CROI 2024 Abstract eBook

Abstract eBook

Poster Abstracts

490

Tissue-Resident TCR Repertoires Linked to HIV Persistence Antoine Chaillon 1 , Alan Wells 1 , Ravi Goyal 1 , Nadia R. Roan 2 , Angela Jones 3 , Karen Beeri 3 , Simon Mallal 3 , Celestine Wanjalla 3 , Magali Porrachia 1 , Gemma Caballero 1 , Pinyi Du 1 , Caroline Ignacio 1 , Davey M. Smith 1 , Sara Gianella 1 1 University of California San Diego, La Jolla, CA, USA, 2 University of California San Francisco, San Francisco, CA, USA, 3 Vanderbilt University, Nashville, TN, USA Background: Clonal expansion of infected CD4+ T cells is a mechanism of HIV persistence, driven by homeostatic, integration site-driven, and antigen-driven proliferation. We profiled the composition and diversity of TCR repertoires across 18 tissues and blood of 19 people with HIV (PWH) from the Last Gift cohort. Methods: Blood and tissues were collected by rapid autopsy in PWH on suppressive ART (N=19, 179 sites). Bulk TCR sequencing (Immunoverse TCR kit) was performed across gastrointestinal (GI, 5 sites), central nervous (CNS, 6 sites), lymphoid (6 sites) and vascular systems (2 sites). Data were analyzed using the mixcr bioinformatic platform. HIV reservoir size (HIV DNA) and activity (HIV RNA) was measured by ddPCR. HIV molecular diversity was obtained from single genome env sequencing. HIV integration site (IS) sequencing was performed for one participant in selected tissues. The VDJdb and McPASTCR databases were used to determine TCR specificities. Generalized mixed effects models were used to examine the association between outcomes (proportion of hyperexpanded clones, TCR diversity) with negative binomial for counts, and gaussian for continuous outcomes, and tissue and HIV reservoir measures as predictors. Results: We observed shared clonotypes in all tissues suggesting migration within and across systems, and substantial expansions of TCR clonotypes in all systems. The CNS exhibited more hyperexpanded TCR clones (mean: 45% [34-61]), compared to GI tract (18% [34-61], p=0.004), lymphoid (13% [8-23], p=0.001) and vascular (24% [16-38], p=0.24). The CNS exhibited significantly lower TCR Chao and HIV DNA diversity compared to other systems (FigA,middle right). Higher transcriptional activity (HIV RNA) and HIV DNA diversity in tissues were associated with increased TCR diversity and lower proportion of hyperexpanded clones (p<0.001). IS sequencing confirmed that proportion of HIV-infected clonally expanded cells was negatively associated with TCR diversity and positively with the proportion of expanded TCR clones. We did not find any evidence for TCR expansions driven by cytomegalovirus or other pathogens. Conclusion: This is the first comprehensive analysis of TCR repertoire landscape across the tissues of PWH. Our findings unveil the expansion and cross-tissue migration of clonal T cells, which are linked to the dynamics of the HIV reservoir. This work sheds light on the interplay between HIV infection and the T cell response, offering insights into the pathogenesis of HIV. The figure, table, or graphic for this abstract has been removed. Single-Cell Multiomics Reveals Trafficking and Enrichment of HIV RNA+ CD4+ T-Cells in Gut Th17 Michelle E Wong 1 , Jack Collora 1 , Timothy Davenport 1 , Oluwabunmi Olaloye 1 , Kenneth Lynn 2 , Emmanouil Papasavvas 3 , Pablo Tebas 2 , Ricardo Morgernstern 2 , Karam Mounzer 4 , Liza Konnikova 1 , Luis J. Montaner 3 , Ya-Chi Ho 1 1 Yale University, New Haven, CT, USA, 2 University of Pennsylvania, Philadelphia, PA, USA, 3 Wistar Institute, Philadelphia, PA, USA, 4 Philadelphia FIGHT, Philadelphia, PA, USA Background: Persistence of HIV RNA+ CD4+ T cells under ART is a major barrier to cure. We examined T cell polarization, clonal expansion, and migration of HIV RNA+ cells between the blood and gut. Methods: We used ECCITE-seq to examine transcriptome, 131 surface protein, T cell receptor (TCR), and HIV RNA in the same single cells using paired blood and gut samples from 11 ART suppressed people with HIV, before and after 20 weeks of interferon alpha2b (Peg-IFN-α2b). Plasma viral load was undetectable at both sampling points, with no change in the size of the reservoir as measured by IPDA. Blood and gut samples from 4 uninfected individuals served as negative controls. Results: We analyzed 245,928 CD4+ T cells from blood and 58,895 from the gut. We found that cytotoxic CD4+ T cells (CD4-CTL) were more abundant in the blood (4.9%) compared to the gut (0.9%)(p=0.019), while Th17 cells were more abundant in the gut (17.4%) than in the blood (8.1%) (p=0.001, paired Wilcoxon rank sum test). Similar distributions were observed in control participants. We detected 75 HIV RNA+ CD4+ cells (mean 452/million) in the blood and 31 HIV RNA+ CD4+ T cells (mean 578/million) in the gut. HIV RNA+ cells were enriched in blood Th17 (22 cells, mean 1639/million blood Th17) and the gut Th17 (14

cells, 1317/million gut Th17). There were more clonal cells in the gut (24.1%) than the blood (16.9%). Of the top 100 largest T cell clones, 72 were only in the blood, 11 were only in the gut, and 17 were identified in both blood and gut. The top 10 blood-only T cell clones were almost exclusively cytotoxic CD4+ T cells (96.8%), consistent with our previous finding. Notably, T cell clones in the gut were highly heterogeneous within clones and between clones, including a mixture of Th1 (42.7%), Trm (15.8%), and Th17 (11.1%) in the 11 gut-only T cell clones, and Th1 (44.4.%), CTL (40.4%) and Th17 (5.4%) in the 17 clones in both blood and gut. Among them, HIV+ T cell clones were mainly CTL (92.2%) in the blood-only clones, Th17 (46.3) and Th1 (36.6%) in the gut-only clones, and Th17 (53.8%) and Th1 (30.8%) in the clones migrated between blood and gut. Conclusion: While expansion within CD4-CTL clones contributes to the persistence of the HIV reservoir in the blood, the gut showcases a diverse landscape of CD4+ T cells, especially Th17 cells. This distinction between blood and gut emphasizes the gut's unique role in HIV persistence and highlights the necessity for specialized therapeutic approaches for each reservoir. Intact Proviruses From Lymph Nodes Are a Preferential Source of Viral Rebound in SHIV- Infected NHP César A Trifone 1 , Corentin Richard 2 , Amélie Pagliuzza 1 , Christine Fennessey 3 , Brandon Keele 3 , Jacob D. Estes 4 , Natasha Clark 5 , Sanath Janaka 5 , Andrés Finzi 1 , David T. Evans 5 , Nicolas Chomont 1 1 Centre de Recherche du CHUM, Montreal, Canada, 2 University College London, London, United Kingdom, 3 Frederick National Laboratory for Cancer Research, Frederick, MD, USA, 4 Oregon Health and Sciences University, Portland, OR, USA, 5 University of Wisconsin–Madison, Madison, WI, USA Background: The persistence of SIV/HIV reservoirs is the main obstacle to a cure and the cause of viral rebound after ART cessation. However, the source of viral rebound remains elusive. We characterized the proviral landscape in various tissues of virally suppressed SHIV-infected rhesus macaques before ART interruption (ATI) and matched it with the env sequences from plasma viruses during rebound. Methods: We used a highly processive and accurate polymerase and PacBio sequencing to obtain near full-length (NFL) genome sequences from blood, lymph node, and gut biopsies in 5 SHIV-infected rhesus macaques who started ART 8 weeks post infection and remained on therapy for 28 weeks. Env sequences (2,554 pb) from plasma rebound viruses 4 weeks after ATI were obtained by single genome sequencing and analyzed using the ElimDupes tool from the HIV Sequences Database to identify matches between intact NFL proviruses and plasma env sequences. Results: Using our novel NFL sequencing approach, a total of 144 proviral sequences were obtained (49 from blood, 63 from lymph nodes and 32 from the gut). 35% of all viral sequences were genetically intact, with a lower proportion in the gut (26%) compared to the blood (42%, p=0.04) and the lymph nodes (41%, p=0.04). Overall, only 2.8% of the proviral sequences were 100% identical, indicating that the SHIV reservoir was mainly composed of unique sequences. Overall, we found that rebounding viruses recovered from plasma more frequently matched with pre-ATI intact proviruses derived from lymph nodes (4 pairs of matched sequences) compared to sequences from blood and the gut (1 and 1 pairs of matched sequences, respectively). Conclusion: The SHIV reservoir is largely composed of non-clonal proviral sequences, suggesting that clonal expansion of the SHIV reservoir has a minor contribution to viral persistence in this model. Our results further suggest that intact proviruses persisting in the lymph nodes may be a preferential source of viral rebound upon ATI in this model. Minimally Invasive Autopsy Confirms HIV Persistence in Multiple Compartments Despite Prolonged cART Adriaan Basson 1 , Nadia Sabet 1 , Tanvier Omar 2 , Melanie Moodie 1 , Monique Nijhuis 3 , Annemarie M. Wensing 3 , Caroline T. Tiemessen 1 , Francois Venter 1 , Ebrahim Variava 1 , Neil Martinson 1 , Maria A Papathanasopoulos 1 1 University of the Witwatersrand, Johannesburg, South Africa, 2 National Health Laboratory Service, Johannesburg, South Africa, 3 University Medical Center Utrecht, Utrecht, Netherlands Background: HIV cure strategies require sophisticated knowledge of the formation and maintenance of latent and active reservoirs of HIV-infected cells. However, the overall paucity of individuals undergoing autopsy have hampered investigation of the anatomical distribution of infected cells during prolonged combination antiretroviral therapy (cART). We report on the largest post mortem study using minimally invasive autopsy on deceased virologically suppressed and unsuppressed adult persons with HIV (PWH) to characterise viral reservoirs.

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Poster Abstracts

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CROI 2024 128