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1

Detecting Apoptotic Cell Death via TUNEL

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For detection of endonucleolytic cleavage of chromatin, characteristic of apoptosis, the terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate nick end-labeling (TUNEL) method was applied, using the In Situ Cell Death Detection Kit, POD kit and including Enzyme solution, Label solution and Converter-POD (Roche, Mannheim, Germany).
Histological slides for quantitation of TUNEL-positive cells were deparaffinized and hydrated. Pretreatment included microwave application with slides placed in 0.01 M citrate buffer (5 min, 360 W). Sections were kept in 1% BSA for 1 h (RT) and afterwards incubated at 37°C with TUNEL mix (TUNEL Enzyme solution: TUNEL label, dilution 1 : 9) for 1 h in a humid chamber. After washing with TRIS buffer, sections were treated for 10 min with methanol/0.3% hydrogen peroxide solution. Thereafter, sections were incubated with Converter-POD solution for 30 min (37°C), rinsed, incubated with DAB (Cell Marque, Rocklin, CA, USA), counterstained with Mayer's hematoxylin and routinely coverslipped.
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2

Ovarian Graft Vascular and Fibrosis Analysis

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Each graft was cut into 5-μm-thick serial sections. Ten sections per transplant, which covered the entire ovarian fragment, were stained with haematoxylin and eosin (H&E).
To detect the functional vascular network, immunostaining was performed in one step. Sections were deparaffinized and rehydrated, and endogenous peroxidase activity was blocked by incubating the sections in 3% hydrogen peroxide for 20 min at room temperature (RT). Non-specific binding sites were blocked by incubation with phosphate-buffered saline (PBS) containing 10% bovine serum albumin for 30 min at RT. The sections were incubated with a ready-to-use anti-fluorescein antibody (Converter-POD, Roche, France), which directly recognized the FITC molecules fixed on dextran, for 30 min at RT. Negative control slides were also performed by replacing the antibody with phosphate-buffered saline (PBS). The 3,3′-diaminobenzidine substrate (K3468, Dako, Belgium) allowed the visualization of positively stained cells, and the sections were counterstained with haematoxylin.
Fibrosis was evaluated using saffron staining. Sections were incubated in 1% saffron solution (Microm Microtech, Francheville, France) in 100% ethanol for 10 min at 37°C.
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3

Quantitative Analysis of Hepatocyte Apoptosis

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TUNEL staining was performed to determine cellular apoptosis post-D-GalN/LPS challenge using the in situ cell death detection kit (cat no. 11684817910; Roche Diagnostics) following the manufacturer's instructions. Cells in each group were fixed with 4% paraformaldehyde at room temperature for 15 min, and dewaxed and hydrated liver tissue sections were permeabilized with 0.1% Triton X-100 solution for 15 min. Then, 50 µl TUNEL reaction mixture (Roche Diagnostics) containing terminal deoxynucleotidyl transferase and fluorescein-dUTP was added into the sample. Subsequently, the cells were incubated at 37°C in the dark for 60 min, washed three times with PBS solution for 5 min. Then, 50 µl Converter-POD (containing anti-fluorescein antibody conjugated with horseradish peroxidase; 1:1,000; cat no. 11684817910; Roche Diagnostics) was added on the sample and incubated at 37°C for 30 min. Substrate solution were added and incubated at room temperature for 10 min. The sample was mounted under glass coverslip with PBS and then (random five fields of view) analyzed under a light microscope at ×20 magnification (Olympus Corporation). Quantification of the percentage of TUNEL-positive cells was performed using Image-Pro Plus software (version 6.0; Media Cybernetics, Inc.).
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4

Apoptosis Analysis in LM3 Cells

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For the apoptosis analysis, LM3 cells were treated with capsaicin, sorafenib or their combination for the indicated times, trypsinized and collected in tubes, and incubated in binding buffer with propidium iodide and FITC-conjugated Annexin V for 10 min in the dark at room temperature. Flow cytometry analysis was used to estimate the cell apoptosis rate. The TUNEL method was applied to visualize the 3′-OH ends of DNA fragments in apoptotic cells according to the manufacturer's protocol (Roche Diagnostics GmbH). LM3 cells were subjected to different treatments for 48 h and fixed in 4% paraformaldehyde. The cells were then submerged in methanol containing 0.3% H2O2 to inhibit endogenous peroxidase activity. Following washing with PBS, cells were covered with proteinase K solution for 10 min. Subsequently, the cells were covered with the TUNEL reaction mixture and incubated for 1 h at 37°C in the dark. After washing in PBS, the cells were placed in Converter-POD (Roche Diagnostics GmbH) and then incubated at 37°C for 30 min. After rinsing in PBS three times for 5 min, the cells were dipped in DAB (Roche Diagnostics GmbH) at room temperature for 10 min and observed under a microscope.
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5

TUNEL Assay for Apoptosis Detection

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The paraffin-embedded sections (5-µm thick) of retinal tissues were deparaffinized, treated with 0.1% Triton X-100 and blocked with 3% H2O2. After washing with PBS, the sections were incubated with the mixture of terminal deoxynucleotidyl transferase (TdT) and fluorescein-labeled dUTP and then treated with converter-POD according to the manufacturer's protocol (Roche, Basel, Switzerland). DAB was added and the sections were counterstained with hematoxylin. Finally, the sections were dehydrated and photographed under OLYMPUS DP73 microscope.
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TUNEL Staining of Frozen Brain Sections

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TUNEL (terminal deoxynucleotidyl dUTP nick-end labeling) staining was carried out according to our published procedure71 (link). In brief, frozen 8-μm coronal sections of the CA1 area were incubated in TUNEL reaction mixture according to kit instructions (Roche Molecular Biochemicals) and The TUNEL reaction incubated in converter-POD (Roche Molecular Biochemicals). Finally, they were treated with DAB-substrate solution.
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7

Quantifying Myocardial Apoptosis via TUNEL

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TUNEL staining was used to measure the rate of apoptosis, as previously described (16 (link)). Following 3 h reperfusion, rat hearts were removed. Myocardial tissue sections were dehydrated in ascending series of ethanol, cleared in xylene and embedded in paraffin. Paraffin-embedded myocardial tissues were cut into sections 5-µm thick, dewaxed with xylene and stained for TUNEL analysis. Sections were penetrated for 8 min with 0.1% Triton X-100 (50 µl; Beyotime Institute of Biotechnology, Haimen, China) and washed 3 times for 5 min each in PBS at 37°C. Sections were then blocked for 10 min by 3% H2O2 and washed 3 times for 5 min each in PBS at 37°C. TUNEL reaction mixture was added to the sections, which were then incubated for 60 min at 37°C in a dark in a humidified environment. Sections were washed 3 times in PBS for 5 min each at 37°C. Converter-POD (50 µl; Roche Diagnostics, Basel, Switzerland) was added to the sections and incubated for 30 min in a humid environment at 37°C. Sections were washed 3 times for 5 min each in PBS at 37°C. Sections were incubated with DAB substrate for 10 min at 15°C and washed 3 times for 5 min each in PBS at 37°C. Finally, sections were stained by hematoxylin for 3 min at 37°C and fixed by neutral balata. TUNEL-positive cells were counted using a fluorescent microscope (Olympus, Tokyo, Japan) at a magnification of ×400.
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8

TUNEL Assay for Cell Death Detection

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For TUNEL staining, an in situ cell death detection kit with horseradish peroxidase (POD; Roche, Basel, Switzerland) was used according to the manufacturer’s protocol. After deparaffinization and rehydration, sections were incubated with protease K (40 μg/mL) for 15 min at 37°C and 3.0% hydrogen peroxide for 5 min to remove endogenous peroxidase. The samples were immersed in TUNEL reaction mixture for 75 min at 37°C in the dark, followed by incubation with Converter-POD (Roche) for 30 min. Images were captured by optical microscopy.
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9

Apoptosis Evaluation via TUNEL Staining

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Apoptosis was evaluated with the TdT-mediated dUTP nick-end labeling (TUNEL) method. Briefly, paraffin-embedded sections were dewaxed, washed with PBS and incubated with Proteinase K for 20 min. After washing with PBS, 50 μL of reaction solution (TUNEL Apoptosis Detection Kit, Roche Applied Science, Mannheim, Germany) was added to each slide at 37°C for 60 min in the dark. After washing, the sections were incubated with 3% hydrogen peroxide for 20 min. Then, 50 μL of Converter-POD (TUNEL Apoptosis Detection Kit, Roche Applied Science, Mannheim, Germany) was added to the sections at 37°C for 30 min. Finally, a DAB Color Development Kit (ZSGB-BIO, Beijing, China) was used to stain the slides. Hematoxylin was used to stain the nuclei. The slides were analyzed using ImageJ Software (National Institutes of Health, Baltimore, MD, United States) at 400× magnification.
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10

Comprehensive Immunohistochemical Tumor Analysis

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Slides (5 µm thick) were autoclaved in Target Retrieval Solution (Dako, S1699, Denmark), incubated in Proteinase K (S3004, Dako, Denmark) or with EDTA- buffer (Prosan, Belgium) according to the immunolabelling for Ki67, CD31, and FITC-dextran, respectively. Endogenous peroxidases were blocked by 3% H2O2/H2O (Merck, Belgium) for 20 minutes, and nonspecific binding was prevented by incubation in PBS/Bovine Serum Albumin 10% (Fraction V, Acros Organics, NJ). Tumor sections were incubated with a mouse monoclonal anti-human Ki-67 antibody (1/100) (clone MIB-1, M7240; DAKO, Denmark), a rat anti-CD31 antibody (1/100) (Ab56299, Abcam, United Kingdom), or a ready-to-use anti-fluorescein antibody (Converter-POD, Roche, France). After 3 washes in PBS or Tris-HCl for CD-31 staining, slides were incubated with an HRP-conjugated secondary antibody, after post antibody blocking (DPVB Blocking, Immunologic NL) for pimonidazole staining, and revealed with Vector DAB (SK-4100, Vector Laboratories, Burlingame, CA, USA). Slides were counterstained with hematoxylin. For lung metastases quantification, six lung sections of 5 µm, spaced by 10 sections of 5 µm, were immunostained with an antibody against human Ki67 as previously described (6 (link)). Metastases were manually counted and classified according to their size (<10 cells, 10 to 50 cells, 50 to 100 cells, >100 cells).
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