Interrogation of rectal mucosal responses to HIV vaccination in the HVTN100B trial using proteomic and metagenomic profiling

Abstract: Traditional assessments of HIV vaccine responses rely on serum-level measurements, overlooking immunity at mucosal portals of viral entry. To address this gap, we leverage untargeted proteomic and shotgun metagenomic profiling of rectal secretions from the HVTN100B trial, an ALVAC-HIV + bivalent subtype C gp120/MF59 regimen with a late boost and characterize the localized impact of vaccination between vaccinated (n=18) and placebo (n=5) arms. We identified 105 differentially expressed proteins, performed functional enrichment, and developed a protein–protein interaction network. Exploratory associations between rectal proteins, Env-specific IgG binding responses, limited antigen-specific IgA reactivity, and microbial taxa in vaccinated HVTN100B participants suggest potential relationships between the mucosal proteome, vaccine immunogenicity, and the local microbial environment. Modest concordance was observed between rectal mucosal proteins and systemic V1V2-specific IgG and CD4⁺ T-cell responses, suggesting distinct patterns of humoral and cellular immune activity upon HVTN100B vaccination. Together, these exploratory findings underscore the value of mucosal interrogation and its potential to inform more targeted approaches to future HIV vaccine development.