Journal: iScience

Article Title: Cellular and molecular profiling of collagenous gastritis implicates pathogenic CD4 + T cells

doi: 10.1016/j.isci.2025.114344

Figure Lengend Snippet: Single cell analysis of patients with collagenous gastritis (A) Workflow for the collection of biopsies from the duodenum and stomach of control and patients with CG. Black and gray arrows indicate which tissues (stomach and duodenum, respectively) were processed by which methods. X indicates the approximate location of all biopsies. (B) Controls (H1-6) and CG biopsies were processed as fresh, unsorted biopsies for gene expression (GEX) libraries; frozen biopsies were CD45-sorted and processed for GEX and T cell receptor (TCR) libraries. CG patient “A” had a pre- and post-steroid biopsy collected for CD45-sorting (“A”; “Apost”), and “D” had a second biopsy (“D2”). (C) UMAP of all patients/samples, both unsorted and CD45-sorted. (D) Violin plot of canonical cluster-defining gene expression across clusters from (C). (E) Cluster frequency per sample. See also and .

Article Snippet: CD45 (Intracellular Domain) (D9M8I) XP® Rabbit mAb #13917 , Cell Signaling Technology , 13917S; RRID: AB_2750898.

Techniques: Single-cell Analysis, Control, Gene Expression

Journal: iScience

Article Title: Cellular and molecular profiling of collagenous gastritis implicates pathogenic CD4 + T cells

doi: 10.1016/j.isci.2025.114344

Figure Lengend Snippet: Patients with Collagenous gastritis have an influx of highly activated T cells (A) CD4 + and CD8 + T cells were quantified by flow cytometry of the duodenum (top row) or stomach (bottom row). (B) Representative flow plots from (A). (C) CD4:CD8 ratio from (A). (D and E) PD-1 expression on duodenal CD8 + (D) or CD4 + T cells (E). (F and G) PD-1 expression on gastric CD8 + (F) or CD4 + T cells (G). (H) Representative CD8 and CD4 stains from tissue sections. All images at 20x objective. Scale bars 500 μm. (I) Quantification of (H) for intraepithelial (top row) or intraepithelial and stromal lymphocytes (bottom) from slides. Total cells per five high power fields (HPFs). (J) Quantification of PD-L1 and PD-1 stained tissue sections. (K) CD4: CD8 ratio from T cells captured by scRNA-seq (see D) in CD45-sorted samples. Significance assessed by the Wilcoxon rank test. (L) Heatmap of differential gene expression comparing control patients to each CG patient sample for CD8 and CD4 scRNA-seq clusters from CD45+ sorted cells. Genes involved in T cell activation/exhaustion are shown. Dot indicates significantly different expression between a patient sample and all control controls. Data are mean ± SEM; flow percentages were compared with a Student’s t test (flow) or Wilcoxon test (histology) followed by a Benjamini-Hochberg correction. Gene expression data compared with a Benjamini-Hochberg-corrected Wilcoxon rank-sum test. ∗ p < 0.05, ∗∗ p < 0.01, ∗∗∗ p < 0.001 See also and .

Article Snippet: CD45 (Intracellular Domain) (D9M8I) XP® Rabbit mAb #13917 , Cell Signaling Technology , 13917S; RRID: AB_2750898.

Techniques: Flow Cytometry, Expressing, Staining, Gene Expression, Control, Activation Assay

Journal: iScience

Article Title: Cellular and molecular profiling of collagenous gastritis implicates pathogenic CD4 + T cells

doi: 10.1016/j.isci.2025.114344

Figure Lengend Snippet: Resident memory CD8 T cells and expanded T cell clonotypes are reduced in patients with CG (A) T cells were sub-clustered from all patients/samples. T RM = Tissue resident memory; T EM = Effector memory; CTL = cytotoxic T lymphocyte. (B) Dot plot of cluster-defining genes for T cell sub-clusters. (C) Sub-cluster frequency per sample. (D) Distribution of T cells split by patient disease status. (E) Barplot of sub-clusters grouped by disease status of the patient. Mean ± SEM; adjusted p -value from BH-adjusted Wilcoxon rank test shown for p-adj <0.1. (F) UMAP from (A) of TCR expansion across all CD45-sorted samples; cells are colored by the TCR frequency. (G) Barplot of unique TCR clonotypes; expanded clonotypes are those with 2+ cells per unique TCR. Percentages above bars indicate the percentage of expanded clonotypes out of the total number of unique clonotypes. (H) Percentage of expanded T cells (2+ cells/clonotype) out of all T cells with TCRs sequenced. (I) Percentage of unique, expanded clonotypes out of all unique clonotypes; similar to (G), but grouped by disease status. Error bars are ±SEM; percentages were compared with a Wilcoxon rank test. See also .

Article Snippet: CD45 (Intracellular Domain) (D9M8I) XP® Rabbit mAb #13917 , Cell Signaling Technology , 13917S; RRID: AB_2750898.

Techniques:

Journal: iScience

Article Title: Cellular and molecular profiling of collagenous gastritis implicates pathogenic CD4 + T cells

doi: 10.1016/j.isci.2025.114344

Figure Lengend Snippet: Memory, Th17, and naive CD4 T cells are reduced, while cytotoxic CD4, Th1, Th2, and Treg populations are increased in patients with CG (A) CD4 T cells were sub-clustered from all patients/samples. (B) Dot plot of cluster-defining genes for CD4 T cell sub-clusters. (C) CD4 sub-cluster frequency per sample. (D) Distribution of T cells, colored by patient disease status. (E) Barplot of CD4 sub-clusters grouped by disease status of patient. Mean ± SEM; adjusted p -value from BH-adjusted Wilcoxon test shown for p-adj <0.1. (F) UMAP from (A) of CD4 clonal expansion across all CD45-sorted samples; cells are colored by the TCR clone frequency. (G) Barplot of unique CD4 TCR clonotypes; expanded clonotypes are those with 2+ cells per unique TCR. Percentages above bars indicate the percentage of expanded clonotypes out of the total number of unique clonotypes. “Patient H5” had fewer than 20 TCRs sequenced and was omitted from the plot. (H) Percentage of expanded T cells (2+ cells/clonotype) out of all T cells with TCRs sequenced (left); percentage of unique, expanded clonotypes out of all unique clonotypes, similar to (G), but grouped by disease status. Error bars are ±SEM; percentages were compared with a Wilcoxon rank test. N.S. not significant. See also .

Article Snippet: CD45 (Intracellular Domain) (D9M8I) XP® Rabbit mAb #13917 , Cell Signaling Technology , 13917S; RRID: AB_2750898.

Techniques:

Journal: iScience

Article Title: Cellular and molecular profiling of collagenous gastritis implicates pathogenic CD4 + T cells

doi: 10.1016/j.isci.2025.114344

Figure Lengend Snippet: Effects of steroid treatment on pre-existing TCR clonotypes and possible future therapies for CG (A) Hallmark Gene Set Enrichment Analysis of all cells from CD45-sorted patient “A”, comparing pre- and post-steroid gene expressions. (B) TCR clones sequenced from patient “A” show the distribution of clonotypes that were shared between time points (pre- and post-steroids) and expanded (2+ cells); expanded but not shared; shared but not expanded; or neither shared nor expanded (not). Percentage of total clone pool for each timepoint shown. (C) Alluvial plot from patient “A” showing unique TCR clones that were expanded (2+ cells) and shared between the two time points (pre- and post-steroids). Flow between bars indicates which sub-cluster the TCR clones were shared between. (D) The top four expanded TCR clones shared between pre- and post-steroids for patient “A” and their T cell sub-clusters of origin. Y axis indicates the total number of T cells captured in each shared clonotype. TCR chains are listed below every four clones. (E) Heatmap of scaled gene expression for T cell activation genes across T cell sub-clusters. Dot indicates significantly different expression between the CG and control samples for a particular gene/cluster. (F) Same as (E), but across CD4 sub-clusters. (G) Expression of IL5 and IL13 in the Th2 subcluster. (H) Differential gene expression analysis was performed across each T cell sub-cluster. Normalized JAK3 expression shown for T cell subclusters in which p-adj ≤0.05. Adjusted p -value and log2 fold-change (LFC) displayed. (I) Same as (H) but for CD4 sub-clusters in which p-adj ≤0.05. (J) Normalized ITGA4 expression shown for T cell subclusters in which p-adj ≤0.05. Adjusted p -value and log2 fold-change (LFC) displayed. (K) Same as (J), but for CD4 sub-clusters in which p-adj ≤0.05. (L) Normalized MADCAM1 (ligand for α4 integrin) on endothelial cells. Gene expression significance assessed by the Wilcoxon rank-sum test with a Benjamini-Hochberg correction. See also .

Article Snippet: CD45 (Intracellular Domain) (D9M8I) XP® Rabbit mAb #13917 , Cell Signaling Technology , 13917S; RRID: AB_2750898.

Techniques: Clone Assay, Gene Expression, Activation Assay, Expressing, Control

Journal: Journal of neuroinflammation

Article Title: Treatment with gelsolin reduces brain inflammation and apoptotic signaling in mice following thermal injury.

doi: 10.1186/1742-2094-8-118

Figure Lengend Snippet: Figure 8 Gelsolin affects migration of myeloid-derived cells into brain. CD45+ cells from gelsolin-treated mice 8 h postburn (A) and quantification of infiltrating CD45+ (B) cells in 10 high power fields (HPF) of the periventricle region following gelsolin treatment. Gelsolin positive cells were seen in medial habenular nucleus (MHb), stria medullaris (sm), hippocampal CA field (CA2) and blood vessel (BV). Magnifications are × 400. *P < 0.05, **P < 0.01, and ***P < 0.001 vs. sham-injured mice; #p < 0.05, ##p < 0.01, ###p < 0.001 vs. placebo mice; + +p < 0.01, and +++p < 0.001 vs. Gsn-L mice by ANOVA, Newman-Keuls post-hoc test. Data are means ± SD for n = 6-8.

Article Snippet: Sections used for immunocytochemistry were incubated in 0.3% hydrogen peroxide (H2O2) for 10 min, and incubated free-floating in antibodies (Abs) of polyclonal anti-mouse ionized calcium-binding adapter molecule 1 (Iba-1, 1:1000; Wako, Osaka, Japan), monoclonal anti-mouse CD11b (Mac-1, 1:1000; EuroBioScience, Lund, Sweden), monoclonal anti-mouse CD45 (1:1000; EuroBioScience), or rabbit anti-cleaved caspase-3 (1:50; Cell Signaling, Danvers, MA, USA) with 3% normal goat serum, 0.05%Triton-X in PBS, for 24-48 h rotating at 4°C.

Techniques: Migration, Derivative Assay

Journal: STAR Protocols

Article Title: Assessing in vivo presentation of exogenous antigen in the tumor microenvironment in mice

doi: 10.1016/j.xpro.2023.102185

Figure Lengend Snippet:

Article Snippet: CD45.2 – vF450 (1:100) , Tonbo Biosciences , clone: 104; Cat# 65-0454-U100.

Techniques: Blocking Assay, Recombinant, Selection, Software, Cell Culture, Light Microscopy

Journal: Cancer research

Article Title: Focused Ultrasound Delivers Targeted Immune Cells to Metastatic Brain Tumors

doi: 10.1158/0008-5472.CAN-12-2609

Figure Lengend Snippet: Histological quantification of HER2-specific NK-92 cells accumulating at the tumor site. Effector cells were co-localized with CD45 IHC (upper panel) and Prussian blue histochemistry (lower panel) in the three experimental groups, A. HER2-specific NK-92 cells reaching the tumor were quantitatively assessed (mean ± SEM), B. When NK-92 cells were injected prior to BBBD, the number reaching the tumor was significantly higher than if they were injected following or without BBBD (group 3 vs groups 1 and 2: 0.95 ± 0.23 vs 0.09 ± 0.11, 0.21 ± 0.15, p < 0.01). There was no statistical difference between groups 1 and 2. These results are in agreement with the iron-sensitive MR imaging in Figure 4.

Article Snippet: Expression of CD45 was evaluated on a cell smear of targeted cells using mouse anti-human CD45 (RnD systems, Minneapolis, MN USA) and the procedures described above.

Techniques: Injection, Imaging

Journal: Cancer research

Article Title: Focused Ultrasound Delivers Targeted Immune Cells to Metastatic Brain Tumors

doi: 10.1158/0008-5472.CAN-12-2609

Figure Lengend Snippet: FUS causes the translocation of HER2-specific NK-92 cells from the vasculature into the brain and tumor when they are present in the circulation at the time of BBBD. A, CD45 IHC depicting a vessel from which a large number of cells have extravasated and appear to track to the tumor (indicated by the star). B, the corresponding Prussian blue stained section is shown, colocalizing the HER2-specific NK-92 cells. C, a normal capillary adjacent the tumor but within the sonicated region, shows HER2-specific NK-92 cells forced to the adluminal surface of the vessel. FUS results in HER2-specific NK-92 cells circumventing both the BBB and BTB. D, the corresponding Prussian blue section. These cell distributions were seen exclusively in group 3 animals.

Article Snippet: Expression of CD45 was evaluated on a cell smear of targeted cells using mouse anti-human CD45 (RnD systems, Minneapolis, MN USA) and the procedures described above.

Techniques: Translocation Assay, Staining, Sonication