non primary  (ATCC)

Journal: bioRxiv

Article Title: The tuberculosis-associated microenvironment promotes HIV-1 persistence by impairing CD8+ T cell-mediated viral control

doi: 10.1101/2025.10.14.682453

Figure Lengend Snippet: (A) UMAP plot showing unbiased clustering of CD8+ T cells based on the immune markers CD103, CD69, CD27, CCR7, CD127, CCR5, CD28, HLA-DR, CD38, 287 PD1, CD39, TIGIT. (B) UMAP plots of expression levels of selected immune markers in TB-PE-derived CD8+ T cells. (C) Proportions of CD8+ T cell clusters identified by UMAP analysis. (D) Heatmap of average expression of 12 variably expressed markers across clusters. (E) scRNA/TCR-seq analysis of TB-PE-derived CD8+ T cells from one PLWH/TB, showing TCR specificities for viral antigens. Cytokine and cytotoxic signatures from scRNAseq data are shown (top), with a heatmap of TNF, IFNG, GZMA, and GZMB expression (bottom). (F) Exhaustion signature from scRNAseq data (top), with a heatmap showing relative expression of exhaustion-associated genes TIGIT, LAG3, CTLA4, PDCD1, and HAVCR2 (bottom).

Article Snippet: CD8+ primary T cells were isolated and purified from PBMCs by negative selection using the Human CD8+ T cell isolation kit (Miltenyi Biotec).

Techniques: Expressing, Derivative Assay

Journal: bioRxiv

Article Title: The tuberculosis-associated microenvironment promotes HIV-1 persistence by impairing CD8+ T cell-mediated viral control

doi: 10.1101/2025.10.14.682453

Figure Lengend Snippet: (A) Schematic of the experimental model used to study the effect of TB-PE on CD8+ T cell functionality. (B) Heatmap showing hierarchical clustering of the top 100 variable genes between TB-PE–treated and control CD8+ T cells stimulated with anti-CD3/CD28 antibodies. (C) Volcano plot of differentially expressed genes (DEGs). (D) Gene set enrichment analysis (GSEA) of DEGs (p < 0.05 and absolute logFC > 1) comparing TB-PE–treated and control activated CD8+ T cells. Dot plots illustrate the top 10 upregulated and downmodulated enriched GO biological process terms. (E) Heatmap of normalized expression of selected genes involved in T cell activation. (F) Gene expression levels of GZMB, IFNG, TNF, IL21, and CD69 across conditions. (G) Primary CD8+ T cells were stimulated with anti-CD3/CD28 antibodies in the presence of TB-PE; cells activated in the absence of PE served as controls. Expression of activation markers CD69, CD25, and HLA-DR was measured by flow cytometry after 24h (CD69, CD25) or 48h (HLA-DR). Representative flow plots (left) and quantification of activated cells (right) are shown. (H) Proportions of CD69 (left) or CD25 (right) positive cells stimulated in the presence of an additional TB-PE pool, three independent TB-PE samples (red), or HF-PE (grey). Values are relative to the non-PE control condition (blue). Data are shown as mean ± SD. Each dot represents an independent donor. Statistical significance was determined by paired two-tailed t-test or one-way ANOVA followed by Tukey’s HSD post-test. p ≤ 0.05, p ≤ 0.01. (I) Oxidative phosphorylation measured as oxygen consumption rate (OCR, left) and mitochondrial-dependent ATP production (right). (J) Glycolysis measured as proton efflux rate (PER, left) and glycolysis-dependent ATP production (right). (K) HIF-1α expression in activated CD8+ T cells determined by flow cytometry. Each dot represents an independent donor. Statistical significance was determined by paired two-tailed t-test or one-way ANOVA followed by Tukey’s HSD post-test. p ≤ 0.05, p ≤ 0.01.

Article Snippet: CD8+ primary T cells were isolated and purified from PBMCs by negative selection using the Human CD8+ T cell isolation kit (Miltenyi Biotec).

Techniques: Control, Expressing, Activation Assay, Gene Expression, Flow Cytometry, Two Tailed Test, Phospho-proteomics

Journal: bioRxiv

Article Title: The tuberculosis-associated microenvironment promotes HIV-1 persistence by impairing CD8+ T cell-mediated viral control

doi: 10.1101/2025.10.14.682453

Figure Lengend Snippet: (A) Schematic of the experimental model used to study the effect of TB-PE on anti-HIV-1 CD8+ T cell effector responses. (B) Representative flow cytometry of PLWH-derived CD8+ T cells expressing CD107a/b, TNF-α and IFN-ψ as markers for effector response upon restimulation with HIV-1 peptides in the presence or absence of TB-PE. Cells exposed to no peptides were used as an experimental control. Cells exposed to HF-PE were used as a control to determine the specific effect of TB-PE. (C) Quantification of expression of CD107a/b, TNF-α and IFN-ψ in PLWH-derived CD8+ T cells exposed to TB-PE (n=5; upper) or HF-PE (n=4; bottom). Each data point represents a single donor. Statistical significance was determined by paired t-test, with p < 0.05 considered significant.

Article Snippet: CD8+ primary T cells were isolated and purified from PBMCs by negative selection using the Human CD8+ T cell isolation kit (Miltenyi Biotec).

Techniques: Flow Cytometry, Derivative Assay, Expressing, Control

Journal: bioRxiv

Article Title: The tuberculosis-associated microenvironment promotes HIV-1 persistence by impairing CD8+ T cell-mediated viral control

doi: 10.1101/2025.10.14.682453

Figure Lengend Snippet: (A) Schematic of the experimental model used to study the effect of TB-PE on HIV-1-specific CD8+ T cell cytotoxicity. (B) Representative flow cytometry plots showing p24 levels in HIV-1-infected CD4+ T cells cocultured with CD8+ T cells expanded in the presence or absence of TB-PE. As a control, CD4+ T cells were cultured without CD8+ T cells. Quantification of HIV-1-infected cell killing was performed using samples from four PLWH. Each data point represents a single donor. Statistical significance was determined by paired t-test, with p < 0.05 considered significant.

Article Snippet: CD8+ primary T cells were isolated and purified from PBMCs by negative selection using the Human CD8+ T cell isolation kit (Miltenyi Biotec).

Techniques: Flow Cytometry, Infection, Control, Cell Culture