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8 protocols using clone d33

1

Immunohistochemical Analysis of Biopsy Samples

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The biopsies were fixed in formalin and paraffin-embedded. Paraffin blocks containing sufficient material were selected for immunohistochemical (IHC) staining with the following anti-human monoclonal Abs: eosinophil peroxidase EPX-mAb (clone MM 25-82.2, kindly provided by Mayo Clinic, Scottsdale, USA), GATA-3 (clone L50-823, Cell Marque, Rocklin, USA), T-Bet (clone EPR9302 RabMab, Abcam, Cambridge, UK), and desmin to confirm muscle indemnity (clone D33, Dako, Glostrup, Denmark). The sections were stained with anti-human PD-L1 (clone SP263, Ventana, Bend USA) and anti-human PD-1 (clone NAT105, Abcam, Cambridge, UK). All markers, except for PD-L1, were determined using standardized automated protocols for LEICA BOND MAX II. PD-L1 expression was determined using the Benchmark ULTRA (Roche, Basel, Switzerland). Sections were examined by optical microscopy (Olympus BX40 microscope, DP2-BSW software), and digitalized images were analyzed using ImageJ software (NIH).
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2

Immunohistochemical Analysis of Tumor Markers

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Formalin-fixed tumors were embedded in paraffin using standard procedures. The 5 μm sections were processed and stained with antibodies directed against Ki67 (1:100; Dako, clone MIB-1) and desmin (1:80; Dako, clone D33).
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3

Western Blot Analysis of Desmin and GAPDH

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Cellular homogenates were prepared using RIPA lysis buffer supplemented with protease inhibitors: phenylmethylsulfonyl fluoride (0.4 mM), aprotinin (10 μg/ml), and sodium orthovanadate (10 μg/ml) (Sigma Aldrich). For western blot analyses, equal amount of total cellular proteins were first dissolved by 12% SDS—PAGE electrophoresis, and next transferred at 125 mA for 2 h to PVDF membranes. After blocking non-specific binding with 5% non-fat dry milk (RT, 1 h), the membranes were incubated overnight at 4°C with mouse monoclonal anti-desmin or rabbit polyclonal anti-GAPDH antibodies (1:200, clone D33, Dako and 0.2 μg/ml, G9545, Sigma Aldrich, respectively), followed by 1 h (RT) of incubation with the secondary donkey anti-rabbit or anti-mouse antibodies conjugated with HRP (1:1000, Cell Signaling Technology). The blots were developed using chemiluminescence western blotting detection reagent (Amersham International).
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4

Necropsy and Histochemical Analysis of Degu Tumors

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A complete necropsy was performed on twelve subjects and biopsy samples taken from the other four degus. Tissue samples were fixed in 10% neutral buffered formalin and routinely processed for paraffin embedding. Four-micrometers thick sections were stained with Hematoxylin and Eosin, Goldner’s Trichrome and Periodic-Acid Schiff. Immunohistochemistry was performed on the selected sections using mouse monoclonal antibodies anti-human vimentin (1:50; clone V9, Dako, Glostrup, Danmark), anti-human cytokeratin AE1/AE3 (1:100; Dako, Glostrup, Danmark), desmin (1:50; clone D33, Dako, Glostrup, Danmark) and anti-human c-kit (CD117) (1:300; Dako, Glostrup, Danmark). Antibody binding was detected by EnVision Detection System Peroxidase/DAB +, Rabbit/Mouse (DAKO, Glostrup, Danmark). Tumours were classified according to the WHO classifications of tumors of domestic animals [15 ,16 ,17 ,18 ].
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5

Myogenic Purity Evaluation Protocol

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The myogenic purity of the cultures was monitored by determining the expression of desmin, a cytoskeletal protein that is expressed only in myogenic cells and not in fibroblasts. The number of desmin-positive cells, represented as a percentage of the total number of nuclei, was determined as the myogenic purity of the cell culture, and at least 500 cells were counted. Immunocytochemistry was performed using an antibody specific for desmin, at a dilution of 1:50 (clone D33; DAKO, Denmark). The cells were washed with × 1 phosphate-buffered saline (PBS) and fixed with 100% ethanol for 10 min. The fixation agent was removed by washing three times with × 1 PBS for 5 min. Non-specific binding sites were blocked with 1% FBS diluted in PBS for 30 min. The cells were then incubated with primary antibody against desmin. Specific antibody binding was detected using Alexa Fluor 488 (Invitrogen, USA) directly coupled to the secondary antibody at a dilution of 1:500. The nuclei were fluorescently detected by Hoechst staining (Sigma, USA) at a dilution of 0.0001% w/v. All images were digitalised using ImageJ software.
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6

Immunohistochemical Analysis of Formalin-Fixed Tumors

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Formalin-fixed tumors were embedded in paraffin using standard procedures. The 5 μm sections were processed and stained with antibodies directed against Ki67 (1:100; Dako, clone MIB-1), desmin (1:80; Dako, clone D33) and von Willebrand Factor VIII (1:100; Biocare Medical, #CP039B).
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7

Central Pathology Review of Soft Tissue Tumors

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The central pathology review was performed conjointly by 3 neuropathologists (ATE, PV, EL), a pathologist expert in soft tissue tumors (FL), and a pathologist expert in vascular lesions (MW). For the CNS cases, additional immunohistochemical stainings were performed on paraffin-embedded sections including: CD34 (1:40, clone QBEnd10, Dako, Glostrup, Denmark), smooth muscle actin (SMA) (1:1500, clone 1A4, Dako, Glostrup, Denmark), Desmin (1:400, clone D33, Dako, Glostrup, Denmark), h-caldesmon (1:100, clone h-CALD, Santa Cruz Biotechnology, Dallas, USA), PS100 (1:6000, polyclonal, Dako, Glostrup, Denmark), GFAP (1:200, clone 6F2, Dako, Glostrup, Denmark), neurofilament (1:25, clone 2F11, Dako, Glostrup, Denmark), STAT6 (1:200, clone YE361, Abcam, Cambridge, UK), SSTR2a (1:200, clone UMB1, Abcam, Cambridge, UK) and EMA (1:200, clone GM008, Dako, Glostrup, Denmark). All immunohistochemical stainings were performed in an automatic closed immunostainer (Omnis automate). Orcein staining was also performed.
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8

Evaluating Barrett's Lesion Muscularis

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Slides showing the deepest infiltration level from 33 randomly selected cases were sectioned and stained for smoothelin (Cell Marque Clone R4 A, monoclonal mouse, dilution 1:100) and desmin (Dako, Clone D33, monoclonal mouse, dilution 1:200). The Ventana Ultraview detection system (Roche Diagnostics, Mannheim, Germany) was used for the development of the reactions. The slides were evaluated for the following parameters: Length of muscularis mucosae duplication within the Barrett’s lesion in percent (≤ 5%, > 5 and ≤ 50%, > 50 and ≤ 95%, > 95%); scattered split and notable difference in staining intensity of the SMM vs the DMM. Discrepant cases were reviewed together for a consensual diagnosis.
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