mouse l cells  (ATCC)

Journal: Nature Communications

Article Title: Type I interferon drives T cell responses to amyloid beta in the central nervous system

doi: 10.1038/s41467-026-72262-6

Figure Lengend Snippet: a Representative confocal images of fresh frozen paraffin-embedded (FFPE) cortical sections from APP23-tg mice aged 8, 12, 16, 20, and 24 months. Regions of interest are shown at 20× magnification (LSM700 confocal microscope). T cells (CD3⁺) are indicated by arrows and identified based on marker expression and characteristic morphology. The strong signal observed in the DAPI channel at plaque sites reflects the known intrinsic blue fluorescence of plaque cores . b Quantification of CD3⁺ T cells normalized to total cell count across five timepoints (8, 12, 16, 20, and 24 months). Statistical analysis was performed using ordinary one-way ANOVA with Tukey’s multiple comparisons test. c Quantification of parenchymal and vascular amyloid deposits per tile scan across the same five timepoints. Two-way ANOVA with Tukey’s post hoc test was used for statistical analysis. For 2 (b) + (c) data are presented as mean ± SD. d T-cell count per amyloid plaque (parenchymal vs vascular) in APP23-tg mice aged 16, 20, and 24 months. Statistical significance was assessed using two-way ANOVA with Tukey’s post hoc test. For analyses in ( b – d ), three tile scans per section from three sections per mouse ( n = 3 mice per timepoint) were used. Each tile scan covered an area of 960.25 µm². e Fixed frozen immunofluorescence (IF) images of cortical sections from one representative 24-month-old APP23-tg mouse (top) and age-matched wild-type control (bottom). Left: tile scan at 20× magnification; right: zoomed-in area of interest. f Fixed frozen IF images of a 24-month-old APP23-tg mouse showing a plaque-rich region (top) and a plaque-devoid region (bottom). Left: tile scan at 20× magnification; right: corresponding zoom-in. For 2 (e) + (f) three tile scans per section from three sections per mouse ( n = 3 mice per timepoint) were used. g Spearman correlation analysis between T-cell frequency and amyloid plaque burden, including parenchymal (middle), vascular (right), and total plaque counts (left). The solid line shows the linear regression fit (least-squares), with curved lines indicating the 95% confidence interval of the fit. Spearman’s ρ , p -value, and R ² are indicated in each plot.

Article Snippet: CD3+ T cells were isolated from spleens of Rosa26-Cas9 mice using mouse Pan T-cell isolation kit l (Miltenyi Biotec) according the manufacturer protocol.

Techniques: Microscopy, Marker, Expressing, Fluorescence, Cell Characterization, Immunofluorescence, Control

Journal: Nature Communications

Article Title: Type I interferon drives T cell responses to amyloid beta in the central nervous system

doi: 10.1038/s41467-026-72262-6

Figure Lengend Snippet: a Volcano plot of differential gene expression (DGE) between ISG-expressing microglia and other immune subsets using the Wilcoxon rank-sum test. P -values: Benjamini-Hochberg (BH) adjusted. b Bar plot showing ISG⁺ microglia frequency within total CD45⁺ cells across cohorts ( n = 4 mice/cohort). Statistics: two-way ANOVA. Data are presented as mean + SD. c Volcano plot of DGE between ISG⁺ CD8⁺ T cells and other immune subsets using the Wilcoxon rank-sum test (BH-adjusted P -values). d Bar plot showing ISG⁺ CD8⁺ T cell frequency within CD45⁺ cells ( n = 4 mice/group). Statistics: two-way ANOVA. Data are presented as mean + SD. e Dot plot of average RNA expression and frequency for canonical ISGs across immune subsets. f Left: UMAP showing ISG CD8⁺ T-cell-specific ISG density. Right: Average RNA expression and frequency of the ISG CD8⁺ T-cell signature per mouse (M1-M4). g Spatial transcriptomic visualization of selected ISGs in the cortex of a 24-month-old APP23-tg mouse. h Spatial quantification of ISG expression relative to plaque proximity in 12–14- and 22–24-month-old APP23-tg mice ( n = 5). Regions: inside, adjacent (≤69 μm), and distant (>69 μm). Statistics: Kruskal–Wallis test with Dunn’s correction (* p < 0.0332, ** p < 0.0021, *** p < 0.0002, **** p < 0.0001). (i) Spatial maps of ISG⁺ CD8⁺ T cells and ISG⁺ microglia in a 24-month-old APP23-tg mouse (left: slide overview; right: zoom-in with segmented cells in white). j Spatial distance quantification between ISG expression and plaque-associated microglia (left) or T cells (right). k , l Heatmaps of inferred cell–cell communication (ligand–receptor interactions) showing interaction number (left) and strength (right) with signaling sources on the y -axis. Comparisons include ( k ) APP23-tg vs. Wt (early stage) and l early vs. late stage (APP23-tg).

Article Snippet: CD3+ T cells were isolated from spleens of Rosa26-Cas9 mice using mouse Pan T-cell isolation kit l (Miltenyi Biotec) according the manufacturer protocol.

Techniques: Gene Expression, Expressing, RNA Expression

Journal: Nature Communications

Article Title: Type I interferon drives T cell responses to amyloid beta in the central nervous system

doi: 10.1038/s41467-026-72262-6

Figure Lengend Snippet: a Differential analysis of enriched ligand–receptor interactions using ISG⁺ CD8⁺ T cells as the signaling source. Dot color: communication probability; dot size: p-value (one-sided permutation test, p < 0.05). b UMAP showing Cxcl10 and Cxcr3 RNA expression density across CD45⁺ immune cells. c Violin plots of average Cxcl10 and Cxcr3 expression across immune subsets. d Spatial RNA expression of Cxcl10 in representative regions of a 24-month-old APP23-tg mouse. e Spatial quantification of Cxcl10 relative to amyloid plaques: intraplaque, adjacent (≤69 μm), and distant (>69 μm) in 12–14 and 22–24-month-old mice ( n = 5). Statistics: Kruskal–Wallis with Dunn’s correction (* p < 0.0332, ** p < 0.0021, *** p < 0.0002, **** p < 0.0001). f Chord diagram of Cxcl10-Cxcr3 signaling in late-stage APP23-tg mice. Bar size indicates total signal strength. g Spatial distribution of ISG marker expression near Cxcl10⁺ plaque-associated cells in early-stage (top) and late-stage (bottom) mice. h Transwell migration assays of CXCR3 knockout (KO) vs. non-targeting (NT) control CD8⁺ T cells. Left: schematic (Created in BioRender. D170, P. (2026) https://BioRender.com/ccvdxlm ); right: bar graph of migrated cells/µl ± stimulation (CXCL10, medium, ± blocking antibody). Data: mean ± SEM; dots: biological replicates ( n = 3 per cohort). i Quantification of migrated CXCR3 KO and NT CD8⁺ T cells toward untreated (UT) or ISG-induced CD8⁺ T cell supernatants. Data: mean ± SEM; dots: biological replicates ( n = 3 per cohort). Statistics for ( h , i ): two-way ANOVA with Tukey’s correction (* p < 0.0322; ** p < 0.0021; *** p < 0.0002; **** p < 0.0001; ns = not significant).

Article Snippet: CD3+ T cells were isolated from spleens of Rosa26-Cas9 mice using mouse Pan T-cell isolation kit l (Miltenyi Biotec) according the manufacturer protocol.

Techniques: RNA Expression, Expressing, Marker, Migration, Knock-Out, Control, Blocking Assay

Journal: Nature Communications

Article Title: Type I interferon drives T cell responses to amyloid beta in the central nervous system

doi: 10.1038/s41467-026-72262-6

Figure Lengend Snippet: a Ingenuity Pathway Analysis (IPA) identifying the top upregulated immune signaling pathways in CD45⁺ immune cells from APP23-tg mice versus Wt controls. Significance was determined using a right-tailed Fisher’s exact test and is shown as –log₁₀( p -value). Pathways are ranked by significance ( p -value) and color-coded by activation z-score. b Heatmap showing normalized average RNA expression of selected T-cell activation markers across all cohorts. Color intensity indicates relative expression levels. c Heatmap showing normalized RNA expression of the same activation markers specifically within CD8⁺ T-cell subsets. d Spatial transcriptomic maps of T-cell activation markers in 24-month-old APP23-tg mice. Whole-slide views are shown on the left, with zoomed-in regions of interest on the right. e Number of T-cell clones grouped by clone size (visualized by color gradient) in identified T cell subsets between all cohorts. f Z-score depicting upregulated genes from differential expression analysis in non-expanding clones (absolute clone numbers ≥ 5) and highly expanding clones (absolute clone numbers >200). g Left: UMAP plot of CD45⁺ immune cells overlaid with an expression density gradient of a defined T-cell exhaustion gene signature (Pdcd1, Lag3, Tox). Right: Average RNA expression and expression frequency of the exhaustion signature across all cohorts. h Violin plots comparing average expression levels of exhaustion-associated genes between late-stage APP23-tg and wild-type mice. Statistical significance was assessed using the Wilcoxon rank-sum test. i Spatial transcriptomic visualization of Pdcd1 (PD-1) expression in two selected regions of interest from 24-month-old APP23-tg mice. j Quantification of Pdcd1 RNA expression in relation to plaque proximity: intraplaque, plaque-adjacent (≤69 μm from plaque boundary), and plaque-distant (>69 μm). Analysis was performed in 22–24-month-old APP23-tg mice. Statistical testing was performed using the Kruskal–Wallis test with Dunn’s correction for multiple comparisons; significance levels are shown as *= p < 0.0332, **= p < 0.0021,***= p < 0.0002,****= p < 0.0001) ( k ) Spatial distribution of Pdcd1 expression relative to T-cell markers in a 24-month-old APP23-tg mouse, visualized by density plots highlighting proximity to T-cell-enriched regions.

Article Snippet: CD3+ T cells were isolated from spleens of Rosa26-Cas9 mice using mouse Pan T-cell isolation kit l (Miltenyi Biotec) according the manufacturer protocol.

Techniques: Protein-Protein interactions, Activation Assay, RNA Expression, Expressing, Clone Assay, Quantitative Proteomics