AUTHOR=Siniscalchi Chiara , Di Palo Armando , Russo Aniello , Potenza Nicoletta 

TITLE=Human MicroRNAs Interacting With SARS-CoV-2 RNA Sequences: Computational Analysis and Experimental Target Validation

JOURNAL=Frontiers in Genetics

VOLUME=Volume 12 - 2021

YEAR=2021

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2021.678994

DOI=10.3389/fgene.2021.678994

ISSN=1664-8021

ABSTRACT=Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel RNA virus affecting humans causing a form of acute pulmonary respiratory disorder named COVID-19, declared a pandemic by World Health Organization. MicroRNAs play an emerging and important role in the interplay between viruses and host cells. Although the impact of host microRNAs on SARS-CoV-2 infection has been predicted, experimental data are still missing. 
This study started by a bioinformatics prediction of cellular microRNAs potentially targeting viral RNAs; then, a number of criteria also based on experimental evidence and virus biology were applied, giving rise to 8 promising binding microRNAs. Their interaction with viral sequences were experimentally validated by transfecting luciferase-based reporter plasmids carrying viral target sequences or their inverted sequences into the lung A549 cell line. Transfection of reporter plasmids resulted in a reduction of luciferase activity for 5 out of the 8 potential binding sites, suggesting responsiveness to endogenously expressed microRNAs. Co-transfection of reporter plasmids along with microRNA mimics led to a further and strong reduction of luciferase activity, validating the interaction between miR-219a-2-3p, miR-30c-5p, miR-378d, miR-29a-3p, miR-15b-5p and viral sequences. miR-15b was also able to repress plasmid-driven Spike expression.  Intriguingly, the viral target sequences are fully conserved in more recent variants such as UK variant B.1.1.7 and South Africa 501Y.V2.
Overall, this study provides a first experimental evidence of the interaction between specific cellular microRNAs and SARS-CoV-2 sequences, thus contributing to understand the molecular mechanisms underlying virus infection and pathogenesis to envisage innovative therapeutic interventions and diagnostic tools.