Designing T-cell Based HIV Vaccines using Peptide-MHC Surface Morphology

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DESCRIPTION: This proposal is a renewal application of the Parent R01 project (AI083115). This application builds upon our accomplishments made during the project period wherein our mathematical frameworks enabled us to identify transmitted HIV strains, assess the duration of infection, estimate the number of founder variants establishing a systemic infection, and design a novel genomic HIV incidence assay. This has been a significant and beneficial contribution to the HIV research community. In the present application, we propose to expand our research toward designing prophylactic HIV vaccines. Humoral immunity has been a significant focus of HIV vaccines since the Thai Phase III clinical trial showed 31% vaccine efficacy in reducing HIV acquisition in 2012. Properly arming the other branch of the adaptive immune system, namely, cytotoxic T lymphocytes, is an important task to ensure full protection against breakthrough viruses, as evidenced in many previous studies on elite controllers and non-human primate models. To obtain a vital lesson applicable to next generation T cell vaccines, we will perform an in-depth analysis of the STEP and Phambili vaccine trials, which showed no efficacy even though the vaccine elicited robust HIV-specific CD8+ T cell responses in study participants. Preliminary data gathered in this application has identified a statistically significant signature f vaccine- enhanced viral escapes, which aligns with one of the key hypotheses for the failure of the STEP and Phambili trials. This proposal focuses on defining a novel immune correlate capable of inducing broad T cell responses which would be beneficial for preventing viral escapes. In previous studies of human and mice influenza infections, peptide-MHC surface morphology has been shown to control T cell breadth. By compiling the list of escape-prone and escape-resistant T cell epitopes from the STEP and Phambili trials and the HIV immunology database, we will test a hypothesis that the conformation of the peptide in the groove is a critica feature of escape variation. Our team will employ our newly developed computational algorithms predicting peptide-MHC conformation alongside high resolution X-ray crystallography to test this hypothesis. Once the association between peptide-MHC surface morphology and viral escapes is revealed, this proposal will provide a concrete roadmap for enhancing immunogenicity of vaccines by identifying MHC binding antigens capable of eliciting broad T cell responses, which would potentially be beneficial for suppressing viral escapes. The proposed study will advance HIV vaccine research by offering a novel prospective immune correlate of peptide-MHC surface morphology which can be used to prioritize HIV peptide vaccine candidates for protection and/or long term viral control.