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6 protocols using ab3328

1

Immunoblotting Analysis of Immune Proteins

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Cells were washed with PBS, lysed in sample buffer, boiled for 3 min, resolved by SDS-PAGE and analyzed by immunoblotting using primary antibodies specific for human MX2 (sc-47197 (N-17), Santa Cruz Biotechnology), human TRIM5α (ab4389, Abcam), human PSMB8 (ab3329, Abcam), human PSMB9 (ab3328, Abcam), human PSMB10 (ab77735, Abcam), human PA28A (ab155091, Abcam), human PA28B (ab183727, Abcam), FLAG (HRP-conjugated M2, Sigma), HA (HRP-conjugated 3F10, Sigma) or human α-tubulin (DM1A, Sigma), and detected using either horseradish peroxidase-conjugated secondary antibodies and chemiluminescence (ECL+ western blotting substrate, Pierce) or IRDye®-800CW-labelled secondary antibodies and the LI-COR infrared imaging technology (LI-COR UK LTD).
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2

Immunohistochemical Analysis of APM Components

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For staining the following antibodies and dilutions were used: for TAP1, rabbit polyclonal H-300 (1:100); for TAP2, rabbit polyclonal H210 (1:100), both from Santa Cruz Biotechnology, Inc (Dallas, TX, USA); for LMP2, rabbit polyclonal antibody ab3328 (1:1000); for LMP7, ab3329 (1:500), both from Abcam (Cambridge, United Kingdom). As secondary antibodies, BA-1000 anti-rabbit (1:200) and BA-2000 anti-mouse (1:200) both from Vector Laboratories (Burlingame, CA, USA) were used. The tumors included in the present study were formerly evaluated for LMP10 with ab C-2 (Santa Cruz Biotechnology, Inc) [27] (link), and for HLA class I with mouse monoclonal antibodies HCA-2 and HC-10 [15] (link), [16] (link). Data from these studies have been included in the present study for comparison to other APM components.
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3

Alveolar Macrophage Protein Isolation

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For protein isolation, alveolar macrophages were washed twice with ice cold PBS and lysed with RIPA buffer (50 mM Tris·HCl, pH 7.5, 150 mM NaCl, 1% Nonidet P-40, 0.5% sodium deoxycholate and 0.1% SDS). Samples were centrifuged to remove cell debris and protein concentrations were determined using standard Bradford assays. In all, 10 μg of protein lysates were separated on 10% SDS-PAGE and blotted onto polyvinylidene difluoride membranes (162–0177, Bio-Rad, Hercules, CA, USA). The following antibodies were used: LMP2 (ab3328, Abcam, Cambridge, UK), LMP7 (ab3329, Abcam), 20S α1+2+3+5+6+7 (hereafter called α1–7; clone MCP231, ab2267, Abcam), Psmb5 (detecting β5, ab90867, Abcam), AKT (4685, Cell Signaling, Beverly, MA, USA), p-AKT (4060, pSer473, Cell Signaling), STAT6 (9362, Cell Signaling), p-STAT6 (9361, pTyr641, Cell Signaling), IRF4 (M17, Santa Cruz, Dallas, TX, USA), Arginase 1 (H-52, Santa Cruz), iNOS (610331, BD Transduction Laboratories, Franklin Lakes, NJ, USA), IL4R (ab157162, Abcam), HRP-conjugated anti-β-actin (Sigma-Aldrich), HRP-conjugated anti-rabbit (Abcam) and anti-goat antibodies (Santa Cruz).
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4

Immunoblotting Analysis of Immune Proteins

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Cells were washed with PBS, lysed in sample buffer, boiled for 3 min, resolved by SDS-PAGE and analyzed by immunoblotting using primary antibodies specific for human MX2 (sc-47197 (N-17), Santa Cruz Biotechnology), human TRIM5α (ab4389, Abcam), human PSMB8 (ab3329, Abcam), human PSMB9 (ab3328, Abcam), human PSMB10 (ab77735, Abcam), human PA28A (ab155091, Abcam), human PA28B (ab183727, Abcam), FLAG (HRP-conjugated M2, Sigma), HA (HRP-conjugated 3F10, Sigma) or human α-tubulin (DM1A, Sigma), and detected using either horseradish peroxidase-conjugated secondary antibodies and chemiluminescence (ECL+ western blotting substrate, Pierce) or IRDye®-800CW-labelled secondary antibodies and the LI-COR infrared imaging technology (LI-COR UK LTD).
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5

Western Blot Analysis of Proteasome Subunits

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Total cell lysates containing equivalent protein content were separated by 12% SDS-PAGE and transferred to polyvinylidene difluoride membranes (Millipore, Billerica, MA) via a semi-dry apparatus. Membranes were then blocked in 5% non-fat dry milk (Bio-Rad, Hercules, CA) in Tris-buffered saline with 0.05% Tween-20 (TBST) for 1 h at room temperature, followed by incubation with 3% BSA in TBST containing the respective primary antibodies overnight at 4 °C: β1 (Enzo Life Sciences; PW8140), β2 (Enzo Life Sciences; PW8145), β5 (Thermo Scientific; PA1-977), β1i (Abcam; ab3328), β5i (Abcam; ab3329), β-actin (Novus Biologicals; NB600-501), and β2i (Santa Cruz; sc-133236; 3% milk-TBST used for dilution). Membranes were then washed five times with TBST and incubated with HRP (Horse radish peroxidase)-conjugated secondary antibodies for 1 hour at room temperature. Immunoreactive bands were visualized using SuperSignal West Femto Chemiluminescent Substrate (Thermo Scientific, Rockford, IL) and X-ray film (Thermo Scientific or GeneMate).
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6

Protein Expression Analysis in Whole-Cell Lysates

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Whole-cell lysates were subjected to western blotting to analyze the expression of various proteins using the specific antibodies that follow. Antibodies for PSMA1 (ab3325), PSMB5 (ab3330), PSMB8 (ab3329), PSMB9 (ab3328), ubiquitinated protein (ab140601), p21 (ab109199), cyclin D (ab134175), CDK1 (phospho Y15) (ab47594), and IRE1 (phospho S724) (ab48187) were purchased from Abcam. Anti-actin antibody (#A2066) was purchased from Sigma-Aldrich (St. Louis, MO, USA). Antibodies for cyclin A (sc-271682) and cyclin B1 (sc-166210) were purchased from Santa Cruz Biotechnology (Dallas, TX, USA). Antibodies for cleaved caspase 3 (#9661), PARP (#9532), phospho-histone H3 (Ser10) (#3377), CHOP (#2895), LC3 (#12741), and phospho-eIF2α (S51) (#9721) were purchased from Cell Signaling Technology (Danvers, MA, USA).
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