Project 1: Systemic analysis of the origin and tissue effects of the 68-1 RhCMV/SIV vaccine efficacy-predictive whole blood transcriptomic signature

Project 1 Summary Vaccination of Rhesus macaques (RMs) with SIV insert-expressing 68-1 Rhesus Cytomegalovirus vectors (RhCMV/SIV) elicits an immune response that in 59% of vaccinees can intercept and effectively arrest an early spreading primary SIV infection. The vast majority of vaccinated RM that manifest SIV replication arrest go to completely clear SIV infection, a remarkable outcome with enormous potential clinical significance. This unique pattern of “arrest and clear” efficacy has been linked to major histocompatibility complex (MHC)-E-restricted SIV- specific CD8+ T cell responses and in RMs with MHC-E-restricted CD8+ T cell responses, a protection-predictive innate immune transcriptional response to vaccination in whole blood (the whole blood protection-predictive signature or wbPPTS) that includes a central IL-15 signaling component. RhCMV/SIV vaccinated RM destined for arrest and clear efficacy manifest low baseline IL-15 signaling (IL-15 quiescence) and high post vaccination IL-15 signaling which persists through to SIV challenge. Since IL-15 is the major cytokine regulator of effector memory T cell physiology, including regulation of effector function, activation thresholds, population homeostasis, and homing behavior, these observations that correlation between the magnitude and persistence of IL-15 signaling induction and protection might reflect an IL-15-mediated modulation of the SIV-specific MHC- E-restricted CD8+ T cells, but IL-15 is not the only pathway in the wbPPTS and its unclear whether IL-15 or other components of the wbPPTS contribute to the tissue-based immune programming that enables vaccine efficacy. In this project, we seek to delineate the origin and tissue correlates of the wbPPTS and its IL-15 dependence in order the delineate the fundamental components of vaccine-induced innate immune programming required for efficacy. We will achieve this goal by determining 1) the systemic transcriptomic correlates of the RhCMV/SIV vaccine-induced wbPPTS in peripheral and mucosal lymphoid tissues and its dependence on IL-15 signaling (S.A.1), 2) the specific spatial transcriptomic response to RhCMV/SIV-infected cells in tissues and the direct contribution of vector-infected cells to the local and systemic transcriptomic responses linked to wbPPTS programming (S.A.2), and 3) the mechanisms underlying the association between IL-15 signaling quiescence and generation of the wbPPTS (S.A.3). We expect these data to implicate an underlying immune mechanism for RhCMV/SIV vaccine-induced arrest and clear protection, to provide validated tissue-based immune correlates for clinical translation, and, potentially, to lead to vaccine modifications that would increase the efficacy of CMV- based SIV/HIV vaccines.