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.

^{了解克隆扩增 HIV-1 感染的 CD4 +} T 细胞的驱动因素和标记对于根除 HIV-1 至关重要。我们使用单细胞 ECCITE-seq，它在同一单细胞内捕获表面蛋白表达、细胞转录组、HIV-1 RNA 和 TCR 序列，以追踪来自六个 HIV-1 感染者的纵向存档样本的克隆扩增动力学（在病毒血症和抑制性抗逆转录病毒治疗后）和两个未感染的个体，在未刺激的条件下，在 CMV 和 HIV-1 抗原刺激后。尽管进行了抗逆转录病毒治疗，但持续的抗原和 TNF 反应影响了 T 细胞的克隆扩增。HIV-1 存在于表达BCL2和SERPINB9的 Th1 极化抗原反应 T 细胞中可以抵抗细胞死亡。HIV-1 RNA ⁺ T 细胞克隆的克隆大小较大，在病毒血症期间建立，在病毒抑制后持续存在，并且富含GZMB ⁺细胞毒性效应记忆 Th1 细胞。靶向 HIV-1 感染的细胞毒性 CD4 ⁺ T 细胞和克隆扩增的驱动因素为根除 HIV-1 提供了另一个方向。