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14 protocols using anti snail1

1

Investigating MUC1-C Protein Interactions in Cell Lysates

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Whole cell lysates were prepared using NP-40 lysis buffer containing protease inhibitor cocktail (Thermo Scientific). Nuclear and cytosolic lysates were prepared using the NucBuster nuclear protein extraction kit (Millipore). Soluble proteins were immunoprecipitated with anti-MUC1-C (NeoMarker) or a control IgG. Immunoprecipiates and lysates not subjected to precipitation were analyzed by immunoblotting with anti-MUC1-C (NeoMarker), anti-CRB3 (Abcam), anti-HUGL2 (Genetex), anti-PATJ, anti-SNAIL1 (Santa Cruz Biotechnology), anti-CDC42, anti-ZEB1, anti-phospho-LATS1, anti-LATS1, anti-phospho-YAP, anti-YAP, anti-HDAC1 (Cell Signaling Technology) and anti-β-actin (Sigma). Immunoreactive complexes were detected using horseradish peroxidase-conjugated secondary antibodies (GE Healthcare) and an enhanced chemiluminescence (ECL) detection system (Perkin Elmer Health Sciences).
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2

Quantifying Protein Abundances in Kidney Cells

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The relative protein abundances in kidneys and HK-2 cells were analyzed using western blotting, as described previously (Xu et al., 2012 (link)). The following primary antibodies were used: anti-α-SMA (1:1,000, Sigma), anti-E-cadherin (1:1,000, Cell Signaling Technology), anti-vimentin (1:1,000, Santa Cruz Biotechnology), anti-collagen I (1:1,000, Abcam), anti-collagen IV (1:1,000, Abcam), anti-Wnt1 (1:100, Abcam), anti-Wnt4 (1:150, Santa Cruz Biotechnology), anti-Wnt3 (1:500, Abcam), anti-Wnt2b (1:700, Abcam), anti-Wnt7a (1:300, Abcam), anti-β-catenin (1:1,000, Cell Signaling Technology), anti-Snail 1 (1:1,000, Santa Cruz Biotechnology), anti-PAI-1 (1:1,000, Santa Cruz Biotechnology), and anti-NF-κB p65 (1:1,000, Cell Signal). Horseradish peroxidase-conjugated secondary antibodies (anti-rabbit or anti-mouse or anti-goat IgG, 1:5,000, Jackson ImmunoResearch) were used according to the manufacturer’s instructions. Image analysis software (Image J, National Institutes of Health) was used to determine the gray value of all bands.
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3

Validated Antibody-based Assays for Protein Analysis

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The following antibodies were used for immuno-analyses: anti-RND3 (Cocalico Biologicals), anti-Snail1 (Santa Cruz, sc-28199), anti-E-cadherin (CST, 3195S), anti-claudin (Bioword, BS1063), anti-c-myc (9E10, Santa Cruz, sc-40), and anti-HA (Santa Cruz, SC-7392, SC-805). Even protein loading in the immunoblotting analysis was verified by the intensity of the GAPDH blot (Santa Cruz, sc-20357). The immunostaining, immunoblotting, and immunoprecipitation were conducted as described previously [8 , 20 (link)]. The immunoblotting densitometry was quantified by the Gel Logic 6000 PRO Imaging System (Carestream Health, Inc. Rochester, NY, USA), and the immunofluorescent and immunohistochemical image quantifications were conducted by Leica Application Suite Imaging Software (Version 4.0, Biberach, Germany).
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4

Western Blot Analysis of EMT Markers

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Cells were lysed in lysis buffer. Equal amounts of total proteins were loaded onto 4-12% SDS–PAGE gels and transferred to PVDF membranes (GE Healthcare Life Sciences, NJ, USA). The membranes were blocked with 5% milk dissolved in TBS containing 0.02% Tween 20 and incubated overnight at 4°C with specific primary antibodies. The membranes were subsequently incubated with specific horseradish peroxidase-conjugated secondary antibodies. Protein bands were visualized using a Fusion FX5 system ((Vilber Lourmat, France). The following primary antibodies were used: anti-cleaved caspase 3, anti-E-cadherin, anti-cleaved caspase 9, anti-cleaved PARP1 (Cell Signaling Technology), anti-SNAIL1, anti-Vimentin, anti-Twist, anti-Slug, anti-Zeb1, anti-Nanog, anti-Sox2, anti-CD44 (Santa Cruz), anti-N-cadherin and anti-Oct4 (BD Biosciences), anti-Survivin, anti-CD133 (Abcam), anti-ALDH (Avivasysbio), and anti-β-actin (Sigma).
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5

Western Blot Analysis of Cell Signaling

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The whole-cell extract was obtained in RIPA buffer in the presence of standard protease and phosphatase inhibitors. The protein content was determined with a protein assay reagent (Bio-Rad Laboratories Inc., Hercules, CA, USA), using bovine serum albumin as a standard. Equal protein content of total cell lysates was resolved on polyacrylamide gel (Bolt 4–12% Bis-Tris Plus Invitrogen, Carlsbad, CA, USA), electro-transferred to PVDF membranes (iBlot Invitrogen, Carlsbad, CA, USA) and incubated with specific primary antibodies: anti-YAP (Santa Cruz Biotechnology, Inc., Dallas, TX, USA; sc #101199; dil.1:1000); anti-p-YAP (Cell Signaling Technology, Inc., Beverly, MA, USA; #13008; dil.1:1000); anti-β Actin (MP Biomedicals, Santa Ana, CA, USA; # 69100; dil.1:10000); anti-Rac1, anti-RhoA and anti-Cdc42 (all Cell Biolabs, San Diego, CA, USA; STA-405; dil.1:500); anti-Zeb1 (Abcam, Cambridge, MA, USA; #180905; dil.1:2000); anti-Snail1 (Santa Cruz Biotechnology, Inc., Dallas, TX, USA; sc-271977; dil.1:1000); anti-GSN (Sigma-Aldrich, St Louis, MO, USA; G-4896, dil.1:1000). Membranes were developed using ECL detection reagents (GE Healthcare Life Sciences, Uppsala, Sweden) on a UVITEC imaging system (UVITEC, Cambridge, UK) or ChemiDocMP system (Bio-Rad Laboratories Inc.). Quantitative analysis of western blots was performed using ImageJ (NIH) software [23 (link)].
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6

Western Blot Analysis of Epithelial-Mesenchymal Transition

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Cell lysates (50 μg) were separated by 10% SDS-PAGE. The proteins were transferred to PVDF membrane. After blocking in 5% milk (w/v) at room temperature for 1 h, the membranes were incubated at 4 °C overnight with primary antibodies (1:1000). Following PBST washing for three times with 5 min for each, the membranes were incubated with secondary antibodies (1:7500) at room temperature for 1 h followed by washing and staining. The antibodies were: anti-β-actin (sc-47,778, Santa Cruz Biotechnology), anti-YY1 (sc-1703, Santa Cruz Biotechnology), anti- NF-κB p65 (D14E12, cell signaling), anti-histone (AH433–1, Beyotime, China), anti-E-cadherin (sc-7870, Santa Cruz Biotechnology), anti-vimentin (sc-32,322, Santa Cruz Biotechnology), anti-snail1 (sc-271,977, Santa Cruz Biotechnology) and anti-GAPDH (CST 5174, Cell Signaling Technology).
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7

Western Blot Analysis of EMT Markers

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Western blot analyses were performed as previously described [7 (link)]. List of antibodies used: anti-LY75 (Abcam, Branford, CT, USA and Santa Cruz Biotechnology Dallas, TX, USA), anti-Snail1, anti-FN1, anti-E-cad, anti-EpCAM, anti-AXIN1, anti-WNT3, anti-EVX2, anti-IFFO1, anti-CLDN5, anti-HOOK1, anti-JMJD8, anti-RAMP2, anti-KLF-4, anti-β-actin antibodies (Santa Cruz Biotechnology, Dallas, TX, USA) and anti-Twist1, anti-E-cadherin, anti-N-cadherin, anti-APC2, and anti-Cend1 antibodies (Abcam Branford, CT, USA).
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8

Immunofluorescence Staining of Neural Crest Cells

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Ten days after isolation and culture, the cells were passaged and plated on collagen-coated cover slips overnight, washed in PBS and fixed in 4% paraformaldehyde for 10 min. The fixed cells were washed in PBS and incubated in blocking buffer containing 10% goat serum (Sigma-Aldrich, St. Louis, MO, USA) and 0.3% Triton X-100 (Fluka, St. Louis, MO, USA) at room temperature for 30 min. Cells were then incubated at 4 °C overnight with one of the following primary antibodies: anti-SOX10 (1:200, rabbit polyclonal IgG; Abcam, Cambridge, MA, USA), anti-Snail 1 (1:100, rabbit polyclonal IgG; Santa Cruz, Biotechnology, Inc., Santa Cruz, CA, USA), or anti-p75 (1:400, rabbit polyclonal IgG; Abcam). The next day, the cells were rinsed three times to remove the unbound primary antibodies and then incubated at room temperature for 2 h with secondary antibody (Alexa Fluor 555-conjugated goat anti-rabbit,1:400; Invitrogen). The cell nuclei were counterstained with 4′,6-diamidino-2-phenylindole (DAPI, 1 μg/mL; Invitrogen) in PBS, in the dark and at room temperature for 1 min. After washing, the stained cover slips were removed, mounted on a slide with mounting media, and visualized using a fluorescence microscope (LeicaDM2500; Leica Microsystems GmbH, Wetzlar, Germany) equipped with an EMCCD camera (LucaEM R DL-604M; Andor Technology, Belfast, UK).
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9

Western Blot Analysis of EMT and Stemness Markers

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Cell lysates were measured for protein concentration using BCA kit (Beyotime Biotechnology, Shanghai.). 50 μg of lysates was separated by 10% SDS/PAGE. The proteins were transferred to nitrocellulose membrane. After being blocked in 5% milk (w/v) at room temperature for 1 hour, the membranes were incubated at 4 °C overnight with primary antibodies (1:1,000). Following 1×PBST washing, the membranes were incubated with secondary antibodies (1:3,000) at room temperature for 1 hour followed by ECL staining. The following antibodies were used: anti-Snail1 (sc-271977, Santa Cruz Biotechnology), anti-Slug (sc-166902, Santa Cruz Biotechnology), anti-ZEB1 (sc-515797, Santa Cruz Biotechnology ), anti-ZEB2 (sc-271984, Santa Cruz Biotechnology), anti-Twist (sc-81417, Santa Cruz Biotechnology), anti-DKK1 (sc-374574, Santa Cruz Biotechnology), anti-BMI-1 (sc-390443, Santa Cruz Biotechnology), anti-Oct4 (2750S, Cell Signaling Technology), anti-Nanog (4903S, Cell Signaling Technology), anti-Vimentin (sc-32322, Santa Cruz Biotechnology), anti-GAPDH (5174, Cell Signaling Technology), and anti-β-actin (sc-47778, Santa Cruz Biotechnology). HRP-conjugated anti-rabbit IgG (7074S, Cell Signaling Technology) and HRP- conjugated anti-mouse IgG (7076S, Cell Signaling Technology) were used as secondary antibodies.
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10

Immunoblotting of Cytosolic Proteins

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Cytosolic fractions were prepared as described previously (21) (link). Proteins were separated by SDS-PAGE using 4-12% gradient gel (Invitrogen) and transferred to nitrocellulose membranes (Bio-Rad, Hercules, CA). These membranes were blocked with 5% nonfat milk and probed with anti-β-catenin (BD Transduction Laboratories), anti-phospho-β-catenin (Cell Signaling), anti-VEGF (Santa Cruz), anti-p65 (Santa Cruz), anti-TNF-α (Santa Cruz), anti-Snail 1 (Santa Cruz), or anti-actin (Cell Signaling) antibody. Membranes were then incubated with horseradish-peroxidaseconjugated anti-mouse IgG (Santa Cruz) or anti-rabbit IgG (Santa Cruz) antibody and visualized using ECL system (Santa Cruz). To determine the levels of phosphorylation, relative amounts of β-catenin and Snail1 protein were quantitated using densitometry (Multi Gauge V2.2). Based on the density of each β-catenin and Snail1 protein band, the same amount of β-catenin and snail was adjusted and loaded into each lane.
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