Continuous NRTI-based antiretroviral therapy induces progressive senescence-like reprogramming of alveolar macrophages [snMultiomics]

Background: Advances in antiretroviral therapy (ART) have substantially improved the lives of people with HIV (PWH) and reduced HIV acquisition through pre-exposure prophylaxis (PrEP). However, the long-term effect of ART on the physiological state of cells remains poorly understood. Despite the success of ART in preventing the progression of HIV infection to AIDS, the aging PWH are suffering from a disproportional burden of non-AIDS comorbidities, including lung diseases. Methods: Given the central function of alveolar macrophages (AM) in pulmonary immunity, we evaluated the impact of nucleoside reverse transcriptase inhibitors (NRTI) based ART on AM of PWH and people on PrEP. We employed a retrospective cross-sectional design and evaluated the effects of continuous exposure to ART in the epigenetic and transcript of AM at bulk and single-nucleus multiomics levels. Results: We showed that continuous NRTI-based ART induces a progressive senescence-like pro-inflammatory state in AM, characterized by increased constitutive epigenetic and transcriptomic priming of genes involved in cell cycle arrest (e.g., CDKN1A/p21), components of the senescence-associated secretory phenotype (e.g., IL1A, IL6R, and CXCL8), as well as transcription factors subunits of the AP-1 family (e.g., FOSL1, JUN). At the AM single nucleus level we described a coordinated gene regulatory network linking key pro-inflammatory transcription factors to the transcriptomic alterations induced by ART. The senescence ART-linked epigenetic and transcriptomic changes were strongly dependent on the duration of ART and irrespective of HIV infection. A secondary time independent ART effect was observed for interferon signaling genes. This effect was more pronounced in people on PrEP and impaired AM response to ex vivo challenge with SARS-CoV-2. Conclusion: Combined, our data indicate that continuous NRTI-based ART promotes a dysregulated physiological state in AM, potentially contributing to age-related pulmonary comorbidities in PWH, such as COPD, pulmonary fibrosis, and asthma. PrEP is critically important for preventing HIV acquisition in the most vulnerable populations. By identifying therapeutical gaps in ART our study advocates for optimized or adjuvant therapies to prevent or mitigate potential long-term adverse effects of PrEP and to continuously improve the quality of life of PWH.