Clonal lineage tracing of HIV specific NK memory cells

ABSTRACT Immune memory is a critical aspect of adaptive immunity. The presence of antigen-specific memory cells can provide immune control against infection, and for this reason, immunological memory is a cornerstone of vaccine protection. Adaptive immunity has long been thought to be the sole domain of B and T cells, but exciting new studies of natural killer (NK) cells memory responses has challenged this paradigm. In the case of HIV, there is evidence from animal models that rare NK cells can mount long-lasting memory responses to HIV antigens, but there is limited data that define HIV-specific NK memory in humans. NK memory has been most clearly demonstrated for HCMV, where recent studies have demonstrated the persistence of NK cell clones using a novel method for cell lineage tracking called ASAP-seq. ASAP-seq uses mitochondrial DNA mutations as endogenous barcodes for long-lived NK cell clonotypes, much like receptor rearrangements are used to mark B and T cell lineages. In addition, this method captures protein expression that can be used to identify markers associated with long-lived NK cell clones. ASAP-seq also captures epigenetic data that provides insights into the cellular changes that are associated with the NK memory cells of interest. Here we propose to apply this method to samples from a unique 30-year cohort of HIV infected women, where there are banked longitudinal samples starting prior to HIV-infection. Thus, we will examine NK cell populations before and after HIV infection, which will enable detection of new NK memory cell clones that arise/expand after HIV acquisition. In addition, we will perform ASAP-seq on HIV+ cases with and without HCMV co-infection to control for the potential confounding effect of NK memory responses to HCMV. Together, these complementary approaches are designed to identify NK memory cell clones that are specific to HIV. If HIV-specific NK memory is discovered through this innovative work, it will lay the foundation for many future studies, ranging from basic studies to define epitope specificity, and HIV-specific NK cell phenotype and function to more applied work to harness these responses to prevent and cure HIV infections.