Single-cell immune profiling reveals the impact of antiretroviral therapy on HIV-1-induced immune dysfunction, T cell clonal expansion, and HIV-1 persistencein vivo

Abstract

Despite antiretroviral therapy (ART), HIV-1 persists in proliferating T cell clones that increase over time. To understand whether early ART affects HIV-1 persistence in vivo, we performed single-cell ECCITE-seq and profiled 89,279 CD4+ T cells in paired samples during viremia and after immediate versus delayed ART in six people in the randomized interventional Sabes study. We found that immediate ART partially reverted TNF responses while delayed ART did not. Antigen and TNF responses persisted despite immediate ART and shaped the transcriptional landscape of CD4+ T cells, HIV-1 RNA+ cells, and T cell clones harboring them (cloneHIV-1). Some HIV-1 RNA+ cells reside in the most clonally expanded cytotoxic T cell populations (GZMB and GZMK Th1 cells). CloneHIV-1+ were larger in clone size, persisted despite ART, and exhibited transcriptional signatures of antigen, cytotoxic effector, and cytokine responses. Using machine-learning algorithms, we identified markers for HIV-1 RNA+ cells and cloneHIV-1+ as potential therapeutic targets. Overall, by combining single-cell immune profiling and T cell expansion dynamics tracking, we identified drivers of HIV-1 persistence in vivo.

SARS-CoV-2 Vaccine-Induced T-Cell Response after Three Doses in People Living with HIV on Antiretroviral Therapy Compared to Seronegative Controls (CTN 328 COVAXHIV Study)

“…We found significantly higher frequencies of TNFα-producing Spike-specific CD4 T-cells in PLWH compared to controls. Elevated T-cell production of pro-inflammatory cytokines, such as TNFα, in chronic HIV infection despite suppressive ART has been well characterized [ 16 , 17 , 18 , 19 ]. Whether higher frequencies of TNFα+ CD4 T-cells are associated with better or worse vaccine-induced protection against severe illness in PLWH requires further investigation.…”

Leveraging Novel Integrated Single-Cell Analyses to Define HIV-1 Latency Reversal

“…ECCITE-seq was used to perform CRISPR screens, reliably identify and quantify the heterogeneity present in single cells that received the same guide RNA (gRNA), and further define the mechanisms that control programmed death-ligand 1 (PD-L1) expression [ 98 ]. CITE-seq was applied to profile and compare HIV-1 infected cells during immediate and delayed antiretroviral therapy [ 99 ]. Single-nucleus-based CITE-seq, Intranuclear Cellular Indexing of Transcriptomes and Epitopes (inCITE-seq), was reported that measures quantitative intranuclear protein levels and transcriptomes in cells and tissues [ 100 ].…”