Blocking PD-1 engagement rapidly upregulates innate antiviral and immune functions that associate with HIV reservoir decay [bulkRNA-seq]

The HIV reservoir, a small pool of PD-1+CD4+ T cells that carry integrated HIV genomes, remains a formidable obstacle to HIV cure. The clinical use of PD-1 inhibitors has shown promising results in curbing the HIV reservoir in people with HIV (PWH) and cancer, but the underlying mechanisms are unknown. Here, we demonstrate that anti-PD-1 therapy leads to a decay in the frequency of cells harboring HIV DNA at the end of a two-year follow-up in 9 of 14 PWH receiving pembrolizumab within the CITN-12 clinical trial (NCT02595866). This reduction correlates with an innate immune response, characterized by increased monocyte frequencies and enhanced myeloid cell-specific transcription of interferon-stimulated genes (ISGs), chemokines, antiviral restriction factors, and TLR signaling. These changes emerge as early as 24 hours post-treatment and persist until the end of therapy. Within 24 hours of treatment, we also observe an increase in proliferating effector HIV-specific CD8+ T cells, increased expression of effector T cell genes, and a decline in plasma TGF-β levels. We validate the generalizability of these ISG expression modules across >1,000 publicly available scRNA-seq samples, revealing a consistent association between high ISG expression in peripheral blood mononuclear cells (PBMCs) and lower expression of WNT pathway and Treg gene sets - pathways known to regulate immune quiescence and persistence of the HIV reservoir - in PBMCs from uninfected controls, as well as in samples from individuals with cancer or infections. Furthermore, we demonstrate that ISGs triggered by TLR ligands protect CD4+ T cells from HIV infection in vitro. These findings support a mechanism by which ISGs restrict the HIV reservoir in vivo and define a set of immune signaling pathways that can be used to identify PWH in whom the HIV reservoir may decay upon anti-PD-1 therapy. Bulk RNA sequencing was performed on whole blood collected in PAXgene tubes from participants at the following timepoints: C01D01 (pre-treatment), C01D02 (hours after the first treatment cycle ), and EOT (end of therapy).