CROI 2025 Abstract eBook

Abstract eBook

Poster Abstracts

RNA were adjusted for relevant factors (e.g., age, CD4 + count, antibiotics) and performed at the gut level (models A adjusted for segments; Fig.1 ) and then within each gut segment (models B). Results: Twenty-four participants were included (87.5% male, 63±13 years, median CD4 + T cells 194/ µ L, 87.5% virally suppressed). Main cause of death was cancer (66.7%; 4 of the gut). We observed a large heterogeneity in the bacteriome composition at each taxonomic level, even between anatomically adjacent segments. The large bowel had the highest α diversity, but significant differences were found also between segments within large and small bowel; β diversity showed divergence in bacterial communities between small and large bowel. HIV DNA levels (but not HIV RNA) were higher in small than large bowel segments (101 vs 40 cp/10 6 cells, p=0.003). In models A, 15 genera were associated with HIV burden ( Fig.1 ). In segment specific models B, none of the taxa was consistently associated with HIV burden across all segments: e.g., Clostridium was associated with higher HIV RNA in duodenum, ileum, and rectum only (p≤0.03 all). Some taxa showed opposite associations across segments: e.g., Lachnospira was associated with lower HIV DNA in colon but higher in ileum (p≤0.01 both); Ruminococcus was associated with higher HIV RNA in duodenum but lower in rectum (p≤0.01 both). Conclusions: The local bacteriome has an impact on the size and activity of HIV reservoir in the gut. However, the segment-specificity of the bacteriome and its relationship with local HIV burden suggest the lack of a core bacteriome that could be univocally targeted by therapeutic microbiome modulation across the whole gut. Viral and Microbial Environment in the Male Genital Tract of People Living With HIV Elizabeth Hastie 1 , Aleksander Georgian 1 , Mina Awad 1 , Magali Porrachia 1 , Alan Wells 1 , Gemma Caballero 1 , Brady Lapke 1 , Mattia Trunfio 1 , Sarah LaMere 1 , Stephen A. Rawlings 2 , Davey Smith 1 , Antoine Chaillon 1 , Sara Gianella Weibel 1 1 University of California San Diego, La Jolla, CA, USA, 2 Maine Medical Center, Portland, ME, USA Background: The male genital tract (MGT) is a crucial site for transmission of HIV and co-infecting viruses and functions as an immune-privileged area and key reservoir for HIV, where viral replication can persist despite suppressive ART. The MGT also hosts a distinct microbiota, which may influence viral dynamics and HIV persistence. While previous studies have used semen as a proxy for studying the MGT, here we focus on tissues to investigate the associations between HIV, CMV, EBV, and the genital microbiome. Methods: Fresh MGT tissue (prostate, testes, epididymis, seminal vesicle) was collected during rapid autopsies (<6 hours of death) from PWH enrolled in San Diego’s Last Gift cohort between 2017 and 2024. CMV DNA, EBV DNA, and cell-associated HIV DNA and HIV RNA were quantified by ddPCR. Bacteriome composition was measured by 16SrRNA sequencing. Adjusted, mixed-effect and generalized linear models were used to assess the associations between CMV, EBV, and relative abundance of taxa (predictors) with HIV DNA and HIV RNA levels (outcomes). P-values were adjusted for multiple comparisons. Results: A total of 69 MGT samples from 18 men were analyzed. At time of death, average age was 65 years (range 30-88) and average CD4 + T cell count was 203 cells/ µ L (range 20-513), with 88% of participants virally suppressed. HIV DNA was detected in 42 samples (61%, average 54.3 copies/10 6 cells), RNA in 27 (39%, average 0.067 copies/10 6 cells), CMV in 37 (54%, average 1624.9 copies/10 6 cells), and EBV in 58 (84%, average 608.6 copies/10 6 cells). Viral levels did not differ significantly across tissue types. After adjusting for relevant covariates, levels of EBV DNA, but not CMV DNA, were positively correlated with both cellular HIV DNA and HIV RNA levels across all MGT tissues ( Table 1 ). In the MGT microbiome analysis, Shannon diversity did not significantly vary across tissue types. Across all MGT tissues, two bacterial genera, Rhodospirillaceae

(phylum Proteobacteria) and Pseudonocardia (phylum Actinomycetota), were significantly associated with higher cellular HIV RNA levels (but not HIV DNA). Conclusions: The associations of Rhodospirillaceae and Pseudonocardia with elevated HIV RNA, alongside EBV’s link to higher HIV DNA and RNA, suggest that microbial and viral interactions may drive local inflammation, promoting HIV persistence in the MGT. These findings point to inflammation-driven mechanisms that could be targeted for novel therapeutic strategies aimed at disrupting HIV reservoirs in tissues.

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Transcriptional Profiles of HIV RNA+ Cells in PWH on ART Differ From Those During Active Viremia Julie Frouard 1 , Sushama Telwatte 2 , Xiaoyu Luo 1 , Natalie Elphick 1 , Reuben Thomas 1 , Douglas Arneson 3 , Pavitra Roychoudhury 4 , Atul J. Butte 3 , Joseph K. Wong 3 , Rebecca Hoh 3 , Steven G. Deeks 3 , Sulggi Lee 3 , Steven Yukl 3 , Nadia R. Roan 1 1 Gladstone Institutes, San Francisco, CA, USA, 2 Peter Doherty Institute, Melbourne, Australia, 3 University of California San Francisco, San Francisco, CA, USA, 4 Washington DC VA Medical Center, Washington, DC, USA Background: While HIV RNA+ cells during untreated HIV infection in people with HIV (PWH) have been characterized by scRNAseq, “transcriptionally-active” reservoir cells (HIV RNA+ cells that persist in ART-suppressed PWH) remain poorly uncharacterized. This is due in part to the inefficiency of capturing HIV transcripts using droplet-based scRNAseq analytical approaches. Methods: We developed HIV-seq as a method to increase scRNAseq-based detection of HIV RNA+ cells from PWH. HIV-seq incorporates HIV-specific primers alongside poly-dT during scRNAseq library preparation to enable more efficient capture of HIV transcripts, including non-polyadenylated ones. We performed HIV-seq on longitudinal blood specimens from 3 PWH before vs. after ART suppression, and compared transcriptomic signatures of HIV RNA+ vs. RNA- cells, before and after ART suppression. Results: HIV-seq improved detection of HIV RNA+ cells from PWH by up to 44%, enabling identification of a total of >1,000 HIV RNA+ cells by scRNAseq. While HIV RNA+ cells from before and after ART suppression were both enriched among Tem cells, only those from viremic individuals exhibited a cytotoxic pro inflammatory signature. Relative to their uninfected counterparts, HIV RNA+ cells during viremia exhibited low expression of antiviral factors SERPINA1 and APOBEC3A. Unlike HIV RNA+ cells during viremia, HIV RNA+ cells during ART suppression exhibited an anti-inflammatory signature characterized by elevated TGF-β signaling. These active reservoir cells also predominantly resided among a long-lived population of memory CD4+ T cells expressing high levels of CD127, a major driver of homeostatic proliferation, and BCL2, an anti-apoptotic effector that is a current target for HIV cure therapies. Conclusions: We demonstrate that HIV-seq improves the efficiency of capturing HIV transcripts for scRNAseq analysis, enabling a comparative analysis of HIV RNA+ cells during viremia vs. after ART suppression. Gene signatures reflecting a cytotoxic pro-inflammatory but diminished anti-viral state were harbored by HIV RNA+ cells during viremia, whereas HIV RNA+ cells during ART suppression were defined by pro-survival, immunosuppressive, and homeostatic proliferative gene expression signatures. Hence, active reservoir cells are fundamentally distinct from HIV RNA+ cells during untreated infection. Selective Decay of Different HIV Transcripts After ART Initiation in Chronic Infection Julie Janssens 1 , Cordelia M. Isbell 1 , Sun Jin Kim 1 , Alton Barbehenn 1 , Rebecca Hoh 1 , Michael Peluso 1 , Sulggi Lee 1 , Satish Pillai 2 , Nadia R. Roan 3 , Steven G. Deeks 1 , Steven Yukl 1 , Adam Wedrychowski 4 , Timothy J. Henrich 1 1 University of California San Francisco, San Francisco, CA, USA, 2 Vitalant Research Institute, San Francisco, CA, USA, 3 Gladstone Institutes, San Francisco, CA, USA, 4 San Francisco VA Medical Center, San Francisco, CA, USA Background: In the first year after ART initiation in acute infection, completed and intact HIV RNA decay faster than incomplete or defective HIV RNA. It is

Poster Abstracts

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CROI 2025 135