Journal: Cell Reports Medicine

Article Title: Rewired type I IFN signaling is linked to age-dependent differences in COVID-19

doi: 10.1016/j.xcrm.2025.102285

Figure Lengend Snippet: Gradual age-dependent change in the phenotype of infection-induced CD4 + T cells and B cells (A) UMAP, showing pre-gated CD4 + T cells from the CyTOF dataset. 19 clusters have been produced using a semi-supervised approach with FlowSOM algorithm. UMAP presents all the patients that were part of the dataset and used for clustering, including follow-up measurements of some patients done approximately 2 weeks and 6 months after the first, acute infection phase measurement (details in ). (B) UMAPs, showing the location of cells belonging to the respective group (colored in, whereas gray identifies cells in other groups). Gray outlines indicate cluster regions enriched in infected children or adults. (C) Boxplots, showing relative abundance of infection-induced clusters resulting from the FlowSOM algorithm, calculated per sample within all CD4 + T cells from the CyTOF data. Kruskal-Wallis + Wilcoxon p value. (D) Scatterplots, showing mean Z score normalized CD38 and CCR6 expression in relationship to patient age for infected patients (linear model fitted to data and Spearman’s rank correlation coefficient in black) within CD4 + T cell CyTOF data. (E) UMAP, showing pre-gated B cells from the CyTOF dataset. 15 clusters have been produced using a semi-supervised approach with FlowSOM algorithm. (F) UMAPs, showing the location of cells belonging to the respective group (colored in, whereas gray identifies cells in other groups). Gray outlines indicate cluster regions enriched in infected children or adults. (G) Boxplots, showing relative abundance of infection-induced clusters resulting from the FlowSOM algorithm, calculated per sample within all B cells from the CyTOF data. Kruskal-Wallis + Wilcoxon p values. (H) Scatterplots, showing mean Z score normalized CXCR5 and CD69 expression in relationship to patient age for infected patients (linear model fitted to data and Spearman’s rank correlation coefficient in black) within B cell CyTOF data. (I) Time-dependent stacked line graphs, displaying the relative mean cluster abundance of all activated CD4 + T cell clusters determined by CyTOF. Activated clusters were defined as clusters having above-average Z -scored expression of activation markers (CD25, HLA-DR, CD38, CD137, CD69, and Ki67) compared to other clusters. Patient group color-coded figurines on the right-hand side point out cluster accumulation patterns. (J) Scatterplot, showing the sum of the relative abundance of all activated CD4 + T cell clusters determined by CyTOF.

Article Snippet: CD38 Inh_78c , Tocris, Biotechne , 6391.

Techniques: Infection, Produced, Expressing, Activation Assay

Journal: Cell Reports Medicine

Article Title: Rewired type I IFN signaling is linked to age-dependent differences in COVID-19

doi: 10.1016/j.xcrm.2025.102285

Figure Lengend Snippet: Consequences for local T cell responses and generated antibody profiles (A) Dotplot, showing scaled average expression of genes in TCRab + T cells, subset from the nasal swab scRNA-seq data. Clusters, increased with infection (0, 4, 5, 6, and 7). A total of 8 clusters have been produced using a graph-based approach as implemented in Seurat package (KNN graph with Louvain community detection). A horizontal line splits the dotplot in two parts; genes above the line were curated based on the presence of clusters with pronounced ISG signature and include other genes useful for annotation; genes below the line were found to be differentially expressed between the clusters (FindMarkers Seurat function). (B) Scatterplots showing CD38 and TNF genes transcription (average scaled expression in clusters 0, 4, 5, 6, and 7, expanded with infection) for each donor, plotted against donor’s age, using TCRab + T cells, subset from nasal swab scRNA-seq data. Linear models fitted to the data points and Spearman’s rank correlation coefficients. (C) Stacked bar chart showing relative expression strength of heavy-chain genes encoding for the different IgG and IgA isotypes in plasmablasts (B cell cluster 12, PBMC scRNA-seq experiment). Plasmablasts, expressing either of the heavy-chain genes, were pre-selected. Expression values for each gene were calculated and normalized to the total expression of all heavy-chain genes. (D) Boxplots of S1-specific IgG (left) and IgA (right) antibody titers for the acute infection phase and follow-up measurements done approximately 2 weeks and 6 months later. Titers for second and third time points are normalized to the first time point for each patient (fold change and ratio). Wilcoxon p values.

Article Snippet: CD38 Inh_78c , Tocris, Biotechne , 6391.

Techniques: Generated, Expressing, Infection, Produced

Journal: Cell Reports Medicine

Article Title: Rewired type I IFN signaling is linked to age-dependent differences in COVID-19

doi: 10.1016/j.xcrm.2025.102285

Figure Lengend Snippet: Mechanistic in vitro studies link age-dependent rewiring of type I IFN responsiveness with in vivo -detected opposite activation profiles (A) Overview of the workflow used to study the responsiveness to type I IFN and IL-1b. PBMCs from uninfected children and adults were stimulated with either SEB or a combination of SEB, ODN CpG2216, B18R, and recombinant IFNa. In a parallel experiment series, different concentrations of IFNa as well as combinations of SEB, ODN CpG2216, IL-1b, and IL-1b inhibitor anakinra were tested. After 4 days of incubation, phenotypic differences in activation marker expression were determined by flow cytometry, while cell culture supernatants were used for cytokine and chemokine quantification. Experiments focused on IL-1b and anakinra influence were only measured in cytokine proteomics. (B) Boxplot of arcsinh-transformed median CD38 fluorescence intensity in proliferating CD4 + T cells, showing influence of CpG2216-mediated activation on CD38 expression. Wilcoxon test p values. Dropout in uninfected children group SEB condition is due to low cell number. (C) Boxplot of arcsinh-transformed median CD38 fluorescence intensity in proliferating CD4 + T cells, showing influence of CpG2216-mediated activation and IFNa (30 ng/mL) on CD38 expression in children. Wilcoxon test p values. Dropouts in SEB and SEB+IFNa perturbations are due to low cell number. (D) Boxplots of CD38 median signal intensity in proliferating CD4 + T cells, separated into CD45RA − (violet filling) memory and CD45RA + naive subpopulations, showing the difference in CD38 upregulation in response to CpG2216-mediated activation and IFNa release between memory and naive CD4 + T cells. Wilcoxon test p values. Dropout in uninfected children, SEB perturbation is due to low cell number. (E) Boxplot of IFNa concentration measured in cell culture supernatant and normalized to values detected in SEB condition for each patient, showing the effectiveness of CpG2216 in provoking IFNa release as well as of B18R in reducing the concentration of soluble IFNa. Dropout in uninfected children is due to low cell number. (F) Heatmap, showing scaled average log concentration of the 18 cytokines measured in co-culturing experiments for different perturbations using PBMC. (G) Line plots, showing the dependence of IFNg, IL-21, and IL-1b concentrations on the IFNa concentration. Wilcoxon p values. (H) Scatterplot, illustrating the correlation between donor age and IL-1b concentration in supernatant when PBMCs are stimulated with SEB and CpG.

Article Snippet: CD38 Inh_78c , Tocris, Biotechne , 6391.

Techniques: In Vitro, In Vivo, Activation Assay, Recombinant, Incubation, Marker, Expressing, Flow Cytometry, Cell Culture, Transformation Assay, Fluorescence, Concentration Assay