Journal: Cancers

Article Title: Exploring Spatial Heterogeneity of Immune Cells in Nasopharyngeal Cancer.

doi: 10.3390/cancers15072165

Figure Lengend Snippet: Figure 1. Differential expression profiles in CD45+ segments from ‘immune-rich cancer cell islets’ and ‘surrounding stromal leukocyte’ regions in NPC. (a) AOIs were generated based on cell expression of the morphological markers CD45 (red), PanCK (cyan), and CD8 (magenta) from the ROIs, and the collected oligonucleotides were quantified using the GeoMx® DSP system. (b) Biplot principal component analysis showing ROI segments (AOIs) as well as protein markers on the first and second components from ‘immune-rich cancer cell islets’ and ‘surrounding stromal leukocyte’ regions. (c) Heatmap demonstrating DE proteins between ‘immune-rich cancer cell islets’ and ‘surrounding stromal leukocyte’ regions (Mann–Whitney test, p-value < 0.05). (d) Twenty DE proteins’ correlation map (Pearson’s correlation, significance taken at |r| > 0.7, p-value < 0.05).

Article Snippet: Glass slides containing 5 μm sections of the FFPE TMAs were stained with DNA stain (SYTOTM 13 Green Fluorescent Nucleic Acid Stain, Invitrogen, Waltham, MA, USA), fluorescently labelled antibodies against CD8 (CD8-AF666/Cy5, clone OTI3H6, Origene, Rockville, MD, USA), PanCK (pan-Cytokeratin-AF568/Cy3, clone AE1 + AE3, Novus Biologicals, Littleton, CO, USA), and CD45 (CD45-AF615/Texas Red, clone 2B11 + PD7/26, Novus Biologicals, Eaglewood, CO, USA) (Figure S1 and Table 1).

Techniques: Quantitative Proteomics, Generated, Expressing, MANN-WHITNEY

Journal: bioRxiv

Article Title: Vascular endothelial growth factor-D improves lung vascular integrity during acute lung injury

doi: 10.1101/2024.12.16.628787

Figure Lengend Snippet: A) NICHES analysis of AFs, mesothelial cells, pericytes, gCap, and aCap in human microvascular niche yields a quantitative cell-cell signaling atlas of AF-aCap, AF-gCap, Mesothelial-aCap, Mesothelial-gCap, Pericyte-aCap, and Pericyte-gCap visualized by low-dimensional UMAP embedding. B) FeaturePlot of top differentially expressed L/R pairs ANGPT1 - TEK , SLIT2 - ROBO4 , VEGFD - KDR , BMP5-BMPR2 , ADM - RAMP2 , WNT5A - FZD6 , PTN - RACK1 , OXT - EDNRB , and ADCYAP1 - VIPR1 from NICHES analysis C) Top 10 differentially expressed L/R pairs between different cell-cell interaction signals processed through NICHES and plotted in DoHeatmap. D) Immunostaining of representative L/R pairs from AF to microvascular endothelial cells, including SLIT2 - ROBO4 , ADM - RAMP2 , BMP5 - BMPR2 , and VEGFD - VEGFR2 in human lung section. ITGA8 is a marker for AF; PRX is a marker for microvascular endothelial cells. Scale bar 20 μm.

Article Snippet: Tissue samples were then stained with antibodies: SLIT2 (Thermo Fisher Scientific, # PA5-31133), ROBO4 (R&D Systems, # AF2366), ADM (Bioss, # BS-0007R), RAMP2 (Santa Cruz Biotechnology, # sc-365240), BMP5 (Thermo Fisher Scientific, # PA5-78878), BMPR2 (Thermo Fisher Scientific, # MA5-15827), VEGFD (Thermo Fisher Scientific, # PA5-13300), VEGFR2 (Santa Cruz Biotechnology, # sc-6251), ITGA8 (Novus Biologicals, # AF4076), PRX (Novus Biologicals, # NBP1-89598) overnight at 4 °C followed by staining with secondary antibodies (RT, 1 hour) and DAPI (RT, 5 min).

Techniques: Immunostaining, Marker

Journal: bioRxiv

Article Title: Vascular endothelial growth factor-D improves lung vascular integrity during acute lung injury

doi: 10.1101/2024.12.16.628787

Figure Lengend Snippet: A) NICHES analysis of AFs, mesothelial cells, pericytes, gCap, and aCap in human microvascular niche yields a quantitative cell-cell signaling atlas of AF-aCap, AF-gCap, Mesothelial-aCap, Mesothelial-gCap, Pericyte-aCap, and Pericyte-gCap visualized by low-dimensional UMAP embedding. B) FeaturePlot of top differentially expressed L/R pairs ANGPT1 - TEK , SLIT2 - ROBO4 , VEGFD - KDR , BMP5-BMPR2 , ADM - RAMP2 , WNT5A - FZD6 , PTN - RACK1 , OXT - EDNRB , and ADCYAP1 - VIPR1 from NICHES analysis C) Top 10 differentially expressed L/R pairs between different cell-cell interaction signals processed through NICHES and plotted in DoHeatmap. D) Immunostaining of representative L/R pairs from AF to microvascular endothelial cells, including SLIT2 - ROBO4 , ADM - RAMP2 , BMP5 - BMPR2 , and VEGFD - VEGFR2 in human lung section. ITGA8 is a marker for AF; PRX is a marker for microvascular endothelial cells. Scale bar 20 μm.

Article Snippet: Tissue samples were then stained with antibodies: SLIT2 (Thermo Fisher Scientific, # PA5-31133), ROBO4 (R&D Systems, # AF2366), ADM (Bioss, # BS-0007R), RAMP2 (Santa Cruz Biotechnology, # sc-365240), BMP5 (Thermo Fisher Scientific, # PA5-78878), BMPR2 (Thermo Fisher Scientific, # MA5-15827), VEGFD (Thermo Fisher Scientific, # PA5-13300), VEGFR2 (Santa Cruz Biotechnology, # sc-6251), ITGA8 (Novus Biologicals, # AF4076), PRX (Novus Biologicals, # NBP1-89598) overnight at 4 °C followed by staining with secondary antibodies (RT, 1 hour) and DAPI (RT, 5 min).

Techniques: Immunostaining, Marker

Journal: bioRxiv

Article Title: Vascular endothelial growth factor-D improves lung vascular integrity during acute lung injury

doi: 10.1101/2024.12.16.628787

Figure Lengend Snippet: B) HLMVECs were cultured in an ECIS plate for 48 hours to reach the plateau, followed by SU5416 (5 μM) treatment. After another 1 hour, cells were treated with VEGF-D (2 μg/mL). The electrical resistance was monitored in real-time for 10 hours after drug treatment. Cells without drug treatment were used as controls. B) HLMVECs were transfected with VEGFR2 siRNA or control siRNA, then replating into ECIS plate. After reaching a plateau, cells were treated with VEGF-D or PBS. Electrical resistances were monitored. C) HLMVECs were transfected with VEGFR2, and control siRNA followed by re-seeding into a new plate. Cells were treated with VEGF-D or PBS for 45 minutes, followed by a TNF-α (1 ng/mL) challenge for another 5.5 hours. The protein expression of ICAM-1, IκBα, and NFκB in all conditions was determined through western blot. D-E) control ( VEGFR2 fl/fl ) or VEGFR2 iECKO at age of the 6 – 8 weeks were injected with tamoxifen 5 times on alternative days. After resting for 30 – 32 days after the last injection, mice were challenged with intratracheal injection of LPS (0.25 mg/kg) with concurrent treatment with VEGF-D (225 μg/kg). After 18 hours of injury, the total number of WBCs were counted in the BAL fluid across different experimental conditions. G) The H/E staining of lungs from control ( VEGFR2 fl/fl ) or VEGFR2 iECKO mice followed by LPS and LPS+VEGFD treatment. Images are representative of 6–9 lung specimens for each condition. Scale bar 150 μm. I) The lung pathological index was calculated in LPS and LPS+VEGFD conditions between control and VEGFR2 iECKO mice. n = 4 - 6 per treatment group. Data presented as mean ± SEM. * indicates p<0.05.

Article Snippet: Tissue samples were then stained with antibodies: SLIT2 (Thermo Fisher Scientific, # PA5-31133), ROBO4 (R&D Systems, # AF2366), ADM (Bioss, # BS-0007R), RAMP2 (Santa Cruz Biotechnology, # sc-365240), BMP5 (Thermo Fisher Scientific, # PA5-78878), BMPR2 (Thermo Fisher Scientific, # MA5-15827), VEGFD (Thermo Fisher Scientific, # PA5-13300), VEGFR2 (Santa Cruz Biotechnology, # sc-6251), ITGA8 (Novus Biologicals, # AF4076), PRX (Novus Biologicals, # NBP1-89598) overnight at 4 °C followed by staining with secondary antibodies (RT, 1 hour) and DAPI (RT, 5 min).

Techniques: Cell Culture, Transfection, Control, Expressing, Western Blot, Injection, Staining