MicroRNA signature from extracellular vesicles of HCV/HIV co-infected individuals differs from HCV mono-infected

Hepatitis C virus (HCV) coinfection with human immunodeficiency virus (HIV) has a detrimental impact on disease progression. Increasing evidence points to extracellular vesicles (EVs) as important players of the host-viral cross-talk. The microRNAs (miRNAs), as essential components of EVs cargo, are key regulators of normal cellular processes and also promote viral replication, viral pathogenesis, and disease progression. We aimed to characterize the plasma-derived EVs miRNA signature of chronic HCV infected and HIV coinfected patients to unravel the molecular mechanisms of coinfection. EVs were purified and characterized from 50 plasma samples (21 HCV mono- and 29 HCV/HIV co-infected). EV-derived small RNAs were isolated and analyzed by massive sequencing. Known and de novo miRNAs were identified with miRDeep2. Significant differentially expressed (SDE) miRNA identification was performed with generalized linear models and their putative dysregulated biological pathways were evaluated. Study groups were similar for most clinical and epidemiological characteristics. No differences were observed in EVs size or concentration between groups. Therefore, HCV/HIV co-infection condition did not affect the concentration or size of EVs but produced a disturbance in plasma-derived EVs miRNA cargo. Thus, a total of 149 miRNAs were identified (143 known and 6 de novo) leading to 37 SDE miRNAs of which 15 were upregulated and 22 downregulated in HCV/HIV co-infected patients. SDE miRNAs regulate genes involved in inflammation, fibrosis, and cancer, modulating different biological pathways related to HCV and HIV pathogenesis. These findings may help to develop new generation biomarkers and treatment strategies, in addition to elucidate the mechanisms underlying virus-host interaction. KEY MESSAGES: HCV and HCV/HIV displayed similar plasma-EV size and concentration. EVs- derived miRNA profile was characterized by NGS. 37 SDE miRNAs between HCV and HCV/HIV were observed. SDE miRNAs regulate genes involved in inflammation, fibrosis and cancer.Open Access funding provided thanks to the CRUE-CSIC agreement with Springer Nature. This work has been supported by grants from (1) Institute of Health Carlos III, Spain [PI18CIII/00020/ to AFR], (2) PID2021–126781OB-I00 funded by MCIN/AEI/10.13039/501100011033 and by “ERDF A way of making Europe”, (3) The SPANISH AIDS Research Network RD16CIII/0002/0002 - ISCIII – FEDER, (4) Centro de Investigación en Red en Enfermedades Infecciosas (CIBERINFEC) CB21/13/00044, (5) the National Agency for Scientific and Technology Promotion (ANPCyT) (PICT 2017 Nº713), and (6) the National Research Council (CONICET, PIP 2021-2023). V.C. received funding form the Asociación Universitaria Iberoamericana de Postgrado (AUIP) for the Academic Mobility Scholarship Program. P.V., E.D.M., and M.V.P. are members of the CONICET-Research Career Program. V.C. is a fellow from ANPCyT. The funder’s had no role in the study design, data collection and analysis, decision to publish, or the preparation of the manuscript.S