SARS-CoV-2 accessory proteins ORF3a and ORF6 alter the miRNome of human lung epithelial cells

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.

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.

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.