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23 protocols using sc 9068

1

Comprehensive Immunohistochemistry Protocol for Skin Tissue

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Paraffin or frozen 5 µm sections of skin tissue samples were stained with the following antibodies: CD31 antibody (1:100, ab28364 Abcam) for detection of endothelial cells; Calponin (1:100, EP798Y, Abcam) and α-SMA (1:200, ab5694, Abcam) for detection of perivascular cells, and F4/80 (1:100, ab6640, Abcam) for assessing macrophages in vivo. Collagen type I (1:200, ab21286, Abcam), collagen type IV (1:100, AB756, Chemicon), collagen type XVIII (1:100, sc-32720, Santa Cruz), collagen type VI (1:50, sc-167530, Santa Cruz), and fibronectin (1:500, sc-9068, Santa Cruz) were used for extracellular matrix and basement membrane evaluation. Incubation with primary antibody was followed by FITC or Texas Red labeled secondary antibody (1:500, Vector Laboratories). Nuclei were stained with Hoechst 33342 fluorescent dye (Thermo Scientific).
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2

Temporal Corneal Protein Expression Analysis

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Corneas (n = 4) were harvested at 2, 4, 7, 14, 28 days and ground and then homogenized in RIPA lysis buffer containing a mixture of protease and phosphatase inhibitor. Lysates were then centrifuged at 12,000 × g for 10 min at 4°C and supernatants were harvested, and the concentration was valued with a bicinchoninic acid assay kit. Subsequently, samples were mixed with 5X SDS-PAGE loading buffer and boiled for 10 min at 100°C. Equivalent amount of protein were run in a 10–12% SDS-PAGE gel and then transferred to PVDF membrane. Membranes were cut properly and immersed in 5% milk for 2 h at room temperature, and then incubated overnight at 4°C with primary antibodies for HMGB1 (1:500 dilution, ab18256, Abcam), VEGF (1:1000 dilution, ABS82, Sigma Aldrich), TNF-α(1:1000 dilution, ab6671, Abcam), Fibronectin (1:1000 dilution, sc-9068, Santa Cruz Biotechnology), GAPDH (1:1000 dilution, ab181602, Abcam) and β-actin (1:1000 dilution, no4967, Cell Signalling Technology). On the following day, secondary antibody (1:5000 dilution) incubation was managed for 2 h at room temperature. Protein expression was measured by the Odyssey® Sa Two-colour infrared laser imaging system (Licor, United States). The images were analyzed by Image-Pro Plus 6.0.
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Histological Assessment of Tissue Response

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After the periods of 7, 15, 30, and 60 days, the animals were euthanized by an anesthetic overdose. The polyethylene tubes were removed with the surrounding tissue and fixed in 10% buffered formalin at pH 7.0. The specimens were embedded in paraffin, serially cut into 5 μm sections, and stained with hematoxylin-eosin or submitted to immunohistochemistry by using an indirect immunoperoxidase technique for FN (primary antibody rabbit, SC-9068, Santa Cruz Biotechnology, CA, USA) and TN (primary antibody rabbit, SC-20932, Santa Cruz Biotechnology, CA, USA). The specimens were also submitted to the procedures suppressing the use of primary antibodies to the negative control.
The inflammatory infiltrate at the open end of the tubes was scored according to previous studies[4 (link)9 ] as follows: 0, few inflammatory cells or no reaction; 1, <25 cells and mild reaction; 2, between 25 and 125 inflammatory cells and moderate reaction; and 3, 125 or more inflammatory cells and severe reaction (×400 magnification). Fibrous capsules were considered thin when <150 μm and thick when ≥150 μm. Immunolabeling for FN and TN was defined as the presence of brownish color in the extracellular matrix. The criteria for establishing the adopted scores were 0, absence of immunolabeling; 1, low immunolabeling standard; 2, moderate immunolabeling standard; and 3, high immunolabeling standard (×1000 ).
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4

Signaling Pathway Analysis via Western Blotting

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Cells were treated with TDPN or DMSO in time-dependent and dose-dependent manners. The cells were harvested by scraping and underwent lysis in RIPA buffer. The BCA method (Thermo Scientific) was used for protein concentration determination. The extracts were analyzed by SDS-PAGE followed by Western blotting with appropriate antibodies.
The following antibodies were used for Western blotting: p21 (catalogue no. 2947), AKT (9272), phosphorylated AKT (9271S), ERK (4695), Slug (9585S), and GAPDH (2118) were from Cell Signaling Technology; E-cadherin (610181) and Zo-1 (610966) were from BD Science Transduction; cyclin E (sc-247), cyclin D1 (sc-246), p53 (sc-126), phosphorylated ERK (sc-7383), collagen I (sc-25974), collagen III (sc-28888), and fibronectin (sc-9068) were from Santa Cruz Biotechnology; and MMP-1 (444209) was from Calbiochem. The secondary antibodies used in the Western blotting were anti-mouse (PI-2000; Vector Laboratories) anti-rabbit (PI-1000; Vector Laboratories), and anti-goat (AP-107P; Millipore). The blots were analyzed using the ImageJ software. The relative change in the ratio of the target protein to the DMSO control was determined.
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5

Comprehensive Immunohistochemistry Protocol for Skin Tissue

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Paraffin or frozen 5 µm sections of skin tissue samples were stained with the following antibodies: CD31 antibody (1:100, ab28364 Abcam) for detection of endothelial cells; Calponin (1:100, EP798Y, Abcam) and α-SMA (1:200, ab5694, Abcam) for detection of perivascular cells, and F4/80 (1:100, ab6640, Abcam) for assessing macrophages in vivo. Collagen type I (1:200, ab21286, Abcam), collagen type IV (1:100, AB756, Chemicon), collagen type XVIII (1:100, sc-32720, Santa Cruz), collagen type VI (1:50, sc-167530, Santa Cruz), and fibronectin (1:500, sc-9068, Santa Cruz) were used for extracellular matrix and basement membrane evaluation. Incubation with primary antibody was followed by FITC or Texas Red labeled secondary antibody (1:500, Vector Laboratories). Nuclei were stained with Hoechst 33342 fluorescent dye (Thermo Scientific).
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6

Kidney Cryosection Immunohistochemistry

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Kidney cryosections were fixed with 3.7% paraformalin for 15 minutes at room temperature. After blocking with 10% donkey serum for 30 minutes, the slides were immunostained with primary antibodies against fibronectin (sc-9068, Santa Cruz Biotechnology), rabbit polyclonal anti-collagen I (234167, EMD Millipore).
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7

Western Blot Analysis of Protein Markers

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Protein lysates were prepared in the presence of PIC (protease–inhibitor complex) and PMSF. Twenty microgram aliquots were separated on 8% sodium dodecyl sulphate polyacrylamide electrophoresis gels, and the proteins were transferred onto a polyvinylidene difluoride membrane (Merck Millipore). The membrane was incubated for 1 h in blocking buffer (tris-buffered saline containing 0.1% Tween (TBS-T), and 5% nonfat dry milk) followed by incubation overnight at 4 °C with the primary antibodies for DICER1 (CST, D38E7, 1:1000), TGFBI (Abcam, ab170874, 1:2000), FOXP1 (CST, 4402, 1:1000), FN1 (Santa Cruz, sc-9068, 1:200), CDH1 (CST, 3195s, 1:1000), and CDH2 (CST, 14215s, 1:1000). After washing with TBS-T, the blot was incubated with horseradish peroxidase (HRP)-conjugated secondary antibody or IRDye800-conjugated secondary antibody and the signals were visualized using an enhanced chemiluminescence system according to the manufacturer’s instructions (Kodak) or Odyssey (LI-COR). The uncropped and unprocessed scans of the most important blots are provided in the Source Data file.
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8

Quantitative Immunofluorescence Imaging

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Cells were incubated with primary antibodies against fibronectin (sc-9068, Santa Cruz; 1:100) or FAP (AF3715, R&D Systems; 10 μg ml−1), followed by incubation with Alexa Fluor 488-conjugated secondary antibodies (Molecular Probes, Eugene, OR; 1:200). The fluorescence intensity was quantitated using ImageJ software.
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9

Isolation of Asthmatic Airway Smooth Muscle Cells

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Human bronchial biopsies were obtained from patients with asthma or from non-asthma/non-COPD (controls) that underwent bronchoscopy for diagnostic reasons at the Clinic of Pneumology, University Hospital Basel, Switzerland. Each patient gave a written consent for using one additional biopsy sample for scientific investigations. The local Ethics Board (EKNZ 2016-01057, 7 July 2016, Ethic commission Northwest- and Central Switzerland, EKNZ) approved the protocol. The clinical parameters of all tissue donors are presented in Table 1.
The primary ASMCs were isolated from the biopsies (obtained from five patients with asthma and five controls) after removing the epithelium and cultivated in a specific medium (DMEM supplemented with 5% fetal calf serum, 1mM sodium pyruvate, 1 × MEM vitamin mix, 1 × non-essential amino acid mix, and 10mM HEPES; all Thermo Fisher Scientific, Basel, Switzerland) [48 (link)]. Positive staining for fibrillar α-smooth muscle actin (ab5694, Abcam, Cambridge, UK) and negative staining for fibrillar fibronectin (#sc-9068, Santa Cruz, Santa Cruz, CA, USA) and E-cadherin (#610181, BD Bioscience, Allschwil, Switzerland) characterized ASMCs. All experiments were performed between passages 3 and 8.
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10

Immunofluorescence Analysis of Cellular Signaling

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NRK-52E cells cultured on coverslips were fixed with 4% PFA for 15 minutes at RT. After blocking with 1% BSA for 30 minutes, the slides were immunostained with primary antibodies for p-AMPK (sc-33524; Santa Cruz Biotechnology CA, USA), p-Smad3 (ab52903; Abcam Cambridge, MA, USA), E-cadherin, (sc-8426; Santa Cruz Biotechnology CA, USA), α-SMA (ab5694; Abcam Cambridge, MA, USA), fibronectin (sc-9068; Santa Cruz Biotechnology CA, USA), and type IV collagen (sc-9301; Santa Cruz Biotechnology CA, USA). Next, the slides were stained with a secondary antibody (Alexa) and mounted with mounting media (Dako, San Diego, CA, USA) using 4, 6-diamidino-2-phenylindole to visualize the nuclei (Sigma Aldrich). Slides were viewed under a Leica TSL-SL confocal microscope. Staining intensity was measured using Image J analysis software ((Mac OS X; National Institute of Mental Health Bethesda, Maryland, USA)
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