Systems Biology of Diffusion Impairment in HIV

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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.