HIV-1 infection of human tonsils activates CD4+ T cell oxidative phosphorylation and myeloid NLRP3 inflammasome activation

Abstract Human immunodeficiency virus type 1 (HIV-1) leads to a chronic, incurable infection that causes immune activation, resulting in chronic inflammation in people with HIV-1 (PWH) despite virologic suppression on antiretroviral therapy (ART). The mechanisms underlying this chronic inflammation are multifactorial, but significant literature supports the role of lymphoid structures as reservoirs for viral latency and centers of immune activation. A systematic analysis of the cell type-specific transcriptomic changes induced by HIV-1 infection in lymphoid tissue has not been conducted. Human tonsil explants from four distinct donors were infected with HIV-1 ex vivo. Single-cell RNA sequencing (scRNA Seq) was performed to evaluate the represented cell types and the impact of infection, including differential gene expression, and associated inflammatory signaling pathways. Most of the cells (80%) are lymphocytes with nearly equivalent representation from T (38%) and B (42%) lymphocytes. We also identify smaller populations of NK, epithelial, and myeloid cells. CD4+ T cells demonstrated the highest levels of HIV-1 transcript expression. Highly infected CD4+ T cells also exhibited increased expression of genes involved in the respiratory electron transport pathway. Cells in the myeloid compartment that expressed low levels of HIV-1 transcript demonstrated increased expression of genes involved in the NLRP3 inflammasome pathway, suggesting that these cells may play a “bystander” role in HIV-associated inflammatory pathogenesis. We propose a model in which HIV-1-infected CD4+ T cells activate oxidative phosphorylation pathways, resulting in excess ATP efflux. Bystander myeloid cells may sense the resulting extracellular ATP, thereby triggering NLRP3 inflammasome activation, proinflammatory signaling pathways, and pyroptotic cell death. These observations support important mechanistic understanding to drive the development of therapeutic and care strategies to eradicate disease in PWH.