Journal: Nature Aging

Article Title: Anti-uPAR CAR T cells reverse and prevent aging-associated defects in intestinal regeneration and fitness

doi: 10.1038/s43587-025-01022-w

Figure Lengend Snippet: a , Surface uPAR expression as determined by flow cytometry on isolated intestinal crypts from young (3 months) and old (20 months) mice ( n = 3 per group). b , Percentage of uPAR + cells that are either EpCAM + CD45 − or EpCAM − CD45 + as determined by flow cytometry on isolated intestinal crypts from old (20 months) mice ( n = 3 per group). c , Surface uPAR expression in SPiDER-β-gal + cells as determined by flow cytometry on isolated intestinal crypts from old (20 months) mice ( n = 3 per group). d , Representative co-immunofluorescence of uPAR (red) and EdU (green) in the proximal jejunum of aged (20 months old mice) ( n = 3 mice). White arrows signal uPAR + EdU − cells. e , Percentage of uPAR + cells that are EdU + or EdU − in the proximal jejunum of aged (20 months) mice ( n = 3 mice). f , Representative co-immunofluorescence of uPAR (red) and p21 (green) in the proximal jejunum of aged (20 months) mice ( n = 3 mice). White arrows signal uPAR + cells. g , Percentage of uPAR + cells that are p21 + or p21 − in the proximal jejunum of aged (20 months) mice ( n = 3 mice). h – k , uPAR + and uPAR − cells from isolated intestinal crypts of duodenum, jejunum and ileum (whole small intestine) from old (20 months) mice were FACS sorted and subjected to scRNA-seq ( n = 4 mice per group pooled into two replicates per group). i , Uniform Manifold Approximation and Projection (UMAP) visualization of small intestinal cell types generated by 10X chromium protocol. Color scale indicates differences in density of cellular populations between uPAR + and uPAR − cells. j , Pathway analysis using enrichR comparing differentially expressed genes between uPAR + versus uPAR − cells in scRNA-seq data. Size scale represents number of genes in each ontology, and color scale represents degree of significance. k , UMAP visualization of small intestinal cell types generated by 10X chromium protocol. Color scale indicates log 2 fold change (log2FC) in senescence signature between uPAR + and uPAR − cells. Right: quantification of the proportion of uPAR + and uPAR − cells contributing to the senescence signature. l – n , scRNA-seq of small intestinal non-immune cell types in the whole small intestine of young (25–30 years old) and old (65–70 years old) subjects generated by 10X chromium protocol ( n = 1 per group). m , Split-violin plot indicates the expression level of PLAUR in the ISC and epithelial lineage. Boxplots display median (center line) and interquartile range (box). n , Pathway analysis using enrichR comparing differentially expressed genes between non-immune PLAUR + vs PLAUR − cells in scRNA-seq data. Size scale represents number of genes in each ontology, and color scale represents degree of significance. o – q , scRNA-seq of small intestinal immune cell types in the whole small intestine of young (25–30 years old) and old (65–70 years old) subjects generated by 10X chromium protocol ( n = 1 per group). p , Split-violin plot indicates the expression level of PLAUR in B cells, myeloid cells and T cells. Boxplots display median (center line) and interquartile range (box). q , Pathway analysis using enrichR comparing differentially expressed genes between immune PLAUR + versus PLAUR − cells in scRNA-seq data. Size scale represents number of genes in each ontology, and color scale represents degree of significance. r , Multiplex immunofluorescence of uPAR, ki-67, p21, γH2A.X, cleaved caspase-3, CD45, CD31, E-cadherin and DAPI in human intestinal samples from subjects aged 51–91 years ( n = 3 subjects). Green arrows highlight uPAR + p21 + cells, pink arrows highlight uPAR + γH2A.X + cells. s , Percentage of cells in the tissues from t that are uPAR + CD45 + uPAR + , CD68 + uPAR + or E-Cadherin + uPAR + ( n = 3 subjects). t , Percentage of E-Cadherin + uPAR + from t that are Ki-67 − , p21 + , Ki-67 − and p21 + , γH2A.X + , or Ki-67 − , p21 + and γH2A.X + ( n = 3 subjects). Shown are results of one independent experiment ( a –t ). Data are mean ± standard error of the mean (s.e.m.) ( a –c , e , g , s–t ). Significance was determined using a two-tailed unpaired Student’s t -test ( a –c , e , g ), two-tailed Fischer’s exact test ( j , n , q ) or two-tailed Wilcoxon rank-sum test (* P < 0.05,** P < 0.01, *** P < 0.001, **** P < 0.0001 ( m , p ). Illustration was created with Biorender.com ( h ).

Article Snippet: The following antibodies were used: uPAR (AF807, R&D), AF555-Ki-67 (558617, BD Biosciences), AF647-γH2A.X (ab195189, Abcam), AF488-E-cadherin (3199S, Cell Signaling Technology), AF647-p21 (8587S, Cell Signaling Technology), AF488-CD31 (42777, Cell Signaling Technology), AF555-CD45 (19744, Cell Signaling Technology), AF750 cleaved caspase-3 (97774S, Cell Signaling Technology), and AF555-donkey anti goal ( A21432 , Invitrogen).

Techniques: Expressing, Flow Cytometry, Isolation, Immunofluorescence, Generated, Multiplex Assay, Two Tailed Test

Journal: Nature Communications

Article Title: Cardiomyocyte gene programs encoding morphological and functional signatures in cardiac hypertrophy and failure

doi: 10.1038/s41467-018-06639-7

Figure Lengend Snippet: Hypertrophy-stage-specific p53 signaling activation. a Bar plot showing the statistical significance of the overlap between modules detected from co-expression analysis with or without hypertrophy-stage cardiomyocytes. The most strongly overlapping module pairs are selected from Supplementary Fig. . Modules are ordered by significance level. The red line indicates the threshold for hypertrophy stage-specific modules. b KEGG pathway enrichment of 12 hypertrophy stage-specific modules identified in a and Supplementary Fig. . c Co-expression network analysis of M7. d Representative images of Cdkn1a mRNA smFISH in the heart from mice at 2 weeks after pressure overload. Wheat germ agglutinin (WGA) and DAPI are used as markers of the plasma membrane and nucleus, respectively. Scale bar, 20 μm. e Bar plots showing the distribution of cells corresponding to the single-cell fluorescent intensity of Cdkn1a mRNA detected by smFISH in the heart after sham and TAC (weeks 2 and 8) operation. f Heatmap showing the enrichment of GO and KEGG pathway terms in 12 hypertrophy stage-specific modules. g Immunohistochemical staining of gH2A.X and p21 in the heart of mice at 2 weeks after pressure overload. WGA and DAPI are used as markers of the plasma membrane and nucleus, respectively. Arrows indicate the nuclei of gH2A.X and p21 double-positive cardiomyocytes. Scale bar, 20 μm

Article Snippet: The sections were incubated with the following antibodies overnight at 4 °C: mouse monoclonal anti-p21 antibody conjugated to Alexa Fluor 647 (1:50; sc6246 AF647; Santa Cruz Biotechnology) and rabbit polyclonal anti-γH2A.X (phospho S139) antibody (1:100; ab2893; Abcam).

Techniques: Activation Assay, Expressing, Clinical Proteomics, Membrane, Immunohistochemical staining, Staining

Journal: Nature Communications

Article Title: Cardiomyocyte gene programs encoding morphological and functional signatures in cardiac hypertrophy and failure

doi: 10.1038/s41467-018-06639-7

Figure Lengend Snippet: Distinct gene programs and their pathogenicity in human cardiomyocytes. a Co-expression network of human cardiomyocytes. Dot colors indicate module colors, matching the colors in b . b Heatmap showing the enrichment of GO and KEGG pathway terms in each module. c t-SNE visualization of human cardiomyocytes (71 normal and 340 dilated cardiomyopathy (DCM) cardiomyocytes). Cells (dots) are colored according to the cell clusters in Supplementary Fig. . d t-SNE plots of human cardiomyocytes colored by the expression of each module. e Heatmap showing the relative average expression for characteristic genes across the five modules. Representative genes are also indicated. f t-SNE plots of human cardiomyocytes colored by the expression of each gene. g Representative images of CDKN1A mRNA smFISH of the DCM heart. WGA and DAPI are used as markers of the plasma membrane and nucleus, respectively. Scale bar, 20 μm. h Bar plots showing the distribution of cells corresponding to the single-cell fluorescent intensity of CDKN1A mRNA detected by smFISH in the normal and DCM hearts. i Subnetwork analysis of human M1. j Scatter plot showing the relationship between M1 and M2 expression. DCM cardiomyocytes are separated into two groups: responder ( n = 59) and non-responder ( n = 281). k Heatmap showing the significance of gene overlaps between human and mouse modules. The table is colored by −log 10 ( P -value), obtained with Fisher’s exact test, according to the color legend below the table

Article Snippet: The sections were incubated with the following antibodies overnight at 4 °C: mouse monoclonal anti-p21 antibody conjugated to Alexa Fluor 647 (1:50; sc6246 AF647; Santa Cruz Biotechnology) and rabbit polyclonal anti-γH2A.X (phospho S139) antibody (1:100; ab2893; Abcam).

Techniques: Expressing, Clinical Proteomics, Membrane