Central Nervous System T-cell immune architecture, and not HIV burden, tracks with cognition under long-term viral suppression

Mattia Trunfio; Gemma Caballero; Vanessa Gomez-Moreno; Simon A Mallal; Celestine N Wanjalla; Angela Jones; Karen Beeri; Alan Wells; Sarah LaMere; Ben Gouaux; Donald R Franklin; Michael Corley; Ronald J Ellis; David J Moore; Scott L Letendre; Davey Smith; Antoine Chaillon; Sara Gianella

doi:10.1371/journal.ppat.1014351

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Central Nervous System T-cell immune architecture, and not HIV burden, tracks with cognition under long-term viral suppression

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Central Nervous System T-cell immune architecture, and not HIV burden, tracks with cognition under long-term viral suppression

Mattia Trunfio, Gemma Caballero, Vanessa Gomez-Moreno, Simon A Mallal, Celestine N Wanjalla, Angela Jones, Karen Beeri, Alan Wells, Sarah LaMere, Ben Gouaux, …

PLoS pathogens, Vol.22(6)

2026

DOI: https://doi.org/10.1371/journal.ppat.1014351

PMID: 42296122

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Abstract

Despite effective antiretroviral therapy, HIV persists in the central nervous system (CNS) and may contribute to neuroinflammation and cognitive impairment. How viral persistence, immune responses, and regional CNS T-cell architecture relate to cognitive functioning remains unclear. We performed a cross-sectional, multi-compartmental immune-genomic study in 12 people with HIV on long-term viral suppression enrolled in the Last Gift rapid autopsy program. Quantitative HIV reservoir measures (total-episomal DNA, unspliced-multiply spliced RNA) and paired αβ T-cell receptor repertoire (TCRR) sequencing were performed in peripheral blood mononuclear cells and five CNS regions: hippocampus, frontal motor cortex, basal ganglia, occipital cortex, and spinal cord. Cognitive performance was assessed within one year of death. Tissue-resolved associations between cognition and HIV reservoir, TCRR architecture (richness, diversity, clonality), and pathogen-specific T-cell clonotypes (HIV, CMV, EBV, and riboflavin derivatives) were evaluated using participant-clustered multivariable models. False discovery rate was applied. HIV DNA and RNA were detectable across all tissues but were not associated with cognitive performance or TCRR metrics. Peripheral TCRR architecture was unrelated to cognition, whereas higher TCRR richness and diversity in the hippocampus and spinal cord were associated with worse verbal, motor, and attention/working memory scores. Higher TCRR richness in the spinal cord was also associated with better recall. T-cell receptor clonotype frequency distributions differed across CNS regions, consistent with regional immune compartmentalization. Epitope-inference analyses revealed pathogen-dependent associations: higher number of HIV-specific T-cell clonotypes in the basal ganglia was associated with better global and attention/working memory scores, whereas riboflavin derivative-specific clonotypes in frontal motor cortex were associated with better motor performance. CMV-specific clonotypes showed nominal associations with worse learning and memory. CNS-localized T-cell receptor architecture and antigenic imprinting related more closely to neurocognitive variability than quantitative measures of HIV persistence under viral suppression, highlighting regional specialization of T-cell responses as a potential correlate of brain health.

Details

Title: Central Nervous System T-cell immune architecture, and not HIV burden, tracks with cognition under long-term viral suppression
Authors/Creators: Mattia Trunfio - University of California System
Gemma Caballero - University of California System
Vanessa Gomez-Moreno - University of California System
Simon A Mallal - Vanderbilt University Medical Center
Celestine N Wanjalla - Vanderbilt University Medical Center
Angela Jones - Vanderbilt University Medical Center
Karen Beeri - Vanderbilt University Medical Center
Alan Wells - University of California System
Sarah LaMere - University of California System
Ben Gouaux - University of California San Diego
Donald R Franklin - University of California San Diego
Michael Corley - University of California San Diego
Ronald J Ellis - University of California San Diego
David J Moore - University of California San Diego
Scott L Letendre - University of California System
Davey Smith - University of California System
Antoine Chaillon - University of California System
Sara Gianella - University of California San Diego
Publication Details: PLoS pathogens, Vol.22(6)
Publisher: Public Library of Science; SAN FRANCISCO
Number of pages: 22
Identifiers: 991005896086507891
Murdoch Affiliation: Research and Innovation Office; Institute for Immunology and Infectious Diseases
Language: English
Resource Type: Journal article

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