Understanding the molecular mechanisms underlying the role of the vaginal microbiome in HIV acquisition risk is an essential step toward safer and more effective HIV prevention. We hypothesized that the resident microbiota regulates micro(mi)-RNAs that can interfere with host pathways exploited by the virus. MiRNAs are endogenous short non-coding RNA molecules that are stably carried in circulation by extracellular vesicles and exert post-transcriptional epigenetic regulation with emerging significance in HIV infection. Their role in the anti-viral mucosal barrier function is unknown.
The study utilized 112 cervicovaginal specimens from healthy reproductive-age women collected during the luteal phase of the menstrual cycle. All subjects were confirmed negative for sexually transmitted infections at the time of sampling. Vaginal microbiota was classified by Nugent scores and microbiome sequencing. Levels of miRNAs were quantified in extracellular vesicles isolated from the cervicovaginal secretions using the EdgeSeq global transcriptome platform. Differential expression (DE) was determined using Bioconductor DESeq2. miRNA target prediction was performed using miRNAtap Bioconductor package.
Cervicovaginal miRNA profiles varied by both Nugent score categories (0-3 scores – normal, 4-6 – intermediate, and 7-10 – bacterial vaginosis, BV) and by metagenome classification. Higher microbiome diversity was associated with higher number of significantly dysregulated miRNAs (373 in BV versus 119 in Nugent 4-6 compared to Nugent 0-3, FDR<0.1, p<0.01). The miRNAs dysregulated by BV overlapped with 66% of the miRNAs which were up or down regulated in G. vaginalis-dominated compared to L. crispatus-dominated metagenomes. The gene ontology predictions based on BV-dysregulated miRNAs identified enrichment for 88 genes previously validated as part of the HIV-host interactome facilitating infection. Gene clusters identified with highest stringency included proteasome and chaperonin pathways, virus entry receptor clusters, host signaling pathways downstream from NF-KB, TNFα, T-cell receptor and the MAPK cascade. Highest enrichment scores were achieved for the TCP-1 ring complex which interacts with the HIV Vif.
We identified miRNAs regulated by vaginal dysbiosis that may facilitate immune imbalance and cellular pathways associated with HIV risk.