Differentially-regulated miRNAs in COVID-19: A systematic review

Novel protective circulating miRNA are associated with preserved vitamin D levels in patients with mild COVID-19 presentation at hospital admission not progressing into severe disease

PURPOSE

Low vitamin D levels were reported to negatively influence the outcomes of acute COVID-19, as well as other biochemical markers were linked to COVID-19, including microRNAs (miRNAs). This study aimed to prospectively evaluate miRNAs and vitamin D relationship in predicting COVID-19 outcomes.

METHODS

COVID-19 patients were part of a previously reported cohort and enrolled in a matched-ratio based on the presence/or not of severe disease at hospital admission. 25(OH) vitamin D levels and miRNAs expression were evaluated.

RESULTS

Patients affected by non-severe COVID-19 were characterized by a higher expression of miRNAs hsa-miR-3115 and hsa-miR-7151-3p, as compared to those affected by severe disease. In non-severe patients, these miRNAs were more frequently expressed in those who subsequently did not develop worsening outcomes. In addition, patients with miRNA-7151 expression and without worsening disease were characterized by higher 25(OH) vitamin D levels and lower prevalence of vitamin D deficiency.

CONCLUSIONS

The expression of two novel miRNAs was reported for the first-time to be associated with a less severe COVID-19 form and to prospectively predict the occurrence of disease outcome. Furthermore, the association observed between vitamin D deficiency and lack of miRNA-7151 expression in COVID-19 patients with worse outcomes may support the hypothesis that the co-existence of these two conditions may have a strong negative prognostic role.

MSC-extracellular vesicle microRNAs target host cell-entry receptors in COVID-19: in silico modeling for in vivo validation

BACKGROUND

Coronavirus disease 2019 (COVID-19) has created a global pandemic with significant morbidity and mortality. SARS-CoV-2 primarily infects the lungs and is associated with various organ complications. Therapeutic approaches to combat COVID-19, including convalescent plasma and vaccination, have been developed. However, the high mutation rate of SARS-CoV-2 and its ability to inhibit host T-cell activity pose challenges for effective treatment. Mesenchymal stem cells (MSCs) and their extracellular vesicles (MSCs-EVs) have shown promise in COVID-19 therapy because of their immunomodulatory and regenerative properties. MicroRNAs (miRNAs) play crucial regulatory roles in various biological processes and can be manipulated for therapeutic purposes.

OBJECTIVE

We aimed to investigate the role of lyophilized MSC-EVs and their microRNAs in targeting the receptors involved in SARS-CoV-2 entry into host cells as a strategy to limit infection. In silico microRNA prediction, structural predictions of the microRNA-mRNA duplex, and molecular docking with the Argonaut protein were performed.

METHODS

Male Syrian hamsters infected with SARS-CoV-2 were treated with human Wharton's jelly-derived Mesenchymal Stem cell-derived lyophilized exosomes (Bioluga Company)via intraperitoneal injection, and viral shedding was assessed. The potential therapeutic effects of MSCs-EVs were measured via histopathology of lung tissues and PCR for microRNAs.

RESULTS

The results revealed strong binding potential between miRNA‒mRNA duplexes and the AGO protein via molecular docking. MSCs-EVs reduced inflammation markers and normalized blood indices via the suppression of viral entry by regulating ACE2 and TMPRSS2 expression. MSCs-EVs alleviated histopathological aberrations. They improved lung histology and reduced collagen fiber deposition in infected lungs.

CONCLUSION

We demonstrated that MSCs-EVs are a potential therapeutic option for treating COVID-19 by preventing viral entry into host cells.

The potential of circulating microRNAs as novel diagnostic biomarkers of COVID-19: a systematic review and meta-analysis

INTRODUCTION

The COVID-19 pandemic has caused an unprecedented health threat globally, necessitating innovative and efficient diagnostic approaches for timely identification of infected individuals. Despite few emerging reports, the clinical utility of circulating microRNAs (miRNAs) in early and accurate diagnosis of COVID-19 is not well-evidenced. Hence, this meta-analysis aimed to explore the diagnostic potential of circulating miRNAs for COVID-19. The protocol for this study was officially recorded on PROSPERO under registration number CRD42023494959.

METHODS

Electronic databases including Embase, PubMed, Scopus, and other sources were exhaustively searched to recover studies published until 16th January, 2024. Pooled specificity, sensitivity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic ratio (DOR), positive predictive value (PPV), negative predictive value (NPV), and area under the curve (AUC) were computed from the metadata using Stata 14.0 software. Risk of bias appraisal of included articles was carried out using Review Manager (Rev-Man) 5.3 package through the modified QUADAS-2 tool. Subgroup, heterogeneity, meta-regression and sensitivity analyses were undertaken. Publication bias and clinical applicability were also evaluated via Deeks' funnel plot and Fagan nomogram (scattergram), respectively.

RESULT

A total of 43 studies from 13 eligible articles, involving 5175 participants (3281 COVID-19 patients and 1894 healthy controls), were analyzed. Our results depicted that miRNAs exhibit enhanced pooled specificity 0.91 (95% CI: 0.88-0.94), sensitivity 0.94 (95% CI: 0.91-0.96), DOR of 159 (95% CI: 87-288), and AUC values of 0.97 (95% CI: 0.95-0.98) with high pooled PPV 96% (95% CI: 94-97%) and NPV 88% (95% CI: 86-90%) values. Additionally, highest diagnostic capacity was observed in studies involving larger sample size (greater than 100) and those involving the African population, demonstrating consistent diagnostic effectiveness across various specimen types. Notably, a total of 12 distinct miRNAs were identified as suitable for both exclusion and confirmation of COVID-19 cases, denoting their potential clinical applicability.

CONCLUSION

Our study depicted that miRNAs show significantly high diagnostic accuracy in differentiating COVID-19 patients from healthy counterparts, suggesting their possible use as viable biomarkers. Nonetheless, thorough and wide-ranging longitudinal researches are necessary to confirm the clinical applicability of miRNAs in diagnosing COVID-19.

High Serum miR-361-3p Predicts Early Postdischarge Infections after Autologous Stem Cell Transplantation

BACKGROUND

Autologous hematopoietic stem cell transplantation (AHSCT) is currently the backbone of the treatment of multiple myeloma (MM) and relapsed and refractory lymphomas. Notably, infections contribute to over 25% of fatalities among AHSCT recipients within the initial 100 days following the procedure. In this study, we aimed to evaluate three selected miRNAs: hsa-miR-155-5p, hsa-miR-320c, and hsa-miR-361-3p, in identifying AHSCT recipients at high risk of infectious events up to 100 days post-transplantation after discharge.

MATERIALS AND METHODS

The study group consisted of 58 patients (43 with MM, 15 with lymphoma) treated with AHSCT. Blood samples were collected from all patients at the same time point: on day +14 after transplantation.

RESULTS

Fifteen patients (25.9%) experienced infectious complications after post-transplant discharge within the initial +100 days post-transplantation. The median time to infection onset was 44 days (interquartile range, 25-78). Four patients required hospitalization due to severe infection. High expression of hsa-miR-361-3p (fold change [FC], 1.79; P=0.0139) in the patients experiencing infectious complications and overexpression of hsa-miR-320c (FC, 2.14; P<0.0001) in patients requiring hospitalization were observed. In the multivariate model, both lymphoma diagnosis (odds ratio [OR], 6.88; 95% confidence interval [CI], 1.55-30.56; P=0.0112) and high expression of hsa-miR-361-3p (OR, 3.00; 95% CI, 1.40-6.41; P=0.0047) were independent factors associated with post-discharge infectious complications occurrence. Our model in 10-fold cross-validation preserved its diagnostic potential with an area under the receiver operating characteristic curve of 0.78 (95% CI, 0.64-0.92).

CONCLUSION

Elevated serum hsa-miR-361-3p emerges as a promising biomarker for identifying patients at risk of infection during the early post-discharge period, potentially offering optimization of the prophylactic use of antimicrobial agents tailored to the specific risk profile of each AHSCT recipient.

Human microRNA sequencing and cytomegalovirus infection risk after kidney transplantation

Cytomegalovirus (CMV)-seropositive kidney transplant recipients (KTRs) with detectable CMV-specific cell-mediated immunity according to the QuantiFERON-CMV assay (QTF-CMV) are expected to have adequate immune protection. Nevertheless, a proportion of patients still develop CMV infection. Human microRNAs (hsa-miRNAs) are promising biomarkers owing to their high stability and easy detection. We performed whole blood miRNA sequencing in samples coincident with the first reactive QTF-CMV after transplantation or cessation of antiviral prophylaxis to investigate hsa-miRNAs differentially expressed according to the occurrence of CMV infection. One-year incidence of CMV viremia was 55.0% (median interval from miRNA sequencing sampling of 29 days). After qPCR validation, we found that hsa-miR-125a-5p was downregulated in KTRs developing CMV viremia within the next 90 days (ΔCt: 7.9 ± 0.9 versus 7.3 ± 1.0; P = .011). This difference was more evident among KTRs preemptively managed (8.2 ± 0.9 versus 6.9 ± 0.8; P < .001), with an area under the receiver operating characteristic curve of 0.865. Functional enrichment analysis identified hsa-miR-125a-5p targets involved in cell cycle regulation and apoptosis, including the BAK1 gene, which was significantly downregulated in KTRs developing CMV viremia. In conclusion, hsa-miR-125a-5p may serve as biomarker to identify CMV-seropositive KTRs at risk of CMV reactivation despite detectable CMV-CMI.

The biomarkers' landscape of post-COVID-19 patients can suggest selective clinical interventions

In COVID-19 clinical symptoms can persist even after negativization also in individuals who have had mild or moderate disease. We here investigated the biomarkers that define the post-COVID-19 clinical state analyzing the exhaled breath condensate (EBC) of 38 post COVID-19 patients and 38 sex and age-matched healthy controls via nuclear magnetic resonance (NMR)-based metabolomics. Predicted gene-modulated microRNAs (miRNAs) related to COVID-19 were quantified from EBC of 10 patients and 10 controls. Finally, clinical parameters from all post-COVID-19 patients were correlated with metabolomic data. Post-COVID-19 patients and controls showed different metabolic phenotype ("metabotype"). From the metabolites, by using enrichment analysis we identified miRNAs that resulted up-regulated (hsa-miR146a-5p) and down-regulated (hsa-miR-126-3p and hsa-miR-223-3p) in post-COVID-19. Taken together, our multiomics data indicate that post-COVID-19 patients before rehabilitation are characterized by persistent inflammation, dysregulation of liver, endovascular thrombotic and pulmonary processes, and physical impairment, which should be the primary clinical targets to contrast the post-acute sequelae of COVID-19.

Virtual high-throughput screening: Potential inhibitors targeting aminopeptidase N (CD13) and PIKfyve for SARS-CoV-2

Since the outbreak of the novel coronavirus nearly 3 years ago, the world's public health has been under constant threat. At the same time, people's travel and social interaction have also been greatly affected. The study focused on the potential host targets of SARS-CoV-2, CD13, and PIKfyve, which may be involved in viral infection and the viral/cell membrane fusion stage of SARS-CoV-2 in humans. In this study, electronic virtual high-throughput screening for CD13 and PIKfyve was conducted using Food and Drug Administration-approved compounds in ZINC database. The results showed that dihydroergotamine, Saquinavir, Olysio, Raltegravir, and Ecteinascidin had inhibitory effects on CD13. Dihydroergotamine, Sitagliptin, Olysio, Grazoprevir, and Saquinavir could inhibit PIKfyve. After 50 ns of molecular dynamics simulation, seven compounds showed stability at the active site of the target protein. Hydrogen bonds and van der Waals forces were formed with target proteins. At the same time, the seven compounds showed good binding free energy after binding to the target proteins, providing potential drug candidates for the treatment and prevention of SARS-CoV-2 and SARS-CoV-2 variants.