Fundació irsiCaixa-HIVACAT, Institut de Recerca en Ciències de la Salut Germans Trias i Pujol (IGTP), Hospital Germans Trias, Universitat Autònoma de Barcelona, 08916 Badalona, Spain; Veterans Affairs San Diego Healthcare System, San Diego, CA 92161, USA; Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA.
Antiviral Res. 2013 Nov;100(2):420-8. doi: 10.1016/j.antiviral.2013.07.017. Epub 2013 Aug 6.
Previous studies of the effect of ART on gene expression in HIV-infected individuals have identified small numbers of modulated genes. Since these studies were underpowered or cross-sectional in design, a paired analysis of peripheral blood mononuclear cells (PBMCs), isolated before and after ART, from a robust number of HIV-infected patients (N=32) was performed. Gene expression was assayed by microarray and 4157 differentially expressed genes (DEGs) were identified following ART using multivariate permutation tests. Pathways and gene ontology (GO) terms over-represented for DEGs reflected the transition from a period of active virus replication before ART to one of viral suppression (e.g., repression of JAK-STAT signaling) and possible prolonged drug exposure (e.g., oxidative phosphorylation pathway) following ART. CMYC was the DEG whose product made the greatest number of interactions at the protein level in protein interaction networks (PINs), which has implications for the increased incidence of Hodgkin's lymphoma (HL) in HIV-infected patients. The differential expression of multiple genes was confirmed by RT-qPCR including well-known drug metabolism genes (e.g., ALOX12 and CYP2S1). Targets not confirmed by RT-qPCR (i.e., GSTM2 and RPL5) were significantly confirmed by droplet digital (ddPCR), which may represent a superior method when confirming DEGs with low fold changes. In conclusion, a paired design revealed that the number of genes modulated following ART was an order of magnitude higher than previously recognized.
先前关于抗逆转录病毒疗法（ART）对感染 HIV 个体基因表达影响的研究，仅鉴定到少数可调节的基因。由于这些研究的效力不足或设计为横断面研究，我们对大量 HIV 感染者（N=32）的外周血单个核细胞（PBMC）进行了配对分析，这些细胞在接受 ART 前后被分离。采用微阵列法检测基因表达，使用多元置换检验，我们在接受 ART 后鉴定到 4157 个差异表达基因（DEGs）。DEGs 所反映的途径和基因本体（GO）术语过度表达，反映了从 ART 前病毒复制活跃期到病毒抑制期（如 JAK-STAT 信号通路的抑制）的转变，以及 ART 后可能存在的长期药物暴露（如氧化磷酸化途径）。CMYC 是 DEG 中产物在蛋白质相互作用网络（PINs）中相互作用最多的基因，这对 HIV 感染者中霍奇金淋巴瘤（HL）发病率增加具有重要意义。通过 RT-qPCR 证实了多个基因的差异表达，包括众所周知的药物代谢基因（如 ALOX12 和 CYP2S1）。未通过 RT-qPCR 证实的靶标（即 GSTM2 和 RPL5）通过液滴数字 PCR（ddPCR）得到显著证实，ddPCR 可能是确认具有低倍数变化的 DEGs 的更优方法。总之，配对设计表明，接受 ART 治疗后调节的基因数量比以前认识的要高一个数量级。
