HIV genetic variability and isomiR presence: Effect on the effectiveness of anti-HIV microRNAs

MORANDO, NICOLAS; ROSENZVIT, MARA C; PANDO MARIA A; RABINOVICH D

Montreal

Conferencia; 23rd International AIDS Conference (AIDS 2020: Virtual); 2020

IAS

Introduction:microRNAs (miRNAs), have proven to play an important role in HIV infection. In particular, the role of miRNAs that target the nef gene is at this time of great interest on HIV latency research. miRNAs can undergo a series of post-transcriptional modifications which yield a set of isoforms of the canonical miRNA sequence (isomiRs), that could differ significantly in terms of complementarity/affinity for the canonical target site.Objectives:To predict in silico the potential effect of miRNAs/isomiRs in nef gene regulation taking into account i) HIV genetic variability, and ii) variability among canonical miRNAs and isomiRs. Methods:Target-miRNA hybridization free energy (ΔG) was calculated for all possible mRNA-miRNA pairs (Two State Melting software, DINAMelt Server) for 43 HIV nef sequences from Argentina and Brazil (subtypes B and C and five BF recombinants forms), and miRNAs reported to target nef (miR-1290, miR-196b, miR-223-3p, miR-29a-3p, miR-29b-3p, miR-326). For each miRNA, ΔG obtained with different target sequences were statistically compared using t tests. Additionally, the 10 most abundant isomiR sequences for each miRNA were included (IsomiR Bank). Target RNA secondary structure was predicted (mfold web server software, UNAFold). Results:nef genes from different HIV strains were predicted to bind to the same miRNA with different ΔG, with ΔG differences of up to 3.7 kcal/mol. Statistically significant differences between HIV belonging to different subtype/recombinant strains were found for all miRNAs except miR-223-3p (p-values: 0.026 - 7.5x10-5). Most isomiRs were predicted to bind their target with the same or higher (less favourable) ΔG than the canonical miRNA (maximum difference: 11.2 kcal/mol), whereas for miR-196b and miR-223-3p there were isomiRs that bound their target with lower (more favourable) ΔG than the canonical miRNA. Analysis of predicted target RNA secondary structures revealed that for almost all miRNAs the canonical sequence can find its target site more accessible, except for miR-29b-3p. Conclusions:Our results revealed that HIV strains belonging to different subtypes/recombinants may be differentially susceptible to miRNA-mediated silencing and that isomiRs differ from the canonical miRNA in target binding energy and are not always less effective gene silencers than their canonical counterparts. These results should be taken into consideration for miRNA study in the context of HIV latency research.