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22 protocols using anti pdgfrα

1

Fluorescent Western Blotting of PDGFRα

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HEK293T cells were seeded (7.5 × 106 cells) into 90 mm dishes and transfected with wild-type or mutated PDGFRα expression vectors using Lipofectamine 3000. Forty-eight h after, the transfected cells were lysed using the Mem-PER Plus membrane protein extraction kit (Thermo Fisher Scientific), and proteins were visualized via fluorescent western blotting. Briefly, proteins were resolved by SDS-PAGE and transferred onto PVDF membranes. Next, membranes were blocked and incubated with antibodies using the protocol described above. The anti-PDGFRα (#5214, Cell Signaling Technology) and anti-phosphotyrosine (4G10) antibodies were used as the primary antibodies, and IRDye 680RD donkey anti-rabbit IgG and IRDye 800CW donkey anti-mouse IgG (LI-COR, Lincoln, NE, USA) were used as the secondary antibodies. Fluorescence detection and quantification were performed using Odyssey CLx (LI-COR).
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2

Cardiac Tissue Analysis Post-Infarction

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After the reperfusion, fresh heart biopsies were fixed in 4% paraformaldehyde overnight at 4°C and embedded in paraffin. Sections into 5-μm slices were stained with hematoxylin-eosin (H&E) or Masson’s trichrome for assessment of fibrosis. Tissues for immunofluorescence were submerged in liquid nitrogen and then embedded in optimal cutting temperature (OCT) solution (Sakura Finetek, USA) on dry ice to be frozen completely. Cardiomyocyte hypertrophy was examined in the peri-infarct zone. Myocyte cross-sectional areas were measured using Image J software (National Institutes of Health) in frozen sections stained with 5 μg/ml wheat germ agglutinin (WGA-Alexa Fluor® 488 conjugate, Invitrogen, USA). Five parts were chosen in the WGA images (200X) including left top, right top, middle, left bottom, and right bottom, and six cells were analyzed for each part. In other experiments, the hearts were excised for Masson staining to evaluate the cardiac remodeling. For inflammatory cell infiltration and PDGFR protein expression, immunofluorescence staining with anti-CD45 (Cell Signaling Technology, USA) and anti-PDGFRα (Cell Signaling Technology, USA) in frozen sections was conducted. Then the number of CD45+ cells/field were quantified by Image J software (National Institutes of Health, USA).
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3

Protein Extraction and Western Blot

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Tissue or cells were homogenized in lysis buffer containing 50 mmol/L Tris–HCl (pH 7.5), 150 mmol/L NaCl, 1% IGEPAL CA-630, 0.1% SDS, 0.5% deoxycholic acid, 1 mmol/L EDTA, 0.1 mmol/L Na3VO4, 1 mmol/L NaF, 50 μmol/L phenylmethylsulfonyl fluoride (PMSF), 5 μg/mL aprotinin, and 5 μg/mL leupeptin. Following SDS-PAGE, immunoblotting was performed using the following antibodies: anti-YAP (Cell Signaling #14074, 1:1000), anti-cardiac troponin T (Thermo Fisher MA5-12960, 1:2000), anti-GFP (Cell Signaling #2956, 1:1000), anti-GAPDH (Cell Signaling #5174, 1:1000), anti-PDGFRα (Cell Signaling #3174, 1:1000), anti-Hsp47 (Enzo Life Sciences #ADI-SPA-470, 1:1000), and anti-tubulin (Sigma, T-6199, 1:1000). Densitometry was performed using NIH ImageJ software.
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4

Signaling Pathway Antibody Validation

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Anti Insulin Receptor β (4B8) (#3025)(1:1000 working dilution); Anti IGF-1 Receptor β (#3027) (1:1000); Anti Akt2 (D6G4) (#3063) (1:1000); Anti phospho-IGF-1 Receptor β (Tyr1135/1136) / Insulin Receptor β (Tyr1150/1151) (19H7) (1:500); Anti Phospho-Akt (Ser473) (193H12) (#4058) (1:1000); Anti phospho-PDGFR-α (Tyr754) (#2992) (1:1000); Anti PDGFR-α (#3174) (1:1000) were supplied by Cell Signalling Technology®. Pan 14-3-3 (K-19) (#sc-629) (1:1000) was from Santa Cruz Biotechnology Inc. Anti phospho-IRS1 (Tyr 608) (#09-432) (1:1000) and anti IRS1 (#06-248) (1:500) were supplied by Millipore™. Secondary antibody; Goat anti-Rabbit IgG (H + L) Cross-Adsorbed Secondary Antibody, HRP (#A16104) (1:4000) was supplied by Invitrogen.
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5

Protein Extraction and Western Blotting

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Cells were lysed with a NP-40 lysis buffer containing protease inhibitor cocktail (Roche, 11697498001), followed by measurement of total protein concentration. A total 20 μg protein of the lysates was resolved by 4–15% precast SDS-polyacrylamide gel electrophoresis gel (Bio-Rad). After transfer, polyvinylidene fluoride membranes were blotted with anti-GAPDH (Cell Signaling, 5174), anti-FSP-1 (Millipore, 07-2274, Abcam, ab27957, and Abnova H00006275-M01), anti-VEGFR-2 (Cell Signaling, 9698), anti-N-cadherin (Cell Signaling, 13116), anti-α-SMA (Abcam, ab5694), anti-NF-κB (Cell Signaling, 8242), anti-Snail (Cell Signaling, 3879s), anti-Erg (Cell Signaling, 97249), anti-Slug (Cell Signaling, 9585s), anti-PDGFR-α (Cell Signaling, 3164), anti-PDGFR-β (Cell Signaling, 3169), anti-PDGF-AA (Millipore, 07-1436), and anti-PDGF-BB (Millipore, 07-1437) antibodies at 1:1000 dilution. Proteins were detected with horseradish peroxidase-conjugated antibodies specific for either rabbit or mouse IgG (Bio-Rad), followed by ECL development (GE Healthcare, RPN2232). Uncropped scans of all immunoblots are provided in Supplementary Fig. 9.
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6

Histological Analysis of Embryonic Lung Development

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Embryos and tissues were fixed in 10% formalin overnight, dehydrated in 100% ethanol, and embedded in paraffin. 8-µm-thick sections were used for hematoxylin-eosin, periodic acid-Schiff (PAS), trichrome, and immunohistochemistry staining. The following primary antibodies were used for immunostaining: anti-LYVE1 (R&D Systems), anti-PROX1 (Abcam), anti-PECAM1 (R&D Systems; clone: 693102), anti–pro-surfactant protein C (pro-SPC; EMD Millipore), anti-Clara cell 10 (CC10; Santa Cruz Biotechnology, Inc.), anti-Podoplanin (Abcam), anti–Caveolin-1 (BD), anti-PDGFRα (Cell Signaling Technology), anti-PDGFRβ (Cell Signaling Technology), anti-SM22α (Abcam), anti-WT1 (Santa Cruz Biotechnology, Inc.), anti-Vimentin (Santa Cruz Biotechnology, Inc.), anti-Desmin (Dako), and anti-NG2 (EMD Millipore). Detailed histology procedures can be found on the University of Pennsylvania Molecular Cardiology Research Center Histology and Gene Expression Core website. Microscopic images were taken on a microscope (Eclipse 80i; Nikon) connected to a camera (DS-Ri1; Nikon). Alveolar wall thickness (averaging 50–100 measurements per embryo) and alveolar area (averaging the total alveolar area in 5–15 vision fields per embryo) were performed in Elements software (Nikon) using a 40× objective.
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7

Western Blot Analysis of Signaling Proteins

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Cells and liver tissues were lysed or homogenized in RIPA buffer containing a cocktail of protease inhibitors (Santa Cruz, CA) according to the manufacturer's instruction. Protein extracts were loaded onto 12% acrylamide gels (Bio-Rad) and transferred onto nitrocellulose membranes. Protein bands were visualized with ECL-chemiluminescent kit (GE Healthcare, Piscataway, NJ). The antibodies against anti-PDGFRα, PDGFRβ, ERK, AKT, phosphorylated ERK (Thr202/Tyr204) and phosphorylated AKT (Ser473) were purchased from Cell Signaling Technology (Danvers, MA). GLI2 and GLI3 antibodies were purchased from Proteintech (Rosemont, IL). The antibodies against β-actin was purchased from Abcam (Cambridge, MA).
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8

Adipose Tissue Histological and Molecular Analysis

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For morphological analysis, adipose tissues were thoroughly fixed in 10% formalin, paraffin-embedded, sectioned and stained with haematoxylin and eosin (H&E). Immunohistochemistry assays were performed using VECTASTAIN ABC kit (Vector Laboratories). Co-immunofluorescence staining was performed by incubation with rabbit anti-Ki67 (Cell Marque Tissue Diagnostics) or anti-PDGFRα (Cell Signalling Technology) followed by FITC-anti-rabbit IgG in combination with Cy3-anti-SMA antibody (Sigma). For x-Gal (5-Bromo-4-chloro-3-indolyl beta-D-galactopyranoside, Sigma) staining, adipose tissues were fixed using 10% neutral buffered formalin for 1 h, whole-mount x-Gal stained, paraffin-embedded, sectioned, and then nuclear fast red counterstained. For RNAscope, adipose tissues were fixed in 10% formalin, cryo-embedded, and then sectioned at 20 to 30 microns for histological analysis. In situ RNAscope assays for Pdgfra and Spry1 were performed according to RNAscope fluorescent multiplex assay instructions (ACDBio). Images were captured using Canon EOS camera and remote imaging software (Canon), or a Leica SP8 confocal microscope.
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9

Immunohistochemical Profiling of Stromal Cells

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Sections on microslides were deparaffinized with xylene, hydrated using a diluted alcohol series, and immersed in 0.3% H2O2 in methanol to quench endogenous peroxidase activity. Sections were treated with TE buffer (10 mM Tris and 1 mM EDTA, pH 9.3) at 98°C for 30 min. To reduce non-specific staining, each section was blocked with 4% bovine serum albumin in PBS with 0.1% Tween 20 for 30 min. The sections were then incubated with anti- SMA (1∶100, Millipore, Billerica, MA, USA), anti-FAP (1∶100, Abcam), anti-FSP1 (1∶100, Millipore), anti-PDGFRα (1∶100, Cell Signaling Technology), anti-PDGFRβ (1∶100, Abcam), anti-CD34 (1∶100, Dako, Glostrup, Denmark) and anti-CD68 (1∶1000, Dako) in PBST containing 3 mg/ml goat globulin (Sigma, St. Louis, MO, USA) for 60 min at room temperature, followed by three successive washes with buffer. Sections were then incubated with an anti-mouse/rabbit antibody (Envision plus, Dako) for 30 min at room temperature. The chromogen used was 3,3′-diaminobenzidine (Dako). Sections were counterstained with Meyer’s hematoxylin. Omitting the primary antibody provided negative controls for immunostaining.
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10

Immunohistochemical Characterization of Tumor Microenvironment

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Sections on microslides were deparaffinized with xylene, hydrated using a diluted alcohol series, and immersed in 0.3% H2O2 in methanol to quench endogenous peroxidase activity. Sections were treated with TE buffer (10 mM Tris and 1 mM EDTA, pH 9.3) at 98°C for 30 min. To reduce non-specific staining, each section was blocked with 4% bovine serum albumin in PBS with 0.1% Tween 20 for 30 min. The sections were then incubated with anti-Tenascin-C monoclonal antibody (1:100, Abcam, UK), anti- SMA (1:100, Millipore, USA), anti-FAP (1:100, Abcam, UK), anti-FSP1 (1:100, Millipore, USA), anti-PDGFRα (1:100, Cell Signaling Technology, USA), anti-PDGFRβ (1:100, Abcam, UK), anti-CD34 (1:100, Abcam, UK), HIF1α (1:100, BD, USA) and anti-CD68 (1:1000, Dako, Denmark) in PBST containing 3 mg/ml goat globulin (Sigma, St. USA) for 60 min at room temperature, followed by three successive washes with buffer. Sections were then incubated with an anti-mouse/rabbit antibody (Envision plus, Dako, Denmark) for 30 min at room temperature. The chromogen used was 3, 3’-diaminobenzidine (Dako, Denmark). Sections were counterstained with Meyer’s hematoxylin. Omitting the primary antibody provided negative controls for immunostaining.
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