Journal: Cellular and Molecular Gastroenterology and Hepatology

Article Title: An Epigenetic Basis for Sustained Inflammatory Epithelial Progenitor Cell States in Crohn’s Disease

doi: 10.1016/j.jcmgh.2025.101665

Figure Lengend Snippet: Cells expressing ISP markers in colonic mucosa in CD tissue. ( A–B ) Representative single channel ( A ) and merged ( B ) images of immunostaining for LCN2, CD74, HLA-DR in biopsies from study subjects, quantified in ( C ) (N = 2 subjects per group, n = 11–16 crypts analyzed per biopsy, average per subject plotted on graph). Asterisk denotes an ISP. ( D ) Correlation analysis comparing abundance of ISPs in tissue (N = 4) as quantified at transcript level (scRNA-seq) to quantification at protein level (immunostaining) in matched subjects (N = 4). P values: ( C ) Welch’s t -test (unpaired, 2-tailed); ( D ) nonparametric Spearman correlation (2-tailed).

Article Snippet: Real-time quantitative polymerase chain reaction (RT-qPCR) was performed with TaqMan probes (TBP1: Hs00427621_m1; LCN2: Hs01008571_m1; HLA-DRA: Hs00219575_m1; HLA-DPA1: Hs00410276_m1; CD74: Hs00269961_m1) and TaqMan Fast Universal PCR Master Mix 2X (Catalog #4352042).

Techniques: Expressing, Immunostaining

Journal: Cellular and Molecular Gastroenterology and Hepatology

Article Title: An Epigenetic Basis for Sustained Inflammatory Epithelial Progenitor Cell States in Crohn’s Disease

doi: 10.1016/j.jcmgh.2025.101665

Figure Lengend Snippet: ISP state can be experimentally induced in patient-derived colonoids. ( A ) Schematic of experimental approach and data presentation. ( B ) Expression of ISP marker genes in colonoids from CD or control subjects (N = 3 each, Passage = 4–6). ( C ) Correlation analysis of HLA-DRA gene expression in the study subjects’ biopsies (scRNA-seq data, epithelial cluster) vs HLA-DR protein expression in colonoids (N = 4 controls and 5 Crohn's) from corresponding subjects (flow cytometry), comparing colonoids grown either in stem cell-enriching expansion medium ( black squares ) or differentiation medium ( open circles ). ( D ) Representative images of immunostaining for LCN2, CD74, HLA-DR in colonoids from study subjects. Asterisk denotes an ISP. Quantified in ( E ): N = 2 lines (n = 12 high power fields) per group, Passage = 7–8. ( F ) Quantification (flow cytometry) of %HLA-DR+ cells in colonoids treated with the inflammatory cocktail (20 ng/mL IL-1beta, 100 ng/mL TNF-alpha, 1 μg/mL flagellin, and 10 ng/mL IL-6) for 24 hours (N = 7 or 8 lines from control subjects or patients with CD, respectively, Passage = 6–8). P values: ( B ) Mann-Whitney test (unpaired, 2-tailed), ( E–F ) ordinary 2-way analysis of variance with Sidak’s multiple comparisons.

Article Snippet: Real-time quantitative polymerase chain reaction (RT-qPCR) was performed with TaqMan probes (TBP1: Hs00427621_m1; LCN2: Hs01008571_m1; HLA-DRA: Hs00219575_m1; HLA-DPA1: Hs00410276_m1; CD74: Hs00269961_m1) and TaqMan Fast Universal PCR Master Mix 2X (Catalog #4352042).

Techniques: Derivative Assay, Expressing, Marker, Control, Gene Expression, Flow Cytometry, Immunostaining, MANN-WHITNEY

Journal: Cellular and Molecular Gastroenterology and Hepatology

Article Title: An Epigenetic Basis for Sustained Inflammatory Epithelial Progenitor Cell States in Crohn’s Disease

doi: 10.1016/j.jcmgh.2025.101665

Figure Lengend Snippet: HLA-DR+HLA-DP+ cells from colonoids subjected to inflammatory cocktail express ISP marker genes. ( A ) Schematic: Colonoids from from control subjects or patients with CD were treated with the inflammatory cocktail for 24 hours and subjected to flow cytometry sorting of HLA-DR+ and HLA-DR+HLA-DP+ populations, as well as total live cells to use as control. ( B ) Quantification (flow cytometry) of %HLA-DR+HLA-DP+ cells in colonoids treated with the inflammatory cocktail for 24 hours. One line each from control subject or patient with CD, N = 3 independent experiments repeated in different passages (Passage = 4–6). ( C ) Expression of ISP marker genes HLA-DPA1, HLA-DRA, CD74, and LCN2, in cell populations sorted as described in ( A ) from control or CD colonoids. One line each from control subject or patient with CD, N = 3 independent experiments repeated in different passages (Passage = 4–6), representative data from 1 experiment are shown. P values: ( B ) ordinary 2-way analysis of variance with Sidak’s multiple comparisons.

Article Snippet: Real-time quantitative polymerase chain reaction (RT-qPCR) was performed with TaqMan probes (TBP1: Hs00427621_m1; LCN2: Hs01008571_m1; HLA-DRA: Hs00219575_m1; HLA-DPA1: Hs00410276_m1; CD74: Hs00269961_m1) and TaqMan Fast Universal PCR Master Mix 2X (Catalog #4352042).

Techniques: Marker, Control, Flow Cytometry, Expressing

Journal: Frontiers in Immunology

Article Title: Macrophage migration inhibitory factor–CD74 axis drives vascular smooth muscle cell–induced M1 macrophage polarization to exacerbate intracranial aneurysm inflammation

doi: 10.3389/fimmu.2025.1682762

Figure Lengend Snippet: Hypomethylation of MIF and CD74 in dataset GSE75434 . (A-C) Methylation data quality control. (D) Genomic distribution of methylation probes. (E, F) Significantly reduced methylation levels at MIF and CD74 loci in IAs versus control arteries. ** and * indicate p-values less than 0.01 and 0.05, respectively.

Article Snippet: Experimental groups were: (1) Control VSMCs + Macrophages; (2) Secretory VSMCs + Macrophages; (3) Secretory VSMCs + Macrophages + 10 μg/mL anti-human MIF monoclonal antibody (Abcam); (4) Secretory VSMCs + Macrophages + 5 μM CD74 inhibitor BMS-582949 (MedChemExpress).

Techniques: Methylation, Control

Journal: Frontiers in Immunology

Article Title: Macrophage migration inhibitory factor–CD74 axis drives vascular smooth muscle cell–induced M1 macrophage polarization to exacerbate intracranial aneurysm inflammation

doi: 10.3389/fimmu.2025.1682762

Figure Lengend Snippet: Cell-cell communication analysis. (A) Global communication network showing interaction strength between major cell types. (B) Interaction weights for MIF ligand-receptor pairs. (C) Chord diagram highlighting MIF-CD74/CD44 signaling between VSMCs and M1-like macrophages. (D) Increased interaction strength and number between secretory VSMCs and M1-like macrophages in IAs. (E) Differential signaling pathway activity between secretory VSMCs and M1-like macrophages across conditions. (F) Heatmap showing communication probability for key pathways between secretory VSMCs and M1-like macrophages. (G) Expression patterns of key MIF axis components (Mif, Cd74, Cd44) across cell types.

Article Snippet: Experimental groups were: (1) Control VSMCs + Macrophages; (2) Secretory VSMCs + Macrophages; (3) Secretory VSMCs + Macrophages + 10 μg/mL anti-human MIF monoclonal antibody (Abcam); (4) Secretory VSMCs + Macrophages + 5 μM CD74 inhibitor BMS-582949 (MedChemExpress).

Techniques: Activity Assay, Expressing

Journal: Frontiers in Immunology

Article Title: Macrophage migration inhibitory factor–CD74 axis drives vascular smooth muscle cell–induced M1 macrophage polarization to exacerbate intracranial aneurysm inflammation

doi: 10.3389/fimmu.2025.1682762

Figure Lengend Snippet: Secretory VSMCs drive macrophage M1 polarization via the MIF-CD74 axis. (A, B) qPCR analysis of iNOS and Arg1 expression in macrophages following Transwell co-culture. Secretory VSMCs increase iNOS and decrease Arg1; anti-MIF antibody or CD74 inhibitor (BMS-582949) attenuates this effect. (C) Flow cytometry quantification of CD86 + macrophages. Secretory VSMCs increase CD86 + proportion; inhibition of MIF or CD74 reduces it. (D, E) qPCR validation of MIF knockdown efficiency in VSMCs and its effect on macrophage iNOS/Arg1 expression in co-culture. MIF knockdown reverses secretory VSMC-induced polarization. (F) Flow cytometry shows MIF knockdown reduces CD86 + macrophage proportion induced by secretory VSMCs. (G, H) qPCR analysis of macrophages treated with secretory VSMC conditioned medium (CM). CM increases iNOS and decreases Arg1; CD74 inhibition reverses this. (I) Flow cytometry shows CD74 inhibition reduces CM-induced increase in CD86 + macrophages. Data are mean ± SEM; P < 0.01, P < 0.05 versus control; ##P < 0.01, #P < 0.05 versus secretory VSMC group (One-way ANOVA with Tukey’s post hoc test).

Article Snippet: Experimental groups were: (1) Control VSMCs + Macrophages; (2) Secretory VSMCs + Macrophages; (3) Secretory VSMCs + Macrophages + 10 μg/mL anti-human MIF monoclonal antibody (Abcam); (4) Secretory VSMCs + Macrophages + 5 μM CD74 inhibitor BMS-582949 (MedChemExpress).

Techniques: Expressing, Co-Culture Assay, Flow Cytometry, Inhibition, Biomarker Discovery, Knockdown, Control