Journal: bioRxiv

Article Title: The lung extracellular matrix protein landscape in severe early-onset and moderate chronic obstructive pulmonary disease

doi: 10.1101/2023.10.20.562391

Figure Lengend Snippet: FFPE lung tissue sections from control and COPD donors were stained using immunohistochemistry for ECM and ECM-associated proteins with specific signals being detected with Nova red (red) and counterstained with hematoxylin (blue). Sections were scanned at 40x magnification using a digital slide scanner. Scale bar = 400um. Images are representative of protein detection patterns seen in control donors (n=18), SEO-COPD (n=12), and moderate COPD (n=14). ECM: extracellular matrix; SEO-COPD: Severe early-onset COPD patients; FFPE: formalin fixed paraffin embedded; COL1A1: collagen type I α chain 1; COL6A1: collagen type VI α chain 1; COL6A2: collagen type VI α chain 2; COL14A1: collagen type XIV α chain 1; FBLN2: fibulin 2; FBLN5: fibulin 5; LTBP4: latent transforming growth factor binding protein 4; LUM: lumican; DCN: decorin; VCAN: versican; ELN: elastin.

Article Snippet: Following PBS washes, primary antibodies diluted in 1% BSA/PBS for FBLN5 (1:8000, Mouse Anti-Fibulin 5/DANCE Antibody 1G6A4, Novus Biologicals), DCN (1:1500, Mouse Anti-Dermatan Sulfate Proteoglycan Antibody 6B6, Seikagaku), VCAN (1:200, Mouse Anti-Versican Antibody 2B1, Seikagaku), and ELN (1:400, Rabbit Anti-Elastin Antibody CL55011AP, Cedarlane Labs) were added to the respective sections for 1 hour at room temperature.

Techniques: Control, Staining, Immunohistochemistry, Formalin-fixed Paraffin-Embedded, Binding Assay

Journal: bioRxiv

Article Title: The lung extracellular matrix protein landscape in severe early-onset and moderate chronic obstructive pulmonary disease

doi: 10.1101/2023.10.20.562391

Figure Lengend Snippet: ECM proteins in FFPE tissue sections from controls (n=18), SEO-COPD (n=12), and moderate COPD (n=14) were detected using immunohistochemistry. Parenchyma was isolated and analyzed for percentage positive tissue area and mean intensity of positive pixels of expression for each protein. All 44 donors were available for analysis of COL1A1, COL6A2, FBLN2, LTBP4, LUM, DCN, VCAN, AND ELN, while for COL6A1, COL14A1, and FBLN5 43 donors were available. For each protein, regression coefficients (± 95% CI) were obtained following linear regression and a p value of <0.05 was considered significant. Non-transformed variables are plotted first, followed by log transformed variables. The differences in ECM and ECM-associated proteins in COPD tissue were compared to control in terms of A-C) percentage area and D-F) mean intensity of positively stained pixels. Dark blue-colored bars in light blue colored boxes highlight significant differences. ECM: extracellular matrix; SEO-COPD: Severe early-onset COPD patients; FFPE: formalin fixed paraffin embedded; COL1A1: collagen type I α chain 1; COL6A1: collagen type VI α chain 1; COL6A2: collagen type VI α chain 2; COL14A1: collagen type XIV α chain 1; FBLN2: fibulin 2; FBLN5: fibulin 5; LTBP4: latent transforming growth factor binding protein 4; LUM: lumican; DCN: decorin; VCAN: versican; ELN: elastin.

Article Snippet: Following PBS washes, primary antibodies diluted in 1% BSA/PBS for FBLN5 (1:8000, Mouse Anti-Fibulin 5/DANCE Antibody 1G6A4, Novus Biologicals), DCN (1:1500, Mouse Anti-Dermatan Sulfate Proteoglycan Antibody 6B6, Seikagaku), VCAN (1:200, Mouse Anti-Versican Antibody 2B1, Seikagaku), and ELN (1:400, Rabbit Anti-Elastin Antibody CL55011AP, Cedarlane Labs) were added to the respective sections for 1 hour at room temperature.

Techniques: Immunohistochemistry, Isolation, Expressing, Transformation Assay, Control, Staining, Formalin-fixed Paraffin-Embedded, Binding Assay

Journal: bioRxiv

Article Title: The lung extracellular matrix protein landscape in severe early-onset and moderate chronic obstructive pulmonary disease

doi: 10.1101/2023.10.20.562391

Figure Lengend Snippet: ECM proteins present in FFPE tissue sections from controls (n=18), SEO-COPD (n=12), and moderate COPD (n=14) were detected using immunohistochemistry. Airway walls were isolated and analyzed for percentage area and mean intensity of expression for each protein. The number of airway walls available for the analysis for each protein were COL1A1 (n= 155), COL6A1 (n=150), COL6A2 (n=149), COL14A1 (n=152), FBLN2 (n=158), FBLN5 (n=173), LTBP4 (n=163), LUM (n=158), DCN (n=156), VCAN (n=165), and ELN (n=158). For each protein, regression coefficients (± 95% CI) were obtained following linear regression and a p value of <0.05 was considered significant. Non-transformed variables are plotted first, followed by log transformed variables. The differences in ECM and ECM-associated proteins in COPD tissue were compared to control in terms of A-C) percentage area and D-F) mean intensity of positively stained pixels. Dark blue-colored bars in light blue colored boxes highlight significant differences. ECM: extracellular matrix; SEO-COPD: Severe early-onset COPD patients; FFPE: formalin fixed paraffin embedded; COL1A1: collagen type I α chain 1; COL6A1: collagen type VI α chain 1; COL6A2: collagen type VI α chain 2; COL14A1: collagen type XIV α chain 1; FBLN2: fibulin 2; FBLN5: fibulin 5; LTBP4: latent transforming growth factor binding protein 4; LUM: lumican; DCN: decorin; VCAN: versican; ELN: elastin.

Article Snippet: Following PBS washes, primary antibodies diluted in 1% BSA/PBS for FBLN5 (1:8000, Mouse Anti-Fibulin 5/DANCE Antibody 1G6A4, Novus Biologicals), DCN (1:1500, Mouse Anti-Dermatan Sulfate Proteoglycan Antibody 6B6, Seikagaku), VCAN (1:200, Mouse Anti-Versican Antibody 2B1, Seikagaku), and ELN (1:400, Rabbit Anti-Elastin Antibody CL55011AP, Cedarlane Labs) were added to the respective sections for 1 hour at room temperature.

Techniques: Immunohistochemistry, Isolation, Expressing, Transformation Assay, Control, Staining, Formalin-fixed Paraffin-Embedded, Binding Assay

Journal: bioRxiv

Article Title: The lung extracellular matrix protein landscape in severe early-onset and moderate chronic obstructive pulmonary disease

doi: 10.1101/2023.10.20.562391

Figure Lengend Snippet: ECM differences noted in the different analyzes throughout this study have been summarized here. In the staining and ECM signatures, red or blue arrows indicate higher or lower proportional levels or component scores in COPD respectively, while they denote positive or negative associations with FEV1 respectively. ECM: extracellular matrix; SEO-COPD: Severe early-onset COPD patients; COL1A1: type I collagen α chain 1; COL6A1: type VI collagen α chain 1; COL6A2: type VI collagen α chain 2; COL14A1: type XIV collagen α chain 1; FBLN2: fibulin 2; FBLN5: fibulin 5; LTBP4: latent transforming growth factor binding protein 4; LUM: lumican; DCN: decorin; VCAN: versican; ELN: elastin; FEV1: forced expiratory volume in 1 second.

Article Snippet: Following PBS washes, primary antibodies diluted in 1% BSA/PBS for FBLN5 (1:8000, Mouse Anti-Fibulin 5/DANCE Antibody 1G6A4, Novus Biologicals), DCN (1:1500, Mouse Anti-Dermatan Sulfate Proteoglycan Antibody 6B6, Seikagaku), VCAN (1:200, Mouse Anti-Versican Antibody 2B1, Seikagaku), and ELN (1:400, Rabbit Anti-Elastin Antibody CL55011AP, Cedarlane Labs) were added to the respective sections for 1 hour at room temperature.

Techniques: Staining, Binding Assay

Journal: EMBO Reports

Article Title: Palmitoylation by ZDHHC4 inhibits TRPV1-mediated nociception

doi: 10.1038/s44319-024-00317-0

Figure Lengend Snippet: Reagents and tools table

Article Snippet: Rabbit anti-APT2 , ABclonal , Cat# A15792.

Techniques: Control, Recombinant, Plasmid Preparation, Sequencing, shRNA, Virus, Software, cDNA Synthesis, SYBR Green Assay