Biology subjects

Welbourn, S.

Publications and source records attributed to Welbourn, S..

3 recordsLinked to original sources

bioRxiv2026

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

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

systems biology↗

bioRxiv2025

A scalable proteogenomic framework for dissecting phospho-signaling pathways in primary immune cells

Signaling networks modulated by post-translational modifications orchestrate cellular responses to external cues. Traditional approaches to study these pathways lack the throughput to systematically capture the causal architecture of these signaling pathways at scale. Here, we present an integrated proteogenomic framework that combines saturating genetic perturbations with high-throughput proteomics to systematically map cytokine-induced signaling in primary human T cells. Supporting this framework is simplePhos, a streamlined, low-input phosphoproteomics workflow that enables scalable, time-resolved analysis without the requirement for specialized equipment or robotics. We extensively validate the simplePhos pipeline by applying inflammatory stimuli, including type I and II interferons, lipopolysaccharide, and Sendai virus to primary T cells and myeloid cells, establishing foundational datasets in these treatment contexts. Ultimately, using type I interferon signaling in genetically modified T cells as a model, we demonstrate that combined application of genetic alterations and proteomic analyses can map key signaling nodes in primary immune cells. This represents a powerful strategy to mechanistically interrogate phospho-signaling networks in human immune cells, with broad applications in translational immunology and therapeutic development.

systems biology↗

bioRxiv2021

Novel compound inhibitors of HIV-1NL4-3 Vpu

HIV-1 Vpu targets the host cell proteins CD4 and BST-2/Tetherin for degradation, ultimately resulting in enhanced virus spread and host immune evasion. The discovery and characterization of small molecules that antagonize Vpu would further elucidate the contribution of Vpu to pathogenesis and lay the foundation for the study of a new class of novel HIV-1 therapeutics. To identify novel compounds that block Vpu activity, we developed a cell-based gain of function assay that produces a positive signal in response to Vpu inhibition. To develop this assay, we took advantage of the viral glycoprotein, GaLV Env. In the presence of Vpu, GaLV Env is not incorporated into viral particles, resulting in non-infectious virions. Vpu inhibition restores infectious particle production. Using this assay, a high throughput screen of >650,000 compounds was performed to identify inhibitors that block the biological activity of Vpu. From this screen, we identified several positive hits but focused on two compounds from one structural family, SRI-41897 and SRI-42371. It was conceivable that the compounds inhibited the formation of infectious virions by targeting host cell proteins instead of Vpu directly, so we developed independent counter-screens for off target interactions of the compounds and found no off target interactions. Additionally, these compounds block Vpu-mediated modulation of CD4, BST-2/Tetherin and antibody dependent cell-mediated toxicity (ADCC). Unfortunately, both SRI-41897 and SRI-42371 were shown to be specific to the N-terminal region of NL4-3 Vpu and did not function against other, more clinically relevant, strains of Vpu.

microbiology↗