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14 protocols using anti fap

1

Characterization of Oral Lichenoid Lesion Fibroblasts

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NEOLP or EOLP lesions were isolated and cultured for OLP-MFs. 8 Primary OLP-MFs and 6 normal fibroblasts (NFs) were obtained according to methods described by a previous study (12 (link)). Cultured cells at passages 3-6 were used. OLP-MFs and NFs were examined using anti-cytokeratin (1:100; cat. no. AM06387SU-N; OriGene Technologies, Inc.), anti-vimentin (1:200; cat. no. ab92547; Abcam), anti-α-SMA (1:100; cat. no. ab5694; Abcam) and anti-FAP (1:100; cat. no. ab53066; Abcam) antibodies. Growth and viability of OLP-MFs were assessed using a Cell Counting Kit-8 (CCK-8; Dojindo Molecular Technologies, Inc.) at 24, 48 and 72 h, according to the manufacturer's protocol. The cells were rinsed with PBS and fixed overnight in 3% glutaraldehyde at 4˚C. Subsequently, the samples were dehydrated using the following ethanol gradient: 30, 50, 70, 95 and 100%. The samples were then dehydrated with xylene, air-dried at room temperature and embed with epoxy resin. The specimens were coated with gold. The ultrastructure of OLP-MFs and NFs was compared using a transmission electron microscope (magnification, x1.2k) and scanning electron microscopy (magnification, x700), respectively. The images were processed using Adobe Photoshop CS6 (Version 13.0.1; Adobe Systems, Inc.).
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2

Tumor Protein Extraction and Analysis Protocol

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On day 22, the tumors were excised and proteins were extracted using radioimmunoprecipitation assay buffer (Beyotime Institute of Biotechnology, Inc., Haimen, China) supplemented with protease inhibitor cocktail (100:1; Sigma-Aldrich). Tumor tissues were homogenized prior to western blot and PCR analysis in liquid nitrogen using a mortar and pestle. Total protein concentrations in the supernatant were determined via the Bicinchoninic Acid assay (P0013B; Beyotime Institute of Biotechnology, Inc.). A total of 30 µg protein was loaded per lane for western blot analysis. Protein samples were separated by 10% SDS-PAGE and transferred onto polyvinylidene difluoride membranes (EMD Millipore, Billerica, MA, USA). After blocking with 5% skimmed milk in TBS containing 0.1% Tween 20 (TBST) for 2 h at 37°C, the membranes were incubated with anti-FAP (1:500; 28244; Abcam) or anti-β-actin (1:1,000; sc-130657; Santa Cruz Biotechnology, Inc., Dallas, TX, USA) primary polyclonal antibodies at 4°C overnight. After washing four times with TBST for 10 min, the membranes were incubated with the goat anti-rabbit HRP-conjugated secondary antibody (1:5,000; sc-2054; Santa Cruz Biotechnology, Inc.) for 1 h at 37°C. After washing with TBST as described above, the bands were visualized using enhanced chemiluminescence reagents (WBKLS0100 EMD Millipore).
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3

Immunohistochemical Analysis of Tumor Samples

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FaDu tumors were excised and paraffin-embedded, followed by the standard dehydration process.41 (link) The tumor samples were cut into 5-µm sections and stained with hematoxylin and eosin (H&E). The sections were dewaxed and antigen retrieval was performed in a sodium citrate buffer. The following antibodies were used: anti-FAP (Abcam) and anti-A27 (GenScript Corporation). Biotinylated secondary antibodies (goat anti-rabbit; Jackson ImmunoResearch Laboratories, Suffolk, UK) were used and detection was performed with Vectorstain Elite ABC reagent and Vector ImmPact DAB Peroxidase substrate (Vector Laboratories, Burlingame, CA).
DU145 tumors were excised at 36 dpi, followed by paraformaldehyde fixation, and then cut into 100-µm sections. The blood vessels and cell proliferation were detected with anti-CD31 antibody (BD Pharmingen, San Jose, CA) and anti-Ki67 antibody (BD Pharmingen), respectively.
The examination of tumor sections was conducted with an MZ16 FA fluorescence stereomicroscope (Leica, Buffalo Grove, IL) equipped with a digital charge-coupled device camera (Leica). Digital images (1,300 to 1,030-pixel images) were processed using Adobe Photoshop 7.0 software (San Jose, CA).
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4

Protein Expression Analysis of Cells and Exosomes

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The expression of α-SMA, FAP, glyceraldehyde 3-phosphate dehydrogenase (GAPDH), CD63, and CD81 proteins were detected by WB. Total protein was extracted from cells or exosomes using RIPA reagent (Invitrogen, USA), according to the manufacturer’s instructions. The protein samples from each group were added to the loading wells, and electrophoresis was completed when the bromophenol blue indicator migrated to the bottom of the separation rubber. A piece of polyvinylidene fluoride film slightly larger than the separation glue was cut, and the film was spread flat on the glue for film turning. After the transfer was completed, the cells were blocked for 2 h. The PVDF membrane was cut into appropriate sizes and placed in 15 ml centrifuge tubes containing anti α-SMA (1:1000, Abcam), anti FAP (1:1000, Abcam), anti GAPDH (1:10,000, Abcam), anti CD63 (1:1000, Abcam), or anti CD81 (1:1000, Abcam) antibodies followed by overnight incubation at 4℃. The next day, after incubating the secondary antibody, appropriate amount of ECL working solution was added, and the multi-functional gel imaging system was used for development.
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5

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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6

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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7

MSC Differentiation under EV Treatment

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MSCs were plated in 6-well plates and cultured for 28 days. KMBC-EVs (2×1010 particles/well) and H69-EVs (2×1010 particles/well) were added to the cell culture every 7 days. After 28 days, cells were collected, plated on coverslips, fixed using 4% paraformaldehyde, permeabilized and incubated with anti-α-SMA antibody (Abcam, Cambridge, MA), rabbit polyclonal antibody anti-FAP (10 µg/ml) (Abcam, Cambridge, UK) or goat polyclonal antibody anti-Vimentin (1:50) (Santa Cruz, Dallas, TX), overnight at 4°C. Cells were washed and incubated with secondary antibody for 1 hour, then mounted with Prolong Gold Antifade Reagent with DAPI (Life Technologies, Grand Island, NY) and visualized by fluorescence microscopy (Olympus IX71, Olympus America, Center Valley, PA).
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8

Biomarker Expression Analysis in Samples

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The ALOX15, USP7 and hnRNPA1 expression were assessed by western blotting analysis and samples were normalized to GAPDH. Protein extraction was blocked with PBS-5% fat-free dried milk at room temperature for 1 h and incubated at 4 °C overnight with anti-ALOX15 (1:1000, Santa cruz), anti-hnRNPA1 (1:1000, Santa cruz), anti-CD63 (1:2000, Abcam), anti-TSG101 (1:1000, Santa Cruz), anti-Alix (1: 1000, Santa Cruz), anti-ubiquitin (1:1000, Santa Cruz), anti-α-SMA (1: 1000, Abcam), anti-FAP (1: 1000, Abcam), andti-FSP1 (1: 1000, Abcam), anti-CEA (1:1000, Abcam), anti-CK-18 (1:1000, Abcam) and anti-GAPDH (1:3000, Santa Cruz) antibodies respectively.
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9

Comprehensive Western Blot Analysis

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Western blotting assays were performed as previously described [16 (link)]. The primary antibodies were as follows: anti-vimentin, anti-FAP, anti-αSMA, anti-LYVE-1, and anti-PAI-1 (Abcam, Cambridge, MA, USA); anti-phospho-AKT (Ser 473), anti-AKT, anti-phospho-ERK1/2 (T202/Y204), anti-ERK1/2, anti-p38, anti-phospho-p38, anti-JNK, anti-phospho-JNK, anti-VE-cadherin, anti-phospho-VE-cadherin (Y685) and anti-GAPDH (CST, Massachusetts, USA). The secondary antibodies were horseradish peroxidase-conjugated anti-rabbit or anti-mouse immunoglobulin-G antibody (Abcam, Cambridge, MA, USA).
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10

Immunofluorescence Analysis of Mouse T Cells

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The immunofluorescence analysis was performed using anti-CD8+ (Abcam, Cambridge, UK) primary antibodies directed against mouse T cells and visualized with a fluorescence microscope (IX51; Olympus, Tokyo, Japan). For two-colour immunofluorescence analysis, the isolated fibroblasts were fi fl and incubated with anti-vimentin, anti-α-SMA, or anti-FAP (Abcam) and then with goat anti-mouse IgG fluorescein-conjugated antibodies for detecting vimentin or with goat anti-rabbit IgG fluorescein conjugate antibodies (Calbiochem, Merck Serono, China) for detecting FAP and α-SMA. Immunofluorescence was visualized using a fluorescence microscope.
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