Identifying drivers of genital inflammation and HIV acquisition in women living in sub-Saharan Africa

PROJECT SUMMARY The majority of HIV worldwide is transmitted following heterosexual intercourse and women are twice as likely to contract HIV from heterosexual sex than men. Mucosal tissues in the female genital tract (FGT) therefore represent the frontline of transmission since they are the site at which HIV infection is first established in most

incident cases. FGT microbiota composed of diverse communities of bacteria with low Lactobacillus abundance are associated with elevated mucosal inflammation, increased numbers of cervical HIV target cells, and over four-fold higher risk of HIV acquisition. In our prior work with the FRESH (Females Rising through Education,

Support and Health) study, we demonstrated that these high-risk bacterial communities are present in over 60% of young, healthy, black South African women. The specific mechanisms by which vaginal microbiota contribute to HIV acquisition risk remain unknown. To address these knowledge gaps, we will utilize samples from 1200

FRESH participants with longitudinal blood and genital sampling, including pre- and post-infection samples from 102 women who went on to acquire HIV. In Aim 1.1 we will generate multi-omics datasets characterizing vaginal microbiota utilizing metagenomics, metatranscriptomics, fungal internally transcribed spacer (ITS) sequencing,

culturomics, microbial whole genome sequencing (WGS), and metabolomics. We will complement this in Aim 1.2 with a comprehensive characterization of the host FGT mucosal environment by assessing genital inflammatory chemokines and cytokines, cervical flow cytometric cell phenotype, and cervical single cell RNA

sequencing (scRNAseq) profiles, combined with in-depth behavioral and demographic metadata. These complex multi-omics datasets and metadata will then be integrated in Aim 1.3 following critical quality control, transformation, and imputation of data from each modality. Modern supervised integration techniques will be

used to identify multi-omics profiles predictive of genital inflammation and HIV acquisition. Novel candidate vaginal bacterial strains, functions, and/or metabolites will then be validated in Aim 2 using innovative in vitro and in vivo models, including an organ-on-a-chip model, cervical and vaginal organoids, and a humanized mouse

model. [In addition, we will test candidate features and hypotheses based upon our extensive preliminary data and established work in the field]. Overall, this project will identify specific bacterial strains and molecules, along with host cellular lineages and sensing pathways, that mediate microbiota-induced genital inflammation and

increased HIV acquisition risk. It will also validate much needed novel model systems that test the interactions of microbiota, host, and HIV to provide critical resources to develop the mechanistic understanding needed to advance the field.