Intragenic transcription from defective HIV proviruses triggers interferon responses in myeloid cells

Abstract

ABSTRACT The persistent HIV-1 reservoir includes a subset of cells harboring transcriptionally repressed latent HIV-1 that contributes to rebound upon antiretroviral treatment (ART) interruption. However, the majority of the reservoir consists of defective proviral genomes with mutations that prevent production of HIV-1 virions. People with HIV (PWH), even with suppression of viremia, demonstrate comorbidities of the central nervous system, heart, gut, and general aging-associated inflammation. Previously, we identified a transcriptionally active element within the envelope gene (env) of HIV-1, which mediates the expression of aberrant HIV-1 RNAs. We hypothesize that spurious expression of defective proviruses contributes to the general inflammation that drives these comorbidities. We observed correlations between levels of inflammatory cytokines in serum of PWH and levels of HIV-1 transcripts from this intragenic promoter. To investigate the impact of defective proviruses, we employed CRISPR-Cas9 to render the 5′ long terminal repeat (LTR), which acts as the enhancer and promoter for proviral transcription, non-functional. HIV-1-infected cells harboring this deletion produce significantly higher levels of IP-10 and IL-8 in vitro in both monocytic cell lines and primary monocyte-derived macrophages. Transcripts generated from the env promoter include a 5′ cap and polyA tail, and the induction of IP-10 expression was dependent on the cytosolic innate immune sensing pathway components MDA5 and MAVS and not cGAS and RIG-I. We propose that defective HIV proviruses contribute to chronic inflammation in PWH through an MDA5-dependent induction of type I interferon pathways. IMPORTANCE People with HIV-1 are at higher risk of developing age-associated comorbidities and immune exhaustion even when receiving antiviral treatments and having no detectable viremia. Transcription and translation have been documented from latent and defective proviruses, but their impact on inflammation associated with chronic HIV-1 infection remains poorly understood. The significance of this work is in identifying a role for defective HIV-1 proviruses and correlating their transcription in triggering a type I interferon response. These results highlight the importance of the persistent defective HIV-1 proviruses and understanding their impact on driving chronic inflammation to inform future strategies to assure people with HIV-1 healthy living and aging. People with HIV-1 are at higher risk of developing age-associated comorbidities and immune exhaustion even when receiving antiviral treatments and having no detectable viremia. Transcription and translation have been documented from latent and defective proviruses, but their impact on inflammation associated with chronic HIV-1 infection remains poorly understood. The significance of this work is in identifying a role for defective HIV-1 proviruses and correlating their transcription in triggering a type I interferon response. These results highlight the importance of the persistent defective HIV-1 proviruses and understanding their impact on driving chronic inflammation to inform future strategies to assure people with HIV-1 healthy living and aging.