Journal: Nature Communications

Article Title: CD248-targeted BBIR-T cell therapy against late-activated fibroblasts in cardiac repair after myocardial infarction

doi: 10.1038/s41467-025-56703-2

Figure Lengend Snippet: a UMAP clustering of 13441 cardiac interstitial cells (left) and fibroblasts (right) isolated from C57BL/6 J wild-type (WT) mice at 7 and 14 days post-sham and post-MI surgery. Each dot represents a single cell. The expression of known marker genes annotated cell type. b UMAP and violin plots depict Postn , Acta2 , and Comp expression in fibroblasts. c Triple IF staining for periostin (green) and αSMA (red) in the peri-infarct zone of the hearts of C57BL/6 J WT mice 0, 7, 14, 21, and 28 days after MI surgery. Nuclei were stained blue. Scale bar = 100 μm. Quantification of the number of periostin + αSMA + F-Myo and periostin + αSMA - F-Act in each high-power field (HPF). n = 5 mice at each time point after MI. d Flow cytometry of fibroblasts isolated from hearts of C57BL/6 J WT and Pdgfra-CRE:tdTomato mice. Total cardiac fibroblasts were lineage traced by pdgfrα. F-Myo and F-Act were marked with antibodies against periostin-AF488 and αSMA-AF647. Quantification of the pdgfrα + fibroblast ratio in live cells, periostin + fibroblasts ratio in pdgfrα + fibroblasts, periostin + αSMA + F-Myo ratio in pdgfrα + fibroblasts, and periostin + αSMA - F-Act ratio in pdgfrα + fibroblasts. n = 5 mice at each time point after MI. e Spatial distribution of the F-Act and F-Myo subpopulation in mouse heart sections from sham and 10 days post-MI conditions, visualized through the integration of scRNA-seq and stereo-seq methodologies. c, d Data are the mean ± SEM and p -values are displayed in the bar charts, one-way ANOVA followed by Tukey’s multiple comparisons tests. Source data are provided as a Source Data file.

Article Snippet: The antibodies used in this study included Periostin (Abcam, ab14041), αSMA-Alexa Fluor 647 (Novus, NBP2-34522), CD248-Alexa Fluor 647 (Santa Cruz, sc-377221), CD3-FITC (BioLegend, 317306 for human and 100204 for mouse), CD4-APC (BioLegend, 344614 for human and 100412 for mouse), CD8-PE (BioLegend, 344706 for human and 100708 for mouse), and goat anti-rabbit IgG (1:1000, Invitrogen, A11008 for Alexa Fluor 488).

Techniques: Isolation, Expressing, Marker, Staining, Flow Cytometry

Journal: Nature Communications

Article Title: CD248-targeted BBIR-T cell therapy against late-activated fibroblasts in cardiac repair after myocardial infarction

doi: 10.1038/s41467-025-56703-2

Figure Lengend Snippet: a Triple IF staining for periostin (green) and CD248 (red) in the peri-infarct zone of the hearts of C57BL/6J WT mice 0, 7, 14, 21, and 28 days after MI surgery. Nuclei were stained blue. Scale bar = 100 μm. Quantification of the periostin + CD248 + cell to DAPI ratio in each HPF. n = 5 mice at each time point after MI. Triple IF staining of periostin, αSMA, COMP (stained green), and CD248 (stained red) in the hearts of MI mouses ( b ) and a patient with ischemic cardiomyopathy ( c ). Nuclei were stained blue. Scale bar =100 μm. IF staining of mouse heart was repeated in heart sections from 5 independent mice, while IF of human heart was repeated 5 times in heart sections from one patient with ischemic cardiomyopathy, yielding similar results. d Flow cytometry of cells isolated from hearts of C57BL/6 J WT mouses and Pdgfra-CRE:tdTomato mice. Total cardiac fibroblasts were lineage traced by pdgfrα. Quantification of the CD248 + cell ratio in live cells, pdgfrα + fibroblast ratio in CD248 + cells, CD248 + cell ratio in pdgfrα + fibroblasts, periostin + CD248 + cell ratio in pdgfrα + fibroblasts, CD248 + cell ratio in periostin + activated fibroblasts, and periostin + activated fibroblasts in CD248 + cells. n = 5 mice at each time point after MI. a, d Data are the mean ± SEM and p -values are displayed in the bar charts, one-way ANOVA followed by Tukey’s multiple comparisons tests. Source data are provided as a Source Data file.

Article Snippet: The antibodies used in this study included Periostin (Abcam, ab14041), αSMA-Alexa Fluor 647 (Novus, NBP2-34522), CD248-Alexa Fluor 647 (Santa Cruz, sc-377221), CD3-FITC (BioLegend, 317306 for human and 100204 for mouse), CD4-APC (BioLegend, 344614 for human and 100412 for mouse), CD8-PE (BioLegend, 344706 for human and 100708 for mouse), and goat anti-rabbit IgG (1:1000, Invitrogen, A11008 for Alexa Fluor 488).

Techniques: Staining, Flow Cytometry, Isolation

Journal: Nature Communications

Article Title: CD248-targeted BBIR-T cell therapy against late-activated fibroblasts in cardiac repair after myocardial infarction

doi: 10.1038/s41467-025-56703-2

Figure Lengend Snippet: a Schematic diagram of the structure of the BBIR-T system. Created in BioRender. Haiting, C. (2025) https://BioRender.com/l46n352 . b Schematic images of dcAv. BBIR-28-137ζ and CD19. CAR-137ζ sequence. c Western blotting shows exogenous CD3ζ expression in HEK-293T cells transduced with lentivirus (LV)-dcAv.BBIR and LV-anti-CD19.CAR. The samples derive from the same experiment and that gels/blots were processed in parallel. Quantifying the relative protein expression of CD3ζ to GAPDH. n = 4 cell culture wells of each group. d Flow cytometry of human peripheral T cells transduced with LV-dcAv.BBIR and LV-anti-CD19.CAR. Quantifying GFP + cells ratio to total T cells and biotin + cells ratio to GFP + cells. n = 5 cell culture wells of each group. e Western blotting by BF shows CD248 expression in NIH-3T3 cells with or without Cd248 overexpression(OE) or knockout(KO). The samples were derived from the same experiment and that gels/blots were processed in parallel. Quantifying the relative protein expression of CD248 to GAPDH. n = 4 cell culture wells of each group. f Triple IF staining of periostin, αSMA, COMP (green), and biotinylated anti-CD248 F(ab’)2 (shorted as BF) (red) in the peri-infarct zone 14 days after MI surgery. Nuclei were stained blue. Scale bar =100 μm. Each experiment was repeated 5 times independently with similar results. c-e Data are the mean ± SEM and p -values are displayed in the bar charts, one-way ANOVA followed by Tukey’s multiple comparisons tests. Source data are provided as a Source Data file.

Article Snippet: The antibodies used in this study included Periostin (Abcam, ab14041), αSMA-Alexa Fluor 647 (Novus, NBP2-34522), CD248-Alexa Fluor 647 (Santa Cruz, sc-377221), CD3-FITC (BioLegend, 317306 for human and 100204 for mouse), CD4-APC (BioLegend, 344614 for human and 100412 for mouse), CD8-PE (BioLegend, 344706 for human and 100708 for mouse), and goat anti-rabbit IgG (1:1000, Invitrogen, A11008 for Alexa Fluor 488).

Techniques: Sequencing, Western Blot, Expressing, Transduction, Cell Culture, Flow Cytometry, Over Expression, Knock-Out, Derivative Assay, Staining

Journal: Cell reports

Article Title: Netrin-1 feedforward mechanism promotes pancreatic cancer liver metastasis via hepatic stellate cell activation, retinoid, and ELF3 signaling.

doi: 10.1016/j.celrep.2023.113369

Figure Lengend Snippet: Figure 6. Netrin-1 interference suppresses metastasis and increases survival in murine PDAC models (A) Mice were pretreated with mAbNtn1 for 2 days and intrasplenically injected with 50,000 Ink4a.1 cells. Antibody treatment (10 mg/kg) continued every 2 days until liver harvest at day 14. Percentage tumor area in the liver was quantified as before (n = 5). (B) Kaplan-Meier graph showing survival of mice in- jected intrasplenically with 20,000 Ink4a.1 cells using mAbNtn1 (n = 16) as adjuvant treatment or vehicle (n = 19). Note that three mAbNtn1-treated mice have not recurred beyond day 200. (C) Immunohistochemistry of CK17-stained livers from C57Bl/6J mice injected via portal vein injection with KPC3 cells (left) and treated with IgG control or mAbNtn1, n = 10/group. Percentage of tumor metastasis area was quantified as before, n = 5 sec- tions/mouse. Note the significant reduction in mice treated with anti-Netrin-1 antibody (right). Scale bars, 200 mm. (D) Normalized Netrin-1 expression in KPC3 cells, normal liver, hepatic KPC3 metastases from control IgG-treated mice, and hepatic KPC3 metastases from mAbNtn1-treated mice as quantified by western blot. (E) Kaplan-Meier plot showing survival of KPC mice treated with IgG vehicle and mAbNtn1 antibodies. The vehicle group (n = 17) had MS = 18 days, while the mAbNtn1 group (n = 11) had MS 42 days, a doubling of lifespan. All experiments were completed at least in duplicate. Statistical analysis was completed using two-tailed Student’s t test (***p < 0.001, ****p < 0.0001).

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-netrin 1 antibody [EPR5428] Abcam ab126729 Human/Mouse ELF3 Antibody R&D Systems AF5787 RXRa (D6H10) Rabbit mAb Cell Signaling 3085S ELF3 Polyclonal Antibody Invitrogen PA5-89261 Normal Rabbit IgG Cell Signaling 2729P RARa/Retinoic Acid Receptor a Antibody (C-1) Santa Cruz Biotechnology sc-515796 Mouse (G3A1) mAb IgG1 Isotype Control Cell Signaling 5415S Anti-Desmin antibody [Y66] Abcam ab32362 Smooth muscle actin Polyclonal antibody ProteinTech 14395-1-AP Goat anti-Rabbit IgG (H + L) Cross-Adsorbed Secondary Antibody, Alexa FluorTM 532 Invitrogen A-11009 Goat anti-Rabbit IgG (H + L) Cross-Adsorbed Secondary Antibody, Alexa FluorTM 555 Invitrogen A-21428 Anti-CD9 antibody [EPR2949] Abcam ab92726 UNC5B (D9M7Z) Rabbit mAb Cell Signaling 13851 Purified Mouse Anti-Flotillin-1 BD Biosciences 610820 Cytokeratin 17 Monoclonal Antibody (CK17) Thermo Fisher 606–540 RARg1 (D3A4) XP Rabbit mAb Cell Signaling 8965S Anti-Retinoid X Receptor beta/RXRB antibody Abcam ab221115 RXRg Antibody (G-6) Santa Cruz Biotechnology sc-514134 Actin Antibody (H-6) Santa Cruz Biotechnology sc-376421 Alix (3A9) Mouse mAb Cell Signaling 2171S Alexa Fluor 647 anti-mouse/human CD324 (E-Cadherin) Antibody Biolegend 147307 Vimentin (D21H3) XP Rabbit mAb Cell Signaling 5741S alpha-Smooth Muscle Actin Antibody (1A4/asm-1) - Azide and BSA Free Novus Biologicals NBP2-34522 mAbNtn1 Patrick Mehlan N/A Bacterial and virus strains Edit-R Mouse Unc5b hEF1a All-in-one Lentiviral sgRNA Horizon Discovery VSGM11942-247910466 Edit-R Mouse Elf3 mCMV All-in-one Lentiviral sgRNA Horizon Discovery VSGM11942-248070215 Edit-R Mouse Ntn1 Lentiviral sgRNA Horizon Discovery VSGM10144-246774776 Biological samples BxPC-3 ATCC CRL-1687 Capan-2 ATCC HTB-80

Techniques: Injection, Adjuvant, Immunohistochemistry, Staining, Control, Expressing, Western Blot, Two Tailed Test

Journal: Experimental & Molecular Medicine

Article Title: PGC-1α mediates migrasome secretion accelerating macrophage–myofibroblast transition and contributing to sepsis-associated pulmonary fibrosis

doi: 10.1038/s12276-025-01426-z

Figure Lengend Snippet: Key resource details.

Article Snippet: Novus , NBP2-34522AF405 , α-SMA antibody (1A4/asm-1) (Alexa Fluor 405).

Techniques: Recombinant, Staining, Clinical Proteomics, Isolation, Bicinchoninic Acid Protein Assay, Membrane, Pore Size, Software