Transcriptional profiling of experimental CD8+ lymphocyte depletion in rhesus macaques infected with SIVmac239. Macaca mulatta

CD8+ T-cells inhibit virus replication in SIV-infected rhesus macaques (RM). However, it is unclear to what extent the viral suppression mediated by CD8+ T-cells reflects direct killing of infected cells as opposed to indirect, non-cytolytic mechanisms. In this study, we used functional genomics to investigate potential mechanisms of in vivo viral suppression mediated by CD8+ lymphocytes. Eight chronically SIVmac239-infected RMs underwent CD8+ lymphocyte depletion, and RNA from whole blood was obtained prior to depletion, at the nadir of CD8+ lymphocytes (5 days post-depletion), and during the repopulation phase (11 days post-depletion). Principal components analysis demonstrated that overall gene expression during the nadir of CD8+ T-cells was highly divergent from other intervals. Conversely, the genomic signature of samples from the CD8+ cell rebound phase was similar to that of pre-depletion samples. During CD8+ lymphocyte depletion we detected a strongly significant decrease in the expression of the genes encoding CD8α and CD8β chains, consistent with the near complete CD8+ T-cell depletion measured by flow cytometry. Of note, we observed significant down-regulation of the expression of genes encoding for factors that can suppress SIV replication, including the CCR5-binding chemokine CCL5/Rantes, several retroviral restriction factors (TRIM10, TRIM15, APOBEC3G/H) and defensins. Reduced expression of various genes related to T cell activation and proliferation was also observed. Collectively, these data indicate that depletion of CD8+ lymphocytes in SIV-infected RMs is associated with the establishment of a pattern of gene expression that may result in increased intrinsic permissivity to virus replication. Overall design: A total of 60 RNA samples were hybridized on to Rhesus Affymetrix 3' Expression arrays. The study was composed of 8 replicate rhesus macaques subjected to SIVmac239 infection and followed over infection, during subsequent treatment with monocloncal antibody OKT8F to deplete CD8+ T lymphocytes, antiretroviral therapy to suppress virus. Samples were taken at various time points during acute and chronic infection, after CD8+ cell depletion, after CD8+ cell reconstition, and during ART suppression of virus.

CD8+ T细胞可抑制猿猴免疫缺陷病毒（SIV）感染恒河猴（RM）体内的病毒复制，但目前尚不清楚CD8+ T细胞介导的病毒抑制作用在多大程度上依赖于对感染细胞的直接杀伤，而非间接非溶细胞机制。本研究采用功能基因组学技术，探究CD8+淋巴细胞介导的体内病毒抑制潜在机制。研究对8只慢性感染SIVmac239的恒河猴实施CD8+淋巴细胞耗竭，并分别在耗竭前、CD8+淋巴细胞耗竭低谷期（耗竭后5天）以及细胞复增殖期（耗竭后11天）采集全血RNA样本。主成分分析结果显示，CD8+ T细胞耗竭低谷期的整体基因表达谱与其余时间区间存在显著差异；与之相反，CD8+细胞反弹阶段的样本基因组特征与耗竭前样本高度相似。在CD8+淋巴细胞耗竭过程中，研究人员检测到编码CD8α与CD8β链的基因表达显著下调，这与流式细胞术测得的近乎完全的CD8+ T细胞耗竭结果相符。值得注意的是，本研究观察到多种可抑制SIV复制的因子编码基因表达显著下调，包括CCR5结合趋化因子CCL5/RANTES、多种逆转录病毒限制因子（TRIM10、TRIM15、APOBEC3G/H）以及防御素。此外，多种与T细胞活化及增殖相关的基因表达也出现下调。综上，上述数据表明，SIV感染恒河猴体内的CD8+淋巴细胞耗竭会伴随建立一种基因表达模式，该模式可能提升宿主细胞对病毒复制的内在易感性。总体实验设计：共计60份RNA样本在恒河猴Affymetrix 3'表达芯片上完成杂交。本研究包含8只经SIVmac239感染的恒河猴重复样本，对其开展感染随访，并在后续使用单克隆抗体OKT8F耗竭CD8+ T淋巴细胞、采用抗逆转录病毒疗法抑制病毒复制期间采集样本。样本采集时间点覆盖急性与慢性感染期、CD8+细胞耗竭后、CD8+细胞重建后以及抗逆转录病毒疗法抑制病毒期间的多个关键节点。