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23 protocols using β actin hrp

1

Establishment and Characterization of DDLPS Cell Lines

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LPS141, a primary human cell line derived from a high grade retroperotineal DDLPS, was kindly provided by Dr. Jonathan Fletcher (DCFI, Boston, MA). Human DDLPS cell lines Lipo224, Lipo224B, Lipo246, Lipo815, and Lipo863B were established in our laboratory from surgically resected human retroperitoneal DDLPSs and maintained as previously described18 (link). Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM 1X) supplemented with 10% FBS, 100 U/mL penicillin, and 100 μg/mL streptomycin, or as otherwise described in figure legends. All the established DDLPS cell lines were DNA fingerprinted using short tandem repeat DNA fingerprinting3 (link) (cell line STR results have been previously reported3 (link); STR for Lipo815 is reported in Supplementary Table 1).
Recombinant Human HGF was purchased from R&D Systems, and the Met inhibitors, EMD1214063 and SU11274, were purchased from Chemitek and Selleckchem, respectively. Antibodies used for western blot analyses or for immunohistochemistry were purchased from the following manufacturers: Met, pMet (Tyr1234/Tyr1235), AKT, pAKT (Ser473), ERK, pERK (Y202/T204) (Cell Signaling), CD31 (BD Pharmingen), Ki67 (Thermo/Lab Vision), and β-actin-HRP (Santa Cruz Biotechnology).
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2

Western Blotting for Protein Profiling

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Western blot analyses were carried out with 100µg of whole cell extract derived as previously reported (Gonzalez et al., 2011 (link)). Membranes were blocked and incubated with primary antibodies in 4% milk (Sigma-Aldrich, #A3059) in TBS-T (Bio-Rad, #161–0372, with 0.05%) Tween 20) at 4°C overnight. Nuclear and cytoplasmic enriched fractions were isolated as reported (Gonzalez et al., 2009 (link)). Mouse monoclonal β-Actin-HRP (Santa Cruz, #47778), anti-GAPDH (Abcam, #ab9484), and rabbit polyclonal anti-Histone H3 (Cell Signaling, #9715) were used to confirm equal loading. Primary antibodies from Cell Signaling included anti-EZH2 (#5246), anti-DDR2 (#12133), anti-DDR1 (#5583), anti-phospho-FAK (Y925) (#3284), anti-FAK (#13009), anti-E-cadherin (#3195), anti-phospho-p44/42 MAPK (ERK1/2) (Thr202/Tyr204) (#4370), anti-p44/42 MAPK (ERK1/2) (#4695), anti-phospho-SRC Family (Tyr416) (#21010, anti-Src (#2109), anti-SLUG (#9585) and anti-Vimentin (#5741); from Abcam anti-Collagen I (#AB34710) and anti-CK18 (#AB189444); from R&D Systems phospho-DDR2 (Y740) (#MAB25382); and from Santa Cruz Biotechnology anti-ZEB1 (#SC-81428).
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3

Maintenance and Characterization of TNBC Cell Line MDA-MB-231

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Human triple-negative breast cancer (TNBC) cells MDA-MB-231 were maintained in DMEM (Hyclone, Cramlington, UK) supplemented with antibiotics (penicillin 50 U/mL; streptomycin 50 µg/mL) and 10% fetal bovine serum (Hyclone, Cramlington, UK) at 37 °C. The culture medium was changed every three days, and cells were passaged once a week when the culture reached 95% confluence. Cell viability measured using trypan blue dye exclusion was higher than 99% in all experiments. All in vitro experiments were repeated at least three times. Antibodies to PD-L1, Akt, phospho-Akt, phospho-ERK, Snail, p21, and β-tubulin were obtained from Cell Signaling Technology (Cell Signaling, Beverly, MA, USA). Antibodies to ERK, Survivin, RhoA, Rac1, Cdc42, c-Fos, c-Myc, and β-actin HRP were obtained from Santa Cruz Biotechnology, Inc. (Santa Cruz, CA, USA). COX2 antibody was obtained from Abcam (Cambridge, UK).
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4

Immunoblotting Analysis of Cell Signaling

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Antibodies specific for cyclooxygenase-2 (COX-2) and inducible nitric oxide synthase (iNOS) were procured from Cayman Chemical Company (Ann Arbor, MI). Antibodies specific for ERK1/2, p38, JNK, CDK2, CDK4, p27, p53, p21, cytochrome c, cyclin E1, cyclin D1 and β-Actin-HRP were purchased from Santa Cruz Biotechnology (Santa Cruz, CA), while p-ERK1/2, p-p38, p-JNK, Bax, Bcl-2, cleaved-caspase 3, cleaved-caspase 9, and proliferating cell nuclear antigen (PCNA) were purchased from cell signaling (Beverly, MA). 2-Acetylaminofluorene (2-AAF), 2-β mercaptoethanol (BME), bovine serum albumin (BSA), dimethyl sulfoxide (DMSO), diethylnitrosamine (DEN), dithiothreitol (DTT), Dulbecco's Modified Eagle's Medium (DMEM), Fetal bovine serum (FBS), streptomycin, penicillin, ethylenediaminetetraacetic acid (EDTA) disodium salt, trypsin/EDTA solution, 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), phenylmethylsulphonyl fluoride (PMSF), propidium iodide (PI), RNase A, protease inhibitor cocktail set-I, Tris buffer, Triton X-100 and Tween-20 were from Sigma Chemicals Co. (St. Louis, MO). All other chemicals and reagents used were of highest purity commercially available.
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5

Western Blot Analysis of Apoptosis Markers

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Acrylamide/bis‐acrylamide, 30% solution (Sigma A3699), 1.5 m Tris‐HCl, pH 8.8 (Teknova T1588), Tris HCl Buffer 0.5 m solution, sterile pH 6.8 (Bio Basic SD8122), Ammonium persulfate (Sigma A3678), UltraPure 10% SDS (Invitrogen 15553‐027), TEMED (Thermo Fisher Scientific 17919), Dithiothreitol (DTT) (BIO‐RAD 1610610) Tris Base (Fisher Bioreagents BP152), Glycine (Fisher Bioreagents BP381), 4x Laemmli sample buffer (BIO‐RAD 1610747), TWEEN 20 (Sigma P9416), Mini Trans‐Blot filter paper (BIO‐RAD 1703932), Nitrocellulose Membranes 0.45 µm (BIO‐RAD 1620115), Western Blotting Luminol Reagent (Santa Cruz sc‐2048). Antibodies; cleaved caspase‐3 (Cell Signaling, 9664S), caspase‐3 (Santa Cruz, sc‐7272). GSDME (Abcam, ab215191), β‐actin‐HRP (Santa Cruz, sc‐47778), HMGB‐1‐HRP (BioLegend, 651411), HSP90 (Santa Cruz, sc‐13119), Goat anti‐Rabbit IgG Secondary Antibody (Thermo Fisher Scientific, 31460), Goat anti‐Mouse IgG (Thermo Fisher Scientific, G‐21040)
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6

Western Blot Analysis of A20 and Caspase-1

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Equally seeded cell cultures were lysed in lysis buffer (20 mM Tris HCl (pH 7.4), 200 mM NaCl, 1% Nonidet P-40) and were denatured in 4x Laemmli buffer. Proteins were separated by Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis (SDS-PAGE), transferred to a nitrocellulose membrane followed by incubation overnight at 4°C with primary antibody against A20 (1:1000, SC- 166692, Santa Cruz Biotechnology), caspase-1 p20 (1:1000, SC-22165, Santa Cruz) and HRP-conjugated secondary goat anti-rabbit (1:2500, DAKO) in Tris-buffered Saline supplemented with 0.05% Tween-20 and 5% nonfat dry milk. Detection was performed with chemiluminescence (Western Lightning Plus-ECL, PerkinElmer) using an Amersham Imager 600 (GE Healthcare). After imaging, blots were incubated with directly labeled primary antibody β-actin-HRP (1:10000, Santa Cruz) for 15 minutes as loading control.
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7

Western Blot Protein Analysis Protocol

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Cells were lysed in NP40 lysis buffer (1% Nonidet P-40, 50 mM Tris (pH 7.5), 150 mM NaCl, 10% glycerol) containing protease inhibitor cocktail (Roche Molecular Biochemicals) and treated with 2× Laemmli sample buffer (Bio-Rad, 1610737) at 95°C for 10 min. The cell lysates were cleared by centrifugation at 14,000 rpm at room temperature for 15 min. Protein extracts were resolved by AnyKD SDS-PAGE gel (Bio-Rad, 4569034) and transferred to a polyvinylidene fluoride (PVDF) membrane (Millipore) and analyzed by immuno-blotting with the following antibodies: β-actin HRP, Santa Cruz (sc-4778) (WB, 1:5,000); SKI (G8, Santa Cruz), WB (1:2,000). Membranes were washed in PBS-T (1× PBS with 0.1% tween-20) and incubated with the following appropriate secondary antibodies from Jackson ImmunoResearch Laboratories: donkey anti-mouse HRP (715–035–150). The secondary antibody was used at a 1:10,000 dilution in 1× PBS-T with 5% BSA. Protein bands were visualized following exposure of the membranes to ECL substrate solution (ThermoFisher) and imaged using Image Lab software. For the original raw gel images of western blot shown in figures, see Supplementary Figure 2.
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8

Protein Expression Analysis by Western Blot

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Total proteins were extracted from cells, and western blotting was performed as previously reported33 (link). The primary antibodies used were: PCNA (Cell Signaling Technology, Danvers MA, USA; #13110; dilution 1:5000); Hexokinase II (EPR20839; 1:500), HIF1α(1:1000), GLUT1 (1:2000), N cadherin (5D5; 1:1000), and Snail/Slug (1:1000), all procured from Abcam (Cambridge, UK); and β-actin-HRP (Santa Cruz Biotechnology, Dalla TX, USA; C4; dilution 1:1000). Western blotting experiments from biological replicates showed similar expression data, attesting to the reproducibility of the results. For band quantification, images were analyzed using Image Lab software (Bio-Rad, Hercules, California, USA). For band quantification, images were analyzed using IMT i-Solution software Martin Microscope Company, Easley, USA).
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9

Immunoblot Analysis of Cellular Proteins

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Cell lysates were harvested in RIPA buffer supplemented with HALT protease inhibitor and stored at -20°C. Proteins were separated on a 4–12% SDS-PAGE gel and blotted on PVDF membranes. Immunoblots were performed using antibodies directed against HA (sc-7392, Santa Cruz Biotechnology), p115 RhoGEF (sc-74565, Santa Cruz Biotechnology), ROCK1 (sc-5562, Santa Cruz Biotechnology), c-Src (sc18, Santa Cruz Biotechnology), β-actin-HRP (sc-47778, Santa Cruz Biotechnology), endothelial cell growth factor receptor (EGFR; Cell Signaling; D3881), Streptavidin-HRP (Thermo Scientific; 21130), UL44 (CA006-100, Virusys), and TurboID (AS204440, Agrisera) and if required, with the appropriate HRP conjugated secondary antibodies (anti-mouse sc-25409 and anti-rabbit sc-2357).
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10

Immunoblotting of NRG1 and Downstream Signaling

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Immunoblotting was performed as described previously (1 (link)). The following antibodies were used: anti-NRG1 β1 (R&D, AF-396-NA), anti-CD74 (Abcam, ab22604), anti-HSP90 (Cell Signaling Technology, No. 4877), anti-ERBB3 (Cell Signaling Technology, No. 4754), anti-phosphoERBB3 (Cell Signaling Technology, No. 4791), ERK1/2 (Cell Signaling Technology, No. 9102), anti-phosphoERK1/2 (Cell Signaling Technology, No. 9106), anti-AKT (Cell Signaling Technology, No. 9272), anti-phosphoAKT (Cell Signaling Technology, No. 9271), and β-actin-HRP (Santa Cruz Biotechnology, sc-47778). Secondary antibodies were IRDye800CW donkey anti-goat IgG (H+L; Licor, 925–32214), IRDye 680LT donkey anti-mouse IgG (H+L; Licor, 925–68022), and IRDye 800CW goat anti-rabbit IgG (H+L; Licor, 926–32211). Fluorescence detection was performed on Odyssey CLx Imaging System (Licor).
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