Spatial regulation of CD8+ T cells at the HLA-E-NKG2A axis drives HIV persistence in Lymph Node B Cell Follicles

B cell follicles (BCF) in the lymph node are a major sanctuary for HIV reservoirs. Immune regulatory mechanisms hindering cytolytic CD8+ responses at these sites, are poorly characterized, likely enabling HIV persistence. Spatial transcriptomics and high- dimensional histocytometry were used to define CD8+ T cell function and immune regulation in LN follicles of people Living with HIV (PLWH), at various stages of ART- treatment. Histocytometry demonstrated that CD8+ T cells infiltrating BCF mostly lacked granzyme B expression, coinciding with reduced chromatin access at cytolytic gene loci in dissociated lymph node cells. Spatial transcriptomics confirmed the immune regulatory microenvironment of HIV-infected BCF, particularly exhibiting upregulation of HLA-E. Additional FACS analysis identified a subset of LN CD8+ T cells expressing the NKG2A-interacting partner of HLA-E, with reduced granzyme B expression. These findings reveal regulation of follicular CD8+ T cells at the HLA-E- NKG2A axis as a key mechanism for HIV immune evasion. Overall design: Samples were extracted from participant lymph nodes and peripheral blood. ATAC-Seq data was generated from 6 Lymph Node residing CD8+ T cells and 5 Peripheral blood CD8+ T cells, with two samples paired between peripheral Lymph Node and Blood samples. RNA-Seq data were generated from 3 Lymph Node CD8+ T cells and 4 Peripheral Blood CD8+ T cells, with three paired samples between the Lymph Node and Blood samples.