CROI 2025 Abstract eBook

Abstract eBook

Poster Abstracts

607

CSF Memory B Cells Exhibit Distinct Molecular Footprints in Treated PWH Paraskevas Filippidis 1 , Michael J. Corley 2 , Serena Spudich 1 , Meng Wang 1 , Jennifer Chiarella 1 , Allison Nelson 1 , Bibhuprasad Das 1 , Steven H. Kleinstein 1 , Shelli Farhadian 1 1 Yale University, New Haven, CT, USA, 2 Weill Cornell Medicine, New York, NY, USA Background: Neutralizing B cell responses are critical for sustained viral control in people with HIV (PWH). However, whether B cell alterations contribute to viral persistence in the central nervous system is unknown. To address this gap, we profiled the single B cell receptor (BCR) repertoire and transcriptomes in cerebrospinal fluid (CSF) and blood of PWH and people without HIV (PWoH) to examine B cell molecular phenotypes and trafficking in the context of antiretroviral therapy (ART). Methods: We enrolled asymptomatic, virally suppressed PWH (n=7) and demographically matched PWoH (n=6) for single cell RNA and BCR-seq from paired CSF and peripheral blood mononuclear cells (PBMC), using 5’ V(D)J 10x Genomics. This “discovery set” comprised 102,313 CSF cells and 186,397 PBMC. We subsequently validated the single cell transcriptomic data by performing 10X single nucleus sequencing in a second, independent cohort of 6 PWH on suppressive ART and 5 PWoH, with features similar to the first cohort, comprising of 43,403 CSF nuclei and 76,974 PBMC nuclei. Results: 19,380 high quality B cells were included in the discovery set. These were sub-clustered into naive, atypical, memory B cells (MBC), and plasmablasts. Clonal diversity was similar between PWH and PWoH in both CSF and blood. Shared clonotypes between blood and CSF were detected in only 1/7 PWH and 2/6 PwoH, accounting for <1% of the total number of clonotypes in each individual. Both IgM and IgG MBC showed reduced V gene mutation frequencies in the blood of PWH compared to PWoH (1.74% v 3.97%, p=0.004 for IgM; 5.43% v 7.65%, p=0.004 for IgG), consistent with previous reports. However, IgG MBC exhibited a higher difference in mutation frequency across tissues (CSF minus blood) between PWH and PWoH (1.46% v -1.45%, p=0.008), suggesting potential antigen-driven BCR selection or altered B cell trafficking in the CSF of PWH. Differential gene expression in CSF revealed a distinct MBC transcriptional signature in PWH (Fig 1), with pathway analysis highlighting downregulation of antigen presentation and cytokine signaling. These transcriptomic changes were confirmed in a validation set of 10,711 B cell nuclei, where the top downregulated pathways in CSF MBC from PWH included MHC-I and MHC-II presentation, and interferon signaling. Conclusions: Single cell BCR and RNA analyses suggest persistent immune alterations in MBC within the CSF of PWH. Further studies may elucidate the role of B cells in HIV CNS persistence and neuropathogenesis.

regression models, adjusted for age and sex, examined the association between W0 and W96 changes in biomarker concentration with baseline characteristics (CD4 count, composite cognitive test score (NPZ) across 7 domains, duration of known HIV, and smoking status) and randomised treatment arm (longitudinal analysis only). Results: In 238 individuals median age was 38 (IQR 31, 46) years, 87% male and 83% of Caucasian ethnicity. Baseline median log 10 HIV RNA was 4.73 (IQR 4.23, 5.11) copies/mL and CD4 count 350 (IQR 285, 412) cells/ µ L. At W96, most individuals had plasma HIV RNA <50 copies/mL (96% triple-ART, 91% dual-ART, p=0.06) and NPZ score increased by 0.15 (triple-ART) vs 0.27 (dual ART) (p=0.80). At W0, greater concentrations of age-adjusted NfL, GFAP and CXCL10 were statistically significantly associated with lower CD4+ count (all p<0.01) but no other baseline characteristics. At W96 biomarker concentrations decreased (mean change log10 GFAP -0.07 pg/mL, IL-6 -0.15 pg/mL, CXCL10 -0.38 pg/mL, sCD14 -0.03 ng/mL, neopterin -0.28 nmol/L (all p<0.01), NfL -0.02 pg/mL (p=0.08)). A greater decline in neopterin concentration was observed in those randomised to dual-ART compared to triple-ART (mean change log10 -0.30 vs -0.25 nmol/L, respectively. p=0.022; Table ). Biomarker changes were statistically significantly associated with CD4 increase (GFAP, CXCL10, sCD14, neopterin, NfL; p<0.002) but not NPZ-score. Conclusions: Improvements in biomarkers of neuronal health following 2 years of ART were associated predominantly with improvements in CD4 count and partly by randomised drug arm, but not with cognitive function changes. Single-Nucleus Multiomics Reveals Dysfunction in Multiple Glial Cell Types in Brain Tissue of PWH Kriti Agrawal, Junchen Yang, Jay S. Stanley, Chang Lu, Nicholas Jacobs, Haowei Wang, Declan Clarke, Le Zhang, Anita Huttner, Mark Gerstein, Yuval Kluger, Serena Spudich, for the Y-SCORCH Yale University, New Haven, CT, USA Background: Central nervous system (CNS) dysfunction is a recognized complication in some people with HIV (PWH). As part of SCORCH (a large-scale, consortium-wide effort examining transcriptional and epigenetic alterations in the brains of PWH), we aim to identify key cell populations and pathways affected by HIV that may be targeted in therapies for HIV-associated CNS dysfunction in insular cortex (INS), prefrontal cortex (PFC), and ventral striatum (VST). Methods: Nuclei were isolated from frozen post-mortem tissue from INS, PFC, and VST of 20 PWH and 13 donors without HIV (PWoH). We profiled 88 transcriptomes and 86 chromatin accessibility profiles of samples that passed quality control using 10x Genomics Single Cell Multiome ATAC+Gene Expression. Reference atlases were used to identify major cell types (Fig. A). We performed individual-level pseudobulk differential expression (DE) analysis between PWH and PWoH within cell types and regions using EdgeR. ATAC-seq data were processed using Signac for all cell types. Results: PWH and PWoH donors were similar in age (median: 47 vs. 43 years) and gender (20% vs. 23% female). In total, we analyzed transcriptomes of 384,858 cells from PWH and 289,135 cells from PWoH. We identified granular neuronal and glial populations in both groups. Cross-regional DE analysis revealed significant changes in glial populations including oligodendrocytes (Oligo), astrocytes (Astro), and microglia (Micro) in all regions. In PWH Astro, we observed upregulation of complement activation genes (CFI,C4A,C1RL,C1R,C4B) indicative of reactive Astro. Relative to PWoH, there was an increase in the relative abundance of Astro in all three brain regions in PWH, but only the INS was significantly different. SERPINA3, a gene linked to poor prognosis in many neurological diseases, was upregulated in PWH Astro transcriptionally and epigenetically (Fig. B). Micro in PWH exhibited signatures of inflammatory responses and activation. Downregulated genes in PWH Astro, Micro, and Oligo were enriched in synaptic signaling and organization pathways, suggesting functional dysregulation of glial cells. Conclusions: We observed substantial transcriptional and epigenetic alterations in multiple glial cell types, revealing broader glial dysfunction in PWH. The epigenetic nature of these changes helps to elucidate disease etiology and suggests potential targets for therapeutics to suppress these dysfunctional and activated glial cells.

606

Poster Abstracts

608

T-Cell Receptor Repertoire and Cognitive Performance in People With HIV Mattia Trunfio 1 , Davey Smith 1 , Gemma Caballero 1 , Vanessa Gomez-Moreno 1 , Magali Porrachia 1 , Ben Gouaux 1 , David Moore 1 , Ronald Ellis 2 , Scott L. Letendre 1 , Antoine Chaillon 1 , Sara Gianella Weibel 1 1 University of California San Diego, La Jolla, CA, USA, 2 University of California San Diego Medical Center, La Jolla, CA, USA Background: The T cell receptor repertoire (TCR) plays a key role in immune surveillance and regulating inflammation. Alterations in TCR are linked to

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CROI 2025 164