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28 protocols using impact dab

1

Quantification of Cleaved Caspase-3 in PDX Tumors

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PDX 12424 tumours treated with nab-paclitaxel were FFPE. Heat-mediated antigen retrieval was carried out with DAKO Target Retrieval Solution and sections were stained for cleaved CASP-3 (Cell Signaling; 9661), followed by biotinylated goat anti-rabbit (Jackson Immunoresearch; 711-066-152) and ABC-RTU (Vector Laboratories, Inc, Burlingame CA, USA) and visualized with Impact DAB (Vector). Labelled cells were quantified by counting five random fields/slide at × 400 magnification; tumours from three mice per group were used. Since tumours naturally have large areas of necrosis, counts were made by avoiding these areas.
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2

Immunohistochemical Staining Procedure for MS Samples

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Paraffin wax sections were de-waxed, rehydrated and subjected to heat-induced epitope retrieval as described previously [25 (link)]. Following overnight incubation with the primary antibody, sections were incubated with biotinylated secondary antibody and avidin-biotin peroxidase complex with diaminobenzidine as the chromogen (Impact DAB; Vector Laboratories Ltd., Peterborough, Cambridgeshire, UK). Individual antibody details are listed in Additional file 1: Table S2. Snap-frozen, unfixed cryosections were air-dried, fixed in methanol or 4 % paraformaldehyde and quenched with H2O2 before immunostaining. Immunofluorescence staining was performed on wax or snap-frozen sections by sequential antibody incubation and detection, followed by diamidino-2-phenylindole (DAPI) counterstaining. In all instances, sections from each MS case for each antibody were immunostained in the same experimental run to ensure comparability of labelling. All experiments included primary antibody-negative controls and irrelevant species-specific antisera as positive controls. Sections were viewed on a Leica DRMB brightfield microscope (Leica Microsystems, Milton Keynes, Buckinghamshire, UK), a Zeiss Axio Imager under epifluorescence or a Zeiss LSM 710 confocal (Carl Zeiss Ltd., Cambridge, Cambridgeshire, UK).
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3

Bladder Tumor Staging and IHC Analysis

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Bladders were paraffin embedded, sectioned, and stained with hematoxylin–eosin for classification of tumor stage according to the World Health Organization/International Society of Urological Pathology consensus. Tumor staging was performed in a blinded fashion by a board certified genitourinary pathologist. For IHC staining, high-temperature antigen retrieval (18–23 psi/126°C) was performed by immersing the slides in Trilogy (Cell Marque). Endogenous peroxidase activity was blocked for 5 minutes in using Dual Endogenous Enzyme Block (Dako S2003). Primary Antibodies used were KI 67 (Abcam; ab16667) and cleaved caspase-3 (Cell Signaling Technology; ab9661). Slides were stained with Impact DAB (Vector Labs) for 3 minutes and counterstained with hematoxylin (Richard-Allen). For each section, Ki67+ cells were counted in 10 random 400× fields. Immunofluorescence was performed on a separate set of slides which were stained for TUNEL per manufacturer instructions (ApopTag Peroxidase In Situ Apoptosis Detection Kit, Millipore) and counterstained with DAPI (Vector Laboratories). For each section, apoptotic cells were counted in five random fields.
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4

Immunohistochemical Analysis of Protein Expression

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Successive coronal 40 µm sections were collected in every fourth section (160-µm intervals). The sections were incubated sequentially in 0.3% H2O2 in methanol for 1 hour at 23°C, 5% normal goat serum with 0.3% Triton X-100 in 0.01 M PBS for 1 hour at 23°C, primary antibodies (Table 1) for 48 hours at 4°C, and secondary antibody (Table 1) for 2 hours at 23°C. The reaction products were visualized using the Vectastain Elite ABC Rabbit IgG Kit (PK-6101; Vector Laboratories, Newark, CA, USA) and the peroxidase substrate kit imPACT DAB (SK-4105; Vector Laboratories). The sections were examined under a microscope (BZ-X800; KEYENCE).
The immunopositive cells were categorized in 0.5-mm intervals, 2.0 mm rostral, and 6.5 mm caudal to the obex.
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5

Immunohistochemical Analysis of NB Tumors

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Frozen sections of the native NB tumors were fixed in pre-cooled acetone (−20°C) for 10 min, washed with PBS and treated with 0.3% H2O2 solution in PBS at room temperature for 10 min to block endogenous peroxidase activity. The samples were blocked for 1 h in 5% normal horse serum (Vectastain Elite ABC HRP Kit R.T.U.; Vector laboratories, PK-7200). The samples were then incubated with the following primary antibodies diluted in antibody diluent (Dako, S3022), in a humid chamber overnight at 4°C: Collagen 1 (dilution 1:500; Abcam, ab34710), EZH2 (dilution 1:50; Millipore # 07–689) and GLI1 (GLI1-rabbit dilution 1:50, Cell Signaling, #2553). The next day, the sections were washed (3 times, 5 min each) with PBST and incubated with secondary antibodies (Vectastain Elite ABC HRP Kit R.T.U. from Vector laboratories, PK-7200), following manufacturer instructions, and developed using Impact DAB (Vector Laboratories, SK4105). Negative controls were prepared by omitting the primary antibody step. Slides were counterstained with Hematoxylin QS (Vector Labs).
For the hyaluronan acid binding protein (HABP) staining, the sections were blocked using 1% BSA in HBSS at room temperature for 30 min, and incubated with a biotinylated HABP antibody (dilution 1:100; Millipore #385911). A Streptavidin Alexa Fluor 488 conjugate (dilution 1:500, Molecular Probes) was used as a secondary antibody.
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6

Immunohistochemical Analysis of Neuroblastoma

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Sections were deparaffinized and gradually hydrated in xylene and graded ethanol/distilled water solutions before performing antigen retrieval in 1X target retrieval solution (Dako, S1699) in a pressure chamber (SP1 Program, 125°C, 20 s; Pascal S2800, Dako). Samples were cooled to room temperature, treated with peroxidase-blocking solution (Dako, #S2023) for 1 h in a humid chamber and washed 3 times (5 min each) with PBST. Then, samples were blocked for 1 h in 5% normal horse serum (Vectastain Elite ABC HRP Kit R.T.U.; Vector laboratories, PK-7200) and incubated with specific primary antibodies for MYCN (dilution 1:100; Abcam, ab198912), CD31 (dilution 1:50, Abcam, ab28364), Ki67 (dilution 1:100, Abcam, ab15580), overnight at 4°C. After washing with PBST (5 min, 3 times), samples were incubated with secondary antibodies (Vectastain Elite ABC HRP Kit R.T.U.; Vector laboratories, PK-7200), following manufacturer instructions, and developed using Impact DAB (Vector Laboratories, SK4105). Negative controls were prepared by omitting the primary antibody step.
Frozen sections of Neuroblastoma tumors were fixed in pre-cooled acetone (-20°C) for 10 min, washed with PBS, treated immediately with peroxidase-blocking solution and incubated with primary and secondary antibodies as explained above.
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7

Immunohistochemical Assessment of HA-PTEN Expression

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The expression of HA-PTEN protein in tumour tissue section was assessed by immunohistochemistry. Sections (5 μm thick) were obtained from tumours treated with PBS, PTEN-mRNA-PGDP NP, or EGFP-mRNA-PGDP NP. Paraffin-embedded sections were deparaffinized, rehydrated, and washed in distilled water. Samples were then incubated for 20 min with 0.3% hydrogen peroxide (H2O2) at room temperature to quench endogenous peroxidase activity followed by antigen retrieval in citrate buffer (pH 6.0) using a microwave for 10 min (2 times, each time 5 min). After washing with PBS (pH 7.4), the samples were treated with the Avidin/Biotin Blocking kit (Vector) to quench endogenous biotin, and then immersed in blocking buffer (1% BSA, 5% normal goat serum) for 60 min. Tissue sections were then incubated with primary rabbit anti-HA antibody at 4°C overnight in a humid chamber. After being rinsed with PBS, the samples were incubated with biotinylated secondary antibody for 30 min at room temperature, followed by incubation with the avidin–biotin–horseradish peroxidase complex (ABC kit, Vector Laboratories, Inc). Staining was developed with the diaminobenzidine peroxidase substrate kit (Impact DAB, Vector Laboratories, Inc) for 3 min. Sections were then counterstained with hematoxylin (Sigma), dehydrated, and mounted.
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8

Histological Characterization of MRI Features

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Tissue blocks were paraffin-embedded and cut on a microtome into 3–5 µm thick sections. For histological characterization of the MRI features, the following antibodies were used: CD68 (DAKO, clone PG-M1, 1:100), and GFAP (Dako, GA52461-2, 1:100). For immunohistochemistry, slides were incubated with PBS before and blocking in PBS/10% bovine serum albumin for 1 hour at room temperature. Endogenous peroxidase was blocked with 0.3% hydrogen peroxide for 20 min. Slides were incubated with primary antibodies overnight at 4°C. Secondary biotinylated antibody was applied for 1 hour at room temperature followed by the ABC complex reagent (VectorLabs) for one hour. The colour reaction was carried out with ‘ImpactDAB’ (VectorLabs). All counterstainings were done with Haematoxylin. In addition, Luxol Fast Blue staining was used to assess myelination, Prussian Blue for hemosiderin, and Elastica van Gieson staining to highlight elastic lamina in vessel walls. Subsequently, slides were dehydrated in ethanol/xylol and mounted using ‘Entellan’ (Merck Millipore). Slides were scanned using a Hamamatsu slide scanner (Hamamatsu Photonics). Corresponding microphotographs of regions of interest were taken using NDP.view2 viewing software.
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9

Quantitative Analysis of Reactive Astrogliosis

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Reactive astrogliosis was assessed by quantification of glial fibrillary acidic protein (GFAP). Tissue sections were washed in PBS and endogenous peroxidase activity was blocked with 3% H2O2 in methanol for 10 minutes. Sections were then blocked with a solution of 2% goat serum and 0.2% Tween 20 in PBS for one hour and then incubated in blocking buffer overnight at 4°C with a primary antibody against GFAP (ab4674, Abcam, Cambridge, UK; 1:8000). They were then rinsed with PBS and incubated with a biotinylated secondary antibody (Vector Labs, Burlingam, CA; 1:200; 1 h). Immunolabeling was visualized with VECTASTAIN ABC and Impact DAB (Vector Labs). Using SPOT Basic imaging software (Sterling Heights, MI), the dorsal striatum was photographed at 10× magnification across 4–6 coronal sections from each subject (n = 7/group). The camera frame was centered within the dorsal striatum, and GFAP immunoreactivity was quantified within the frame using ImageJ by an observer blinded to the treatment condition. Images were converted to 8-bit, and contrast and brightness were adjusted equally for all images using the default settings (imagej.nih.gov/ij/plugins/plane-brightness). Artifacts were removed if needed, and the percent area of immunolabeling was determined by analyzing the particle area with a threshold set to include only immunolabeled cells.
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10

Immunohistochemical Analysis of Liver Tissue

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For immunohistochemistry analysis, paraffin-embedded liver tissues were cut into 4-μm sections, deparaffinized in xylene, rehydrated through a graded ethanol series, and then subjected to antigen repair by citric acid using the microwave boiling method. Endogenous peroxidase activity was blocked by incubation with 3% hydrogen peroxide at room temperature for 10 min. The slides were incubated with anti-HA antibody (1:400, #3724; Cell Signaling Technology, MA, USA) overnight at 4°C in a humidified chamber. The next day, sections were washed in PBS three times for 5 min each. Secondary antibody was applied for 30 min at 37°C, and color was developed using a diaminobenzidine peroxidase substrate kit (Impact DAB, Vector Laboratories, CA, USA). Sections were then counterstained with hematoxylin, dehydrated, and mounted.
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