Ay, S. | bioRxiv Science

bioRxiv2025

Tracking HIV-1 DNA fate from Cell Culture to Humanized mice Tissues.

Unambiguous identification of HIV reservoirs is essential for their characterization and for developing curative strategies. A major obstacle to curing HIV is the persistence of silent viral genomes in host cells that evade immune detection and resist therapy. Here, we present a fluorescence microscopy-based method for direct in vivo visualization of full-length double-stranded HIV-1 DNA, an achievement not previously realized. To achieve this, we developed an advanced imaging platform adapted for replication-competent HIV-1. This system leverages a bacterial-derived two-component tagging strategy, where a fluorescent protein (OR-GFP), efficiently expressed in xenografted human immune cells, specifically binds to an engineered ANCH3 tag sequence integrated into the viral genome. The tagged virus infects CD4+ T cells both in vitro and in vivo, producing bright nuclear puncta corresponding to individual viral genomes. Multiple nucleation sites within ANCH3 enable a stable, shortened tag form for persistent and long-term tracking. Transcriptional profiling during acute infection revealed both transcriptionally active and silent genomes in spleen, lymph nodes, and bone marrow, with silent forms enriched in lymph nodes and marrow, supporting early reservoir establishment. This live-cell imaging strategy enables high-specificity detection of latent HIV, offering a transformative tool for studying reservoir dynamics and guiding future cure strategies.

microbiology↗

bioRxiv2024

Decoding the biogenesis of HIV-induced CPSF6 puncta and their fusion with the nuclear speckle

Viruses rely on host cellular machinery for replication. After entering the nucleus, the HIV genome accumulates in nuclear niches where it undergoes reverse transcription and integrates into neighboring chromatin, promoting high transcription rates and new virus progeny. Despite antiretroviral treatment, viral genomes can persist in these nuclear niches and reactivate upon treatment interruption, raising the possibility that they could play a role in the establishment of viral reservoirs. The post-nuclear entry dynamics of HIV remain unclear, and understanding these steps is critical for revealing how viral reservoirs are established. In this study, we elucidate the formation of HIV-induced CPSF6 puncta and the domains of CPSF6 essential for this process. We also explore the roles of nuclear speckle scaffold factors, SON and SRRM2, in the biogenesis of these puncta. Through genetic manipulation and depletion experiments, we demonstrate the key role of the intrinsically disordered region of SRRM2 in enlarging nuclear speckles in the presence of the HIV capsid. We identify the FG domain of CPSF6 as essential for both puncta formation and binding to the viral core, which serves as the scaffold for CPSF6 puncta. While the low-complexity regions (LCRs) modulate CPSF6 binding to the viral capsid, they do not contribute to puncta formation, nor do the disordered mixed charge domains (MCDs) of CPSF6. Interestingly, the FG peptide facilitates viral replication. These results demonstrate how HIV evolved to hijack host nuclear factors, enabling its persistence in the host. Of note, this study provides new insights into the underlying interactions between host factors and viral components, advancing our understanding of HIV nuclear dynamics and offering potential therapeutic targets for preventing viral persistence. HighlightsO_LIThe formation of HIV-induced CPSF6 puncta is critical for restoring HIV-1 nuclear reverse transcription. C_LIO_LICPSF6 protein lacking the FG peptide cannot bind to the viral core, thereby failing to form HIV-induced CPSF6 puncta. C_LIO_LIThe FG peptide, rather than low-complexity regions (LCRs) or the mixed charge domains (MCDs) of the CPSF6 protein, drives the formation of HIV-induced CPSF6 puncta. C_LIO_LIThe presence of the FG peptide plays a pivotal role in facilitating viral replication within macrophage-like cells. C_LIO_LIHIV-induced CPSF6 puncta form individually and later fuse with nuclear speckles (NS) via the intrinsically disordered region (IDR) of SRRM2. C_LI

microbiology↗