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5 protocols using phox2b

1

Immunophenotyping of Neuroblastoma Samples

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Samples taken from 17 NB tumors on relapse were kept in culture medium (RPMI-1640) for 24 h or stored in a freezing solution containing 90% of serum and 10% DMSO until use (histological immunophenotyping and DNA extraction). After paraffin embedding, immunohistochemistry phenotyping was carried out. Tumor tissue sections (3 µm) were de-paraffinized and incubated with the immune-cell marker CD45 (LCA) (Mouse Monoclonal Antibody (mAb)—Cell Marque/Roche), and with the NB markers CD56 (MRQ-42) (Rabbit mAb—Cell Marque/Roche), TH (F-11) (Mouse mAb—Santa Cruz Biotechnology), PHOX-2B (EPR14423) (rabbit mAb—Abcam) and S100 (4C4.9) (Mouse Monoclonal Antibody—Ventana/Roche). In some cases, primary Abs were diluted with Ventana/Roche Ab diluent (for TH mAb) or with BOND Primary Antibody Diluent—Leica (for PHOX-2B mAb). The ultraView Universal DAB detection kit from Ventana and the BOND Polymer Refine Detection kit from Leica (for PHOX-2B mAb) were used to detect the binding of primary antibodies. Sections were counterstained with HEMATOXYLIN—Ventana/Roche.
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2

Porcine Skin Gelatin Hydrogel Fabrication

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Gelatin from porcine skin (Type A, SLCC7838), methacrylic anhydride (MA), Irgacure (2‐Hydroxy‐4′‐(2‐hydroxye‐thoxy)‐2‐methylpropiophenone), and PBS were obtained from Sigma‐Aldrich (Wisconsin, U.S.A.). AlamarBlue and qPCR kits were purchased from Bio‐Rad (Hercules, U.S.A). Carbopol ETD 2020 polymer was purchased from Lubrizol (Wickliffe, U.S.A.). Calcein AM and propidium iodide (PI) were obtained from Biotium (Fremont, U.S.A.). HUVEC culture medium (VascuLife VEGF) was purchased from Lifeline Cell Technology (Oceanside, U.S.A.). Conjugated F‐actin and wheat germ agglutinin (WGA) were purchased from ThermoFisher, USA; CD31, Connexin 43, Phox2B and Synaptophysin antibodies were purchased from Abcam, USA.
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3

Comprehensive Histopathological Analysis of Tumors

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Tumors were fixed in 4% formalin, embedded in paraffin, and cut in 4-μm sections for staining. H&E (Histolab Products) staining was performed for histopathological analysis. The slides were blinded for morphological differentiation assessment and evaluated by an independent viewer. TUNEL assay (Abcam, ab206386), using either methyl green or hematoxylin as counterstain, was performed to asses cell death. Quantification was performed using the software QuPath 0.2.3. 3,3’-Diaminobenzidine (DAB) staining was performed using the Autostainer Plus (Dako), and fluorescence staining was performed manually. Heat-induced antigen retrieval was done using sodium citrate buffer (pH 6.0). The antibodies used are PHOX2B (1:1000; Abcam), PHOX2B-AF647 conjugate (1:100; Santa Cruz Biotechnology), Ki67 (1:200; Dako), CD34 (1:200; Santa Cruz Biotechnology), MYCN (1:200; Proteintech), TH (1:1000; Abcam), SOX9 (1:500; Abcam), and LGR5 (1:150; Abcam). Processing and quantification of fluorescence images were performed with ImageJ.
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4

Comprehensive Histopathological Analysis of Tumor Samples

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Tumours and organs were fixed in formalin, embedded in paraffin and then sectioned and stained for histopathologic assessment by a practicing paediatric pathologist (AJG). Stains included haematoxylin and eosin (H&E), Mason trichrome, orcein elastic and Papanicolaou and Giemsa. Immunohistochemical (IHC) staining included NB84 (1:400, Leica, Nussloch, Germany), synaptophysin (1:200, Leica), CD56 (1:100, Leica), PHOX2B (1:1000, Abcam, Cambridge, UK), CD45 (1:400, Leica), CD20 (1:200, Leica) and CD3 (1:200, Leica). For EBV-encoded RNA in situ hybridisation (EBER-ISH), slides were stained using BOND EBER probe (Leica). Images were captured using an Olympus BX53 light microscope and CD73 camera with CellSens software.
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5

Evaluation of PRMT Inhibitors in Neuroblastoma

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Furamidine, pentamidine, hexamidine, and TC-E5003 were purchased from Tocris. Decamidine and SKLB639 were described previously15 (link),17 (link). Antibodies used in this study include PRMT13 (link), PRMT5 (Millipore), aDMA (Cell Signaling), sDMA (Millipore), MYCN3 (link), TH (Millipore), PHOX2B (Abcam), PARP (Cell Signaling), ATF5 (Abcam), Flag (Thermo Fisher Scientific), and β-actin3 (link).
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