Multidimensional single-cell approach probing HIV-1 integration association with non-AIDS defining cancers (Biospecimens/Biocohort)

项目总结 目前对HIV-1感染的治疗方法包括抑制性抗逆转录病毒疗法(ART)，这种疗法可以减少 活跃的病毒复制到几乎检测不到的水平。然而，抗逆转录病毒疗法未能治愈HIV-1感染，因为 病毒以潜伏状态无限期地持续存在。虽然艾滋病毒携带者(PLWH)活得更长，但他们受到 由于抗逆转录病毒治疗制度本身和综合普鲁斯的存在而产生的次要长期后果 在整个人类基因组中。虽然抗逆转录病毒疗法有助于降低艾滋病定义癌症的发病率， 非艾滋病定义癌症(NADC)，如T细胞和B细胞淋巴瘤的发病率一直在上升 在诊所里有记录。尽管之前关于HIV-1整合位点和 癌症患病率：HIV-1在特定部位的整合与非传染性非传染性疾病患病率之间的临床关联 在很大程度上仍未被探索。鉴于这些以前的发现和知识差距，核心假设是 这一提议是，HIV-1整合到或邻近选定的人类基因中，从而改变其表达 导致NADC。具体地说，HIV-1整合可能会扰乱HIV-1相关基因的正常表达 (HAGEs)导致原癌基因上调、肿瘤抑制基因下调和/或改变RNA 剪接模式，从而重新连接产生异常CD4+T和B细胞的基因表达程序 扩张和/或导致NADC的行为。 这项提议的主要目标是询问选定的HIV-1整合部位是否与 抑制治疗下PLWH中NADC发生率的增加和相关生物标志物的预测。至 开始实现这一目标，我们将部署多维方法来同时分析HIV-1 单个细胞水平的整合位点和人类转录本，可通过 艾滋病与癌症标本资源(ACSR)这将是有史以来第一个可以同时 在单细胞水平上询问HIV-1整合位点和人类转录本之间的关系 参与者生物标本。我们手头已经有了一个令人印象深刻的分子和基因组工具箱，它将是 这对于实现本提案的具体目标具有战略意义。这些措施包括：1)部署多维 在ACSR中同时收集HIV-1整合位点和人类转录本的单细胞方法 参与者生物谱(目标1)，和2)组合生成的数据集以定义参与者HIV-1 整合诱导的与NADC相关的生物标记物(目标2)。总的来说，这些研究将揭示病毒 在PLWH和NADC中过度表达的整合位点，将单个病毒整合位点与改变的人类联系起来 潜在地解释NADC发病的基因表达，并对与选择的HIV-1相关的生物标记物进行分类 用于诊断和预后结果的整合事件。未来利用这一知识的研究将在功能上 将特定的HIV-1整合事件定义为NADC的驱动因素，并帮助设计替代治疗机会。

PROJECT SUMMARY Current treatments for HIV-1 infection include suppressive anti-retroviral therapy (ART), which curtails active viral replication to nearly undetectable levels. However, ART fails to cure HIV-1 infection because the virus persists indefinitely in a latent state. While people living with HIV-1 (PLWH) live longer, they are subject to secondary long-term consequences due to the ART regime itself and the presence of integrated proviruses throughout the human genome. Whereas ART facilitated a decrease in the incidence of AIDS defining cancers, an increased incidence of non-AIDS defining cancers (NADC), such as T and B cell lymphomas, has been well documented in the clinics. Despite previous controversies regarding the role of HIV-1 integration site and cancer prevalence, the clinical association between HIV-1 integration in defined sites and NADC prevalence remains largely unexplored. Given these previous findings and gaps in knowledge, the central hypothesis of this proposal is that HIV-1 integration into or nearby select human genes alters their expression thereby causing NADC. Specifically, HIV-1 integration might disrupt the normal expression of HIV-1 Associated GEnes (HAGEs) causing upregulation of proto-oncogenes, downregulation of tumor suppressors and/or altering RNA splicing patterns, consequently rewiring gene expression programs producing abnormal CD4+ T and B cell expansion and/or behaviors leading to NADC. The major goal of this proposal is to interrogate whether select HIV-1 integration sites are associated with increased incidence of NADC in PLWH under suppressive therapy and to predict associated biomarkers. To start accomplishing this goal, we will deploy a multidimensional approach to concurrently profile HIV-1 integration sites and human transcriptomes at the single cell level in a unique cohort available through the AIDS and Cancer Specimen Resource (ACSR). This will be the first ever approach that can simultaneously interrogate the relationship between HIV-1 integration sites and human transcriptomes at the single cell level in participants biospecimens. We already have on hand an impressive molecular and genomic toolset that will be strategic for accomplishing the Specific Aims of this proposal. These include: 1) To deploy a multidimensional single cell approach to simultaneously collect HIV-1 integration sites and human transcriptomes in ACSR participants biospecimens (Aim 1), and 2) to combine the generated datasets to define participants HIV-1 integration-induced biomarkers associated with NADC (Aim 2). Collectively, these studies will reveal viral integration sites over-represented in PLWH with NADC, link individual viral integration sites to altered human gene expression potentially explaining the onset of NADC, and categorize biomarkers linked to select HIV-1 integration events for diagnostic and prognostic outcomes. Future studies using this knowledge will functionally define specific HIV-1 integration events as NADC drivers and help devise alternative therapeutic opportunities.