Journal: Journal of Biological Chemistry

Article Title: Critical Role for GATA3 in Mediating Tie2 Expression and Function in Large Vessel Endothelial Cells

doi: 10.1074/jbc.m109.041145

Figure Lengend Snippet: FIGURE 6. siRNA-mediated knockdown of GATA3 attenuates Ang-1-induced AKT phosphorylation, migration, tube formation, and cell survival in primary human endothelial cells. A, left, HUVEC were transfected with si-control (lanes 1 and 3) or si-GATA3 (lanes 2 and 4) for 2 days, serum-starved for 18 h, and treated in the absence (lanes 1 and 2) or presence (lanes 3 and 4) of Ang-1 for 10 min. Samples were immunoprecipitated with anti-AKT antibody and immunoblotted with phospho-specific AKT antibody. The membrane was stripped and re-probed for total AKT. Right, quantitation of phospho-AKT levels relative to si-control-transfected cells treated in the absence or presence of Ang-1. Data are expressed as mean S.D. from three independent experiments. #, p 0.0001; *, p 0.0001 compared with without Ang-1 control and control plus Ang-1, respectively N.S., nonsignificant. B, modified Boyden chamber assay of HUVEC transfected with si-control (Control) or si-GATA3 (GATA3) and treated in the presence or absence of Ang-1 or VEGF. Shown are the mean S.D. of migrated cells quantified by cell image analyzer in three independent experiments. #, p 0.01; *, p 0.001 compared with minus control and control plus Ang-1, respectively. N.S., nonsignificant. C, tube formation assay of si-control- or si-GATA3-transfected HUVEC plated on collagen gel and overlaid with fibroblast-containing collagen with or without Ang-1. Capillary-like tube morphology was observed under the fluorescent microscopy. Bar, 500 m. Quanti- fication of the tube length (bar graph) was calculated using the cell image analyzer from four arbitral optical images per experiment. Data are expressed as mean S.D. from three independent experiments. #, p 0.005; *, p 0.001 compared with without Ang-1 control and control plus Ang-1, respectively. N.S., nonsignificant. D, HUVEC were incubated with EBM-2 0.5% FBS for 18 h and then further incubated with Dulbecco’s modified Eagle’s medium 0.5% FBS (Starvation) for 24 h in the presence or absence of Ang-1. Cells were harvested and stained with annexin V-fluorescein isothiocyanate. Count of annexin V-positive cells were performed by flow cytometry. Data are presented as mean S.D. from six independent experiments. *, p 0.0001 compared with starvation alone. N.S., nonsignificant.

Article Snippet: Human skin fibroblast (Clonetics) and COS-7 cells (ATCC CRL-1651) were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% heat-inactivated fetal bovine serum (FBS).

Techniques: Knockdown, Phospho-proteomics, Migration, Transfection, Control, Immunoprecipitation, Membrane, Quantitation Assay, Modification, Boyden Chamber Assay, Tube Formation Assay, Microscopy, Incubation, Staining, Flow Cytometry

Journal: bioRxiv

Article Title: SenCat: Cataloging human cell senescence through multiomic profiling of multiple senescent primary cell types

doi: 10.64898/2026.02.05.703986

Figure Lengend Snippet: (A) Overview of the strategy used to identify core senescence markers using ML. Linear regression models were trained on transcriptomic and proteomic datasets from SenCat, and features consistently predictive across all models were assigned average coefficients (weights). (B) The resulting weighted transcriptomic (ML T SENCAT) and proteomic (ML P SENCAT) sets define a senescence score derived from a linear combination of marker expression levels and their respective ML-derived weights. (C) Heatmaps of traditional senescence markers (p16, p21, IL6, GDF15, LMNB1) and ML-derived transcriptomic senescence scores (ML T SENCAT) across 14 different human cell types subjected to senescence-inducing treatments (CTIS, IRIS, OSIS, OIS) or controls (P or EV) from the transcriptomic data. (D) Equivalent heatmaps displaying canonical senescence markers and ML-derived proteomic senescence scores (ML P SENCAT) as in (C), but obtained from the proteomic data. (E) Validation of ML-derived senescence scores on independent transcriptomic (top heatmap) and proteomic (bottom heatmap) datasets (IMR-90 lung fibroblasts external to the SenCat dataset). Quiescent (QUI), proliferating (P), and senescent (SEN) states were analyzed in these datasets. See also Figures S8,9 .

Article Snippet: WI-38 lung fibroblasts (obtained from the NIGMS Human Genetic Cell Repository, Coriell Institute for Medical Research; repository ID AG06814-N) and BJ skin fibroblasts (ATCC, CRL-2522) were cultured in DMEM (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (FBS).

Techniques: Derivative Assay, Marker, Expressing, Biomarker Discovery

Journal: bioRxiv

Article Title: SenCat: Cataloging human cell senescence through multiomic profiling of multiple senescent primary cell types

doi: 10.64898/2026.02.05.703986

Figure Lengend Snippet: (A) Schematic of the experimental design for induction of systemic senescence with doxorubicin and sample collection across time points. (B) Cluster identities assigned to doxorubicin-treated lung samples profiled by snRNA-seq. (C) UMAP projection of lung samples colored by cluster identity. (D) UMAP projections of senescent cells in lung samples across time points. (E) Bar plot showing the number of senescent cells from lung per cluster and condition. (F,G) GSEA plots of gene set association scores for p53, EMT, NF-κB, Apoptosis, and Hypoxia hallmark pathways (F) and senescence signature lists SenePy, SeneSig, SenMayo, hUSI (G); in fibroblast, epithelial, and endothelial clusters on Day 6. (H) Schematic of the analysis pipeline applied to published aging lung snRNA-seq datasets. (I) UMAP projection of aging lung samples showing senescent cell distribution by age group. (J) Schematic of ligand-receptor inference analysis between senescent fibroblasts and non-senescent epithelial cells. (K) Chord diagram displaying ligand-receptor interactions between senescent fibroblasts (sender cells) and non-senescent epithelial cells (receiver cells) inferred through CellPhoneDB. (L) Dot plot showing expression of the specified ligands across fibroblast clusters at 23 months of age. (M) Schematic and GSEA plot explaining and displaying TGFβ signaling pathway increase during aging in non-senescent epithelial cells at 23 months versus 3 months. See also Figures S11-13 .

Article Snippet: WI-38 lung fibroblasts (obtained from the NIGMS Human Genetic Cell Repository, Coriell Institute for Medical Research; repository ID AG06814-N) and BJ skin fibroblasts (ATCC, CRL-2522) were cultured in DMEM (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (FBS).

Techniques: Expressing

Journal: The Journal of biological chemistry

Article Title: The novel type II prolyl 4-hydroxylase is the main enzyme form in chondrocytes and capillary endothelial cells, whereas the type I enzyme predominates in most cells.

doi: 10.1074/jbc.273.11.5989

Figure Lengend Snippet: FIG. 1. Contributions of the two isoenzymes to total prolyl 4-hydroxylase activity in cultured cells. Black columns represent type I and hatched columns type II as percentages of total prolyl 4-hydroxylase activity in logarithmic phase (L) and confluent (C) cells. The cell lines studied are adult human skin fibroblasts (AHSF), fetal human skin fibroblasts (FHSF), mouse embryonal fibroblasts (3T3), mouse chondrocytes (MC), human embryonic lung fibroblasts (WI-38), simian virus 40-transformed WI-38 cells (Va-13), and human embryo- nal rhabdomyosarcoma cells (RD). The results are given as the means from two to six separate experiments and their S.D. values or ranges (in the cases of WI-38 cells and logarithmic phase fetal human skin fibro- blasts and Va-13 cells with n 5 2).

Article Snippet: Cell Cultures—The cell lines used here were fetal human skin fibroblasts (ATCC CRL-1475), adult human skin fibroblasts (ATCC CRL1987), human embryonic lung fibroblasts (WI-38, ATCC CCL-75), simian virus 40-transformed WI-38 cells (Va13/WI-38, ATCC CCL 75.1), human embryonal rhabdomyosarcoma cells (RD, ATCC CCL 136), mouse embryonal fibroblasts (3T3, ATCC CCL-92), and mouse chondrocytes, which were obtained from the heads of the ribs of 7-day-old mice.

Techniques: Activity Assay, Cell Culture, Virus, Transformation Assay

Journal: The Journal of biological chemistry

Article Title: The novel type II prolyl 4-hydroxylase is the main enzyme form in chondrocytes and capillary endothelial cells, whereas the type I enzyme predominates in most cells.

doi: 10.1074/jbc.273.11.5989

Figure Lengend Snippet: FIG. 3. Immunofluorescence staining of samples from a fetal human foot with antibodies to prolyl 4-hydroxylase a(I) subunit (A, C, E, and G) and a(II) subunit (B, D, F, and H). A and B, undifferentiated mesenchymal cells are stained strongly with the a(I) antibody (A) but show only a very weak staining with the a(II) antibody (B). Capillaries (arrows) around the mesenchymal cells show strong immunofluorescence with the a(II) antibody (B). C and D, chondrocytes show intensive staining with both a(I) (C) and a(II) (D) antibodies. The synovial cells covering the joints stain strongly with the a(I) antibody (C) and much less so with the a(II) antibody (D). E and F, a strong signal with the a(I) antibody is seen in osteoblasts (arrows) (E), while a weaker but clear signal is seen with the a(II) antibody (F). G, epidermal cells (ep) and dermal (d) fibroblasts show strong staining with the a(I) antibody, whereas the dermal capillaries (arrows) are negative. H, the endothelial cells of the capillaries demonstrate high positivity for the a(II) antibody (arrows), whereas the epidermal cells (ep) and dermal (d) fibroblasts give no signal. The basement membrane below the epider- mis shows a weak staining. Magnification: 3 100, except 3 160 in G.

Article Snippet: Cell Cultures—The cell lines used here were fetal human skin fibroblasts (ATCC CRL-1475), adult human skin fibroblasts (ATCC CRL1987), human embryonic lung fibroblasts (WI-38, ATCC CCL-75), simian virus 40-transformed WI-38 cells (Va13/WI-38, ATCC CCL 75.1), human embryonal rhabdomyosarcoma cells (RD, ATCC CCL 136), mouse embryonal fibroblasts (3T3, ATCC CCL-92), and mouse chondrocytes, which were obtained from the heads of the ribs of 7-day-old mice.

Techniques: Immunofluorescence, Staining, Membrane