HIV reservoirs persist despite successful antiretroviral therapy (ART) and are a major obstacle to the eradication and cure of HIV. The mature monocyte subset, CD14⁺CD16⁺, contributes to viral reservoirs and HIV-associated comorbidities. Only a subset of monocytes harbors HIV (HIV⁺), while the rest remain uninfected, exposed cells (HIV^exp). We developed an innovative single cell RNA sequencing (scRNAseq) pipeline that detects HIV and host transcripts simultaneously, enabling us to examine differences between HIV⁺ and HIV^exp mature monocytes. Using this, we characterized uninfected, HIV⁺, and HIV^exp primary human mature monocytes with and without ART. We showed that HIV⁺ mature monocytes do not form their own cluster separately from HIV^exp but can be distinguished by significant differential gene expression. We found that ART decreased levels of unspliced HIV transcripts potentially by modulating host transcriptional regulators shown to decrease viral infection and replication. We also identified and characterized mature monocyte subpopulations differentially impacted by HIV and ART. We identified genes dysregulated by ART in HIV^exp monocytes compared to their uninfected counterpart and, of interest, the junctional protein ALCAM, suggesting that ART impacts monocyte functions. Our data provide a novel method for simultaneous detection of HIV and host transcripts. We identify potential targets, such as those genes whose expression is increased in HIV⁺ mature monocytes compared to HIV^exp, to block their entry into tissues, preventing establishment/replenishment of HIV reservoirs even with ART, thereby reducing and/or eliminating viral burden and HIV-associated comorbidities. Our data also highlight the heterogeneity of mature monocyte subsets and their potential contributions to HIV pathogenesis in the ART era.

中文翻译：

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通过创新的 scRNAseq 管道识别单核细胞、HIV 和 ART 的相互作用：通往病毒库和 HIV 相关合并症的途径。

尽管抗逆转录病毒治疗（ART）取得了成功，但艾滋病毒储存库仍然存在，并且是根除和治愈艾滋病毒的主要障碍。成熟的单核细胞亚群 CD14 ⁺ CD16 ⁺有助于形成病毒库和 HIV 相关合并症。只有一部分单核细胞携带 HIV (HIV ⁺ )，而其余的细胞则未受感染，处于暴露状态 (HIV ^exp )。我们开发了一种创新的单细胞 RNA 测序 (scRNAseq) 流程，可同时检测 HIV 和宿主转录本，使我们能够检查 HIV ⁺和 HIV ^exp成熟单核细胞之间的差异。利用这一点，我们对使用和不使用 ART 的未感染、HIV ⁺和 HIV ^{exp原代人类成熟单核细胞进行了表征。}我们表明，HIV ⁺成熟单核细胞不会与 HIV ^exp分开形成自己的簇，但可以通过显着差异的基因表达来区分。我们发现，ART 可能通过调节宿主转录调节因子来降低未剪接的 HIV 转录本的水平，从而减少病毒感染和复制。我们还确定并描述了受 HIV 和 ART 影响不同的成熟单核细胞亚群。^{我们在 HIV感染单}核细胞中发现了 ART 失调的基因，与未感染的单核细胞相比，以及令人感兴趣的连接蛋白 ALCAM，这表明 ART 影响单核细胞功能。我们的数据提供了一种同时检测 HIV 和宿主转录本的新方法。我们确定了潜在的靶标，例如与 HIV ^exp相比，在 HIV ⁺成熟单核细胞中表达增加的那些基因，以阻止它们进入组织，即使使用 ART 也能防止 HIV 储存库的建立/补充，从而减少和/或消除病毒负荷和与艾滋病毒相关的合并症。我们的数据还强调了成熟单核细胞亚群的异质性及其在 ART 时代对 HIV 发病机制的潜在贡献。