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4 protocols using human osteoactivin gpnmb anti goat

1

Immunohistochemical Analysis of Kidney Cancer

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Hematoxylin and eosin staining was performed by standard methods. Histology was reviewed by a pathologist experienced in evaluating kidney cancer. Immunohistochemistry for TFE3 and GPNMB was performed as previously described [28 ]. Primary antibodies were as follows: Human Osteoactivin/GPNMB anti goat (R&D Systems; 1:800); TFE3 anti rabbit (Sigma Aldrich; 1:800). Spectral karyotyping and TFE3 was performed as previously described [29 (link)] and outlined in Supplementary Methods.
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2

Immunohistochemical Profiling of Tumor Samples

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Five-micron thick formalin-fixed paraffin-embedded sections were cut from all available tumor blocks. IHC staining and H&E staining were performed by either VitroVivo Biotech (Rockville, MD) or the Molecular Histopathology Laboratory at the Frederick National Laboratory for Cancer Research (Frederick, MD) using standardized methodologies. IHC staining was performed using either Human Osteoactivin/GPNMB anti-goat (R&D Systems, Minneapolis, MN), TFE3 anti-rabbit (Sigma Aldrich, Burlington, MA), Phospho-S6 Ribosomal Protein (Ser235/236) anti-rabbit (Cell Signaling Technology, Danvers, MA), or Phospho-4-E-BP1 (Thr37/46) anti-rabbit (Cell Signaling Technology, Danvers, MA). For selected tumors, an immunohistology panel was performed evaluating HMB45 (Agilent Dako, Carpinteria, CA), Melan-A (Abcam, Waltham, MA), Pan-cytokeratin (Novus Biologicals, Centennial, CO), Cytokeratin 7 (Abcam, Waltham, MA), Cathepsin K (Abcam, Waltham, MA), and Carbonic anhydrase IX (Cell Signaling Technology, Danvers, MA). Images were captured using an AxioScan.Z1 Slide Scanner (Zeiss, Oberkochen, DE).
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3

Immunohistochemistry of Melanoma Markers

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Five-micron thick formalin-fixed paraffin-embedded sections were deparaffinized and blocked with methanol containing 30% H2O2. Antigen retrieval was performed with Citrate buffer at pH 6.0 in a steamer cooker. Slides were blocked in PBS with normal rabbit serum, incubated with primary antibodies overnight and with secondary antibodies conjugated with biotin for 40 min at room temperature. Signal was detected with streptavidin-HRP for 40 min at room temperature. DAB (3,3′-diaminobenzidine) counterstaining was performed by diluting DAB 1:40 in DAB buffer plus H2O2 for 2 min and Hematoxylin for 10 seconds (Vector Laboratories). Pictures were obtained with an AxioScan.Z1 Slide Scanner (Zeiss, Oberkochen, DE). The primary antibodies were used as follows: Human Osteoactivin/GPNMB anti goat (R&D Systems, Minneapolis, MN; 1:800), MITF anti mouse (EMD Millipore, Billerica, MA;1:50); TFE3 anti rabbit (Sigma Aldrich; 1:800), TFEB anti rabbit (Bethyl Laboratories, Montgomery, TX; 1:200).
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4

Quantifying Lysosomal Activity in Cells

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Reagents were obtained from the following sources: human TFEB (4240) anti‐rabbit from Cell Signaling Technology; antibody to murine TFEB from Bethyl laboratories (A303‐673A); human TFE3 anti‐rabbit from Sigma Aldrich (#SAB4200803), antibody to Cadherin 16 from Novus Biologicals (NBP1‐59248); human osteoactivin/GPNMB antigoat from R&D Systems; mouse anti‐LAMP1 was from Santa Cruz (1D4B). DMEM, RPMI, and fetal bovine serum (FBS) were from Euroclone; lentiviral plasmids sh‐RNAs, amino acids, and blasticidine were from Sigma Aldrich; Torin 1 (cat. no. 4247) from Tocris; LysoTracker DND99 (L7528) and DQ Green BSA (D12050) were from Thermo Fisher; siRNAs were purchased as SMART pool from Dharmacon.
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