Background MicroRNAs (miRNAs) have a crucial role in regulating immune response against infectious diseases, showing changes early in disease onset and before the detection of the pathogen. Thus, we aimed to analyze the plasma miRNA profile at COVID-19 onset to identify miRNAs as early prognostic biomarkers of severity and survival. Methods and results Plasma miRNome of 96 COVID-19 patients that developed asymptomatic/mild, moderate and severe disease was sequenced together with a group of healthy controls. Plasma immune-related biomarkers were also assessed. COVID-19 patients showed 200 significant differentially expressed (SDE) miRNAs concerning healthy controls, with upregulated putative targets of SARS-CoV-2, and inflammatory miRNAs. Among COVID-19 patients, 75 SDE miRNAs were observed in asymptomatic/mild compared to symptomatic patients, which were involved in platelet aggregation and cytokine pathways, among others. Moreover, 137 SDE miRNAs were identified between severe and moderate patients, where miRNAs targeting the SARS CoV-2 genome were the most strongly disrupted. Finally, we constructed a mortality predictive risk score (miRNA-MRS) with ten miRNAs. Patients with higher values had a higher risk of 90-days mortality (hazard ratio = 4.60; p -value < 0.001). Besides, the discriminant power of miRNA-MRS was significantly higher than the observed for age and gender (AUROC = 0.970 vs. 0.881; p = 0.042). Conclusions SARS-CoV-2 infection deeply disturbs the plasma miRNome from an early stage of COVID-19, making miRNAs highly valuable as early predictors of severity and mortality.
Background: Interest in microbiome research has increased exponentially in recent years. However, the growth in the number of studies has outpaced the standardization of the processing and analysis of microbiome samples. This lack of standardization represents a major limitation that hampers the replication of results across studies and the clinical translation of research findings. The major source of variation in microbiome results on the experimental side are differences in the methods of DNA extraction from fecal samples. In this study, we aimed to compare the metagenomic profiles obtained by using two commercially available DNA extraction kits, and their effects on microbiome diversity, composition and associations to phenotypes. Methods and Results: We compared two commonly used DNA extraction kits, the AllPrep DNA/RNA Mini Kit (APK) and the QIAamp Fast DNA Stool Mini Kit (FSK), in 745 paired samples from two independent population cohorts: Lifelines-DEEP (LLD, n = 292), and 500 Functional Genomics project (500FG, n = 453). We evaluated the performance of both methods for DNA yield and quality and explored whether the DNA extraction protocol introduces heterogeneity in microbiota composition and diversity or in phenotype–microbiome associations. In both cohorts, APK protocol yields a higher DNA concentration and alpha diversity, with 25% and 10% more bacterial species being detected in comparison to the FSK method in LLD and 500FG cohorts, respectively. Both extraction kits result in markedly different community composition and microbial abundances, with >80% of species being differentially abundant in both cohorts. Species belonging to Firmicutes and Actinobacteria show increased abundances in the APK protocol, whereas Bacteroidetes and Proteobacteria are more prevalent in FSK samples. These differences lead to significant variations in the phenotypic association profile with gut microbes.Conclusions: The results of this study further reinforce that choice of DNA extraction method impacts metagenomic profile of human gut microbiota. We demonstrate that accounting for differences in fecal sample processing is essential for improving the reproducibility of microbiome research findings.
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