Transcriptional Crosstalk between DUX4-FL and HIV

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Abstract HIV eradication strategies aim to clear residual HIV transcription, from a pool of latently infected memory CD4+ T cells, that persist in people living with HIV (PLWH) treated with an effective antiretroviral therapy (ART). These cells harbor a provirus poised to viral rebound upon a sequential recruitment, at the HIV promoter, of host transcription elongation factors, the viral Tat protein and host chromatin remodelers (a process called Tat- mediated transcription). Long-term block of this residual HIV transcription, in different models of HIV latency, using an inhibitor of Tat, results in an heterochromatinization and a loss of RNA polymerase II at the HIV promoter, along with preventing viral rebound. Thus, our premise is that transcriptional and chromatin remodeling inhibitors along with Tat inhibitors can be used in the block-and-lock functional cure approaches, aimed at reducing residual viremia during ART and limiting viral rebound. Additionally, gaining fresh insightful knowledge on the connections between these factors and HIV transcription will help leverage them as antiviral targets. We have uncovered a direct positive relationship between the expression of the full-length isoform of the double homeobox protein 4 (DUX4-FL) expression and HIV infection in primary blood CD4+T cells. DUX4-FL robustly activates HIV transcriptional activity by promoting both residual and Tat-mediated HIV transcription. Furthermore, HIV enhances DUX4-FL transcription suggesting a positive transcriptional crosstalk between HIV and DUX4-FL. DUX4-FL is a strong transcription factor that is mostly expressed in disease phenotypes, such as facioscapulohumeral muscular dystrophy and cancers, but has never been described to regulate HIV. In disease, DUX4-FL typically regulates expression of evolutionally or immune adaptative genes, resulting in toxicity and/or evasion from the immune system. DUX4-FL has also been described to open compacted chromatin by recruiting histone variants or chromatin remoders promoting long-lasting chromatin relaxation. Importantly, strategies to neutralize the overexpression of DUX4-FL in mice have shown to be safe and provide benefits. To explore the role of DUX4-FL in the context of HIV transcription, we propose to identify and quantify DUX4 isoforms expressed in relevant HIV productive or latent models. This will ensure the significance of our studies, since DUX4-FL is not expected to be expressed in blood CD4+T cells. We will define the mechanism by which DUX4-FL upregulates HIV transcription. We will study the direct DUX4-FL recruitment to the HIV promoter, its impact on epigenetic marks, and uncover cellular proteins complexed with DUX4-FL via a multipronged approach, including proteomics, genomics and cell-based approaches. The overarching goal of this study is to explicitly establish whether DUX4-FL, or complexed proteins, are important for HIV transcriptional regulation, with the longstanding objective of exploiting these factors for HIV functional cure approaches.