Journal: Nature Communications

Article Title: PRC2-AgeIndex as a universal biomarker of aging and rejuvenation

doi: 10.1038/s41467-024-50098-2

Figure Lengend Snippet: a Average DNAm levels at CpGs across the whole genome (left panel), at LMRs ranked by the level of their PRC2 binding in hESCs (center panel) and within high-PRC2 regions (right panel) from 8 different tumor and normal samples. Data were obtained from TCGA WGBS datasets, (see Supplementary Data ). Error bars on the right show 95% confidence intervals for average DNAm across high-PRC2 LMRs for each sample. b Average DNAm levels at CpGs across the whole genome (left panel) and at LMRs ranked by the level of their PRC2 binding in hESCs (right panel) from young vs old human oligodendrocytes. (WGBS dataset, GSE107729, n = 6). c Average DNAm levels at CpGs across the whole genome (left panel) and at LMRs ranked by the level of their PRC2 binding in hESCs (middle panel), correlation between average DNAm at high-PRC2 LMRs and the number of passages (right panel, shaded area of line plot represents 95% CI) in in vitro cultured fibroblasts (GSE79798, n = 5). High-PRC2 LMRs are highlighted with dotted red boxes.

Article Snippet: Neonatal fibroblasts were purchased from Cell Applications (#106-05n) and old fibroblasts were isolated from skin tissue collected from deceased healthy individuals.

Techniques: Binding Assay, In Vitro, Cell Culture

Journal: Nature Communications

Article Title: PRC2-AgeIndex as a universal biomarker of aging and rejuvenation

doi: 10.1038/s41467-024-50098-2

Figure Lengend Snippet: a Average DNAm levels of neonatal and old passaged fibroblasts, and CD4 T-cells, at CpGs across the whole genome (left panel) and at the LMRs ranked by the level of EZH2-binding data of the same respective tissue (middle panels). Bottom panels show heatmaps of LMR rank number, ordered by EZH2 binding in their respective tissue (top heatmap) and in hESCs (bottom heatmap). Heatmaps are colored by EZH2 binding in the same respective tissue, i.e. purple/orange represents high and low-ranked neonatal/old LMRs ordered by neonatal/old fibroblasts PRC2 binding, respectively, and red/blue represent high and low-ranked CD4 T-cells LMRs ordered by CD4 T-cells PRC2 binding, respectively. Right panel shows the correlation of mean methylation of high-PRC2 LMRs against age or passage number. b Average methylation levels at LMRs ranked by PRC2 binding in hESCs for neonatal fibroblasts (left panels) and old fibroblasts (right panels). c Average DNAm levels of LMRs calculated from neonatal and old samples merged (all passages), ranked by PRC2 binding in hESCs (left panel) and correlation between methylation and age for high-PRC2 LMRs of both neonatal and old in vitro passaged fibroblasts (right panel). d Heatmap of normalized read density of the high-PRC2 neonatal/old LMRs in neonatal and old fibroblasts (passage 2). WGBS Neonatal and old fibroblasts were generated by our lab (GSE253987, n = 3 for neonatal samples (one donor) and n = 3 for old samples (one donor)), CD4 T-cell samples are the same as used in Fig. (6 samples 18–86 years old, GSE79798 and 2 samples 0 and 103 years old, GSE31263). ChIP data for fibroblast and CD4 T-cells were generated by our lab (GSE253987, two donors pooled at passage 2 for neonatal fibroblasts, three donors pooled at passage 2 for old fibroblasts, three donors pooled for CD4 T-cells). High-PRC2 LMRs are highlighted with dotted red boxes. Line plots with >3 samples plotted have a shaded area representing 95% CI.

Article Snippet: Neonatal fibroblasts were purchased from Cell Applications (#106-05n) and old fibroblasts were isolated from skin tissue collected from deceased healthy individuals.

Techniques: Binding Assay, Methylation, In Vitro, Generated

Journal: Biology

Article Title: Chemical Composition, Antioxidant Capacity, and Anticancerous Effects against Human Lung Cancer Cells of a Terpenoid-Rich Fraction of Inula viscosa

doi: 10.3390/biology13090687

Figure Lengend Snippet: IVL DCM decreased the viability of A549 cells. ( A ) MTT assay was used to measure the viability of A549 and HDFn cells treated with the indicated concentrations of IVL DCM for 24, 48, or 72 h. Data represents the mean ± SEM of the percent viability of treated cells compared to vehicle-treated cells. Data are the mean of three independent experiments ( n = 3). *** p < 0.001, **** p < 0.0001. ( B ) A549 cells treated with the indicated concentrations of IVL DCM for 24 h were stained with DAPI nuclear stain. DAPI fluorescence was imaged at 20X magnification using a BioTek Cytation 5 reader. ( C ) A549 cells were treated with the indicated concentrations of IVL DCM for 24 h and then stained with crystal violet. The micrographs represent stained cells imaged at 20X magnification by light microscopy using the Invitrogen EVOS ® FL Cell Imaging System.

Article Snippet: A549 human lung adenocarcinoma cells, the most common subtype of NSCLC, which accounts for approximately 85% of lung cancer cases [ ], human normal neonatal fibroblasts (HDFn), SK-OV-3 (human ovarian cancer), MCF-7 (human breast cancer), MDA-MB-231 (human breast cancer), HepG2 (human liver cancer), and HCT116 (human colorectal cancer) cells were obtained from ATCC and cultured at 37 °C and 5% CO 2 in a humidified incubator.

Techniques: MTT Assay, Staining, Fluorescence, Light Microscopy, Imaging

Journal: ACS Applied Materials & Interfaces

Article Title: Zinc-Releasing Fibrous Scaffolds Modulate Fibroblast, Endothelial, and Macrophage Interactions for Vascularized Tissue Engineering

doi: 10.1021/acsami.5c16589

Figure Lengend Snippet: Expression of different proteins after transformation of the fibroblasts into myofibroblasts and differentiated HDFn cells. Left and middle panel: immunofluorescence images of intracellular vimentin (red) and α-smooth muscle actin (α-SMA) (green) expressed by HDFn cells after incubation for 7 and 14 days on different fibrous scaffolds labeled using immunocytochemistry. Scale bar = 50 μm. (A and B) and (C and D); the fluorescence intensity of the protein markers, vimentin, and α-SMA for days 7 and 14, respectively, was analyzed using ImageJ software. Quantification of growth factor (E) bFGF and (F) VEGF concentration in cell-cultured media on predetermined days (1, 3, 5, and 7). One-way ANOVA with Tukey’s post hoc test was used to calculate statistical significance, and data were expressed as the mean ± SD; n = 4 per group for the cell viability test (where * p < 0.05, ** p < 0.01, and *** p < 0.001).

Article Snippet: Primary dermal fibroblast normal; human, neonatal (HDFn, PCS, 201-010TM), fibroblast basal medium (PCS, 201–030), fibroblast growth kit-serum free (PCS, 201–040), streptomycin-amphotericin B solution (PCS, 999–002), trypsin–EDTA for primary cells (PCS, 999–003) and trypsin neutralizing solution (PCS, 999–004), HUVEC (CRL-1730TM), F–12K medium (30–2004), and fetal bovine serum (FBS, 30–2020) were purchased from ATCC (Manassas, VA, USA).

Techniques: Expressing, Transformation Assay, Immunofluorescence, Incubation, Labeling, Immunocytochemistry, Fluorescence, Software, Concentration Assay, Cell Culture