Systems Biology of Diffusion Impairment in HIV

摘要 一氧化碳(DLCO)扩散能力受损的机制，影响超过50% HIV+个体，人们对此知之甚少。尽管对生活质量有重大影响，但没有治疗方法 死亡率。识别HIV+个体DLCO损伤的分子途径并发展其能力 因此，预测有DLCO损害风险的HIV+个体对于改善护理至关重要。在这 建议，我们构建了一种系统建模方法来识别分子和临床途径 与HIV+个体的DLCO损害有关。我们收集了多个平行的分子数据集，集成了详细的 肺功能、放射学和超声心动图测量，以建立一个全面的系统- 建立HIV中DLCO异常的水平模型，并开发DLCO易感性恶化的预测模型。 我们的初步数据表明，某些miRNAs，如低氧诱导的和代谢活跃的 MIR-210可能在HIV的DLCO异常中发挥重要作用，然后我们进行假设检验 确定miRNAs对肺上皮细胞和内皮细胞的影响的实验。我们利用我们的油井- 500多名携带相关生物素的艾滋病毒携带者的表型队列，以实现以下目标： 目的1：通过结合临床特征和-DLCO损伤的分子机制，确定DLCO损伤的关键分子通路。 来自HIV+患者肺部的组学数据。我们将利用高通量的RNA测序和质量 用分光光度法定量测定支气管肺泡液和肺组织中的miRNAs、mRNAs、微生物组和代谢物 HIV阳性个体的上皮细胞具有详细的肺功能、放射学和超声心动图 构建DLCO概率网络模型的措施。关键路径将得到验证。目标2：实现 从临床特征、转录组、微生物组和代谢物确定DLCO下降的预测标志 在易于获取的临床标本中的数据。我们将建立预测模型来识别有风险的个人 根据Easy收集的组学数据，出现DLCO损害或显著下降 可接近的组织(来自血清和外周血单核细胞的miRNA和代谢谱；口腔的微生物组)； 再加上详细的临床和表型数据。目标3.调查全系统的关系 HIV阳性个体中HIV诱导的miRNAs与肺上皮和内皮基因重编程之间的关系。 基于我们的初步数据，我们将检验来自HIV+个体的PBMC释放miRNAs的假设 它们被输送到肺上皮细胞和内皮细胞，从而调节基因表达、代谢 功能和活跃性。这些研究调查了一种全新的艾滋病毒媒介传播模式。 通过细胞外miRNA信号与肺细胞产生直接治疗相关性，因为miRNA水平可以 通过增强或抑制特定的miRNAs进行调节。该项目将利用现有资源来 确定DLCO损害的复杂关联和因果关系，确定新的治疗靶点 和生物标志物，并改善对艾滋病毒携带者的护理。

ABSTRACT Mechanisms of impairment of diffusing capacity for carbon monoxide (DLco), which affects over 50 percent of HIV+ individuals, are poorly understood. No therapies exist despite significant impact on quality of life and mortality. Identifying molecular pathways of DLco impairment in HIV+ individuals and developing ability to predict HIV+ individuals at risk of DLco impairment is thus of utmost importance for improving care. In this proposal, we construct a systems’ modeling approach to identify molecular and clinical pathways contributing to DLco impairment in HIV+ individuals. We collect multiple parallel molecular datasets integrated with detailed pulmonary function, radiographic, and echocardiographic measurements to build a comprehensive, systems- level model of DLco abnormalities in HIV and to develop predictive models of susceptibility to DLco worsening. As our preliminary data suggest that certain miRNAs, such as the hypoxia-induced and metabolically active miR-210, may play an important role in DLco abnormalities in HIV, we then perform hypothesis-testing experiments to determine the impact of miRNAs on lung epithelial and endothelial cells. We utilize our well- phenotyped cohort of over 500 HIV+ individuals with associated biospecimens to execute the following aims: Aim 1: To identify key causal molecular pathways of DLco impairment by integrating clinical features and – omics data from the lung in HIV+ individuals. We will utilize high-throughput RNA sequencing and mass spectrometry to quantify miRNAs, mRNAs, the microbiome, and metabolites in bronchoalveolar fluid and lung epithelial cells in HIV+ individuals with detailed pulmonary function, radiographic, and echocardiographic measurements to construct probabilistic network models of DLco. Key pathways will be validated. Aim 2: To identify predictive signatures of DLco decline from clinical features, transcriptomic, microbiome, and metabolite data in easily accessible clinical specimens. We will build predictive models to identify individuals at risk of developing DLco impairment or having significant decline based on –omics data collected from easily accessible tissues (miRNA and metabolic profiles from serum and PBMCs; microbiome of the oral cavity), coupled with detailed clinical and phenotypic data. Aim 3. To investigate the systems-wide relationship between HIV-induced miRNAs and lung epithelial and endothelial gene reprogramming in HIV+ individuals. Based on our preliminary data, we will test the hypothesis that PBMCs from HIV+ individuals release miRNAs that are delivered to lung epithelial and endothelial cells and consequently regulate gene expression, metabolic function, and activity. These studies investigate an entirely novel paradigm of HIV-mediated communication with pulmonary cells via extracellular miRNA signaling with direct therapeutic relevance as miRNA levels can be modulated by augmentation or inhibition of specific miRNAs. This project will leverage existing resources to identify complex associations and causal relationships in DLco impairment, identify novel therapeutic targets and biomarkers, and improve care of HIV+ individuals.