Nuclear landscape of HIV-1 integration in microglia - unexplored HIV-1 reservoirs

联合抗逆转录病毒疗法(CART)的引入大大改善了对艾滋病毒-1感染的管理，以及艾滋病毒-1感染者的健康和预期寿命。虽然病毒载量可以通过CART有效地控制，但转录沉默，但具有复制能力的病毒持续整合到宿主基因组中，在全身不同的解剖位置创建长期的储存库。这些长期储存在记忆T细胞、巨噬细胞和脑小胶质细胞中的细胞，是目前的治疗方法无法达到的，阻碍了HIV-1的功能性治愈。病毒隐藏在人类基因组中的位置对病毒的命运具有功能性后果。我们之前在T细胞上的工作，潜伏着HIV-1的主要避难所，已经开始探索3D宿主基因组组织和HIV-1整合位点选择之间的联系。我们发现HIV-1并不是随机定位其基因组，而是偏爱外层空间壳，与核孔复合体(NPC)下开放的染色质结构域相关。最近，我们发现HIV-1通常以具有超级增强子(SE)调控元件的细胞类型特定基因簇为靶标。虽然一些研究报道了染色质介导的HIV-1在小胶质细胞中转录沉默的机制，但对病毒在这些细胞中的整合部位几乎一无所知。在这里，我们建议从基因组学的角度研究HIV-1在小胶质细胞中的整合和潜伏时间，并研究在HIV-1生命周期中可能有助于整合和沉默事件的DNA特征和染色质因素。我们建议确定HIV-1的整合位点，定义染色质特征，并将基因组联系映射到整合的病毒基因组。LUSIC实验室将专注于病毒感染的细胞生物学和基因组学，而Herrmann团队将通过分析这些复杂的基因组数据并生成与病毒相关的小胶质细胞染色质图谱和基因组接触的总体情况，为该项目做出贡献。我们将与SPP提案的其他成员共同努力，我们将直接与Vassilis Roukos(IMB Mainz)和Irina Solovei(LMU Munich)合作，通过荧光原位杂交(FISH)和高通量显微镜显示HIV-1及其整合到小胶质细胞中的基因组区域。

The introduction of combinatorial antiretroviral therapy (cART) has significantly improved the management of HIV-1 infection as well as the health and life expectancy of HIV-1 infected individuals. While viral loads can be efficiently controlled by cART, transcriptionally silenced, but replication competent virus persists integrated into the host genome, creating long-lasting reservoirs in different anatomical sites throughout the body. These long-lived reservoirs in memory T cells, macrophages and brain microglia, are unreachable by current treatments and impede a functional HIV-1 cure .Where the virus is hidden in the human genome has functional consequences for the viral fate . Our previous work on T cells, major sanctuaries of latent HIV-1, has started exploring the link between 3D host genome organization and HIV-1 integration site selection. We showed that HIV-1 does not position its genome randomly but prefers the outer spatial shells, associated with the open chromatin domains underneath the nuclear pore complex (NPC). More recently we discovered that HIV-1 commonly targets clusters of cell type specific genes with super-enhancer (SE) regulatory elements. Whereas several studies report on the mechanisms of chromatin mediated transcriptional silencing of HIV-1 in microglia, almost nothing is known about the integration sites of the virus in these cells. Here we propose to study HIV-1 integration and latency in microglia through a genomics view-point and to investigate DNA features and chromatin factors that could contribute to integration and silencing events in HIV-1 life cycle. We propose to identify the integration sites of HIV-1, to define the chromatin signatures and to map the genome contacts with respect to the integrated viral genome. Lusic lab will focus on the cell biology and genomics of viral infection, while the Herrmann group will contribute to the project by analysing these complex genomics data and generating an overall picture of chromatin profiles and genomic contacts relevant for the virus in microglial cells. We will join forces with other members of the SPP proposal, and we will collaborate directly with Vassilis Roukos (IMB Mainz) and Irina Solovei (LMU Munich) to visualize HIV-1 and genomic regions where it integrates in microglia by fluorescence in situ hybridization (FISH) and high-throughput microscopy.