Distinct miRNAs associated with various clinical presentations of SARS-CoV-2 infection

Circulating miRNA profiles in COVID-19 patients and meta-analysis: implications for disease progression and prognosis

We compared circulating miRNA profiles of hospitalized COVID-positive patients (n = 104), 27 with acute respiratory distress syndrome (ARDS) and age- and sex-matched healthy controls (n = 18) to identify miRNA signatures associated with COVID and COVID-induced ARDS. Meta-analysis incorporating data from published studies and our data was performed to identify a set of differentially expressed miRNAs in (1) COVID-positive patients versus healthy controls as well as (2) severe (ARDS+) COVID vs moderate COVID. Gene ontology enrichment analysis of the genes these miRNAs interact with identified terms associated with immune response, such as interferon and interleukin signaling, as well as viral genome activities associated with COVID disease and severity. Additionally, we observed downregulation of a cluster of miRNAs located on chromosome 14 (14q32) among all COVID patients. To predict COVID disease and severity, we developed machine learning models that achieved AUC scores between 0.81-0.93 for predicting disease, and between 0.71-0.81 for predicting severity, even across diverse studies with different sample types (plasma versus serum), collection methods, and library preparations. Our findings provide network and top miRNA feature insights into COVID disease progression and contribute to the development of tools for disease prognosis and management.

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

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is responsible for coronavirus disease of 2019 (COVID-19) that infected more than 760 million people worldwide with over 6.8 million deaths to date. COVID-19 is one of the most challenging diseases of our times due to the nature of its spread, its effect on multiple organs, and an inability to predict disease prognosis, ranging from being completely asymptomatic to death. Upon infection, SARS-CoV-2 alters the host immune response by changing host-transcriptional machinery. MicroRNAs (miRNAs) are regarded as post-transcriptional regulators of gene expression that can be perturbed by invading viruses. Several in vitro and in vivo studies have reported such dysregulation of host miRNA expression upon SARS-CoV-2 infection. Some of this could occur as an anti-viral response of the host to the viral infection. Viruses themselves can counteract that response by mounting their own pro-viral response that facilitates virus infection, an aspect which may cause pathogenesis. Thus, miRNAs could serve as possible disease biomarkers in infected people. In the current review, we have summarised and analysed the existing data about miRNA dysregulation in patients infected with SARS-CoV-2 to determine their concordance between studies, and identified those that could serve as potential biomarkers during infection, disease progression, and death, even in people with other co-morbidities. Having such biomarkers can be vital in not only predicting COVID-19 prognosis, but also the development of novel miRNA-based anti-virals and therapeutics which can become invaluable in case of the emergence of new viral variants with pandemic potential in the future.

Empagliflozin Improves the MicroRNA Signature of Endothelial Dysfunction in Patients with Heart Failure with Preserved Ejection Fraction and Diabetes

Endothelial dysfunction represents a key mechanism underlying heart failure with preserved ejection fraction (HFpEF), diabetes mellitus (DM), and frailty. However, reliable biomarkers to monitor endothelial dysfunction in these patients are lacking. In this study, we evaluated the expression of a panel of circulating microRNAs (miRs) involved in the regulation of endothelial function in a population of frail older adults with HFpEF and DM treated for 3 months with empagliflozin, metformin, or insulin. We identified a distinctive pattern of miRs that were significantly regulated in HFpEF patients compared to healthy controls and to HFpEF patients treated with the sodium glucose cotransporter 2 (SGLT2) inhibitor empagliflozin. Three miRs were significantly downregulated (miR-126, miR-342-3p, and miR-638) and two were significantly upregulated (miR-21 and miR-92) in HFpEF patients compared to healthy controls. Strikingly, two of these miRs (miR-21 and miR-92) were significantly reduced in HFpEF patients after the 3-month treatment with empagliflozin, whereas no significant differences in the profile of endothelial miRs were detected in patients treated with metformin or insulin. Taken together, our findings demonstrate for the first time that specific circulating miRs involved in the regulation of endothelial function are significantly regulated in frail HFpEF patients with DM and in response to SGLT2 inhibition. SIGNIFICANCE STATEMENT: We have identified a novel microRNA signature functionally involved in the regulation of endothelial function that is significantly regulated in frail patients with HFpEF and diabetes. Moreover, the treatment with the SGLT2 inhibitor empagliflozin caused a modification of some of these microRNAs in a direction that was opposite to what observed in HFpEF patients, indicating a rescue of endothelial function. Our findings are relevant for clinical practice inasmuch as we were able to establish novel biomarkers of disease and response to therapy.

In silico analysis of SARS-CoV-2 genomes: Insights from SARS encoded non-coding RNAs

The recent pandemic caused by Severe Acute Respiratory Syndrome Coronavirus-2 has resulted in enormous deaths around the world. Clues from genomic sequences of parent and their mutants can be obtained to understand the evolving pathogenesis of this virus. Apart from the viral proteins, virus-encoded microRNAs (miRNAs) have been shown to play a vital role in regulating viral pathogenesis. Thus we sought to investigate the miRNAs encoded by SARS-CoV-2, its mutants, and the host. Here, we present the results obtained using a dual approach i.e (i) identifying host-encoded miRNAs that might regulate viral pathogenesis and (ii) identifying viral-encoded miRNAs that might regulate host cell signaling pathways and aid in viral pathogenesis. Analysis utilizing the first approach resulted in the identification of ten host-encoded miRNAs that could target the SARS, SARS-CoV-2, and its mutants. Interestingly our analysis revealed that there is a significantly higher number of host miRNAs that could target the SARS-CoV-2 genome as compared to the SARS reference genome. Results from the second approach resulted in the identification of a set of virus-encoded miRNAs which might regulate host signaling pathways. Our analysis further identified a similar "GA" rich motif in the SARS-CoV-2 and its mutant genomes that was shown to play a vital role in lung pathogenesis during severe SARS infections. In summary, we have identified human and virus-encoded miRNAs that might regulate the pathogenesis of SARS coronaviruses and describe similar non-coding RNA sequences in SARS-CoV-2 that were shown to regulate SARS-induced lung pathology in mice.

Identifying MicroRNA Markers That Predict COVID-19 Severity Using Machine Learning Methods

Individuals with the SARS-CoV-2 infection may experience a wide range of symptoms, from being asymptomatic to having a mild fever and cough to a severe respiratory impairment that results in death. MicroRNA (miRNA), which plays a role in the antiviral effects of SARS-CoV-2 infection, has the potential to be used as a novel marker to distinguish between patients who have various COVID-19 clinical severities. In the current study, the existing blood expression profiles reported in two previous studies were combined for deep analyses. The final profiles contained 1444 miRNAs in 375 patients from six categories, which were as follows: 30 patients with mild COVID-19 symptoms, 81 patients with moderate COVID-19 symptoms, 30 non-COVID-19 patients with mild symptoms, 137 patients with severe COVID-19 symptoms, 31 non-COVID-19 patients with severe symptoms, and 66 healthy controls. An efficient computational framework containing four feature selection methods (LASSO, LightGBM, MCFS, and mRMR) and four classification algorithms (DT, KNN, RF, and SVM) was designed to screen clinical miRNA markers, and a high-precision RF model with a 0.780 weighted F1 was constructed. Some miRNAs, including miR-24-3p, whose differential expression was discovered in patients with acute lung injury complications brought on by severe COVID-19, and miR-148a-3p, differentially expressed against SARS-CoV-2 structural proteins, were identified, thereby suggesting the effectiveness and accuracy of our framework. Meanwhile, we extracted classification rules based on the DT model for the quantitative representation of the role of miRNA expression in differentiating COVID-19 patients with different severities. The search for novel biomarkers that could predict the severity of the disease could aid in the clinical diagnosis of COVID-19 and in exploring the specific mechanisms of the complications caused by SARS-CoV-2 infection. Moreover, new therapeutic targets for the disease may be found.

Unpacking COVID-19 Systems Biology in Lung and Whole Blood with Transcriptomics and miRNA Regulators

COVID-19 is a systemic disease affecting tissues and organs, including and beyond the lung. Apart from the current pandemic context, we also have vastly inadequate knowledge of consequences of repeated exposures to SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the virus causing COVID-19, in multiple organ systems and the whole organism scales when the disease evolves from a pandemic to an endemic state. This calls for a systems biology and systems medicine approach and unpacking the effects of COVID-19 in lung as well as other tissues. We report here original findings from transcriptomics analyses and differentially expressed genes (DEGs) in lung samples from 60 patients and 27 healthy controls, and in whole blood samples from 255 patients and 103 healthy individuals. A total of 11 datasets with RNA-seq transcriptomic data were obtained from the Gene Expression Omnibus and the European Nucleotide Archive. The identified DEGs were used to construct protein interaction and functional networks and to identify related pathways and miRNAs. We found 35 DEGs common between lung and the whole blood, and importantly, 2 novel genes, namely CYP1B1 and TNFAIP6, which have not been previously implicated with COVID-19. We also identified four novel miRNA potential regulators, hsa-mir-192-5p, hsa-mir-221-3p, hsa-mir-4756-3p, and hsa-mir-10a-5p, implicated in lung or other diseases induced by coronaviruses. In summary, these findings offer new molecular leads and insights to unpack COVID-19 systems biology in a whole organism context and might inform future antiviral drug, diagnostics, and vaccine discovery efforts.

RNA Sequencing Demonstrates That Circular RNA Regulates Avian Influenza Virus Replication in Human Cells

Circular RNAs (circRNAs) are involved in diverse biological processes. Avian influenza virus (AIV) can cross the species barrier to infect humans. Here, we employed RNA sequencing technology to profile circRNA, microRNA, and mRNA expression in human lung carcinoma cells in response to AIV or human influenza A virus (IAV) infection at viral replication. The analysis revealed that the expression of 475 common circRNAs were significantly regulated. The 381 and 1163 up-regulated circRNAs were induced by AIV at 8 and 16 h, respectively. Subsequently, gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses were also conducted for the AIV-specific up-regulated circRNAs. Moreover, the circRNAs were characterized, of which six were verified by quantitative real-time PCR. We further confirmed that expression of the selected circRNAs only increased following AIV infection. Knocking down the selected circRNAs promoted AIV proliferation, and overexpression of three of the candidate circRNAs restricted AIV replication and proliferation. We further analyzed that AIV-specific up-regulated circRNA mechanisms might function through the ceRNA network to affect the “Endocytosis” pathway and the “Cell cycle process”. These data provide the first expression profile of AIV-specific up-regulated circRNAs and shed new light on the pathogenesis of AIV infection. Our findings also suggest that these circRNAs serve an important role in AIV infection.

Circulating microRNA signatures associated with disease severity and outcome in COVID-19 patients

Background

SARS-CoV-2 induces a spectrum of clinical conditions ranging from asymptomatic infection to life threatening severe disease. Host microRNAs have been involved in the cytokine storm driven by SARS-CoV-2 infection and proposed as candidate biomarkers for COVID-19.

Methods

To discover signatures of circulating miRNAs associated with COVID-19, disease severity and mortality, small RNA-sequencing was performed on serum samples collected from 89 COVID-19 patients (34 severe, 29 moderate, 26 mild) at hospital admission and from 45 healthy controls (HC). To search for possible sources of miRNAs, investigation of differentially expressed (DE) miRNAs in relevant human cell types in vitro.

Results

COVID-19 patients showed upregulation of miRNAs associated with lung disease, vascular damage and inflammation and downregulation of miRNAs that inhibit pro-inflammatory cytokines and chemokines, angiogenesis, and stress response. Compared with mild/moderate disease, patients with severe COVID-19 had a miRNA signature indicating a profound impairment of innate and adaptive immune responses, inflammation, lung fibrosis and heart failure. A subset of the DE miRNAs predicted mortality. In particular, a combination of high serum miR-22-3p and miR-21-5p, which target antiviral response genes, and low miR-224-5p and miR-155-5p, targeting pro-inflammatory factors, discriminated severe from mild/moderate COVID-19 (AUROC 0.88, 95% CI 0.80-0.95, p<0.0001), while high leukocyte count and low levels of miR-1-3p, miR-23b-3p, miR-141-3p, miR-155-5p and miR-4433b-5p predicted mortality with high sensitivity and specificity (AUROC 0.95, 95% CI 0.89-1.00, p<0.0001). In vitro experiments showed that some of the DE miRNAs were modulated directly by SARS-CoV-2 infection in permissive lung epithelial cells.

Conclusions

We discovered circulating miRNAs associated with COVID-19 severity and mortality. The identified DE miRNAs provided clues on COVID-19 pathogenesis, highlighting signatures of impaired interferon and antiviral responses, inflammation, organ damage and cardiovascular failure as associated with severe disease and death.