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7 protocols using anti p53 do 7

1

Immunohistochemical Analysis of P53 and PTEN

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Cell lines were fixed using neutral formalin and included into paraffin to build TMA (Tissue Microarrays) sections. Then, sections were deparaffined, rehydrated and incubated with primary antibodies anti-P53 (DO-7, Dako) or anti-PTEN (6H2.1, Dako). Subsequently, the immunocytochemistry assay was performed with streptavidin-biotin technique, using the Immunostainer Techmate 500 (Dako), and the results were visualized by Envision System (DakoCytomation).
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2

Immunohistochemical Analysis of Gastrointestinal Markers

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Immunostaining was carried out on 3‐μm‐thick paraffin sections. After deparaffinization and rehydration, the sections were heated in Envision FLEX target retrieval solution (pH 6.0 or 9.0; Dako) for 20 min and washed 2 × 5 min in phosphate‐buffered saline. Endogenous peroxidase was blocked with 3% hydrogen peroxide for 5 min. Nonspecific binding was blocked with 1.5% normal serum in phosphate‐buffered saline for 35 min at room temperature. Immunohistochemical staining was performed as described previously. Immunohistochemical analysis used anti‐p53 (DO7; Dako), anti‐MUC2 (Ccp58; Novocastra), anti‐MUC5AC (CLH2; Novocastra), anti‐MUC6 (CLH5; Novocastra), anti‐CD10 (56C6; Novocastra), Annexin A10 (polyclonal; Novusbio), and anti‐Ki67 (MIB1, monoclonal; DAKO). Detailed data are presented in Table S2.
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3

Comprehensive Immunohistochemical Analysis of Tissue

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Sections of formalin-fixed, paraffin-embedded tissue blocks were cut at a 3–4-μm thickness for immunohistochemical analysis using an extensive panel of antibodies, including anti-p53 (DO7; DAKO, Copenhagen, Denmark), anti-MUC2 (Ccp58; Novocastra Laboratories, Newcastle, UK), anti-MUC5AC (CLH2; Novocastra Laboratories), anti-MUC6 (CLH5; Novocastra Laboratories), anti-CD10 (56C6; Novocastra Laboratories), anti-caudal-related homeobox transcription factor 2 (CDX2; DAK-CDX2, ready to use; Agilent Technologies), anti-β-catenin (clone 14; Becton Dickinson), and anti-Ki-67 (MIB1, monoclonal; DAKO) antibodies. The sections were prepared, dried, deparaffinized, and rehydrated before subjecting to microwave treatment (H2500, Microwave Processor; Bio-Rad Laboratories, Hercules, CA, USA) in citrate buffer (pH 6.0) for 5 min. The slides were counterstained with hematoxylin, dehydrated, and then mounted. Immunohistochemical staining was examined using the Envision+ System (DAKO).
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4

Immunohistochemical Profiling of DLBCL

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IHC was performed on a total of 130 samples using the DAKO EnVison detection Kit (Dako, Glostrup, Denmark) in accordance with the manufacturer’s instructions. Freshly cut 4-um FFPE sections were subjected to heat-induced antigen retrieval in EDTA buffer (PH = 9.0) for 2–3 min. A panel of primary antibodies was utilized in our study, including anti-CD10 (clone 56C6, 1:50, Novocastra), anti-BCL6 (clone PG-B6p, 1:40, Dako), anti-MUM1 (clone MUM1p, 1:50, Dako), anti-BCL2 (clone 124, 1:100, Dako), anti-C-MYC (clone EP121, 1:75, Zhongshan) and anti-P53 (DO-7, 1:100, Dako). IHC staining was performed with colour development carried out using 3,3′-diaminobenzidine tetrahydrochloride.
According to the requirements and recommendations of the 2016 revised WHO classification system, the expression statuses of BCL2 and C-MYC were identified in all samples. Cutoff values of 50% for BCL-2 expression and 40% for C-MYC expression was used to identify DEL [9 (link)]. Germinal centre B-cell (GCB)/non-GCB types were grouped according to Han’s algorithm [14 (link)], which is based on immunostaining against CD10, BCL-6 and MUM1, using a cut-off of 30% for each antibody.
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5

Western Blot Protein Analysis Protocol

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Cells were washed twice on ice with PBS before adding protein lysis buffer (1× protease inhibitor cocktail, Roche, Basel, Switzerland, 1.5mM EDTA, 1mM DTT, 10% glycerol, 25mM HEPES, pH 7.6). The protein concentration was determined by the Bradford assay (BioRad, Hercules, CA) using BSA as a standard. Total protein (20μg) was resolved by 10% SDS-PAGE for subsequent western blot analysis using antibodies against the following proteins (diluted in TTBS (Tween–Tris Buffered Saline: 0.02% Tween-20 in 100mM Tris-CL [pH 7.5], 1:1000) as indicated): anti-p53 (DO7, DAKO, Glostrup, Denmark), anti-NKX2-1 (sc-53136, Santa Cruz, Santa Cruz, CA), anti-Sp1 (sc-14027, Santa Cruz, CA), anti-p65 (sc-8008, Santa Cruz, CA), anti-Snail (sc-28199, Santa Cruz, CA), anti –NF-Y (sc-17753, Santa Cruz, CA), anti-vimentin (sc-6260, Santa Cruz, CA), anti-IKKβ (sc-271782, Santa Cruz, CA), ant-α-tubulin (sc-5266, Santa Cruz, CA), anti-p21 (sc- 6246, Santa Cruz, CA) and anti-E-cadherin (cat. 610182, BD Biosciences, Franklin Lakes, NJ). The gel was transferred to a Hybond-C Extra membrane (GE Healthcare, Little Chalfont, UK) and immunoblotted with primary antibody, as indicated in the figure legends. Anti-mouse or rabbit IgG conjugated to horseradish peroxidase was used as the secondary antibody for detection using an ECL western blot detection system.
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6

Immunohistochemical Analysis of CLIC4, p53, TGF-β, TNF-α, and α-SMA

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For immunohistochemical analysis, 3-µm thick tissue sections were mounted on organosilane-coated slides (3-aminopropyltriethoxysilane; Sigma Chemical Co., St. Louis, MO, USA). Deparaffinization, rehydration and antigen retrieval were performed using Trilogy (Cell Marque, CA, USA) diluted in distilled water (1:100) and heated in a Pascal pressure cooker. Endogenous peroxidase and nonspecific antibody reaction were blocked with 3% hydrogen peroxide and Protein Block (Thermo Scientific, Runcorn, UK), respectively. The tissues were incubated with primary antibodies anti-CLIC4 (EPR14253, Abcam, 1:4000, 60'), anti-p53 (DO7, DAKO, 1:400, 60'), anti-TGF-β (3C11, Santa Cruz, 1:500, 60'), anti-TNF-α (52B83, Santa Cruz, 1:400, overnight) and anti-α-SMA (1A4, DAKO, 1:800, 60'). Antibodies were detected using the HiDef DetectionTM HRP Polymer system (Cell Marque) and reaction was developed with diaminobenzidine as chromogen (DAB, Sigma Chemical, St Louis, MO, USA). The sections were counterstained with Mayer's hematoxylin and mounted in Permount® (Fisher Scientific, Fair Lawn, NJ, USA). Replacement of the primary antibodies with bovine serum albumin was used as negative control and human melanoma tissue served as positive control.
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7

Immunohistochemical analysis of ARID1A and p53

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Immunohistochemical analyses were performed on formalinfixed paraffin-embedded specimens. Antigen retrieval was performed by autoclaving the samples in 10 mM citrate buffer (pH 6.0) for 10 min. Anti-ARID1A (HPA005456; 1:2000; Sigma-Aldrich, St Louis, MO, USA) and anti-p53 (DO-7; 1:100; Dako, Glostrup, Denmark) antibodies were used as primary antibodies. An automated stainer (Dako) was used in accordance with the manufacturer's protocol. ChemMate EnVision (Dako) methods were used for detection. For p53 staining, diffuse and complete lack of staining were regarded as abnormal expression patterns. For ARID1A, areas devoid of expression, occupying > 10% of lesions, were regarded as significant.
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