Innate immune signatures to a partially-efficacious HIV vaccine predict correlates of HIV-1 infection risk

The pox-protein regimen tested in the RV144 trial is the only vaccine strategy demonstrated to prevent HIV-1 infection. Subsequent analyses identified antibody and cellular immune responses as correlates of risk (CoRs) for HIV infection. Early predictors of these CoRs could provide insight into vaccine-induced protection and guide efforts to enhance vaccine efficacy. Using specimens from a phase 1b trial of the RV144 regimen in HIV-1-uninfected South Africans (HVTN 097), we profiled innate responses to the first ALVAC-HIV immunization. PBMC transcriptional responses peaked 1 day post-vaccination. Type I and II interferon signaling pathways were activated, as were innate pathways critical for adaptive immune priming. We then identified two innate immune transcriptional signatures strongly associated with adaptive immune CoR after completion of the 4-dose regimen. Day 1 signatures were positively associated with antibody-dependent cellular cytotoxicity and phagocytosis activity at Month 6.5. Conversely, a signature present on Days 3 and 7 was inversely associated with Env-specific CD4+ T cell responses at Months 6.5 and 12; rapid resolution of this signature was associated with higher Env-specific CD4+ T-cell responses. These are the first-reported early immune biomarkers of vaccine-induced responses associated with HIV-1 acquisition risk in humans and suggest hypotheses to improve HIV-1 vaccine regimens.
Author summary The innate immune response is the body’s initial defense against pathogens and is linked to and shapes the subsequent adaptive immune response, which can confer long-lasting protection. For a vaccine with partial efficacy, such as the RV144 HIV vaccine regimen, identifying early innate responses that are linked with adaptive responses—particularly those for which evidence has accumulated that they might be important for protection—could help a more efficacious version be developed. In the HVTN 097 study, the RV144 prime-boost (ALVAC-HIV and AIDSVAX B/E) vaccine regimen was given to South African participants. We characterized the innate response to the first dose of ALVAC-HIV in these participants and identified gene expression signatures present within the first few days that were associated with antibody and T-cell responses to the full vaccine regimen measured up to 1 year later. As these antibody and T-cell responses have previously been implicated in protection, our findings suggest ways of refining the RV144 regimen and also have broader applications to vaccine development.