CROI 2025 Abstract eBook

Abstract eBook

Poster Abstracts

the risk of opportunistic infections and non-AIDS-related morbidity and mortality. Understanding the mechanisms driving this immune dysfunction is critical for developing targeted therapies. Methods: We performed single-cell RNA sequencing (scRNA-seq) and single cell VDJ sequencing (scVDJ-seq) on peripheral blood mononuclear cells (PBMCs) from INRs (n= 10), immune responders (IRs, n= 14), and healthy controls (HCs, n= 9). We developed scGeneANOVA, a novel mixed model differential gene analysis tool, to detect differentially expressed genes and pathways. We performed flow cytometry and bulk RNA-seq to PLWH cohort (23 INRs and 37 IRs) to validate the corelation. In addition, we developed the Viral Identification and Load Detection Analysis (VILDA) tool to quantify HIV-1 transcripts and investigate their relationship with host gene expression. Results: We had identified 8 major clusters and 51 subclusters within 232,369 PBMC cells across 33 samples. The scGeneANOVA tool identified critical genes and pathways that were missed by traditional analysis methods, and revealed that INRs exhibit a dysregulated interferon (IFN) expression profile. RNA velocity and TCR tracing showed an increased tendency toward an exhaustion prone differentiation trajectory in the CD4 + T cells of INRs, with fewer cells differentiating into effector cells. Transcriptional analysis on bulk RNA-seq cohort and public data validated the role of IFN in driving CD4 + T cell exhaustion. The VILDA tool showed higher levels of HIV-1 transcripts in INRs, suggesting that the size and transcriptional activity of the HIV-1 reservoir are closely linked to IFN signaling activation in INRs. Conclusions: This study revealed that INRs exhibit a dysregulated IFN response, closely associated with CD4 + T cell exhaustion. This immune exhaustion was identified as a key factor contributing to immune recovery failure. These findings point to the central role of IFN signaling and HIV-1 reservoirs in INR related immune dysfunction. The identification of key genes and pathways offers potential biomarkers and therapeutic targets for improving immune recovery in this vulnerable population. Variability in Immunometabolic Signatures Among People w/ HIV Defines Immune Outcomes and Progression Simon Gressens 1 , Mohamed R. Joma 1 , Rachelle Saleh 1 , Lara Tabet 1 , Cassiopée Adam 1 , Julien Pansiot 1 , Katia Bourdic 2 , Guislaine Carcelain 2 , Nicolas Noel 2 , Olivier Lambotte 2 , Mireille Laforge 1 1 Institut national de la santé et de la recherche médicale (Inserm), Paris, France, 2 Assistance Publique Hôpitaux, Paris, France Background: HIV infection leads to significant loss of CD4 T lymphocytes (CD4TL), compromising immune function despite antiretroviral therapy (ART). People living with HIV (PLHIV) can be categorized as immune responders (IR) or immune non-responders (INR) based on their ability to achieve immune reconstitution. IR restore CD4TL counts >500 cells/mm³, while INR remain below this threshold despite ART. CD4TL subpopulations show distinct metabolic signatures based on their functions. Upon in-vitro activation, Glut1 expression rises supporting glycolysis along with the upregulation of the activation markers. Recent research has shown that CD4TL from PLHIV exhibit bioenergetic defects, particularly in INR, with a downregulation of TFAM, a regulator of mitochondrial biogenesis. In addition, the release of mitokines in the plasma is associated with mitochondrial stress. These mitochondrial dysregulations impair immune functions. We carried a study in PLHIV to describe mitochondrial defects in PLVIH to understand how IR despite those defects could achieve their immune reconstitution. Methods: We included 30 PLHIV based on age, ART length, undetectable virus, CD4TL count and CD4/CD8 ratio. We performed a multiapproach immuno metabolic profiling of CD4TL and their subpopulations using flow cytometry, biochemistry, and Seahorse analysis, combined with NMR metabolomics and secretome analysis on plasma. Results: CD4TL from INR displayed reduced mitochondrial mass, increased non mitochondrial oxygen consumption, lower TFAM, increased activation markers (CD25, CD69, HLA-DR, CD95, PD-1), less naive CD4TL ( p=0.007 ), and more TEMRA ( p=0.002 ) compared to healthy donors (HD) and IR. However, both groups exhibited bioenergetic defects; yet IR can compensate through enhanced mitochondrial biogenesis by increasing TFAM and functional mitophagy, maintaining immune integrity. Upon in-vitro activation, INR did not upregulate Glut1 despite elevated activation markers (c ompared to HD: ns for IR; p<0.001 for INR ). Both groups had high GDF15 in plasma, but INR showing significantly higher levels ( compared to HD: p=0.022 for IR; p<0.001 for INR ).

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Virulent HIV-1B: Clinical Challenges and Proteomic Insights Kavita Mehta 1 , Mareva Delporte 2 , Victoria Rios Vazquez 3 , Marc J. T. Blaauw 4 , Louise E. van Eekeren 3 , Albert L. Groenendijk 5 , Wilhelm A. Vos 6 , Evy Blomme 2 , Sarah Gerlo 2 , Bram Vrancken 7 , Philippe Lemey 7 , Sofie Rutsaert 2 , Andre van der Ven 3 , Linos Vandekerckhove 2 , for the 2000HIV Human Functional Genomics Partnership Program 1 Ghent University, Ghent, Belgium, 2 HIV Cure Research Center, Ghent University, Ghent, Belgium, 3 Radboud University Medical Center, Nijmegen, Netherlands, 4 Elisabeth-TweeSteden Ziekenhuis, Tilburg, Netherlands, 5 Erasmus University Medical Center, Rotterdam, Netherlands, 6 OLVG, Amsterdam, Netherlands, 7 Katholieke University Leuven, Leuven, Belgium Background: A virulent HIV-1 subtype B clade (VB) first reported in 2022 (Wymant et al . 2022), is linked to higher viral loads (VL), faster CD4+ T-cell decline, and greater transmissibility. This presents significant challenges for clinical management due to its faster disease progression. The study aims to elucidate the effects of VB on clinical outcomes and host proteomic profiles. Methods: Viral genetic analysis was performed on 1,895 people living with HIV (PLWH) on ART from the 2000HIV cohort using partial env and pol sequencing of gDNA samples extracted from CD4+ T-cells. Phylogenetic analysis using IQ-TREE (subtype B), confirmed the presence of VB. The profiling of 2,367 proteins was assessed using proximity extension assay technology (OLINK proteomics). Associations of VB with clinical parameters were assessed using the Wilcoxon Rank-Sum Test. Differential protein expression analysis between VB and non-VB was performed using a linear regression model adjusting for covariates such as age, smoking status, and other factors that accounted for at least 3% of the variance in the plasma proteome. Results: The VB was confirmed in 32 participants (male, diagnosed between 2004-2019, median ART duration before sampling: 9.93 years). Tropism profiles were R5 (n=22), X4 (n=3), and mixed-tropic (n=2) (Fig1A). VB participants had higher pre-cART VL(p=0.00099) and zenith VL (p =0.013), and more rapid CD4+ T-cell decline. Proteomic analysis revealed significant differential expression in 10 out of 2,376 proteins between VB and non-VB post-ART (Fig1B). Some of these proteins are already known to be involved in HIV progression. Notably, IDO1, an important player in tryptophan metabolism and immune regulation, was upregulated, potentially contributing to heightened immune dysregulation in VB. Additionally, IL-1B and ARF6 were upregulated, suggesting a more severe inflammatory response and modulation of crucial HIV life cycle processes, respectively. In contrast, TREH, a protein involved in carbohydrate metabolism, was downregulated which may indicate metabolic disturbances. Trehalose, TREH's substrate, was shown to inhibit HIV post-entry by modulating autophagy, possibly affecting viral replication. Conclusions: VB is linked to more severe clinical outcomes and distinct proteomic changes, especially in immune response, inflammation, and metabolism, which may contribute to the clade's aggressiveness. Despite a decade of ART, proteomic profile changes persist in individuals with VB. Single-Cell Multi-Omics Uncovers the Immune Heterogeneity in HIV-Infected INRs Xiaosheng Liu 1 , Leidan Zhang 2 , Ling Chen 2 , Liyuan Zheng 2 , Jia Tang 2 , Fada Wang 2 , Yang Han 2 , Xiaojing Song 2 , Wei Cao 2 , Taisheng Li 2 1 Tsinghua University, Beijing, China, 2 Peking Union Medical College Hospital, Beijing, China Background: Immunological non-responders (INRs) are people living with HIV-1 who fail to achieve full immune reconstitution despite long-term effective antiretroviral therapy (ART). This incomplete recovery of CD4 + T cells increase The figure, table, or graphic for this abstract has been removed.

Poster Abstracts

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CROI 2025