da Conceicao Viviane N, Dyer Wayne B, Gandhi Kaushal, Gupta Priyanka, Saksena Nitin K
Centre for Virus Research, Westmead Millennium Institute, Westmead Hospital, University of Sydney, Darcy Road, Sydney, Westmead, NSW 2145 Australia.
Centre for Virus Research, Westmead Millennium Institute, Westmead Hospital, University of Sydney, Darcy Road, Sydney, Westmead, NSW 2145 Australia ; Retroviral Genetics Division, Centre for Virus Research, Westmead Millennium Institute, Sydney, Westmead, NSW 2145 Australia.
Mol Cell Ther. 2014 Apr 3;2:11. doi: 10.1186/2052-8426-2-11. eCollection 2014.
Although the host gene expression in the context of HIV has been explored by several studies, it remains unclear how HIV is able to manipulate and subvert host gene machinery before and after highly active antiretroviral therapy (HAART) in the same individual. In order to define the underlying pharmaco-genomic basis of HIV control during HAART and genomic basis of immune deterioration prior to HAART initiation, we performed a genome-wide expression analysis using primary peripheral blood mononuclear cells (PBMC) derived from 14 HIV + subjects pre-highly active antiretroviral therapy (HAART) (time point-1 or TP1) with detectable plasma viremia and post-HAART (time point-2 or TP2) with effective control of plasma viremia (<40 HIV RNA copies/mL of plasma).
Genomic RNA extracted from the PBMCs was used in microarray analysis using HT-12V3 Illumina chips. Illumina®BeadStudio Software was used to obtain differentially expressed (DE) genes. Only the genes with p value <0.01 and FDR of <5% were considered for analysis. Pathway analysis was performed in MetaCore™ to derive functional annotations. Functionally significant genes were validated by qRT-PCR.
Between TP1 and TP2, 234 genes were differentially expressed (DE). During viremic phase (TP1), there was an orchestrated and coordinated up-regulation of immune, inflammation and antiviral genes, consistent with HIV infection and immune activation, which comprised of genes mainly involved in antiviral action of interferons and their signalling. In contrast, the therapy-mediated control phase (TP2) showed systematic down-regulation of these pathways, suggesting that the reduction in plasma viremia with HAART has a considerable influence on reducing the immune activation, thereby implying a definitive role of HIV in subverting the human gene machinery.
This is the first study to show the evidence for the differential regulation of gene expression between the untreated and treated time points, suggesting that gene expression is a consequence of cellular activation during plasma viremia. Affirmation to these observations comes from down-modulation of genes involved in cellular activation and inflammation upon initiation of HAART coinciding with below detectable levels of plasma viremia.
尽管多项研究已对HIV背景下的宿主基因表达进行了探索，但仍不清楚HIV在同一患者接受高效抗逆转录病毒治疗（HAART）之前和之后如何操纵和颠覆宿主基因机制。为了确定HAART期间HIV控制的潜在药物基因组学基础以及HAART开始前免疫恶化的基因组基础，我们使用来自14名HIV阳性患者的原代外周血单核细胞（PBMC）进行了全基因组表达分析，这些患者在高效抗逆转录病毒治疗（HAART）前（时间点1或TP1）血浆病毒血症可检测，在HAART后（时间点2或TP2）血浆病毒血症得到有效控制（血浆中HIV RNA拷贝数<40/mL）。
从PBMC中提取的基因组RNA用于使用HT-12V3 Illumina芯片的微阵列分析。使用Illumina®BeadStudio软件获得差异表达（DE）基因。仅考虑p值<0.01且FDR<5%的基因进行分析。在MetaCore™中进行通路分析以获得功能注释。通过qRT-PCR验证功能显著的基因。
在TP1和TP2之间，有234个基因差异表达（DE）。在病毒血症期（TP1），免疫、炎症和抗病毒基因出现了协调上调，这与HIV感染和免疫激活一致，这些基因主要参与干扰素的抗病毒作用及其信号传导。相比之下，治疗介导的控制期（TP2）显示这些通路系统性下调，这表明HAART使血浆病毒血症降低对减少免疫激活有相当大的影响，从而暗示HIV在颠覆人类基因机制中起决定性作用。
这是第一项显示未经治疗和治疗时间点之间基因表达差异调节证据的研究，表明基因表达是血浆病毒血症期间细胞激活的结果。对这些观察结果的肯定来自于HAART开始时与血浆病毒血症低于可检测水平同时发生的细胞激活和炎症相关基因的下调。
