Lung Microbiome and Pulmonary Inflammation/Immunity in HIV Infection

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DESCRIPTION (provided by applicant): The lung compartment in Human Immunodeficiency Virus (HIV) infection is characterized by chronic inflammation and severe immunologic derangements. While some of the inflammatory changes may be due to chronic stimulation by HIV in the lung, correlation between these changes and the lung viral load is poor. Thus other factors are likely driving the chronic inflammatory state in the lung. Given the known immunodeficiency in these patients, colonization of the respiratory tract with new or increased numbers of infectious pathogens is highly likely and easily could be contributing to chronic inflammation. Thus we hypothesize that the lung inflammatory and immunologic environment in HIV-infected subjects is directly related to the host microbiome rather than the pulmonary HIV burden, that the immunodeficiency seen leads to a more diverse pulmonary microbiome compared to uninfected subjects, and that highly active antiretroviral therapy (HAART) returns the pulmonary microbiome towards normal. We will make use of a large existing cohort of bronchoalvoelar lavage samples to begin exploring lung microbiomes in normal volunteers and HIV-infected subjects and correlate these with measures of local pulmonary inflammation. These cohorts include HIV-infected subjects with COPD and those studied prior to starting antiretroviral and followed longitudinally for 6-12 months. We will also prospectively study the microbiome along the entire respiratory tract from the oropharynx to the alveoli to determine if what is found in the upper tract can predict lower respiratory microbiomes. To accomplish our goals we propose the following Specific Aims. (1) To compare the respiratory microbiome between HIV-infected subjects and normal volunteers; (2) To directly correlate the relationship between the respiratory microbiome and the pulmonary inflammatory milieu in HIV-infected subjects and normal volunteers; (3) To determine if highly active antiretroviral therapy alters the pulmonary microbiome and local inflammatory response; and (4) To compare the respiratory microbiome in HIV-infected subjects and normal volunteers from the oropharynx to the alveoli. In depth analysis will start with 16s and 18s rRNA sequencing to paint a broad picture of the microorganisms present in the lung. Detailed metagenomic shotgun sequencing will be performed on prospectively identified species to characterize significant gene pools which may directly impact the pulmonary immunologic and inflammatory milieu These studies will greatly enhance our understanding of the lung environment in both health and disease and lead to potential new models defining pulmonary homeostasis.