Genomic Analysis of Immunity and Lung Inflammation in HIV Infection

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DESCRIPTION (provided by applicant): The lung compartment HIV infection is characterized by chronic inflammation and severe immunologic derangements. While improvement is seen on highly active antiretroviral therapy (HAART), these patients still are susceptible to lung disease, especially those mediated by chronic inflammation. Furthermore, immune reconstitution is frequently characterized by poorly functioning lymphocytes due to a phenomenon called immunosenescence, or accelerated aging. Immunosenescence is caused by chronic antigenic stimulation, usually by viruses. In this regard, we have shown that HIV can persist in the lung in patients on HAART. Importantly, immunosenescence is associated with a chronic inflammatory state. Thus in this project we hypothesize that persistent antigenic stimulation by whole HIV or HIV proteins leads to an immunosenescent lung phenotype and chronic lung inflammation which contribute to the late complications associated with HIV infection. To address this hypothesis we will make use of two well characterized longitudinal cohorts of HIV-infected subjects we have recruited since 2000 to examine inflammatory and immunologic responses to HAART. We will recruit these subjects back for a longterm follow up visit to assess whether baseline, early HAART findings, or late HAART findings predict the development of long term HIV pulmonary complications. To accomplish our goals we propose the following Specific Aims: (1) To assess HIV-infected subjects who have been on treatment for three years or longer for pulmonary complications using a respiratory questionnaire, pulmonary function testing, chest CT imaging, and bronchoalveolar lavage. (2) To assess the pulmonary and peripheral blood HIV viral load and virome in patients on longterm HAART by measuring acellular HIV and cellular HIV RNA and HIV DNA in bronchoalveolar lavage fluid and blood. (3) To assess lung inflammation in HIV-infected subjects at the genomic level after longterm HAART using nanostring sequencing transcriptome analysis of lung and blood specimens. (4) To assess immune and inflammatory potential in subjects on long-term HAART by measuring cellular activation makers, T cell phenotypes, cytokine and chemokine release, and antigen specific T cell responses. Given our long history of studying HIV-infected subjects we have a large baseline HIV population with well-defined baseline clinical and immunologic characteristics which provide us a unique opportunity to look at longitudinal long term follow-up. Since chronic inflammation is likely at the root of most pulmonary complications in long term HIV infection, this work could have broad reaching implications on the management of these patients.