Department of Medicine, University of California, San Francisco, California, USA.
Department of Medicine, San Francisco Veterans Affairs Medical Center, San Francisco, California, USA.
J Virol. 2023 Jan 31;97(1):e0125422. doi: 10.1128/jvi.01254-22. Epub 2022 Dec 21.
Posttreatment controllers (PTCs) are rare HIV-infected individuals who can limit viral rebound after antiretroviral therapy interruption (ATI), but the mechanisms of this remain unclear. To investigate these mechanisms, we quantified various HIV RNA transcripts (via reverse transcription droplet digital PCR [RT-ddPCR]) and cellular transcriptomes (via RNA-seq) in blood cells from PTCs and noncontrollers (NCs) before and two time points after ATI. HIV transcription initiation did not significantly increase after ATI in PTCs or in NCs, whereas completed HIV transcripts increased at early ATI in both groups and multiply-spliced HIV transcripts increased only in NCs. Compared to NCs, PTCs showed lower levels of HIV DNA, more cell-associated HIV transcripts per total RNA at all times, no increase in multiply-spliced HIV RNA at early or late ATI, and a reduction in the ratio of completed/elongated HIV RNA after early ATI. NCs expressed higher levels of the IL-7 pathway before ATI and expressed higher levels of multiple cytokine, inflammation, HIV transcription, and cell death pathways after ATI. Compared to the baseline, the NCs upregulated interferon and cytokine (especially TNF) pathways during early and late ATI, whereas PTCs upregulated interferon and p53 pathways only at early ATI and downregulated gene translation during early and late ATI. In NCs, viral rebound after ATI is associated with increases in HIV transcriptional completion and splicing, rather than initiation. Differences in HIV and cellular transcription may contribute to posttreatment control, including an early limitation of spliced HIV RNA, a delayed reduction in completed HIV transcripts, and the differential expression of the IL-7, p53, and TNF pathways. The findings presented here provide new insights into how HIV and cellular gene expression change after stopping ART in both noncontrollers and posttreatment controllers. Posttreatment control is associated with an early ability to limit increases in multiply-spliced HIV RNA, a delayed (and presumably immune-mediated) ability to reverse an initial rise in processive/completed HIV transcripts, and multiple differences in cellular gene expression pathways. These differences may represent correlates or mechanisms of posttreatment control and may provide insight into the development and/or monitoring of therapeutic strategies that are aimed at a functional HIV cure.
治疗后控制器（PTCs）是少数能够限制抗逆转录病毒治疗中断（ATI）后病毒反弹的感染 HIV 的个体，但其中的机制尚不清楚。为了研究这些机制，我们在 ATI 前后的时间点，定量分析了 PTCs 和非控制器（NCs）的血细胞中各种 HIV RNA 转录本（通过逆转录液滴数字 PCR [RT-ddPCR]）和细胞转录组（通过 RNA-seq）。在 PTCs 和 NCs 中，ATI 后 HIV 转录起始并未显著增加，而完整的 HIV 转录本在两组中均在早期 ATI 时增加，并且多剪接的 HIV 转录本仅在 NCs 中增加。与 NCs 相比，PTCs 表现出更低水平的 HIV DNA，在所有时间点，细胞相关 HIV 转录本与总 RNA 的比例更高，早期或晚期 ATI 时多剪接的 HIV RNA 没有增加，并且早期 ATI 后完成/延伸的 HIV RNA 比例降低。NCs 在 ATI 前表达更高水平的 IL-7 途径，并且在 ATI 后表达更高水平的多种细胞因子、炎症、HIV 转录和细胞死亡途径。与基线相比，NCs 在早期和晚期 ATI 期间上调了干扰素和细胞因子（特别是 TNF）途径，而 PTCs 仅在早期 ATI 期间上调了干扰素和 p53 途径，并在早期和晚期 ATI 期间下调了基因翻译。在 NCs 中，ATI 后的病毒反弹与 HIV 转录完成和剪接的增加有关，而不是起始。HIV 和细胞转录的差异可能导致治疗后控制，包括早期限制剪接的 HIV RNA，延迟减少完整的 HIV 转录本，以及 IL-7、p53 和 TNF 途径的差异表达。本研究提供了新的见解，了解了 HIV 和细胞基因表达在非控制器和治疗后控制器停止 ART 后的变化。治疗后控制与早期限制多剪接 HIV RNA 增加的能力有关，与延迟（可能是免疫介导）逆转初始进程性/完整 HIV 转录本增加的能力有关，以及细胞基因表达途径的多个差异。这些差异可能代表治疗后控制的相关因素或机制，并为开发和/或监测旨在实现功能性 HIV 治愈的治疗策略提供了思路。
