Journal: STAR Protocols

Article Title: Protocol for large-scale, high-yield, high-purity extracellular vesicle purification from human plasma

doi: 10.1016/j.xpro.2026.104428

Figure Lengend Snippet: Fusion assay demonstrating the uptake of EVs from different fractions by cells EV populations were stained with DiI dye, then incubated with hTERT-HUVEC cells for 16 h. Cells were then fixed and DNA was stained with DAPI. Images taken at 20X and 100X magnification. Scale bar=10 μm

Article Snippet: hTERT-HUVEC (Human Telomerase Reverse Transcriptase (hTERT), Human umbilical vein endothelial cells (HUVEC)) , ATCC , CRL-4053 TM.

Techniques: Single Vesicle Fusion Assay, Staining, Incubation

Journal: Nature Biomedical Engineering

Article Title: Bioengineered immunocompetent preclinical trial-on-chip tool enables screening of CAR T cell therapy for leukaemia

doi: 10.1038/s41551-025-01428-2

Figure Lengend Snippet: a , The compartmentalized bone marrow chip (middle) was populated with human bone marrow cells (right) to replicate the in vivo counterpart (left). The whole scanning of the leukaemia bone marrow chip (bottom right) with central sinus (RFP-HUVECs in red), medullary cavity and endosteum (DiD-labelled osteoblasts in yellow). The 3D view of perivascular niche (top right) in bone marrow with hematopoietic cells (CD45 + in red), vascular cells (CD31 + in orange) and nuclei in blue (DAPI). Representative images were from one of the three technical replicates with similar results ( n = 3). Schematic (left part) was adapted from smart.servier.com . Schematic (right part) was created in BioRender (C.M. (2025), https://BioRender.com/wlbhoxu ), b , scRNA-seq profiling of the bone marrow cellularity on-chip, highlighting the presence of most hematopoietic (immune) and non-hematopoietic (bone marrow stroma) cells. c , scRNA-seq profiling of primary bone marrow mononuclear cells, which was comparatively mapped to that of on-chip bone marrow niche. d , The cellularity where B cell populations were excluded to reveal bone marrow niche immune populations. In addition to the bone marrow stromal cell populations seeded to build the stromal environment, macrophage, basophil/mast cells and megakaryocyte/platelets were generated on-chip during culture. e , The presence of stromal compartment. HUVECs in red (RFP), Reh B-ALL cells in green (GFP) and mesenchymal cells in purple (DiD labelling). The white arrowheads indicate Reh B-ALL cells. f , The presence of hematopoietic cells. Lymphoid (left): CD8 + T cells in cyan and CD4 + T cells in red. The top white arrowheads indicate CD4 + T cells, and the bottom arrowheads indicates CD8 + T cells. Myeloid (right): monocyte (CD14 + ) in cyan, HUVECs (CD31 + ) in green and Reh B-ALL cells (CD19 + ) in red. The white arrowheads indicate monocytes. g , The deposition of ECMs such as laminin (green) and collagen IV (purple). Reh B-ALL cells in red. The white arrowheads indicate Reh B-ALL cells. Representative images were from one of the three technical replicates with similar results ( n = 3).

Article Snippet: Primary human umbilical vein endothelial cells (HUVECs; catalogue number C2519A, Lonza), VE-CAD-GFP-expressing HUVECs (catalogue number cAP-0001VECAD-GFP, Angio-Proteomie) and RFP-expressing HUVECs (catalogue number cAP-0001RFP, Angio-Proteomie) were cultured in Endothelial Cell Growth Medium-2 BulletKit (EGM-2; catalogue number CC-3162, Lonza) and used within passage 5.

Techniques: In Vivo, Generated

Journal: Nature communications

Article Title: Stress-induced RNA-chromatin interactions promote endothelial dysfunction.

doi: 10.1038/s41467-020-18957-w

Figure Lengend Snippet: Fig. 1 High glucose and TNFα induce a profound gene expression and phenotypic change. a HUVECs were treated in biological duplicates as Day 0: 25 mM mannitol as normal glucose and osmolarity control (NM); Day 3: combined treatment consisting 25 mM D-glucose and 5 ng/mL TNFα (H + T) for 3 days; and Day 7: H + T treatment for 7 days. Each group of treated cells was subjected to single-cell RNA-seq (scRNA-seq), Hi-C, and iMARGI assays. b t-SNE plot of scRNA-seq (4000–15,000 cells per sample) showed clear separation by treatment condition into three distinct clusters. c Principal component analysis of scRNA-seq data: single cells are plotted in the first two PC space and are labeled in red (Day 0, i.e., NM), green (Day 3, i.e., 3-day H + T treatment), and blue (Day 7, i.e., 7-day H + T treatment). d Expression heatmap (z-scaled) of top DE genes in single ECs grouped into functional pathways. Cells were ordered by increasing SERPINE1 expression (per each sample separately) and binned per 100 cells for the analysis. A total of 269 bins in Day 0, 177 bins in Day 3, and 148 bins in Day 7. e t-SNE plots of the expression level of selected genes in each single cell across the time course. The RNA levels are represented by log-normalized unique molecular identifier counts. f mRNA levels of eNOS and α-SMA in NM vs. H + T-treated HUVECs and cells untreated (NT) or treated with TGF-β (10 ng/mL) and IL-1β (5 ng/mL; T + I) for 3 or 7 days. The respective control was set as 1. Relative eNOS level: data represent mean ± SEM from five independent experiments; relative α-SMA level in H + T treatment: data represent mean ± SEM from seven independent experiments; relative α-SMA level in T + I treatment: data represent mean ± SEM from four independent experiments. *P = 0.0067, 0.0087, 0.0057, and 0.0017 from left to right based on ANOVA with Bonferroni as post hoc test. g Cell morphology under bright field (BF), immunofluorescent staining of α-SMA, and VE-cadherin (VE-cad), phalloidin staining of cytoskeleton, and DRAQ5 (DRAQ) staining of the nuclei. Representative images from five independent experiments are shown. Scale bar of BF = 100 µm; scale bars of (immuno)fluorescent staining = 50 µm. Source data are provided as a Source data file.

Article Snippet: Plasmid transfection was performed using the CytofectTM HUVEC Transfection kit (Cell Applications) following the manufacturer’s protocol in 6-well or 12-well plates.

Techniques: Gene Expression, Control, RNA Sequencing, Hi-C, Labeling, Expressing, Functional Assay, Staining

Journal: Nature communications

Article Title: Stress-induced RNA-chromatin interactions promote endothelial dysfunction.

doi: 10.1038/s41467-020-18957-w

Figure Lengend Snippet: Fig. 2 Overview of time-course Hi-C and iMARGI data. a, b Proportions of intrachromosomal (yellow) and interchromosomal read pairs (blue) in Hi-C (a) and iMARGI data (b) at the three time points (columns). c An example of interchromosomal iMARGI read pairs mapped to chromosome 2 near LINC00607 (left) and chromosome 7 near SERPINE1 (right). The RNA end (pink) and the DNA end (green) of each read pair is linked by a horizontal line. d Examples of overlapping iMARGI read pairs on a contact matrix from the RNA end (rows) to the DNA end (columns) with SEs (marked in light blue and in SE tracks) in control (Day 0) ECs. Genome region: chr1:75,000,0000–chr1:125,000,000. Resolution = 200 kb. e Proportions of iMARGI read pairs with the RNA ends (pink) or the DNA ends (green) in Day 0 (Ctrl) and Days 3 and 7 (H + T) ECs mapped to HUVEC SEs. Dotted line: the relative size of HUVEC SEs compared to the size of the genome. Source data are provided as a Source data file.

Article Snippet: Plasmid transfection was performed using the CytofectTM HUVEC Transfection kit (Cell Applications) following the manufacturer’s protocol in 6-well or 12-well plates.

Techniques: Hi-C, Control

Journal: Nature communications

Article Title: Stress-induced RNA-chromatin interactions promote endothelial dysfunction.

doi: 10.1038/s41467-020-18957-w

Figure Lengend Snippet: Fig. 4 Inhibition of LINC00607 attenuates SERPINE1 induction and EC dysfunction. a Illustration of LINC00607 genomic locus and gene structure and LNA GapmeRs targeting of LINC00607 RNA. b HUVECs were transfected with scramble (scr) or two LNAs targeting LINC00607. LINC00607 RNA and SERPINE1 mRNA levels were quantified. Data represent mean ± SEM from seven independent experiments. c qPCR of LINC00607 in subcellular fractionations of HUVECs transfected with scr, LNA1, or LNA2. Data represent mean ± SEM from four independent experiments. d RNA-seq was performed with cells transfected as in b in biological replicates. Heatmap is plotted based on z-scaled log-transformed gene expression levels. e, f ECs transfected with scr or LNA1 and then treated by H + T were used in e monocyte adhesion assay and in f SA-β-gal assay. In e, the number of attached monocytes to ECs were quantified. Data represent mean ± SEM from eight independent experiments performed with peripheral blood-derived monocytes from four individual donors. Representative images show the attachment of fluorescently labeled peripheral blood-derived monocytes to ECs for experiments performed with monocytes from three different donors. In f, ECs with positive β-gal staining were quantified. The positively stained cell number in scr control was set to 100 (%). f Data represent mean ± SEM from four independent experiments respectively. Scale bar = 200 μm. * denotes p = 0.0289, 0.0013, 0.001, 0.0001, 0.0025, and 0.024 from left to right (in b) and p = 0.0023, 0.0079, and 0.0249 from left to right (in c) between indicated groups based on ANOVA followed by Bonferroni post hoc test (in b and c); p = 0.0039 (in e) and 0.0014 (in f), as compared to scr group based on two-tailed paired t test (in e and f). Source data are provided as a Source data file.

Article Snippet: Plasmid transfection was performed using the CytofectTM HUVEC Transfection kit (Cell Applications) following the manufacturer’s protocol in 6-well or 12-well plates.

Techniques: Inhibition, Transfection, RNA Sequencing, Transformation Assay, Gene Expression, Cell Adhesion Assay, Derivative Assay, Labeling, Staining, Control, Two Tailed Test