A proteomic signature of HIV infection: insights into new vaccine and drug targets

An estimated 33.3 million adults and children are infected with human immunodeficiency virus (HIV), and 2.6 million new cases are diagnosed every year. Therefore, there is a pressing need for a prophylactic vaccine and an efficient cure for HIV. An effective prophylactic vaccine would provide protection by inducing neutralising antibodies and also elicit a robust cytotoxic lymphocyte response to eliminate virus-infected cells. CD8+ T-cells detect and kill virus-infected cells after recognising viral peptide antigens presented by Human Leukocyte Antigen (HLA) class I molecules. CD4+ T-cells play a central role in adaptive immunity by licensing immune action against pathogens after recognising peptides bound to HLA class II molecules. A hallmark of HIV infection is the tropism of the virus for CD4+ T-cells, leading to an immunocompromised state in infected individuals. Two of the three major aims of this study were to identify HIV-derived peptides that may form targets of antiviral CD8+ and CD4+ T-cells. A proteomics-based approach was utilised to characterise HLA class I- and class II-bound ligands isolated from antigen presenting cells expressing disease relevant HLA molecules and selected HIV antigens. This study was able to generate one of the largest datasets of naturally presented HLA-bound peptides with around 20000 class I and 10000 class II peptides identified and characterised. Within this large dataset of constitutively presented peptides, 22 class I- and 17 class II-restricted HIV-derived ligands were identified, including previously documented T cell epitopes and several novel peptides. These previously unreported determinants included a HLA-B57-restricted peptide bearing a novel kynurenine post-translational modification. The immune reactivity towards selected peptides was subsequently measured in healthy and HIV-infected individuals. A subset of HIV-infected individuals control their viremia and do not go on to develop AIDS. This observation is frequently associated with possession of the protective HLA-B*57:01 allele. There was an efficient selection of HIV envelope derived peptides by this allele compared to other disease associated HLA allotypes. This leads to the speculation that this property of HLA-B57 may be associated with protection during HIV infection. While antiretroviral therapy has vastly improved the quality of life of those suffering from HIV, interruption of therapy leads to the reemergence of the virus. The third aim of this project was to explore the proteomes of latently infected cells, which remain the major impediment to a cure for HIV. A well-established CD4+ T-cell line model of latency (J-Lat cells) was used to generate a comprehensive quantitative protein expression map of latently infected J-Lat cells and to follow changes in protein expression after viral reactivation by TNF-alpha. More than 9000 proteins and their modifications were identified and quantitated in latent and reactivated cells, making this study the largest of its kind. Several key pathways were perturbed in latently infected cells including proteins involved in cell signalling, energy generation, and transcription factors. This data highlights that latently infected cells have a discrete proteomic signature and has unveiled new drug and immunotherapeutic targets that could be used to eliminate this pool of virus