HIV-specific CD8⁺ T-cells in tonsils express exhaustive T_RM-like signatures

Abstract

Lymphoid tissues are an important HIV reservoir site that persists in the face of antiretroviral therapy and natural immunity. Targeting these reservoirs by harnessing the antiviral activity of local tissue resident memory ( T_RM) CD8⁺ T-cells is of great interest, but limited data exist on T_RMs within lymph nodes of people living with HIV (PLWH). Here, we studied tonsil CD8⁺ T-cells obtained from PLWH and uninfected controls from South Africa. We show that these cells are preferentially located outside the germinal centers (GCs), the main reservoir site for HIV, and display a low cytolytic and transcriptionally T_RM-like profile that is distinct from blood. In PLWH, CD8⁺ T_RM-like cells are highly expanded and adopt a more cytolytic, activated and exhausted phenotype characterized by increased expression of CD69, PD-1 and perforin, but reduced CD127. This phenotype was enhanced in HIV-specific CD8⁺ T-cells from tonsils compared to matched blood. Single-cell profiling of these cells revealed a clear transcriptional signature of T-cell activation, clonal expansion and exhaustion ex-vivo. In contrast, this signature was absent from HIV-specific CD8⁺ T-cells in tonsils isolated from a natural HIV controller, who expressed lower levels of cell surface PD-1 and CXCR5, and reduced transcriptional evidence of T-cell activation, exhaustion and cytolytic activity. Thus, we show that HIV-specific T_RM-like CD8⁺ T-cells in tonsils from non-HIV controllers are enriched for activation and exhaustion profiles compared to those in blood, suggesting that lymphoid HIV-specific CD8⁺ T_RM cells are potentially ideal candidates for immunotherapy to modulate their ability to targeting the HIV reservoirs.