Journal: Stem Cell Research & Therapy

Article Title: Exosomes derived from human umbilical cord mesenchymal stem cells inhibit vein graft intimal hyperplasia and accelerate reendothelialization by enhancing endothelial function

doi: 10.1186/s13287-020-01639-1

Figure Lengend Snippet: Morphology and characterization of hucMSCs and hucMSC-exosomes. a The fibroblast-like morphology of hucMSCs shown in light microscopy images (× 40). b Surface markers of hucMSCs analysed by flow cytometry. hucMSCs were positive for CD29, CD44, and CD90 and were negative for CD34 and CD45. c MSCs displayed the ability of adipogenic differentiation (× 40). d MSCs displayed the ability of chondrogenic differentiation (× 40). e Morphology of exosomes under transmission electron microscopy. Scale bar, 100 nm. f The size distribution of exosomes measured by Image-Pro Plus software. g Western blotting analyses of the exosome surface markers (CD9, CD81, and CD63)

Article Snippet: Blots were incubated with the appropriate primary antibodies, including CD9 (1:1000, Proteintech), CD63 (1:1000, Proteintech), CD81 (1:1000, BOSTER, Wuhan, China), inducible nitric oxide synthase (iNOS,1: 1000, Abcam), endothelial nitric oxide synthase (eNOS, 1:1000, Abcam), VEGF-A (1: 1000, Abcam), CD31 (1:1000, Abcam), AKT (1:1000,Cell Signaling, Boston, USA), p-AKT(,1:1000, Cell Signaling), ERK1/2 (1:1000, Cell Signaling), p-ERK1/2 (1:1000, Cell Signaling), and GAPDH (1:2000, Proteintech).

Techniques: Light Microscopy, Flow Cytometry, Transmission Assay, Electron Microscopy, Software, Western Blot

Journal: Cellular and Molecular Gastroenterology and Hepatology

Article Title: The Appendix Orchestrates T-Cell Mediated Immunosurveillance in Colitis-Associated Cancer

doi: 10.1016/j.jcmgh.2022.10.016

Figure Lengend Snippet: Appendectomy significantly alters intratumor T-cell immunity in mice. Paraffin-embedded sections of the colon from each mouse taken at the AOM/DSS protocol endpoint in the appendectomy (n = 16) and control (n = 10) groups were stained with anti-CD3 or anti-CD8 antibodies. ( A ) Representative CD3+ cell immunostaining of colonic tumors after appendectomy or sham laparotomy (control). ( B ) Quantification of intratumor CD3+ T-cell density by an automated observer-independent process using Aperio ImageScope software in the appendectomy and control groups. ( C ) Representative CD8+ immunostaining of colonic tumors after appendectomy or sham laparotomy (control). ( D ) Quantification of intratumor CD8+ T-cell density in the appendectomy and control groups. All colonic tumors from individual mice of the appendectomy (n = 13) and control (n = 12) groups subjected to the AOM/DSS protocol were resected and pooled. Intratumor CD3+ T-cells were isolated. Flow cytometry was performed to label CD3, CD4, CD8, CD62L, CD44, and PD1. Dot plots comparing intratumor cell labeling between the 2 groups in terms of ( E ) percentage of CD3+CD44 high cells among CD3+ cells, ( F ) CD62L low /CD62L high ratio among CD3+CD44 high cells, ( G ) percentage of PD1 high among CD3+ cells, ( H ) percentage of CD4+CD44 high cells among CD4+ cells, ( I ) CD62L low /CD62L high ratio among CD4+CD44 high cells, ( J ) percentage of PD1 high among CD4+ cells, ( K ) percentage of CD8+CD44 high cells among CD8+ cells, ( L ) CD62L low /CD62L high ratio among CD8+CD44 high cells, and ( M ) percentage of PD1 high among CD8+ cells. ( N ) Scatter plot of CD3+ cells isolated from appendectomy and control mice stained for CD62L (x-axis) and for CD44 (y-axis). The red number represents the percentage of labeled cells. ( O ) T cells were isolated from pooled colonic tumors of individual mice subjected to the AOM/DSS protocol after appendectomy (n = 13) and sham laparotomy (n = 12). 100,000 cells per mouse were stimulated or not with a cocktail of phorbol myristate acetate-ionomycin. Dot plot represents production of TNF-α and IFN-γ by stimulated T cells from the appendectomy and control groups measured by ELISA. In all dot plots , the error bars represent the 25th, 50th (median), and 75th interquartile ranges. Comparisons of 2 groups were performed using Mann-Whitney test with 2-tailed P value. P value <.05 was considered statistically significant.

Article Snippet: Then, cells were incubated for 20 minutes at 4°C in the dark with a cocktail of antibodies directed against CD3 (APC-Vio770, 130-119-793; Miltenyi), CD4 (FITC, 130-118-692; Miltenyi), CD8 (PE-Vio770, 130-119-123; Miltenyi), CD62L (APC, 130-112-837; Miltenyi), CD44 (PE, 130-118-694; Miltenyi), and PD1 (PE-CF594, 562523 BD).

Techniques: Control, Staining, Immunostaining, Software, Isolation, Flow Cytometry, Labeling, Enzyme-linked Immunosorbent Assay, MANN-WHITNEY

Journal: iScience

Article Title: Immunometabolic adaptation in monocytes underpins functional changes during pregnancy

doi: 10.1016/j.isci.2024.109779

Figure Lengend Snippet:

Article Snippet: CD163 human antibody (clone GHI/61.1) , Miltenyi , Cat#130-123-249; RRID: AB_2819455.

Techniques: Recombinant, Adhesive, Sequencing, Modification, DC Protein Assay, Staining, Imaging, Enzyme-linked Immunosorbent Assay, Bicinchoninic Acid Protein Assay, Gene Expression, Software, Saline

Journal: Cell Reports Medicine

Article Title: Lymph node and tumor-associated PD-L1 + macrophages antagonize dendritic cell vaccines by suppressing CD8 + T cells

doi: 10.1016/j.xcrm.2023.101377

Figure Lengend Snippet: PD-L1 + macrophages are mobilized by DC vaccines in GBM patients (A) Expression of CD274 / cd274 (PD-L1) across indicated datasets (n = 287 patients). (B) Correlation between CD274 vs. M1/M2 macrophage fraction in TCGA cancer types (C1, n = 1,313; C2, n = 1,210, C3, n = 688; C4, n = 222, C5, n = 2; C6, n = 111). (C) Z scores of CoxPH regression of CD274 HIGH macrophages HIGH subgroups, correcting for age, gender, tumor-stage (bladder cancer/BLCA, n = 408; breast cancer/BRCA, n = 1,100; colon adenocarcinoma/COAD, n = 458; GBM, n = 153; head and neck cancer human papillomavirus − /HNSC-HPV − , n = 422; head and neck cancer human papillomavirus + /HNSC-HPV + , n = 98; kidney chromophobe/KICH, n = 66; kidney renal clear cell carcinoma/KIRC, n = 533; kidney renal papillary cell carcinoma/KIRP, n = 290; low-grade glioma/LGG, n = 516; liver cancer/LIHC, n = 371; lung adenocarcinoma/LUAD, n = 515; lung squamous cell carcinoma/LUSC, n = 501; ovarian cancer/OV, n = 303; pancreatic adenocarcinoma/PAAD, n = 179; pheochromocytoma/PCPG, n = 181; prostate adenocarcinoma/PRAD, n = 498; rectum adenocarcinoma/READ, n = 166; sarcoma/SARC, n = 260; melanoma/SKCM, n = 471; stomach adenocarcinoma/STAD, n = 415; thyroid carcinoma/THCA, n = 509; uveal melanoma/UVM, n = 80, Mantel-Cox test). (D and E) log2(metagene expression) of CD274, CD163, CD14, and CD68. (D) Responders vs. non-responders to anti-PD-L1 (atezolizumab/durvalumab) (responders, n = 185 and non-responders, n = 269, where ureter/renal pelvis cancer n = 4, urothelial cancer n = 345, bladder cancer n = 31, esophageal cancer n = 72, renal cell carcinoma n = 2; Mann-Whitney U test). (E) Responders vs. non-responders to anti-PD-1 (nivolumab/pembrolizumab) (responders, n = 183 and non-responders, n = 323, where lung cancer n = 19, GBM n = 19, ureter/renal pelvis cancer n = 7, gastric cancer n = 45, colorectal cancer n = 5, melanoma n = 415, bladder cancer n = 59, hepatocellular carcinoma n = 22, breast cancer n = 14, renal cell carcinoma n = 31, head and neck cancer n = 110; Mann-Whitney U test). (F–J) Analysis of CD45 + fraction of primary and DC vaccinated GBM patients (NCT03395587). Tumor material from day of resection at first diagnosis (primary) or at recurrence after vaccination. (F) Overview of NCT03395587. (G) Frequency of CD4 + /CD8 + of CD3 + cells. (H) Frequency of IFNγ + of CD4 + /CD8 + CD3 + T cells. (G and H) Primary, n = 6; progress vaccine, n = 5, two-way ANOVA, Bonferroni’s multiple comparison. (I) Mean fluorescent intensity of CD163 on CD14 + cells. Primary, n = 15; recurrent DC vaccine, n = 5; two-tailed Student’s t test. (J and K) Immunohistochemistry of tumor slide from unvaccinated and DC vaccinated GBM patients (NCT03395587). (J) Representative images. (K) Correlation between TAM and T cell counts (n = 37 tumor regions from eight unvaccinated/vaccinated, Spearman’s correlation). (L) Mean fluorescent intensity of PD-L1 on CD14 + cells. Primary, n = 15; recurrent DC vaccine, n = 5; two-tailed Student’s t test. (M) Bromodeoxyuridine incorporation in cocultures of PBMC-derived lymphocytes (CD14 depleted PBMC) and TAMs obtained from primary GBM samples with/without anti-PD-L1 blocking (n = 3; area-under-curve-driven two-tailed paired t test). Here, “n” represents different patients (biological replicates) and error bars represent SEM. See also Figure S7 .

Article Snippet: FITC anti-human CD163 (clone: REA812 , Miltenyi Biotec , Cat#130-112-290 RRID: AB_2655475.

Techniques: Vaccines, Expressing, MANN-WHITNEY, Biomarker Discovery, Comparison, Two Tailed Test, Immunohistochemistry, Derivative Assay, Blocking Assay

Journal: Cell Reports Medicine

Article Title: Lymph node and tumor-associated PD-L1 + macrophages antagonize dendritic cell vaccines by suppressing CD8 + T cells

doi: 10.1016/j.xcrm.2023.101377

Figure Lengend Snippet:

Article Snippet: FITC anti-human CD163 (clone: REA812 , Miltenyi Biotec , Cat#130-112-290 RRID: AB_2655475.

Techniques: Control, Recombinant, Lysis, Protease Inhibitor, Western Blot, Staining, Stripping, Liposomes, CRISPR, MTS Assay, ATP Assay, Reverse Transcription, Cell Isolation, Enzyme-linked Immunosorbent Assay, Conjugation Assay, Selection, Drug discovery, Vaccines, Single-cell Analysis, RNA Sequencing, Mutagenesis, Microarray, Purification, Software

Journal: PLoS ONE

Article Title: Hypoxia Regulates CD44 and Its Variant Isoforms through HIF-1α in Triple Negative Breast Cancer

doi: 10.1371/journal.pone.0044078

Figure Lengend Snippet: q-RT-PCR analysis of VEGF and CD44 mRNA expression levels in MDA-MB-231 wild type cells under normoxia (open box), in response to 24 h of hypoxia (black box) (A), and in response to 24 h treatment with 200 µM CoCl 2 (dark-gray box) (B). mRNA expression of VEGF and CD44 in SUM-149 wild type cells under normoxia (open box) and in response to 24 h of hypoxia (hatched box)(C), and in response to 24 h treatment with 200 µM CoCl 2 (cross-hatched box)(D). Values represent Mean ± SEM obtained from three independent experiments. *P<0.05, **P<0.005.

Article Snippet: Briefly, 1–2 mCi of [ 125 I]NaI were incubated with 30 μg of purified mouse monoclonal anti-human CD44 antibody (A3D8, Abcam Inc., Cambridge, MA) in 50–100 μl PBS in an iodogen-coated reaction vial.

Techniques: Reverse Transcription Polymerase Chain Reaction, Expressing

Journal: PLoS ONE

Article Title: Hypoxia Regulates CD44 and Its Variant Isoforms through HIF-1α in Triple Negative Breast Cancer

doi: 10.1371/journal.pone.0044078

Figure Lengend Snippet: (A) Immunoblot analysis of HIF-1α or HIF-2α expression in whole cell extracts from MDA-MB-231 cells stably expressing EV, HIF-1α-shRNA or HIF-2α-shRNA under normoxia or in response to 4 h treatment with 200 µM CoCl 2 . HIF-1β expression was used as a loading control. (B) mRNA expression of HIF-1α, HIF-2α, VEGF, and CD44 in MDA-MB-231 EV cells under normoxia (open box) or following 24 h of 200 µM CoCl 2 (dark-gray box) and in MDA-MB-231 cells stably expressing HIF-1α-shRNA under normoxia (light-gray box) or following 24 h of 200 µM CoCl 2 (cross-hatched box). (C) mRNA expression of HIF-1α, HIF-2α, VEGF, and CD44 in MDA-MB-231 EV control cells under normoxia (open box) or following 24 h of 200 µM CoCl 2 (dark-gray box) and in MDA-MB-231 cells stably expressing HIF-2α-shRNA under normoxia (hatched box) or following 24 h of 200 µM CoCl 2 (wavy-hatched box). Values represent Mean ± SEM of three experiments. *P<0.05, **P<0.005.

Article Snippet: Briefly, 1–2 mCi of [ 125 I]NaI were incubated with 30 μg of purified mouse monoclonal anti-human CD44 antibody (A3D8, Abcam Inc., Cambridge, MA) in 50–100 μl PBS in an iodogen-coated reaction vial.

Techniques: Western Blot, Expressing, Stable Transfection, shRNA, Control

Journal: PLoS ONE

Article Title: Hypoxia Regulates CD44 and Its Variant Isoforms through HIF-1α in Triple Negative Breast Cancer

doi: 10.1371/journal.pone.0044078

Figure Lengend Snippet: (A) Co-registration of RFP expression from optical images (blue), and SPECT images (yellow) showing the overlap of a hypoxic region of high fluorescence with high CD44 antibody localization. Inset shows ex vivo SPECT (left) and optical (right) images of a fresh 2-mm slice from the tumor. (B) In vivo SPECT imaging of a SCID mouse bearing MDA-MB-231-HRE-tdTomato RFP tumor was performed in 64 projections at 30 sec/projection. Following SPECT acquisition, CT images were acquired in 512 projections to allow coregistration. Volume rendered images were created using Amira image processing software. A representative trans-axial slice of decay corrected, volume rendered SPECT/CT images at 48 h demonstrate specific accumulation of radioactivity in the tumor as well as some radioactivity in the liver. The optical image of the excised tumor shows a hypoxic region with intense red fluorescence. (C) Quantification of average intensity from SPECT data obtained from normoxic and hypoxic regions in ex vivo tissue slices demonstrates a statistically significant increase (*P<0.05, n = 3 ) in image intensity in hypoxic regions. Values represent Mean ± SEM from 10 slices obtained from three tumors.

Article Snippet: Briefly, 1–2 mCi of [ 125 I]NaI were incubated with 30 μg of purified mouse monoclonal anti-human CD44 antibody (A3D8, Abcam Inc., Cambridge, MA) in 50–100 μl PBS in an iodogen-coated reaction vial.

Techniques: Expressing, Single Photon Emission Computed Tomography, Fluorescence, Ex Vivo, In Vivo, Imaging, Software, Radioactivity

Journal: Basic Research in Cardiology

Article Title: A DARPin targeting activated Mac-1 is a novel diagnostic tool and potential anti-inflammatory agent in myocarditis, sepsis and myocardial infarction

doi: 10.1007/s00395-021-00849-9

Figure Lengend Snippet: DARPin F7 improves LV function in a murine model of myocarditis by inhibition of monocyte–cardiomyocyte interaction. a Schematic representation of how atomic force microscopy based SCFS was performed. Detachment force ( F detach ) was assessed by repeated removal of monocytes adhering to cardiomyocytes using a leaf spring. Mouse cardiomyocytes used in SCFS were isolated from whole murine hearts. After removal, the murine hearts were connected to a Langendorff perfusion system and perfused with collagenase containing buffers up to 50 min and isolated cardiomyocytes were then cultured in laminin-coated cell-culture dishes. Mouse monocytes were isolated from healthy C57BL/6N mice using a monocyte isolation kit, stimulated with PMA to activate cells and induce Mac-1 conformational change towards the activated conformation. Afterwards, monocytes were treated with DARPins. The negative control was not stimulated with PMA, the positive control was stimulated with PMA but was not treated with DARPins. Cardiomyocytes were stimulated with mouse TNFα before SCFS ( b ) SCFS revealed significantly reduced F detach for stimulated monocytes and cardiomyocytes pre-incubated with F7 compared to the control DARPin ( n = total number of measurements of F detach : negative control n = 97, positive control n = 226, F7 n = 167, Control DARPin n = 162; data from at least five monocyte–cardiomyocyte pairs per treatment group. We aimed for at least 20 measurements of F detach from each pair, *** p < 0.001). c Immunohistochemistry was performed using an anti-CD68 monoclonal antibody (FA-11) or an isotype control followed by incubation with a secondary anti-rat-biotin-conjugated antibody. The Vectastain ® ABC Kit components (containing Avidin-HRP) were then added according to the manufacturer’s instructions. Images were acquired using an AxioImager M2 microscope and analysed using Zen Black 2.3 software. Significantly reduced numbers of macrophages ( brown colour ) were found for mice treated with F7 compared to treatment with the control DARPin and PBS ( n = 10 mice per treatment group, *** p < 0.001). p -values were calculated by one-way ANOVA, Scale bar = 50 µm. d, e Echocardiography was performed under isoflurane anesthesia on a heating/ECG pad. The heart rate was kept above 400/min. The left ventricular (LV) ejection fraction was measured in the parasternal long axis. Echocardiography revealed that mice treated with F7 did not suffer significant reduction in left ventricular ejection fraction (LVEF) on day 14 and day 50 compared to mice treated with the control DARPin or PBS in a murine model of myocarditis. Similar observations were made regarding cardiac output ( f ) and stroke volume ( g ). No differences between treatment groups were observed regarding the left ventricular enddiastolic volume (LVEDV) ( h ) and left ventricular endsystolic volume (LVESV) ( i ). Examples of echocardiographic loops from representative mice are provided online as Online Resource 13–15 ( n = 9 mice per treatment group, *** p < 0.001). p -values were calculated using one-way ANOVA. The error bars indicate SEM

Article Snippet: Immunohistochemistry was performed using an anti-CD68 monoclonal antibody (FA-11, 50 μl per slide, 1:500 dilution; 30 min, RT; Bio-Rad, USA) or an isotype control (Invitrogen, USA).

Techniques: Inhibition, Microscopy, Isolation, Cell Culture, Negative Control, Positive Control, Incubation, Control, Immunohistochemistry, Avidin-Biotin Assay, Software

Journal: Cell reports

Article Title: The Master Regulator protein BAZ2B can reprogram human hematopoietic lineage-committed progenitors into a multipotent state.

doi: 10.1016/j.celrep.2020.108474

Figure Lengend Snippet: (A) Schematic showing the experimental workflow of the first screen with human CD34+ hematopoietic stem and progenitor cells. (B-D) Human CD34+ cells infected with 8 MRs, or 8 combinations of 7 MRs were plated on methocult assays to count colonies of lineages (B) CFU-GEMM, (C) BFU-E and (D) CFU-GM based on morphology. N = 3 donors. Data represented as mean ± SD. (E) Sorted Lineage-GFP+ cells plated on LTC-IC assay followed by counting of colonies. N = 3 donors. Data represented as mean ± SD. Luc vs 8-MR: two-tailed paired t-test **P<0.01, *P<0.05. 8-MR vs 7-MR combinations: two-tailed unpaired t-test with unequal variance. (F-J) Overexpression of a combination of 5 MRs in human CD34+ cells. Lineage-GFP+ cells were FACS analyzed or characterized by in vitro colony assays. (F) Quantification of Lin-CD34+CD38− Stem Progenitors represented for N = 7 donors. (G) Quantification of MPPs represented for N = 7 donors. (H) Quantification of colonies from primary CFC assay N = 6 donors. Data represented as mean ± SD. (I) Quantification of colonies from secondary CFC assay N= 5 donors. Data represented as mean ± SD. (J) Quantification of colonies from LTC-IC CFC assay N = 5 donors. Data represented as mean ± SD. (K-M) Human CD34+ cells transduced with Luciferase or BAZ2B for in vitro analysis. (K) Quantification of the CD34+CD38− multipotent stem progenitor within Lineage-GFP+ cells from N = 5 donors (L) Quantification of colonies from primary CFC assay N = 5 donors. Data represented as mean ± SD. (M) Quantification of colonies from LTC-IC CFC assay N= 5 donors. Data represented as mean ± SD. (B-M) Two-tailed paired t-test, unless specified otherwise **P<0.01, *P<0.05.

Article Snippet: APC mouse Anti-human CD34 (Clone AC136) , Miltenyi , Order # 130-098-139.

Techniques: Infection, Two Tailed Test, Over Expression, In Vitro, Transduction, Luciferase

Journal: Cell reports

Article Title: The Master Regulator protein BAZ2B can reprogram human hematopoietic lineage-committed progenitors into a multipotent state.

doi: 10.1016/j.celrep.2020.108474

Figure Lengend Snippet: (A) Lin-CD34+CD38− cells were transduced with Luciferase or BAZ2B and intra-femoral transplanted into irradiated NSG mice (See STAR Methods, for details). (B-C) FACS analyses of the Lineage-GFP+ population after gene induction (B) Representative FACS plot showing the enrichment of CD34+CD45RA-CD90+ population in BAZ2B vs Luciferase-transduced cells. Percentage fractions for each gate normalized to Lineage-GFP+ fraction represented as mean ± SD from N = 5 donors. (C) Quantification of the CD34+CD45RA-CD90+ normalized to Lineage-GFP+ cells N = 5 donors. Two-tailed paired t-test **P<0.01, *P<0.05. (D-F) Bone marrow FACS analyses of the transplanted NSG mice after 12 weeks. (D) Representative FACS plot showing the enrichment of the engrafted human CD45+ cells in the BAZ2B vs Luciferase-transduced cells. Percentage fractions for hCD45 gate normalized to live cells represented as mean ± SD. CD33+ myeloid and CD19+ lymphoid gates show the lineage potential for the human CD45+ cells. Percentage fractions for hCD33/hCD19 gate normalized to hCD45+ cells represented as mean ± SD. N = 4 donors, 2-3 mice per donor. Bottom panel from top to bottom: basophils, eosinophils, neutrophils, monocytes and lymphocytes derived from human CD45+ cells stained with the Wright-giemsa method. Scale bar: 50 urn. (E) Quantification of engrafted human CD45+ cells within the total live cells of the mouse bone marrow. N= 4 donors; 2-3 mice transplanted per donor. (F) Mean bone marrow engraftment of human CD45+ cells. N = 4 donors. Two-tailed paired t-test **P<0.01, *P<0.05. (G) Quantification of engrafted human CD45+ cells in the spleen and peripheral blood of the transplanted NSG mice. N= 2 donors; 2-3 mice per donor. Two tailed unpaired t-test **P<0.01, *P<0.05. (H) Quantification of the CD33+ myeloid and CD19+ lymphoid fraction normalized to the total human CD45+ cells engrafted in the bone marrow, spleen and peripheral blood. Bone marrow N= 4 donors; 2-3 mice per donor. Spleen and peripheral blood N= 2 donors; 2-3 mice per donor. Two tailed unpaired t-test **P<0.01, *P<0.05.

Article Snippet: APC mouse Anti-human CD34 (Clone AC136) , Miltenyi , Order # 130-098-139.

Techniques: Transduction, Luciferase, Irradiation, Two Tailed Test, Derivative Assay, Staining

Journal: Cell reports

Article Title: The Master Regulator protein BAZ2B can reprogram human hematopoietic lineage-committed progenitors into a multipotent state.

doi: 10.1016/j.celrep.2020.108474

Figure Lengend Snippet: (A) Lineage-CD34+CD38+ committed progenitors were transduced with Luciferase or BAZ2B for in vitro analysis. (B) Quantification of the CD34+CD38− multipotent stem progenitor within Lineage-GFP+ cells from N = 4 donors. (C) Quantification of colonies from primary CFC assay N = 3 donors. Data represented as mean ± SD. (D) Quantification of colonies from LTC-IC CFC assay N= 3 donors. Data represented as mean ± SD. (B-D) Two-tailed paired t-test **P<0.01, *P<0.05. (E) UMAP visualization of the four reference populations FISCs, MPPs, MLPs and Lineage Committed Progenitors in VIPER space. (F) Top 1% of the cells of the four reference populations used for the random forest model, based on their differential density in the UMAP space. (G) Circular visualization of the model classification for Luciferase and BAZ2B samples. Samples closer to the circumference have a definite classification, and the plotting angle for each sample is determined by the weighted average of the model’s classification votes. (H) Heatmap of ATAC-Seq peaks showing unique SAZ2S-induced chromatin-accessible regions. (I) Distribution of BAZ2B-induced unique ATAC-Seq peaks from the transcription start sites. (J) Transcription factors with enriched motifs in the BAZ2B-induced nucleosome-free regions and a predicted VIPER activity > 1. (K) Ridgeline density plots showing VIPER-activity from single-cell RNA-Seq samples for 17 transcription factors (VIPER activity > 1) with enriched motifs in BAZ2B-induced nucleosome-free regions.

Article Snippet: APC mouse Anti-human CD34 (Clone AC136) , Miltenyi , Order # 130-098-139.

Techniques: Transduction, Luciferase, In Vitro, Two Tailed Test, Activity Assay, RNA Sequencing

Journal: Cell reports

Article Title: The Master Regulator protein BAZ2B can reprogram human hematopoietic lineage-committed progenitors into a multipotent state.

doi: 10.1016/j.celrep.2020.108474

Figure Lengend Snippet: (A) Lin-CD34+CD38+ committed progenitors were sorted and transduced with Luciferase or BAZ2B followed by NSG mice transplantation (See STAR Methods, for details). Human hematopoietic engraftment was analyzed after 16 weeks. (B) FACS plot showing engraftment of human CD45+ hematopoietic cells in the mouse bone marrow upon expression of BAZ2B or Luciferase in Lin-CD34+CD38+ committed progenitors. Percentage fractions for hCD45 gate normalized to live cells represented as mean ± SD. CD33+ myeloid and CD19+ lymphoid gates show the lineage potential for the human CD45+ cells. Percentage fractions for hCD33/hCD19 gate normalized to hCD45+ cells represented as mean ± SD. N = 3 donors with 2-3 mice per donor. (C) Quantification of the engraftment of human CD45+ cells with respect to total live cells in the bone marrow, spleen and peripheral blood. Two-tailed unpaired t-test. (D) Quantification of the CD33+ myeloid and CD19+ lymphoid cells with respect to the total human CD45+ hematopoietic cells from Luciferase or BAZ2B-induced multipotent hematopoietic progenitors.

Article Snippet: APC mouse Anti-human CD34 (Clone AC136) , Miltenyi , Order # 130-098-139.

Techniques: Transduction, Luciferase, Transplantation Assay, Expressing, Two Tailed Test

Journal: Cell reports

Article Title: The Master Regulator protein BAZ2B can reprogram human hematopoietic lineage-committed progenitors into a multipotent state.

doi: 10.1016/j.celrep.2020.108474

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: APC mouse Anti-human CD34 (Clone AC136) , Miltenyi , Order # 130-098-139.

Techniques: Blocking Assay, Plasmid Preparation, Virus, Recombinant, Labeling, Transfection, Red Blood Cell Lysis, Gene Expression, Transformation Assay, Mutagenesis, PCR Cloning, Software, Generated, Biomarker Discovery

Journal: iScience

Article Title: Elastic properties of leukemic cells linked to maturation stage and integrin activation

doi: 10.1016/j.isci.2025.112150

Figure Lengend Snippet:

Article Snippet: Human monoclonal CD34-PE , Miltenyi Biotec , Cat#130-120-520; RRID: AB_2811343.

Techniques: Recombinant, Sequencing, Software