Ashokkumar Manickam, Hafer Terry L, Felton Abby, Archin Nancie M, Margolis David M, Emerman Michael, Browne Edward P
Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America.
UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America.
PLoS Pathog. 2025 Apr 8;21(4):e1012467. doi: 10.1371/journal.ppat.1012467. eCollection 2025 Apr.
Human Immunodeficiency virus (HIV) infection is regulated by a wide array of host cell factors that combine to influence viral transcription and latency. To understand the complex relationship between the host cell and HIV-1 latency, we performed a lentiviral CRISPR screen that targeted a set of host cell genes whose expression or activity correlates with HIV-1 expression. We further investigated one of the identified factors - the transcription factor ETS1, and found that it is required for maintenance of HIV-1 latency in both latently infected cell lines and in a primary CD4 T cell latency model. Interestingly, ETS1 played divergent roles in actively infected and latently infected CD4 T cells, with knockout of ETS1 leading to reduced HIV-1 expression in actively infected cells, but increased HIV-1 expression in latently infected cells, indicating that ETS1 can play both a positive and negative role in HIV-1 expression. CRISPR/Cas9 knockout of ETS1 in CD4 T cells from ART-suppressed people with HIV-1 (PWH) confirmed that ETS1 maintains transcriptional repression of the clinical HIV-1 reservoir. Transcriptomic profiling of ETS1-depleted cells from PWH identified a set of host cell pathways involved in viral transcription that are controlled by ETS1 in resting CD4 T cells. In particular, we observed that ETS1 knockout increased expression of the long non-coding RNA MALAT1 that has been previously identified as a positive regulator of HIV-1 expression. Furthermore, the impact of ETS1 depletion on HIV-1 expression in latently infected cells was partially dependent on MALAT1. Additionally, we demonstrate that ETS1 knockout resulted in enhanced abundance of activating modifications (H3K9Ac, H3K27Ac, H3K4me3) on histones located at the HIV-1 long terminal repeat (LTR), indicating that ETS1 regulates the activity of chromatin-targeting complexes at the HIV-1 LTR. Overall, these data demonstrate that ETS1 is an important regulator of HIV-1 latency that impacts HIV-1 expression through repressing MALAT1 expression and by regulating modification of proviral histones.
人类免疫缺陷病毒（HIV）感染受多种宿主细胞因子调控，这些因子共同影响病毒转录和潜伏。为了解宿主细胞与HIV-1潜伏之间的复杂关系，我们进行了一项慢病毒CRISPR筛选，靶向一组宿主细胞基因，其表达或活性与HIV-1表达相关。我们进一步研究了其中一个已确定的因子——转录因子ETS1，发现它在潜伏感染的细胞系和原代CD4 T细胞潜伏模型中维持HIV-1潜伏都是必需的。有趣的是，ETS1在活跃感染和潜伏感染的CD4 T细胞中发挥了不同的作用，ETS1基因敲除导致活跃感染细胞中HIV-1表达降低，但潜伏感染细胞中HIV-1表达增加，这表明ETS1在HIV-1表达中既可以发挥正向作用，也可以发挥负向作用。在接受抗逆转录病毒治疗（ART）抑制的HIV-1感染者（PWH）的CD4 T细胞中，通过CRISPR/Cas9敲除ETS1证实，ETS1维持临床HIV-1储存库的转录抑制。对PWH中ETS1缺失细胞的转录组分析确定了一组在静止CD4 T细胞中由ETS1控制的参与病毒转录的宿主细胞途径。特别地，我们观察到ETS1基因敲除增加了长链非编码RNA MALAT1的表达，该长链非编码RNA先前已被确定为HIV-1表达的正向调节因子。此外，ETS1缺失对潜伏感染细胞中HIV-1表达的影响部分依赖于MALAT1。此外，我们证明ETS1基因敲除导致位于HIV-1长末端重复序列（LTR）的组蛋白上的激活修饰（H3K9Ac、H3K27Ac、H3K4me3）丰度增加，表明ETS1调节HIV-1 LTR处的染色质靶向复合物的活性。总体而言，这些数据表明ETS1是HIV-1潜伏的重要调节因子，它通过抑制MALAT1表达和调节前病毒组蛋白修饰来影响HIV-1表达。
