CROI 2025 Abstract eBook

Abstract eBook

Poster Abstracts

of PLWH during analytical treatment interruption (ATI) with variation in time to rebound. Currently, there is a lack of unbiased identification of ‘omics’ biomarkers that predict viral rebound. The RV254 Thai cohort of PLWH who initiated ART during acute HIV-1 infection (AHI) then underwent ATI provided a unique opportunity for us to use multiomic profiling and machine learning (ML) with explainable AI to identify signatures that could predict viral rebound following ATI. Methods: Peripheral blood cells and plasma were obtained from 27 PLWH from ATI studies with no other intervention in Thailand. Participants were diagnosed during AHI and were on ART for a median of 3 years. Covariates that affect viral load (VL) rebound were first evaluated using ML. Longitudinal multiomics data including proteomics, simultaneous single-cell transcriptomics, chromatin accessibility and surface protein expression at AHI (week 0), 60 weeks after ART initiation, and immediately prior to ATI were analyzed. Cell state identification, differential expression, and pathway analyses were performed to identify markers of rebound. Results: ML approaches identified faster time to VL suppression upon ART initiation as the strongest predictor of time to delayed rebound which was then used as a covariate in our multiomics analyses. Single-cell CITE-seq differential expression analyses showed that CD8 + T cells had the highest number of genes associating with time to rebound at all three timepoints. Surface protein markers measured at the ART timepoints of delayed rebound were markers of T cell activation (CD2, CD48) and proliferation (CD45), while early rebound markers were related to inhibition of immune responses (CTLA-4, PD1, PD-L1). Conclusions: Single-cell omics methods identified the immune population with the strongest effect on HIV-1 rebound. Specific markers of CD8 + T cell activation or inhibition measured during ART associated with time to rebound. Understanding the CD8 + T cell phenotype associated with time to rebound using pathway analysis and integration of other clinical and immunologic data could provide further insight into how natural variation can impact time to viral rebound and inform new intervention strategies focused on CD8 + T cell activation to advance HIV-1 remission. Total HIV-1 Nucleic Acid Increases Precede Plasma RNA Rebound During Pediatric ATI Gabriela Z. L. Cromhout 1 , Nomonde Bengu 1 , Nicholas G. Herbert 2 , Thumbi Ndung'u 1 , Moherndran Archary 1 , Philip Goulder 2 1 Africa Health Research Institute, Mtubatuba, South Africa, 2 University of Oxford, Oxford, UK Background: In the absence of a reliable biomarker for HIV cure/remission, analytical treatment interruptions(ATIs) provide the only means for evaluating cure/remission interventions. Children who acquire HIV in utero are hypothesised to have higher cure potential due to immune ontogeny that restricts the ability of HIV to establish a large latent reservoir in the setting of very early antiretroviral therapy (ART). However, this limited immune exposure to HIV may increase the risk of acute retroviral syndrome (ARS) in children who later undergo ATI in studies designed to assess HIV cure/remission. To monitor for viral rebound, frequent plasma viral load testing is undertaken, but due to low blood sample volumes in children these samples are often diluted, and this reduces assay sensitivity. We hypothesised that Point-of-care (PoC) testing of total nucleic acid (TNA) in whole blood would detect increases in TNA prior to or at viral rebound as measured by standard HIV-1 RNA plasma assays. Methods: To test this hypothesis, we monitored HIV-1 TNA via PoC testing using the Cepheid GeneXpert Qual XC assay, which requires 100ul of whole blood per test. At the same time, we measured plasma HIV-1 RNA via standard testing using the Aptima HIV-1 Quantitative assay which requires 1ml whole blood for 500ul of plasma needed. This monitoring was done in 15 study participants from a very early ART-treated cohort of children living with HIV who underwent ATI in KwaZulu-Natal, South Africa. Results: Plasma viral rebound occurred in 11 of the 15 participants who underwent ATI. In several instances, HIV-1 TNA became detectable prior to the plasma RNA (Fig 1A&B). There were no cases of HIV-1 RNA being detectable without detection of TNA (Fig 1B). In this group of very early ART-treated children, who were aviraemic and had low total HIV-1 DNA loads prior to ATI, plasma viral load and GeneXpert TNA Ct were strongly inversely correlated during the ATI period (r=-0.88, p<0.0001). Conclusions: These data indicate that PoC testing of TNA on whole blood would contribute to safety monitoring in pediatric ATI studies, as a biomarker of imminent plasma HIV-1 RNA rebound. This would enable clinicians to be alerted early to the possibility of ARS and, potentially, the need to reinitiate

ART, depending on the study design. At the same time, the low volume of blood sample required for the TNA assay allows for the frequent screening needed during paediatric ATI studies without compromising sensitivity.

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Consecutive Analytical Treatment Interruption Improves CD8 T-Cell Activity During Viral Control Gabriel Duette 1 , Josefina Marin-Rojas 1 , Samantha K. Cronin 2 , Eunok Lee 1 , Steven G. Deeks 3 , Anthony D. Kelleher 4 , Sarah Palmer 1 1 The Westmead Institute for Medical Research, Westmead, Australia, 2 The University of Sydney, Sydney, Australia, 3 University of California San Francisco, San Francisco, CA, USA, 4 University of New South Wales, Darlinghurst, Australia Background: In the PULSE clinical trial, 68 people living with HIV underwent three consecutive analytical treatment interruptions (ATIs). Of note, 10% of the participants transiently controlled HIV rebound during the 3rd ATI. We investigated whether this virological control is associated with improved antiviral CD8 T-cell function and response to mutationally-constrained and highly-conserved HIV epitopes. Methods: We obtained blood-derived mononuclear cells from four participants enrolled in PULSE: two non-controllers (NCs) with rapid viral rebound during all ATIs and two transient controllers (TCs) with virological control during the 3rd ATI. To evaluate CD8 T-cell functionality during the ATIs, CD8 T-cells were stimulated with HIV peptides to assess cytokine production (IFN-γ/TNF-α) and stained with CellTrace Far-Red to quantify proliferation by flow cytometry. To compare CD8 T-cell cytotoxicity across the ATIs, autologous CD4 T-cells were infected with HIV-NL4-3, co-cultured with CD8 T-cells from each ATI timepoint, and p24 levels were measured by ELISA. Using our novel Immunoinformatics Analysis Pipeline (IMAP), we identified 33 mutationally-constrained and unique Gag-derived HIV epitopes (Gag-IMAP-peptides). The response to these peptides was determined in NC- and TC-derived CD8 T-cells by measuring IFN-γ/TNF-α expression. Results: For TCs, CD8 T-cell proliferation and cytokine production (3- to 34-fold) increased during the viral control timepoints. In contrast, the capacity for CD8 T-cells to proliferate and produce cytokines did not increase across the ATI timepoints for NCs. Moreover, TC-derived CD8 T-cells from the 3rd ATI, where viral rebound is delayed, eliminated HIV-infected CD4 T-cells more efficiently (2- to 5-fold p24 decrease) compared to CD8 T-cells from earlier ATI timepoints. In contrast, within NCs, we observed no consistent enhancement of CD8 T-cell cytolytic response. Both NC- and TC-derived CD8 T-cells responded to the Gag IMAP-peptides, with a 49-fold higher response observed for TC-derived cells. Conclusions: For some participants, repeated exposure to viral antigens during consecutive ATIs results in enhanced CD8 T-cell proliferation, cytokine production and cytotoxicity. The higher potential of CD8 T-cells from transient controllers to recognize mutationally-constrained HIV epitopes may also contribute to their virological control. Importantly, these results indicate that enhanced CD8 T-cell responses are pivotal for achieving viral remission after consecutive ATIs.

Poster Abstracts

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CROI 2025 122