Persistence of HIV-1 in tissue reservoirs of therapy-suppressed, aviremic individuals is a major challenge to HIV-1 cure. The viral reservoir consists of myeloid and lymphoid cells that harbor the virus through long periods of combination anti-retroviral therapy (cART). Until recently, it was thought that HIV-1 provirus remains in a transcriptionally-silent, latent state in these reservoir cells and only resumes viral transcription and virion production upon activation from endogenous or exogenous stimuli. However, it is now evident that in a subset of reservoir cells, the virus remains transcriptionally-active even under cART and continues to generate some levels of viral RNAs and/or proteins. Even in absence of complete viral replication, persistent viral RNA and protein production in these “active” reservoirs pose significant adverse immunologic and virologic consequences. They can contribute to the chronic immune activation as well as impact viral rebound upon treatment interruption. Along with the transcriptionally-silent, latently-infected cells, elimination of these viral transcriptionally-active reservoirs would be necessary to achieve a cure for HIV-1.

Most of our current knowledge of active HIV-1 reservoirs is limited to studies of CD4+ T-cells in the peripheral blood. The nature of active reservoirs in myeloid cells within tissue compartments have remained largely uncharacterized. In our preliminary studies, we have shown that alveolar macrophages (AMs), which are the predominant HIV-1-infected cell-type in the lung, continue to transcribe viral RNAs under long-term cART. We have also shown that, unlike CD4+ T-cells, the levels of viral RNA-positive AMs do not decrease even after years-long therapy. In this study, we propose to comprehensively characterize these active AM reservoirs in therapy-suppressed individuals by addressing three specific questions: (1) how the proviral landscapes and profiles of viral RNA transcripts in AMs compare between cART-naïve and treated individuals, (2) how does the ongoing viral transcription affect immunological functions and survival of the active macrophage reservoirs and (3) do active reservoir macrophages impact viral rebound and replication in the neighboring reactivation-capable AMs and CD4+ T-cells. We will utilize state-of-the-art molecular, cellular and immunological methods and a well-characterized human subject cohort to examine the specific aims. The study will provide fundamental scientific knowledge about a new layer of complexity in HIV-1 persistence and reveal the biological significance of active AM reservoirs. Understanding the molecular mechanisms of continued viral transcription in active AMs and its adverse cellular effects will help in devising tailored strategies for eliminating these myeloid reservoir cells.