Altered microRNA Transcriptome in Cultured Human Airway Cells upon Infection with SARS-CoV-2

Abstract

Numerous proteomic and transcriptomic studies have been carried out to better understand the current multi-variant SARS-CoV-2 virus mechanisms of action and effects. However, they are mostly centered on mRNAs and proteins. The effect of the virus on human post-transcriptional regulatory agents such as microRNAs (miRNAs), which are involved in the regulation of 60% of human gene activity, remains poorly explored. Similar to research we have previously undertaken with other viruses such as Ebola and HIV, in this study we investigated the miRNA profile of lung epithelial cells following infection with SARS-CoV-2. At the 24 and 72 h post-infection time points, SARS-CoV-2 did not drastically alter the miRNome. About 90% of the miRNAs remained non-differentially expressed. The results revealed that miR-1246, miR-1290 and miR-4728-5p were the most upregulated over time. miR-196b-5p and miR-196a-5p were the most downregulated at 24 h, whereas at 72 h, miR-3924, miR-30e-5p and miR-145-3p showed the highest level of downregulation. In the top significantly enriched KEGG pathways of genes targeted by differentially expressed miRNAs we found, among others, MAPK, RAS, P13K-Akt and renin secretion signaling pathways. Using RT-qPCR, we also showed that SARS-CoV-2 may regulate several predicted host mRNA targets involved in the entry of the virus into host cells (ACE2, TMPRSS2, ADAM17, FURIN), renin–angiotensin system (RAS) (Renin, Angiotensinogen, ACE), innate immune response (IL-6, IFN1β, CXCL10, SOCS4) and fundamental cellular processes (AKT, NOTCH, WNT). Finally, we demonstrated by dual-luciferase assay a direct interaction between miR-1246 and ACE-2 mRNA. This study highlights the modulatory role of miRNAs in the pathogenesis of SARS-CoV-2.

Using the power of innate immunoprofiling to understand vaccine design, infection, and immunity

“… 18 RNAseq is commonly partnered with RT-qPCR to look at host mRNA targets involved with viral entry into host cells, the innate immune response including cytokine production, fundamental cellular processes, and interactions between miRNAs and mRNAs to alter host pathways. 19 However, bulk RNAseq can mask which specific cell types are driving disease progressions or resistance. By contrast, single-cell RNAseq (sc-RNAseq) evaluates the individual expression of cells, and thousands at a time.…”

“…When combined, bulk RNAseq and single-cell RNA seq are beneficial in establishing immune and inflammatory mechanisms of infection-induced organ damage. 19 , 20 These tools have been incredibly useful during the SARS-CoV-2 pandemic. Both bulk and single cells are used to understand multivariant SARS-CoV-2 including viral immune evasion.…”

“…Both bulk and single cells are used to understand multivariant SARS-CoV-2 including viral immune evasion. 19 Groups use this technology to understand the expression of mRNAs, proteins, posttranscriptional regulatory agents such as micro-RNAs (miRNA) and long noncoding RNA (lncRNA). 19–21 Combining the expression of miRNAs with the upregulation of different genetic pathways which can be identified via the Kyoto Encyclopedia of Genes and Genomes database (KEGG) sheds light on which secretion and signaling pathways are altered during the course of SARS-CoV-2 infection in the lungs.…”

“… 19 Groups use this technology to understand the expression of mRNAs, proteins, posttranscriptional regulatory agents such as micro-RNAs (miRNA) and long noncoding RNA (lncRNA). 19–21 Combining the expression of miRNAs with the upregulation of different genetic pathways which can be identified via the Kyoto Encyclopedia of Genes and Genomes database (KEGG) sheds light on which secretion and signaling pathways are altered during the course of SARS-CoV-2 infection in the lungs. 19 In addition to peripheral samples, organ tissues can be directly sampled from patients to assess the severity of infection, upregulation of innate immune responses (including inflammatory genes IL-2, IL-6, IL-8, IL-17A, and NF-kB).…”

“… 19–21 Combining the expression of miRNAs with the upregulation of different genetic pathways which can be identified via the Kyoto Encyclopedia of Genes and Genomes database (KEGG) sheds light on which secretion and signaling pathways are altered during the course of SARS-CoV-2 infection in the lungs. 19 In addition to peripheral samples, organ tissues can be directly sampled from patients to assess the severity of infection, upregulation of innate immune responses (including inflammatory genes IL-2, IL-6, IL-8, IL-17A, and NF-kB). 19–22 Upregulation of these cytokines has downstream effects that can lead to organ injury and have therefore been valuable to understand the mechanisms during the pandemic.…”