Single-cell multiomics reveals persistence of HIV-1 in expanded cytotoxic T cell clones

Understanding the drivers and markers of clonally expanding HIV-1-infected CD4(+) T cells is essential for HIV-1 eradication. We used single-cell ECCITE-seq, which captures surface protein expression, cellular transcriptome, HIV-1 RNA, and TCR sequences within the same single cell to track clonal expansion dynamics in longitudinally archived samples from six HIV-1-infected individuals (during viremia and after suppressive antiretroviral therapy) and two uninfected individuals, in unstimulated conditions and after CMV and HIV-1 antigen stimulation. Despite antiretroviral therapy, persistent antigen and TNF responses shaped T cell clonal expansion. HIV-1 resided in Th1-polarized, antigen-responding T cells expressing BCL2 and SERPINB9 that may resist cell death. HIV-1 RNA(+) T cell clones were larger in clone size, established during viremia, persistent after viral suppression, and enriched in GZMB(+) cytotoxic effector memory Th1 cells. Targeting HIV-1-infected cytotoxic CD4(+) T cells and drivers of clonal expansion provides another direction for HIV-1 eradication.

Automated summary

Understanding the driving factors and markers of clonally expanding HIV-1-infected CD4(+) T cells is crucial for the eradication of HIV-1. Utilizing single-cell ECCITE-seq technology, researchers tracked the dynamics of clonal expansion in longitudinally archived samples from HIV-1-infected individuals and uninfected individuals. The study revealed that persistent antigen and TNF responses shaped T cell clonal expansion, even in the presence of antiretroviral therapy. Additionally, HIV-1-infected cytotoxic CD4(+) T cell clones persisted and were enriched in cytotoxic effector memory Th1 cells.