Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of COVID-19. The accessory proteins of SARS-CoV-2 have been reported to attune host immune responses and viral pathogenicity. We have studied the effect of SARS-CoV-2 accessory proteins ORF3a and ORF6 on the expression pattern of miRNAs and their impact on cell signaling pathways in human lung epithelial cells.
Methods and results: The miRNA expression profiling of human lung epithelial cells revealed a subset of 14 and 19 differentially expressed miRNAs (DEMs) in response to SARS-CoV-2 ORF3a and ORF6, respectively. Target prediction tools and subsequent bioinformatic analysis revealed the involvement of DEMs in key signaling pathways like PI3K/AKT, TNF, MAPK, TGF-β, and NF-κB, as a bystander effect of SARS-CoV-2 ORF3a and ORF6. The target genes were validated using real-time PCR and immunoblotting techniques. The results demonstrate that SARS-CoV-2 ORF3a and ORF6 exploit host cellular miRNAs such as hsa-miR-101-3p, hsa-miR-4455, hsa-miR-10b-5p, hsa-miR-940, and hsa-miR-4483, etc. to modulate the key cellular signaling pathways like NF-κB, TGF-β, Ras, IL-17, MAPK, and TNF signaling pathways.
Conclusions: The present study demonstrates that SARS-CoV-2 ORF3a and ORF6 modulate the miRNA expression pattern in human lung epithelial cells. ORF3a exploits miRNAs to trigger a pro-inflammatory response, while ORF6 antagonizes IFN signaling via miRNA dysregulations to help SARS-CoV-2 in evading the host's immune response.
Keywords: COVID-19; SARS-CoV-2; Viral accessory proteins; miRNA-mRNA interaction network; microRNAs.
© 2025. The Author(s), under exclusive licence to Springer Nature B.V.