glance at SARS-CoV-2

“…A recent study distinguished circ_3205 from nasopharyngeal swabs of SARS-CoV-2-infected individuals, synthetized by SARS-CoV-2. 119 Their results conveniently proposed that circ_3205 act as a ceRNA, sponges hsa-miR-298, and by promoting the upregulation of KCNMB4 (potassium calcium-activated channel subfamily M regulatory beta subunit 4) and PRKCE (protein kinase C epsilon) mRNAs contributes to the progression of SARS-CoV-2 infection. 119 Additionally, in another RNA-seq study, 351, 224, and 2,764 circR-NAs were identified from SARS-CoV-2, SARS-CoV, and MERS-CoV, respectively.…”

“…119 Their results conveniently proposed that circ_3205 act as a ceRNA, sponges hsa-miR-298, and by promoting the upregulation of KCNMB4 (potassium calcium-activated channel subfamily M regulatory beta subunit 4) and PRKCE (protein kinase C epsilon) mRNAs contributes to the progression of SARS-CoV-2 infection. 119 Additionally, in another RNA-seq study, 351, 224, and 2,764 circR-NAs were identified from SARS-CoV-2, SARS-CoV, and MERS-CoV, respectively. It was observed that theses coronavirus-derived circRNAs are more abundant and longer than host genome-derived circRNAs.…”