Integrated miR-omics and proteomics reveal the regulatory role of miR in protein networks associated with COVID-19 disease progression

Abstract

Introduction While microRNA (miR) expression profiling has identified potential biomarkers in patients with COVID-19, the regulatory mechanisms by which miRs modulate disease severity remain poorly characterized. We performed integrated miR–proteome analysis to elucidate mechanistic relationships between miR regulation and COVID-19 severity. Method Deidentified plasma samples from 93 participants with acute COVID-19 were categorized by severity using a 12-point symptom scoring system: mild (0–1), moderate (2–4), and severe (5–12). miR and proteomic profiles were analyzed using univariate statistics, pathway analysis, miR-target prediction, and correlation analysis. Differentially expressed miRNAs (DEMs) and differentially expressed proteins (DEPs) between the three severity groups from the original cohort were evaluated in a validation cohort of 94 participants. Results We identified 365 unique miRs and 801 unique proteins that were significantly associated with COVID-19 severity in any of the three comparisons. Ingenuity pathway analysis revealed neutrophil degranulation, cytokine storm, interleukin-10 (IL-10) signaling, and wound healing signaling as top dysregulated pathways in severe versus mild cases, with IL-6 involved in 9 of the 10 most significant pathways. Correlation analysis between miRs and proteins from 93 participants identified 6,559 miR–protein pairs with |r| > 0.5, of which 83.6% were negative correlations, suggesting widespread miR-mediated downregulation of protein expression. A significant correlation (r = 0.43, p < 0.0001) was found between 122 predicted miR–protein pairs found in the discovery cohort and the same miR–protein pairs in the validation cohort. Discussion To our knowledge, this represents the first integrated analysis of circulating miRs and proteins from the same COVID-19 participants and separately in a validation cohort. The high frequency of negative miR–protein correlations combined with target prediction analysis suggests that miRs play regulatory roles in COVID-19 severity-associated pathways. These findings provide mechanistic insights into miR regulation of host immune responses and identify potential biomarkers that could inform therapy of COVID-19.