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

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 the World Health Organization. MicroRNAs (miRNA) play an emerging and important role in the interplay between viruses and host cells. Although the impact of host miRNAs on SARS-CoV-2 infection has been predicted, experimental data are still missing. This study started by a bioinformatics prediction of cellular miRNAs potentially targeting viral RNAs; then, a number of criteria also based on experimental evidence and virus biology were applied, giving rise to eight promising binding miRNAs. Their interaction with viral sequences was experimentally validated by transfecting luciferase-based reporter plasmids carrying viral target sequences or their inverted sequences into the lung A549 cell line. Transfection of the reporter plasmids resulted in a reduction of luciferase activity for five out of the eight potential binding sites, suggesting responsiveness to endogenously expressed miRNAs. Co-transfection of the reporter plasmids along with miRNA 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 United Kingdom variant B.1.1.7 and South Africa 501Y.V2. Overall, this study provides a first experimental evidence of the interaction between specific cellular miRNAs and SARS-CoV-2 sequences, thus contributing to understanding the molecular mechanisms underlying virus infection and pathogenesis to envisage innovative therapeutic interventions and diagnostic tools.

SARS-CoV-2, Cardiovascular Diseases, and Noncoding RNAs: A Connected Triad

“…SARS-CoV-2 may act as a sponge of these miRNAs, being potentially titrated on the viral genome and resulting in an altered regulation of canonical miRNA targets [55]. An additional computational analysis confirmed that the SARS-CoV-2 genome potentially associates with host hsa-miR-3529-3p, hsa-miR-451b, hsa-miR-499b-3p, and hsa-miR-5688 [56,73].…”

“…The data reported by Moazzam-Jazi and coworkers indicate that several human lncRNAs preferentially interact with the 5 end of SARS-CoV-2 rather than the 3 end [66], reinforcing the possibility to design RNA-based vaccines against the 5 end of the virus. Accordingly, H19, MIAT, FENDRR, and linc01505 show BS against the SARS-CoV-2 leader sequence [53,56,73,127].…”

“…A number of in silico studies analyzed the common features of viral 5 UTR, identified conserved motifs in the TRSs and the leader sequence selectively recognized by miRNAs, and identified specific lncRNAs that may negatively modulate viral genome expression and possibly reduce SARS-CoV-2 infectivity [53,56,73,127]. Baldassarre and coworkers [127] described a putative binding of miR-4507, miR-638, miR-3150b-3p, and miR-602 highly expressed in the lung at the 5 UTR of SARS-CoV-2.…”

The role of microRNAs in solving COVID-19 puzzle from infection to therapeutics: A mini-review

“…Under this premise, a relevant inquiry buttressed that some human miRNAs, such as miR-219a-2-3p, miR-30c-5p, miR-378d, miR-29a-3p, and miR-15b-5p, can interact with the viral sequences of SARS-CoV-2. Intriguingly, the outcomes of this investigation stated that the complete complementary target sequences of the aforesaid miRNAs are conserved in some of the newly emerged variants of the virus, i.e., South Africa 501Y.V2 and United Kingdom variant B.1.1.7 ( Siniscalchi et al, 2021 ). Therefore, to obtain an effective and safe miRNA-based treatment for COVID-19, further inquiries should assure that the interactions between human miRNAs and SARS-CoV-2’s genome sequences are conserved in almost all the existing variants of the virus.…”

The Non-Coding RNA Journal Club: Highlights on Recent Papers—9

“…Effective therapeutic strategies against the coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are desperately needed. In a recent issue of Frontiers in Genetics , Chiara Siniscalchi and collaborators [ 5 ] identify some miRNAs targeting SARS-CoV-2 RNA. Specifically, starting with a well-designed bioinformatic analysis that pinpointed eight candidate miRNAs, the authors went on to validate the functional interaction of five miRNAs (namely miR-15b-5p, miR-29a-3p, miR-30c-5p, miR-219a-2-3p, and miR-378d) with viral sequences in a human lung cell line.…”