Understanding HIV-1 persistence in cytotoxic CD4+ T lymphocytes at the single cell level

项目摘要 尽管有有效的抗逆转录病毒治疗（ART），HIV-1仍然存在于潜伏的水库终身。虽然大多数艾滋病毒- 1-感染的细胞死于病毒致细胞病变效应或免疫清除，HIV-1感染的细胞，即使是那些具有活性的细胞， HIV-1表达，可以存活，持续存在和增殖。我们想研究HIV-1是如何感染的 在HIV-1感染者的病毒血症期间，并在病毒抑制下持续存在。了解免疫细胞 HIV-1感染细胞的亚群、免疫程序和细胞标记将确定治疗靶点。的 挑战是HIV-1感染细胞的异质性和稀有性：在ART治疗的病毒抑制个体中， 仅1-100/106（<0.01%）的CD 4 + T细胞具有可诱导的HIV-1。为此，我们分析了CD 4 + T细胞， 病毒血症期间和病毒抑制后的Sabes队列，使用单细胞ECCITEseq捕获单细胞 转录组、蛋白质表达、HIV-1 RNA和T细胞受体序列（TCR）。 我们已经建立了先进的单细胞生物信息学分析管道和机器学习工具。这 这种方法能够对免疫细胞亚群进行多维、高分辨率、单细胞分析， 程序、细胞标记、T细胞克隆扩增和HIV-1 RNA+细胞。我们的单细胞 ECCITEseq发现HIV-1 RNA+细胞上调细胞毒性CD 4 + T细胞基因。使用流式细胞术 通过测量HIV-1 p24蛋白和颗粒酶B表达，我们基于RNA测序的结果得到了验证 一种基于蛋白质的正交方法，揭示了HIV-1通过隐藏在颗粒酶B+细胞毒性效应子中而持续存在。 记忆性CD 4 + T细胞。根据我们从病毒血症样本中获得的结果，我们可以检查罕见的HIV-1 RNA+细胞， 随着时间的推移，使用单细胞ECCITEseq，我们发现，尽管抑制性ART， 坏死因子（TNF）反应持续存在。此外，抗原和TNF应答驱动T细胞增殖， 细胞克隆此外，不同的抗原应答驱动不同的T细胞极化和增殖。总之， 我们假设抗原刺激和TNF应答可以影响T细胞极化，细胞易感性， HIV-1感染、细胞存活和感染细胞增殖，特别是颗粒酶B细胞毒性CD 4 + T细胞。我们的目标是了解为什么HIV-1感染的细胞毒性CD 4 + T细胞可以优先存活，增殖， 并持续存在，与其他T细胞亚群相反。实现这一目标将确定免疫程序， HIV-1持久性和识别HIV-1感染细胞的细胞标志物，以实现更特异的治疗靶向。我们 一种方法是将联合收割机结合尖端的单细胞ECCITEseq和正交验证来研究HIV-1如何 RNA+颗粒酶B+ CTL通过分析细胞亚群、免疫程序 标记物，以及在体内病毒抑制期间罕见HIV-1 RNA+细胞随时间的增殖动力学， 体外总的来说，我们将理解为什么HIV-1优先存在于细胞毒性CD 4 + T细胞中， 促进HIV-1感染的细胞毒性CD 4 + T细胞的存活和增殖的免疫驱动因子，并指导 开发针对HIV-1感染细胞的治疗策略。

PROJECT SUMMARY Despite effective antiretroviral therapy (ART), HIV-1 persists in the latent reservoir lifelong. Although most HIV- 1-infected cells die of viral cytopathic effects or immune clearance, HIV-1-infected cells, even those having active HIV-1 expression, can survive, persist, and proliferate. We want to examine how HIV-1 establishes infection during viremia and persists under viral suppression in people living with HIV-1. Understanding the immune cell subsets, immune programs, and cell markers of HIV-1-infected cells will identify therapeutic targets. The challenge is the heterogeneity and rarity of HIV-1-infected cells: in ART-treated, virally suppressed individuals, only 1–100/106 (<0.01%) CD4+ T cells harbor inducible HIV-1. To this end, we profiled CD4+ T cells from the Sabes cohort during viremia and after viral suppression using single-cell ECCITEseq, which captures single-cell transcriptome, protein expression, HIV-1 RNA, and T cell receptor sequence (TCR) within the same single cell. We have established advanced single-cell bioinformatic analysis pipelines and machine learning tools. This approach enables multi-dimensional, high-resolution, single-cell profiling of immune cell subsets, immune programs, cell markers, T cell clonal expansion, and HIV-1 RNA+ cells at the same time. Our single-cell ECCITEseq found that HIV-1 RNA+ cells upregulated cytotoxic CD4+ T cell genes. Using flow cytometric measurement of HIV-1 p24 protein and granzyme B expression, our RNA-seq based results were validated by a protein-based orthogonal approach, revealing that HIV-1 persists by hiding in granzyme B+ cytotoxic effector memory CD4+ T cells. Based on our results from viremic samples, we can examine the rare HIV-1 RNA+ cells under suppressive ART over time. Using single-cell ECCITEseq, we found that despite suppressive ART, tumor necrosis factor (TNF) responses persist. Furthermore, antigen and TNF responses drive the proliferation of T cell clones. In addition, different antigen responses drive distinct T cell polarization and proliferation. Altogether, we hypothesize that antigen stimulation and TNF responses can shape T cell polarization, cellular susceptibility to HIV-1 infection, cellular survival, and proliferation of the infected cells, particularly granzyme B cytotoxic CD4+ T cells. Our goal is to understand why HIV-1-infected cytotoxic CD4+ T cells can preferentially survive, proliferate, and persist, as opposed to other T cell subsets. Achieving this goal will identify immune programs that drive HIV-1 persistence and identify cell markers for HIV-1-infected cells for more specific therapeutic targeting. Our approach is to combine cutting-edge single-cell ECCITEseq and orthogonal validations to examine how HIV-1 RNA+ granzyme B+ CTLs survive and persist under viral suppression by profiling cell subsets, immune program, markers, and proliferation dynamics for the rare HIV-1 RNA+ cells over time during viral suppression in vivo and in vitro. Overall, we will understand why HIV-1 preferentially persists in cytotoxic CD4+ T cells, identify upstream immune drivers promoting the survival and proliferation of the HIV-1-infected cytotoxic CD4+ T cells, and guide the development of therapeutic strategies specific for HIV-1-infected cells.