Crentsil, E. U. | bioRxiv Science

bioRxiv2026

A Tissue Microenvironment Analogous to Certain Tumor Microenvironments Facilitates HIV Persistence

The HIV reservoir that establishes early upon infection and persists in tissues remains the primary barrier to a functional cure. While progress has been made to study the reservoir in blood compartments and specific cell types, knowledge gaps remain on the tissue microenvironment that facilitates persistence. The development of a novel immunoPET/CT-guided spatial transcriptomics pipeline has enabled the localization of foci of viral infection in tissues, rare events that are challenging to sample. Prior studies leveraging the pipeline have characterized the viral microenvironment (VME) gene signatures, cell types and interactions, and host transcriptome gene drivers of viral persistence. Detailed characterization of the VME revealed multiple shared features with certain tumor microenvironments (TMEs), suggesting shared immunoregulatory and survival mechanisms. In this study, we apply the immunoPET/CT-guided spatial transcriptomics pipeline in the SIVmac239/rhesus macaque model to define immune mechanisms underlying persistent versus transient HIV/SIV reservoirs. We utilize a systematic approach to highlight correlates between the VME and TME transcriptional programs, gene pathways, local tissue neighborhoods, cell-cell interactions, and host transcriptomic drivers. Analysis of broad transcriptional programs revealed SIV-localized spatial enrichment of genes associated with multiple cancer subtypes. The persistent reservoir was characterized by gene pathways of "cold" TMEs (e.g., epithelial to mesenchymal transition, TGF{beta} activation) whereas the transient reservoir was comparable to "hot" TMEs with cytotoxic immune activation. Cell-cell interaction analysis identified regulatory T cells as a key mediator of interactions in both persistent and transient reservoirs. Machine learning identified KRT8, EPCAM, and RRM2, genes with known roles in mediating carcinogenesis, among the top host transcriptomic drivers of the TME phenotype of the persistent VME. Collectively, the findings of this study provide novel and transformative insights on key mechanisms of HIV/SIV persistence and reveal potential targets for immunotherapeutic strategies aimed at reservoir disruption or clearance towards a functional HIV cure.

microbiology↗

bioRxiv2026

A Tissue Virus Microenvironment with Activated Stress Responses Underlies Durable SIV Persistence

HIV persistence during suppressive antiretroviral therapy (ART) remains a central barrier to cure, with the majority of reservoirs residing in gut-associated lymphoid tissues (GALT). Here, we define a spatially organized viral microenvironment (VME) that sustains reservoir durability and governs early viral rebound by comparing animals initiating ART early after infection (transient reservoirs) versus late (persistent reservoirs). Using immunoPET/CT-guided sampling of SIV-infected rhesus macaques combined with spatial transcriptomics, we interrogated tissue sites of viral production during the eclipse phase following analytical treatment interruption (ATI). Our results revealed that viral rebound from persistent reservoirs arises from discrete, transcriptionally active foci enriched in the mucosa lining the gut lumen. Eclipse phase persistent reservoirs were characterized by increased proviral burden and a distinct tissue state marked by activation of stress-response, metabolic, mitochondrial, and cell cycle programs coupled to repression of cytoplasmic translation and increased cellular senescence. These features co-occurred with immunosuppressive cellular architectures resembling tertiary lymphoid structures enriched for Treg cells, innate lymphoid cells, and mast cells, regulated by Treg-centered cell-cell interaction networks. In contrast, transient reservoirs displayed enhanced translational and metabolic activity and were embedded within immune-active environments enriched for CD8 T cells, Th17, Tfh, and activated CD4 T cells. Machine learning identified stress adaptation, hypoxia, metabolic rewiring, and cytoskeletal remodeling pathways as dominant predictors of viral density within persistent VMEs, with strong convergence on programs observed in tumor microenvironments (TME). Orthogonal validation confirmed activation of the integrated stress response (ISR) at sites of viral production in concurrence with results of immunofluorescent microscopy revealing SIV gag expression in two populations primarily in the mucosa, differentiated by the phosphorylation of eIF2. Together, these findings establish the VME as a critical determinant of reservoir persistence, integrating immune regulation, tissue remodeling, and translational control to enable viral survival. This framework suggests that effective HIV cure strategies will require coordinated disruption of VME-supportive functions in addition to targeting infected cells.

microbiology↗