CD8+ T cell stemness precedes post-intervention control of HIV viremia

Interventions to induce lasting HIV remission are needed to obviate the requirement for lifelong antiretroviral therapy (ART). Durable post-intervention control (PIC) of viremia has been achieved in a subset of individuals following broadly neutralizing anti-HIV-1 antibody (bNAb) administration and analytical treatment interruption (ATI)1-4. Prior studies support a role for CD8+ T cells5-9 but the precise features of CD8+ T cells involved in PIC remain unclear. Here we mapped and functionally profiled CD8+ T cell responses to autologous HIV epitopes using longitudinal samples from four ATI trials in bNAb recipients. PIC was associated with superior pre-intervention HIV-specific CD8+ T cell proliferative capacity, stem cell-like memory phenotype, and recall cytotoxicity against autologous HIV peptide-pulsed CD4+ T cells. CD8+ T cell stemness was further increased following bNAb administration without emergence of new clonotypes targeting defined HLA-optimal epitopes. Multimodal single-cell analyses revealed molecular features associated with PIC and HIV-specific CD8+ T cell stemness, including signatures of metabolic fitness and reduced T cell exhaustion. These results identify immune features that precede subsequent PIC to inform the development of combination immunotherapies that will elicit durable HIV remission. Overall design: HIV and CMV epitope-specific CD8+ T cells were isolated from participant PBMCs by FACS using combinations of barcoded fluorescent peptide-HLA tetramers among longitudinal samples collected before (pre) and/or following (post) infusion of broadly-neutralizing antibodies against HIV-1 and analytical treatment interruption. Each sample was also stained with a unique barcoded hashing antibody (HTO) and a panel of commercially available library of barcoded surface antibodies prior to isolation. Gene expression (GEX), antibody-derived tags (ADT), and T cell receptor (VDJ) sequencing libraries were prepared using 10X GEM-X 5' single-cell RNA-sequencing with feature barcode technology before sequencing via the Illumina NextSeq 2000 platform. Funding by Howard Hughes Medical Institute.