Drug screen combining RNA landscape analysis reveals targetable pathways in HIV-1 reactivation

We invesitgated cellular pathways required for HIV-1 activation using HIV-1-suppressing agents. Despite effective antiretroviral therapy, HIV-1-nfected cells continue to produce viral antigens and induce chronic immune exhaustion. Using a novel dual reporter system and a high-throughput drug screen, we identified FDA-approved drugs which can suppress HIV-1 reactivation in both cell line models and CD4+ T cells from virally suppressed, HIV-1-infected individuals. We identified 11 cellular pathways required for HIV-1 reactivation as druggable targets. Using differential expression analysis, gene set enrichment analysis and exon-intron landscape analysis, we examined the impact of drug treatment on the cellular environment at a genome-wide level. Overall design: Drugs treatment of HIV-1-infected T cell clones and CD4+ T cells from HIV-1-infected individual under long term suppressive ARTs for 24 hours. Transcriptome analysis was performed on bulk mRNA from treated samples

本研究采用抗HIV-1制剂，探究了介导HIV-1激活的细胞通路。尽管抗逆转录病毒疗法（antiretroviral therapy, ART）可实现有效的病毒抑制，但HIV-1感染细胞仍可持续产生病毒抗原，并诱发慢性免疫耗竭。本研究借助新型双报告基因系统（dual reporter system）与高通量药物筛选（high-throughput drug screen），在细胞系模型以及来自病毒学抑制状态HIV-1感染者的CD4+ T细胞中，筛选得到可抑制HIV-1再激活的美国食品药品监督管理局（Food and Drug Administration, FDA）获批药物。本研究共鉴定出11条可作为药物靶点的HIV-1再激活必需细胞通路。本研究通过差异表达分析、基因集富集分析（gene set enrichment analysis, GSEA）以及外显子-内含子谱分析，在全基因组层面考察了药物处理对细胞微环境的影响。实验整体设计：将来自接受长期抑制性抗逆转录病毒疗法的HIV-1感染者的HIV-1感染T细胞克隆与CD4+ T细胞进行药物处理，处理时长为24小时。对处理后样本的总mRNA进行转录组分析。