CROI 2024 Abstract eBook

Abstract eBook

Poster Abstracts

499

Gut Microbiome Associations With Intestinal HIV Persistence in ART-Suppressed Pediatric Macaques Nicole Soo 1 , Alexander Grier 1 , Veronica Obregon-Perko 2 , Zain Gohar Siddiqi 2 , Gloria Mensah 2 , Bhrugu Yagnik 2 , Diane G. Carnathan 2 , Julia T. Ngo 2 , Rama R. Amara 2 , Genevieve G. Fouda 1 , Guido Silvestri 2 , Sallie Permar 1 , Ann Chahroudi 2 , Ria Goswami 1 1 Weill Cornell Medicine, New York, NY, USA, 2 Emory University, Atlanta, GA, USA Background: Currently, ~1.5 million children are living with HIV, worldwide. ART cannot clear the HIV reservoir, resulting in the need for life-long adherence to therapy. Using SHIV-infected pediatric rhesus macaques (RMs) on long-term ART, we recently demonstrated transcriptionally active HIV in the gastrointestinal (GI) tract. Interestingly, the GI tract was also the first anatomic site of HIV reactivation after ART interruption. However, factors contributing to viral persistence in the GI tract remain unknown. Here, we tested whether pediatric GI microbiome can influence transcriptionally active HIV in this compartment. Methods: Feces were obtained from SHIV.CH505-infected virally-suppressed infant RMs. All RMs received the same triple-drug ART regimen (TFV+FTC+DTG) and were categorized into early ART (n=7, ART start: 4 days post-infection, pi), intermediate ART (n=9, ART start: 2 wks pi), late ART (n=14, ART start: 8 wks pi) and late ART+ therapeutic vaccine (n=8, ART start: 8 wks pi, vaccine on ART) groups. The fecal microbiome was profiled using 16s rRNA sequencing. Levels of 21 bile acids and 162 polar metabolites in feces were measured by LC-MS. To determine the impact of microbiome on cell-associated (CA)-RNA, we used Analysis of Compositions of Microbiomes with Bias Correction (bacterial taxa) and linear regression models (metabolites). Results: Irrespective of the regimen and duration of treatment, the ratio of SHIV CA-RNA/DNA was higher in the CD4+ T cells of rectal biopsies, compared to blood or lymph nodes. Treatment impacted both fecal-microbial and -metabolomic profiles. After correcting for therapy-based differences, we identified bacterial species Sarcina ventriculi, Lactococcus lactis and Treponema succinifaciens and metabolite adenosine diphosphate to be directly associated with increased SHIV CA-RNA. Additionally, the levels of Eubacterium hallii, Ruminococcus bromii, Terrisporobacter mayombei, D-glucose, D-glucuronic acid, citric acid, D-fructose and 4-hydroxyproline were inversely correlated with CA-RNA in the GI tract. Finally, a statistical mediation analysis indicated that the association of commensal Eubacterium hallii with reduced viral persistence was mediated via D-glucose. Conclusion: In the pediatric RM model, gut microbiome appeared to impact intestinal SHIV persistence. Building a GI microbiome from early life that can dampen HIV persistence and prevent reactivation may contribute to the goal of ART-free viral suppression in children living with HIV. Decreased Frequency of Colon-Resident Memory T-Cells Is Associated With HIV-1 Persistence on ART Camille Vellas 1 , Nived Collercandy 1 , Manon Nayrac 2 , Mary Requena 1 , Justine Latour 1 , Nicolas Jeanne 1 , Karl Barange 1 , Laurent Alric 1 , Guillaume Martin Blondel 1 , Jacques Izopet 1 , Pierre Delobel 1 1 Toulouse University Hospital, Toulouse, France, 2 Centre de Recherche du CHUM, Montreal, Canada Background: The gut is a major target for HIV-1 replication and persistence. Tissue-resident memory (TRM) cells play a crucial role in mucosal immunity but this cell population could be affected by HIV-1 replication in mucosa. Their depletion may contribute to a persistent imbalance in mucosal homeostasis and the persistence of HIV-1 in the gut on ART. Methods: 42 virologically suppressed people living with HIV-1 (PLWH) and 42 uninfected controls were recruited in the ANRS EP61 GALT study. Duodenal, ileal, and colonic biopsies and blood samples were obtained. The frequency and activation/exhaustion phenotype of intestinal-TRM cells was assessed by FACS. Total HIV-1 DNA and residual HIV-1 RNA were quantified in gut samples, and the genetic complexity of HIV-1 quasispecies was assessed by single-molecule real-time next-generation sequencing of env. Recirculating intestinal-TRM cells were defined as CD103+β7hiCD8+ T cells in peripheral blood. The frequency of HIV-1–specific CD8+ T cells among recirculating TRM cells was assessed in 15 PLWH after stimulation with HIV-1 peptide pools and measurement of IFNγ production, degranulation (CD107a), and cell proliferation (CFSE). Results: CD4+ and CD8+ TRM cells were significantly depleted in the colonic mucosa of PLWH versus uninfected controls (P=0.015 and P=0.006 for CD4+ and CD8+ TRM cells, respectively), and their frequency correlated negatively with CD4 nadir (ρ=0.41, P=0.020 and ρ=0.37, P=0.037 for CD4+ and CD8+

TRM cells, respectively). TRM cells express overall lower levels of PD-1, TIGIT, KLRG1 and CD57 than non-TRM cells in all 3 gut segments, but levels are highest in the colon. CD4+ and CD8+ TRM cell frequencies were negatively associated with total HIV-1 DNA and residual HIV-1 RNA, while non-TRM cells were associated with quasispecies genetic complexity (Figure). Recirculating CD8+ TRM cells were enriched in HIV-1-specific T cells (P<0.01 for IFNγ+, CD107a+, and CFSEdim cells in recirculating TRM vs total CD8+ T cells). Conclusion: The frequencies of CD4+ and CD8+ TRM cells remained reduced in PLWH on ART, particularly in the colon. Irreversible damage may have been inflicted on these cell populations prior to initiation of ART. The loss of these cells could promote the persistence of HIV-1 in the colon. Enrichment of HIV-1 specific cells in recirculating TRM supports persistent antigenic stimulation by HIV-1 antigens in the gut mucosa of PLWH on suppressive ART.

Poster Abstracts

501

Monocytes/Macrophages Contribute Only Marginally to the Gut Reservoir of HIV-1 on ART Camille Vellas 1 , Mary Requena 1 , Manon Nayrac 2 , Karl Barange 1 , Laurent Alric 1 , Guillaume Martin-Blondel 1 , Jacques Izopet 1 , Pierre Delobel 1 1 Toulouse University Hospital, Toulouse, France, 2 Centre de Recherche du CHUM, Montreal, Canada Background: Current antiretroviral treatments (ART) are unable to cure HIV-1 infection due to the persistence of latently infected cells. The gut mucosa contains numerous target cells, and high levels of HIV-1 DNA persist in this compartment under ART. CD4+ T cells are the best-characterized reservoir for HIV-1. However, macrophages are abundant long-lived cells in the gut, but their involvement in HIV-1 persistence under ART remains debated. Methods: To investigate the contribution of intestinal monocytes/ macrophages to the HIV-1 reservoir, we collected duodenal (N=8) and colonic (N=8) biopsies from 12 people living with HIV (PLWH) under suppressive ART (viral load <30 copies/mL) for 8 years, included in the ANRS EP61 GALT study. T cells were isolated by positive CD2 magnetic sorting, and monocytes/ macrophages (CD3-CD19-CD56-CD66- CD11c+ HLA-DR+ CD33+ CD14+/-) were sorted by flow cytometry. Cellular DNA was extracted and amplified by REPLI-g. We quantified total HIV-1 DNA by qPCR in the LTR region and integrated proviral DNA by Alu-LTR qPCR. We used the Intact Proviral DNA Assay (IPDA) to estimate the frequency of intact, 5' defective and 3' defective HIV-1 proviruses in monocytes/macrophages and T cells. Results: Total HIV-1 DNA levels in intestinal T cells (positive samples: 8/8 in the duodenum and 8/8 in the colon, median 3,398 copies/10 6 CD4+ T cells [IQR, 1,208-12,312]) were much greater than those in monocytes/macrophages (positive samples: 4/8 in the duodenum and 3/8 in the colon, median 12 copies/10 6 monocytes/macrophages [IQR, 8-22]) (P<0.001). Unintegrated HIV-1 DNA was detected in a third of T cell and monocytes/macrophages positive samples. Using the IPDA assay, we detected intact HIV-1 proviruses in 4/16 of T cell samples but in only 1/6 of monocyte/macrophage samples. Conclusion: We showed that monocytes/macrophages from the intestinal mucosa of both the duodenum and colon of PLWH under suppressive ART can contain HIV-1 DNA, even intact or unintegrated, but at much lower levels (300 fold lower) than those found in T cells. These findings provide further evidence that monocytes/macrophages contribute only marginally to the HIV-1 reservoir in the gut of ART-treated individuals. Background: While HIV-1 group M is responsible for the large majority of HIV infections worldwide, 3 others groups named O, N and P (HIV-1 non-M) are more genetically divergent and concentrated in West-central Africa

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