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11 protocols using ab32052

1

Antibody-based Analysis of Stress Signaling

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Antibodies against phosphorylated (p)-eIF2α (Ser51) (ab32157), p-PKR (Thr451) (ab81303), and total PKR (ab32052) were purchased from Abcam (Cambridge, MA, USA). The antibody against total eIF2α (sc-11386) was purchased from Santa Cruz Biotechnology (Dallas, TX, USA). The monoclonal antibody clone 16F8 against p-PERK (Thr980) (#3179) was purchased from Cell Signaling Technology (Danvers, MA, USA). Antibodies against PERK (20582-1-AP), GADD34 (10449-1-AP), and β-actin (20536-1-AP) were obtained from Proteintech Group (Chicago, IL, USA). The antibody against PRV (PA1-081) was obtained from Invitrogen (Carlsbad, CA, USA), the monoclonal antibody clone 12D10 against puromycin (MABE343) was obtained from Sigma–Aldrich (St. Louis, MO, USA), and the HRP-conjugated IgG secondary antibody was purchased from Jackson ImmunoResearch Laboratories (West Grove, PA, USA). Thapsigargin (Tg) (67526-95-8), salubrinal (324895), and puromycin (540222) were purchased from Sigma–Aldrich. The PP1/PP2A inhibitor okadaic acid (OA) (GC16958) was purchased from GlpBio (Montclair, CA, USA). Lipofectamine 2000 was purchased from Invitrogen.
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2

Quantifying PKR Kinase Activity in Dendritic Cells

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PKR kinase activity was assessed using a combination of an EIF2AK2 kinase enzyme kit (Promega) and ADP‐Glo kinase assay (Promega). DCs were stimulated as previously described to induce kinase activity. After 2 h, whole‐cell extracts were prepared using PKR lysis buffer (50 mM Tris‐HCl [pH 7.5], 1 mM EDTA, 150 mM NaCl, 0.5% Igepal, 12.5 mM beta‐glycerophosphate, 10% glycerol, 1 μg/mL leupeptin, 1 μg/mL pepstatin A, 0.4 mM PMSF). To capture PKR in whole‐cell extract, 96‐well high binding plates (Thermo Fisher) were coated with 10 μg/mL anti‐PKR (ab32052, Abcam) O/N at 4°C. Then, anti‐PKR‐coated wells were blocked with 1%BSA for 30 min and incubated with 10 μg whole‐cell extract for 2 h. Recombinant PKR was used to obtain a protein standard used for quantification (Promega). Wells were incubated with 0.1 mg/mL substrate (myelin basic protein) in 22.5 μL kinase activity buffer (40 mM Tris‐HCl [pH 7.5], 20 mM MgCl2, 50 μM DTT, 0.1 mg/mL BSA, 50 μM ATP) for 1 h at RT. Kinase activity termination and ATP depletion were achieved using the ADP‐Glo reagent (Promega) for 40 min at RT. Final PKR kinase activity was measured by incubation with kinase detection reagent for 30 min at RT, after which the mixture was transferred to a white opaque plate (Corning). Relative light units were detected as a measure for generated ADP and, thus, PKR activity, using the BioTek Synergy HT.
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3

Antibody Detection in Virus Research

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Mouse monoclonal anti-NS5A antibody (9E10) was kindly provided by Dr. Joe Grove (UCL) and has previously been described (Lindenbach et al., 2005 (link)). Antibodies against β-actin (Abcam; ab8226 or ab8227), CypA (Enzo; BML-SA296-0100), CypB (Abcam; ab16045), CypD (Abcam; ab110324), RIG-I (Cell Signaling Technology; #3743) MAVS (Santa Cruz Biotechnology; sc166583), PKR (Abcam; ab32052) and phospho-PKR T446 (Abcam; ab32036) were also used. Secondary IRDye 680- or 800-labelled antibodies and AlexaFluor-conjugated antibodies were obtained from LI-COR Biosciences or Thermo Scientific, respectively. Anti-human interferon alpha/beta receptor chain two antibody (IFNAR2) (Pbl Assay Science, 21385–1) and an IgG2A control antibody (R and D Systems, 4460 MG-100) were used at 2 μg/mL.
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4

Multiprotein Immunofluorescence Analysis

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To examine the presence of STAT1 and PKR, and to test the localization of these proteins in relation to HLA class I and VP1 within the same FFPE sections, we performed combined IF of STAT1/HLA class I and PKR/VP1. Owing to limited resources and a restricted supply of the STAT1 antibody, we performed IF staining in a subset of the samples only. Seventeen samples of especially good quality and size were analyzed. Antigen retrieval and blocking were performed as described in the IHC protocol described earlier. The sections were immunostained sequentially with STAT1 (Ab109320, dilution 1:500, overnight primary incubation at 4 °C), followed by HLA class I (Abcam class I HLA [EMR8/5] Ab70328, dilution 1:1000, 1 hour at room temperature). The same subset of cases were stained for PKR (Abcam Ab32052 at a dilution of 1:700, overnight at 4 °C) and VP1 (Dako antienteroviral VP1 [5D8/1 clone], 1:1000 dilution, overnight at 4 °C). Primary antibodies were detected using species-specific secondary antibodies (antirabbit or antimouse immunoglobulin G [H + L]) conjugated to either Alexa Fluor 488 or Alexa Fluor 555 (Invitrogen) at a dilution of 1:400 for 1 hour at room temperature, together with DAPI 1:1000.
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5

Western Blot Analysis of PKR and eIF2α

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HEK-293 cells were grown in 6-well plates. Before collection, cells were washed with PBS and lysed in Whole-cell lysis buffer (10% glycerol, 0.5 mM EDTA, 1 mM DTT, 2 mM natrium fluoride, 0.2% Triton X-100 in PBS pH 7.4) supplemented with protease and phosphatase inhibitors (Calbiochem). Proteins were separated on 10% polyacrylamide gel and transferred to PVDF membrane (Millipore). The following antibodies were used for detection: total PKR (Abcam #ab32052, 1∶5000 dilution), PKR [pT446] (Abcam #ab32036, 1∶1000), total EIF2α (Santa-Cruz #sc-11386, 1∶1000), EIF2α [pS52] (Life Techonologies #44728G, 1∶1000), RPS14 (Santa-Cruz #sc-68873, 1∶1000), and tubulin (Sigma #T6074, 1∶5000). SuperSignal West Femto Chemiluminescent Substrate (Pierce) was used for detection.
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6

Immunofluorescence Staining of RNA Sensors

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Cells were grown on coverslips (13 mm), washed with 1 mL PBS, and fixed for 10 min in 4% paraformaldehyde in PBS (Affymetrix, High Wycombe, UK). Cells were washed three times with PBS-T for 5 min, followed by permeabilization with 0.25% Triton-X-100 (Sigma) in PBS for 15 min. Samples were washed three times in PBS-T and blocked with ready-made 10% normal goat serum (Life Technologies, Paisley, UK) for 1 h at room temperature. Primary antibodies were diluted in blocking solution: J2 (monoclonal mouse IgG2a kappa chain; Scicons, Susteren, The Netherlands) and TOM20 (Abcam, ab186734) at 1:200 dilution, PKR (monoclonal IgG rabbit anti-human, Abcam, ab32052), MDA5 (monoclonal IgG rabbit anti-human, Abcam, ab126630) at 1:1000. After incubation at RT for 1 h cells were washed (three times 5 min in PBS-T) followed by secondary antibody incubation: For J2, an Alexa fluor™ 488 coupled goat anti-mouse IgG2a (Thermo) was used, otherwise an Alexa fluor™ 594 goat anti-rabbit IgG H + L (Thermo). Both secondary antibodies were diluted in blocking buffer 1:1000 and incubated for 1 hr at RT in the dark. After three washes, the cells were stained with DAPI (Vector Laboratories, Newark, CA, USA) and mounted on slides with ProlongTM Glass Antifade hard mounting medium (Thermo). Cells were imaged using an LSM800 Airyscan confocal microscope (Zeiss, Jena, Germany).
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7

Immunoblotting of Innate Immune Sensors

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Cells were grown in 50 mm Petri dishes followed by lysis in RIPA buffer (150 mM NaCl, 1.0% IGEPAL® CA-630, 0.5% sodium deoxycholate, 0.1% SDS, 50 mM Tris, pH 8.0) and protein quantification was performed using a BCA protein assay (Pierce, Paisley, UK). 30 μg of protein lysate were run on CriterionXT precast 3–8% gradient gels (Bio-Rad, Watford, UK) with a protein ladder (Bio-Rad) in 1× tricine acetate running buffer (Bio-Rad). Proteins were transferred to PVDF membranes (Bio-Rad) using the Trans-Blot Turbo system (Bio-Rad). Membranes were washed in PBS-T (1× PBS, 0.1% Tween) and then blocked in 5% (w/v) skimmed milk in TBS-T for 1 h at room temperature. Primary antibodies against PKR (Abcam, ab32052, Cambridge, UK), RIG1 (Abcam, ab180675), MDA5 (Abcam, ab126630), ADAR (Atlas, B115763, Stockholm, Sweden) were used at a dilution of 1:5000 and anti-actin (Rabbit, Sigma; A2066) at 1:10,000. All antibodies were diluted in a blocking solution and incubated with the membranes at 4 °C overnight. After two washes in TBS-T, the secondary antibody (goat anti-rabbit IgG-HRP, 4030-05, 1:5000, Southern Biotech, Upper Heyford, UK ) in blocking buffer was applied at room temperature for 1 h. After washes in PBS-T, ECL (Bio-Rad) was added, followed by imaging using a chemiluminescence documentation system.
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8

Antibody detection of viral and host proteins

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Rabbit anti-SINV antibody (used at 1 in 200) was a gift from Sondra Schlesinger, Washington University St Louis. Other antibodies were as listed below. They were used at the dilutions indicated and they were incubated either for 2 h at room temperature, or at 4 ℃ overnight. Rabbit anti- YBX1 (Abcam#ab12148, 1 in 300); rabbit anti-VCP (Cell Signaling Technologies, London, UK #2648); mouse anti-G3BP1 (BD, 611126, 1 in 200); goat anti-TIA1 (Santa Cruz sc-1751, 1 in 200); rabbit anti-PKR (Abcam#ab32052); rabbit anti-RIG-I (Abcam#ab45428, 1 in 200); rabbit anti-dsRed (Clontech 632496, 1 in 1000); mouse anti-ATG16L1 (MBL M150–3, 1 in 1000); mouse anti-actin (Sigma-Aldrich, Gillingham, Dorset, A5441, 1 in 7000); rabbit anti LC3 A/B (Cell Signalling#4108 1 in 1000). The antibody against phosphorylated eIF2 alpha was from Cell Signalling (#3398, 1 in 1000). Poly I:C (Roche) was transfected into cells with lipofectamine (Invitrogen) for four hours. Procarta mouse interferon alpha/interferon beta Luminex 2-plex was from Affimetrix (eBiosciences, ThermoFisher Scientific, UK).
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9

Western Blot Analysis of Protein Expression

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Frozen tissues or cells were lysed with RIPA lysis buffer containing PMSF, protease and phosphatase inhibitors (Roche Diagnostics). Protein concentration was quantified using a BCA protein assay kit (Pierce). Samples containing 30 μg of protein were separated by SDS-PAGE gels and transferred to PVDF membranes. The membranes were blocked with 5% fat-free milk before incubation with primary antibodies specifically recognizing PKR (ab32052, 1:1000, Abcam), p-PKR (ab32036, 1:1000, Abcam), human GSDMD (ab210070, 1:1000, Abcam), rabbit anti-human N-GSDMD antibody (EPR20829-408) (ab215203, 1:1000, Abcam) and IL-1β (MAB201, 1:1000, R&D system), α-SMA (1:1000, Proteintech), SM22α (1:1000, Proteintech), calponin (1:1000, Proteintech), caldesmon (1:1000, Proteintech), thrombospondin (1:1000, Proteintech) and osteopontin (1:1000, Proteintech). Immunoreactivity was detected by an enhanced chemiluminescence system, and bands were scanned with a Bio-Rad Imager. Individual band intensity was determined with ImageJ software.
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10

Western Blot Antibody Characterization

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EGFP was detected by anti-GFP rabbit serum A-6455 (Life Technologies), ACTINB was detected by monoclonal anti-β-actin antibody (A5441, Sigma Aldrich), TUBA1A was detected by anti-alpha Tubulin antibody (ab80779, abcam), GAPDH was detected by Anti-GAPDH antibody (G4595, SIGMA Aldrich),PKR was detected by anti-PKR antibody (ab32052, abcam), p-PKR was detected by anti-PKR phospho T451 antibody (ab81303, abcam), eIF2-alpha was detected by anti EIF2S1 antibody (ab26197, abcam), p-eIF2-alpha was detected by anti-EIF2S1 phospho S51 antibody (ab32157, abcam), p-4E-BP1 was detected by anti-phospho-4E-BP1 (ser65) antibody (#9451, Cell Signaling Techonology) and 4E-BP1 was detected by anti-4E-BP1 antibody (#9452, Cell Signaling Technology). Secondary antibodies were horseradish peroxidase (HRP) conjugated Polyclonal Goat Anti-Rabbit antibody (P0448; Dako) and horseradish peroxidase (HRP) conjugated Polyclonal Goat Anti-Mouse antibody (P0447; Dako).
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