Microbiome-Derived Metabolites Shape CD4⁺ T-Cell Differentiations and Immune Aging in Chronic HIV-1 Infection

Da Silva, A. C.; Flantzer, L.; Weinberg, J.; Kyu, S.; Daley-Bauer, L. P.; Santana, A. C.; Talla, A.; Rittgers, A. L.; Welbourn, S.; Gordon, D. E.; Tomalka, J.; Marconi, V. C.; Jones, D. P.; Younes, S.-A.

doi:10.64898/2026.01.13.699280

bioRxiv · 10.64898/2026.01.13.699280

Microbiome-Derived Metabolites Shape CD4⁺ T-Cell Differentiations and Immune Aging in Chronic HIV-1 Infection

Da Silva, A. C.·Flantzer, L.·Weinberg, J.·Kyu, S.·Daley-Bauer, L. P.·Santana, A. C.·Talla, A.·Rittgers, A. L.·Welbourn, S.·Gordon, D. E.·Tomalka, J.·Marconi, V. C.·Jones, D. P.·Younes, S.-A.

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Abstract

The role of aromatic gut-derived bacterial metabolites (GDBMs) in shaping immune cell metabolism and function remains poorly explored. Using ex vivo metabolomic profiling of paired plasma and CD4 T-cells from people living with HIV-1 (PLWH), we identified a network of aromatic GDBMs whose cell-associated abundance, rather than systemic levels, was linked to broad alterations in CD4 T-cell metabolic and functional states. Among these metabolites, p-cresol sulfate (PCS) emerged as a mechanistic prototype investigated in depth. Ex vivo flow cytometry and single-cell RNA sequencing of CD4 T-cells stratified by cell-associated PCS levels revealed dose-dependent enrichment of transcriptional programs associated with impaired differentiation capacity, regulatory-like identity, and cellular senescence. Consistently, in vitro transcriptomic and proteomic analyses of PCS-exposed CD4 T cells demonstrated induction of cell-cycle arrest, mitochondrial dysfunction, and senescence-associated programs, including upregulation of p16 and p21. Integration of these immunometabolic features with measurements of HIV-1 reservoir size in PLWH revealed that CD4 T-cell states defined by cell-associated GDBMs track with intact proviral DNA levels in vivo. Together, these findings define a microbiome-derived axis that reshapes CD4 T-cell metabolism and fate and promotes immune aging-associated states in PLWH. Our data suggest that cell-associated GDBMs may foster immunometabolic CD4 T-cell states previously linked to long-term HIV-1 reservoir persistence in vivo. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC="FIGDIR/small/699280v1_figa1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@faf44aorg.highwire.dtl.DTLVardef@1bc590aorg.highwire.dtl.DTLVardef@79c557org.highwire.dtl.DTLVardef@8b0a64_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract.C_FLOATNO PCS-driven metabolic reprogramming and senescence promoting CD4+ T-cell immune cell aging.Dietary proteins are metabolized by proteolytic gut microbiota into p-cresol, which is absorbed and converted in the liver to PCS. Circulating PCS accumulates in CD4 T-cells, where it activates the aryl hydrocarbon receptor (AhR). AhR signaling reduces glycolysis and mTOR activity, while enhancing TGF-, Wnt/-catenin, and TCF7 pathways, driving a regulatory-like and stem-like transcriptional program. These changes are associated with increased expression of p16 and p21, leading to cell cycle arrest and cellular senescence promoting CD4+ T-cell immune cell aging. C_FIG

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Da Silva, A. C., Flantzer, L., Weinberg, J., Kyu, S., Daley-Bauer, L. P., Santana, A. C., Talla, A., Rittgers, A. L., Welbourn, S., Gordon, D. E., Tomalka, J., Marconi, V. C., Jones, D. P., Younes, S.-A.. 2026-01-14. Microbiome-Derived Metabolites Shape CD4⁺ T-Cell Differentiations and Immune Aging in Chronic HIV-1 Infection. https://doi.org/10.64898/2026.01.13.699280

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