CROI 2025 Abstract eBook

Abstract eBook

Poster Abstracts

497

CD8+ T Cells Shape the HIV Integration Site Landscape According to the Degree of T-Cell Pressure Noemi L. Linden 1 , Alexander McFarland 2 , Ali Danesh 1 , Scott Sherrill-Mix 3 , John Everett 2 , Aoife Roche 2 , Chanson J. Brumme 4 , Zabrina L. Brumme 5 , Itzayana G. Miller 1 , Tan Thinh Huynh 1 , Dennis Copertino Jr 1 , Emma Cook 2 , Tianyu Lu 2 , Frederic Bushman 2 , R. Brad Jones 1 1 Weill Cornell Medicine, New York, NY, USA, 2 University of Pennsylvania, Philadelphia, PA, USA, 3 Michigan State University, East Lansing, MI, USA, 4 BC Centre for Excellence in HIV/AIDS, Vancouver, Canada, 5 Simon Fraser University, Burnaby, Canada Background: HIV elite control in the absence of therapy is marked by a highly clonal integration site landscape. However, the underlying mechanisms remain elusive, impeding the design of therapies that could replicate this exceptional HIV control. We previously demonstrated that elite controller CD8+ T cells reduced HIV integration site diversity, decreased genic integrations, and enriched for integrations in specific gene pathways in a xenograft mouse model. Here we deciphered how varying levels of CD8+ T cell pressure shape HIV integration site characteristics, hypothesizing that the strength of CD8+ T cell response correlates with latency-associated patterns of viral control. Methods: NSG mice were engrafted with memory CD4+ T cells from three human HLA*B27:05 male elite controllers and injected with HIV JRCSF , and either kept untreated (control) or engrafted with autologous memory CD8+ T cells. After monitoring blood cell counts by flow cytometry and qPCR viral load for 8 weeks, spleens were harvested, and total DNA was subjected to linker-mediated PCR for integration site sequencing, analyzed via the AAvengeR pipeline, Reactome pathway analysis, and correlation analysis between integration distributions and immune response. Results: In 57 xenograft mice, CD8+ T cell responses produced varied viral load and cell population outcomes. A strong positive correlation was observed between total CD8+ T cell counts, CD4+ T cell counts, and HLA*B27:05-KK10 tetramer-reactive cells (p.adj.<0.001). Elite controller CD8+ T cells reduced viral load by a median of three orders of magnitude. Decreases in viral load correlated with reductions in total and non-clonal integrations (p.adj.<0.05), while inversely correlating with integrations in repeats (p.adj.<0.05), indicating the preferential persistence of clonal integrations in repetitive genomic loci. The genic integrations persisting in the presence of CD8+ T cells were preferentially associated with functions in chromatin organization, SUMOylation, and transcriptional activation (p.adj.<0.05). Conclusions: Inter- and intra-individual diversity in viral and immune trajectories and integration sites revealed key associations. Similar patterns, including increased HIV reservoir clonality and reduced genic integrations, have been observed in individuals on long-term antiretroviral therapy. These links between CD8+ T cell control and proviral landscape variables suggest the potential to use integration site patterns as a readout of CD8+ T cell strength over time. Anti-IL-10/Anti-PD-1 Dual Blockade Leads to IFN-Related HIV Elite Control Signatures Susan P. Ribeiro 1 , Felipe Ten-Caten 1 , Khader Ghneim 1 , Ana Carolina Santana 1 , Muhammad Bilal Latif 1 , Tamara C. Garcia 1 , Perla Mariana Del Río Estrada 2 , Jeffrey D. Lifson 3 , Mihai G. Netea 4 , Daniel M. Gorman 5 , Bonnie J. Howell 6 , Mirko Paiardini 1 , Hugo Soudeyns 7 , Rafick P. Sekaly 1 1 Emory University, Atlanta, GA, USA, 2 Instituto Nacional de Enfermedades Infecciosas, Mexico City, Mexico, 3 Frederick National Laboratory for Cancer Research, Frederick, MD, USA, 4 Radboud University Medical Center, Nijmegen, Netherlands, 5 Merck & Co, Inc, Kenilworth, NJ, USA, 6 Merck Sharp & Dohme, Rahway, NJ, USA, 7 Centre Hospitalier Universitaire Sainte-Justine, Montreal, Canada Background: Elimination of latently HIV-infected cells remain the biggest challenge to reach a cure. Current immunotherapy approaches have focused on targeting the adaptive arm of the immune system, such as therapeutic vaccines and the passive transfer of broadly neutralizing antibodies. Recent studies showed that epigenetic reprogramming of innate myeloid cells triggered by adjuvants promoted protective interferon-induced antiviral immunity in vaccinees. Methods: In this study, flow cytometry, cytokine array, and single-cell RNA-Seq/ ATAC-Seq were conducted on SIV-infected, virologically suppressed rhesus macaques (RMs) treated with anti-IL-10 and anti-PD-1 antibodies (combo treatment) before analytical treatment interruption (ATI). Results: Ninety percent of the combo-treated RMs (9/10) successfully controlled viremia to levels lower than 10,000 cps/mL for at least 6 months post analytical treatment interruption (ATI), and 40% of these RMs had a significant decrease in the cell-associated viral DNA quantities in lymph nodes (so-called

DNA (P=0.076, 0.014), and higher VL (P=0.0072, 0.0031). In a cross-sectional analysis of all ART-treated PWH, VL was higher in the short and intermediate compared to long ART duration groups (P=0.0044, 0.042), while we did not detect significant differences in CA HIV RNA. Compared to chronic treated PWH, early treated PWH had lower levels of initiated HIV RNA (median 560 vs. 2348 copies/ug; P=0.029) and 5’ elongated HIV RNA (median 14 vs. 50 copies/ ug; P=0.0058) and tended to have lower levels of multiply spliced HIV RNA (P=0.062). These findings persisted after normalization to HIV DNA, with lower levels of initiated HIV RNA per provirus (P=0.054) and 5’ elongated HIV RNA per provirus (P=0.049) in early treated PWH. Compared to chronic treated PWH, elite controllers also tended to have lower levels of initiated HIV RNA (P=0.064) and had lower levels of 5’ elongated HIV RNA (P=0.0029), but these differences disappeared or reversed after normalization to HIV DNA. Conclusions: Elite control was associated with lower infection frequencies but no decrease in HIV transcription per provirus. Early ART start was associated with lower levels of HIV transcriptional initiation but no differences in VL, while increasing duration of ART was associated with lower VL but no detectable changes in CA HIV RNA. Future studies towards HIV-1 cure should target the immune mechanisms that likely underlie these differences. Viral Reservoir Characteristics in Lymphoid Tissues of HIV-1 Elite Controllers Samantha K. Marzi 1 , Chloe M. Naasz 1 , Leah Carrere 1 , Carmen Gasca Capote 2 , Mathias Lichterfeld 1 , Matthieu Perreau 3 , Xu G. Yu 1 , Andrea Mastrangelo 3 1 Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA, 2 Instituto Biomedicina de Sevilla, Sevilla, Spain, 3 Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland Background: Elite controllers maintain undetectable levels of HIV replication in the absence of antiretroviral treatment and are considered as a model for a cure of HIV infection. Recent studies suggest distinct viral reservoir characteristics in blood in such persons, however, viral reservoirs in lymphoid tissues from elite controllers remain largely unexplored. Methods: Paired samples of mononuclear cells from blood (PBMC) and from lymph nodes (LNMC) from two elite controllers (MP032 and MP083) who maintained undetectable viremia for over ten years were studied. Viral reservoir cells were evaluated using full-length individual proviral sequencing (FLIP-Seq) and matched integration site and proviral sequencing (MIP-Seq). Integration site loop amplification (ISLA) was performed to determine proviral integration sites. Results: MP032 had a viral reservoir of 17.36 HIV copies per million PBMC versus 5.91 copies per million LNMC, and MP083 had a reservoir of 11.49 HIV copies per million PBMC versus 5.90 HIV copies per million LNMC. In MP032, a major clone of genome-intact proviruses was found in both the PBMC and the LNMC samples. This clone was integrated in the pericentromeric area of chromosome 10 and made up 67.9% of all intact sequences. In addition, two other intact clones were found in the PBMC, one in the pericentromeric region of chromosome X and the other in a gene desert in chromosome X. MP083 also had one major intact clone that was found in both the PBMC and LNMC samples in a non-genic pericentromeric area of chromosome 12. A smaller clone of intact proviruses was found in a gene desert of chromosome 22, and an additional intact sequence was integrated into the centromeric area of chromosome 19; both of these subdominant clones were detected in PBMC only. Despite this overlap between clonal sequences from PBMC and LNMC, we found that not every proviral sequence was found in both sample types; the majority of un-shared clones of intact proviruses were found in the PBMC, and very few LNMC-only intact viral sequences were detected. Conclusions: Lymph node viral reservoir cells from elite controllers displayed an increased propensity for viral integration into heterochromatin regions of the human genome. Transcriptional repression of intact proviruses in heterochromatin regions in lymphoid tissues is likely to contribute to spontaneous viral control.

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Poster Abstracts

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CROI 2025 126