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5 protocols using af2330

1

Western Blot Analysis of Glioma Cells

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Whole-cell protein extracts were prepared from briefly cultured RCAS-PDGFb (≤ 7 passages) and GL261 glioma cells or primary naïve astrocytes using RIPA lysis buffer (Sigma-Aldrich, St. Louis, MO, USA) containing EDTA-free protease inhibitor cocktail tablets (Roche Diagnostics, Mannheim, Germany). Protein concentration was determined by a BCA protein assay kit (Thermo Fisher Scientific, Waltham, MA, USA), and 20 µg of total protein of each sample was resolved on a 10% SDS-PAGE gel, followed by wet transfer of resolved proteins onto a PVDF membrane (GE Healthcare, Chicago, IL, USA). Membranes were blocked and followed by overnight incubation at 4 °C for murine GPNMB (goat, AF2330; R&D Systems, Minneapolis, MN, USA) and for murine GAPDH (mouse, ab8245; Abcam, Cambridge, UK). Membranes were incubated with a secondary for anti-rabbit HRP antibody at 1:2000 (#7074; Cell Signaling Technology) and for anti-goat with IRDye 680RD (925-68071; Li-Cor, Lincoln, NE, USA), developed with SuperSignal West Pico Chemiluminescence substrate kit (Thermo Fisher Scientific). Signal was detected by Molecular Imager Gel Doc XR system (Bio-Rad, Hercules, CA, USA).
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2

Quantitative Proteomic Analysis of Cellular Lysates

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Frozen tissue samples and cultured cells were lysed in KPi lysis buffer (25 mM K2HPO4/KH2PO4, pH 6.5, 0.1% (v:v) Triton X-100) supplemented with protease inhibitors (Roche) and sonicated 5× for 1 s with 9 min intervals (amplitude 25%). Equal quantities of protein as assessed by bicinchoninic acid assay (Thermo Fisher Scientific, 23225) were resuspended in Laemmli buffer and denatured at 95 °C. Proteins were subsequently separated by SDS-PAGE using a 10% acrylamide gel and transferred to 0.2 µm nitrocellulose membrane (#1704159, Bio-Rad). Blocking of membranes occurred in 5% (w:v) bovine serum albumin (Sigma, A1906) solution in PBS/0.1% Tween-20 (Sigma, P1379) for 1 h at room temperature (RT). Primary antibodies used were targeted against GPNMB (AF2330; R&D Systems), LIMP2 (NB400-129, Novus Biologicals), and galectin-3 (MABT51, Millipore). Furthermore, rabbit-anti-LAMP1 was used (ab24170, Abcam) and mouse-anti-tubulin (Cedarlane, CLT 9002, Burlington, ON, Canada) was used as loading control. Proteins were detected by using specific secondary conjugated antibodies (Alexa FluorTM 488/647) (Molecular Probes). Detection of immunoblots was performed using a Typhoon FLA 9500 fluorescence scanner (GE Healthcare).
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3

GPNMB Expression in Macrophages

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AKR/J, AKRg-, DBA/2J, DBA/2g+ macrophages, and RAW macrophages with or without CRISPR/Cas9 Gpnmb editing were lysed in RIPA buffer and equal protein levels loaded on 4–20% tris-glycine gels. After transfer, membranes were probed with antibodies against GPNMB (AF2330, R&D Systems) and GAPDH (FL-335, Santa Cruz).
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Detailed Western Blotting and Immunofluorescence Protocols

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For Western blotting the following antibodies were used at the concentrations indicated: mouse anti-Rab27a, 1∶10000 [22] (link); rabbit anti R3G, 1∶5000 (a kind gift of J. Myoshi and Y. Takai); mouse anti-GST, 1∶10000 (Sigma G1160); mouse anti-tubulin, 1∶5000 (Sigma T6557); mouse anti-ATP1a1, 1∶5000 (Abcam ab7671); rabbit anti-His, 1∶1000 (Abcam ab9108); mouse anti Pmel17, 1∶500 (Dako M0634); goat anti-GPNMB, 1∶1000 (R&D Systems AF2330); rabbit anti-Annexin A2, 1∶5000 (a kind gift from J. Ayala-SanMartin CNRS/UPMN/ENS).
For immunofluorescence the following antibodies were used at the concentrations indicated: rabbit anti-Rab27a, 1∶200 (purified by R. Singh, Imperial College, UK); mouse anti-ATP1a1, 1∶200 (Thermo MA1-16731); rabbit anti-Rab5a, 1∶50 (Abcam ab18211); rabbit anti-Rab38, 1∶100 (purified by C. Wasmeier, Imperial College, UK [33] (link)); rabbit anti-Mlph (purified by A. Hume, Imperial College, UK [34] (link))
For immunoprecipitation the monoclonal anti-HA (Roche 12CA5) and anti-FLAG (Sigma F3165) were used.
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5

Immunoblot Analysis of Glycosylation

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Immunoblot analysis was performed as described previously (Kawahara et al., 2009). The blotted membraneswere incubated with one of the following antibodies: 9F5 (1 µg ml−1), ED1 (1 µg ml−1; MCA341GA; Serotec), rabbit anti‐Iba1 (1 µg ml−1;019‐19741; Wako), goat anti‐GPNMB (1 µg ml−1;AF2330; R&D Systems), rabbit anti‐furin (1:500; PA1‐062; Affinity BioReagents), goat anti‐CD40 (1:100; T‐20; Santa CruzBiotechnology), goat anti‐CD86 (1:500; 421340; Genezyme Techne), or mouse anti‐β‐actin (1:2,000; AC15; Sigma–Aldrich) antibodies.
To determine the amount of N‐linked glycosylation, the cell lysate from rat type 1 MG was first denatured in 1% sodium dodecyl sulfate (SDS) (5 min, 60°C). Deglycosylation was then performed with 60 U ml−1 peptide‐N‐glycosidase F (PNGase F;Boehringer Mannheim) in phosphate buffer [0.2M Na2HPO4‐NaOH (pH 7.5) containing 10 mM EDTA, 0.5% NonidetP‐40, and protease inhibitors] for 24 hr at 37°C (SDS concentration during the PNGase F incubation: 0.05%). O‐Glycan chains were analyzed via digestion with α‐2,3,6,8,9‐neuraminidase (sialidase; Calbiochem) and endo‐α‐N‐acetylgalactosaminidase (O‐glycosidase; Calbiochem), according to the manufacturer's instructions. Removal of sugar chains was analyzed by using SDS‐PAGE and immunoblotting as described above.
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