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14 protocols using anti rip1

1

Immunoblot and Co-IP Protocol for Necroptosis

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Antibodies used for immunoblots were as follows: anti-ASS1 (Polaris, San Diego, CA, USA), anti-LC3 (Sigma), anti-p62 (Sigma), anti-RIP1 (Cell Signaling), anti-caspase 8 (Cell Signaling), anti-BCL-2 (Cell Signaling), anti-cIAP1 (Cell Signaling), anti-cleaved PARP (Cell Signaling), anti-caspase 3 (Imgenex, San Diego, CA, USA), anti-RIP3 (Abcam, Cambridge, MA, USA), anti-Atg5 (Santa Cruz, Dallas, TX, USA), anti-Atg7 (Microbiology Laboratories, Woburn, MA, USA), and anti-actin (Sigma). Cells were lysed in RIPA buffer and protein concentrations were determined by BCA kit (Pierce, Waltham, MA, USA). In all, 25–40 μg of proteins was resolved by NuPAGE (Invitrogen) and transferred onto PVDF membranes (Immobilon-P, Millipore, Darmstadt, Germany). Antibody detection was accomplished using enhanced chemiluminescence (Western Lightning, PerkinElmer, Melville, NY, USA).
For co-IP, SK-LMS-1 cells were treated with PBS, 1 μg/ml ADI-PEG20, 20 μM chloroquine, or both for 3 days. Following treatment, cells were lysed in 0.2% NP-40 buffer and protein concentration was determined by BCA kit (Pierce). Lysates were incubated with anti-RIP1 (Cell Signaling) and protein A/G beads (Pierce). The immunoprecipitates were subsequently immunoblotted with anti-RIP3 (Abcam), anti-RIP1 (Cell Signaling), anti-caspase 8 (Cell Signaling) and anti-actin (Sigma) as described above.
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2

Western Blot Antibody Analysis

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Western immunoblotting was accomplished as previously described (25 (link),26 (link)) using the following primary antibodies: anti-caspase-9 (Assay Designs); anti-FLAG and anti-β-actin (Sigma); anti-p65, anti-NF-κB2, anti-IκBα, phospho-IκBα, anti-laminA/C, anti-α-tubulin, anti-NIK, anti-RIP1, anti-cIAP1, anti-cIAP2, anti-Apaf1, anti-myc (Cell Signaling Technology); anti-K48, anti-Ki-67, and K63-linkage specific ubiquitin, and anti-Ki-67 (Abcam). Secondary antibodies were horseradish peroxidase-conjugated anti-rabbit IgG and anti-mouse IgG antibodies (Cell Signaling Technology).
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3

Protein Phosphorylation Analysis in GCs

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Protein isolation and Western Blot were conducted as previously described26 ,27 (link). In brief, GCs were lysed after 1 to 5 days of culture using RIPA buffer containing protease and phosphatase inhibitors (PI, Thermo Fisher Scientific, Waltham, USA). A total of 10 µg protein per lane was loaded on a 12 % SDS gel and run under constant current (30 mA/gel). After blotting (100 V, 65 min) and blocking with 5 % non-fat dry milk in Tris-buffered saline with Tween 20 (TBS-T, 50 mM Tris-HCl, 150 mM NaCl, 0.1 % Tween 20, pH 7.4), anti-pRIP1(S166), anti-pRIP3(S227) both from Cell Signaling Technology (Danvers, MA, USA) and anti-pMLKL(T357/S358) antibodies were administered to decorate these phosphorylated proteins. To visualize specific binding, HRP-conjugated goat anti-rabbit antibody (Jackson ImmunoResearch Inc., West Grove, PA, USA) was used. As loading controls, anti-RIP1, anti-RIP3 (both from Cell Signaling Technology, Danvers, MA, USA), anti-MLKL (ab184718, Abcam, Cambridge, UK) and anti-β-actin (A5441, Sigma-Aldrich, St. Louis, MI, USA) antibodies were used. Preabsorption of anti-pMLKL was previously published27 (link). All experiments were carried out five times if not described otherwise.
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4

Western Blot Analysis of Cellular Signaling

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Total cell lysates (50 μg protein) were resolved on SDS-PAGE, and processed according to standard protocols. The monoclonal antibodies used for Western blotting included: anti-β-Actin (Sigma, St. Louis, MO, USA); anti-caspase-3 (Cell Signaling, Danvers, MA, USA). The polyclonal antibodies used included anti-phospho-p44/p42 MAP kinase (T202/Y204) and anti-p44/p42 MAP kinase; anti-phospho-JNK and anti-JNK1-3; anti-phospho-AKT (S473) and anti-AKT; anti-phospho-p65 (S536) NF-κB and anti-p65 NF-κB, anti-phospho-STAT3 (Y705) and anti-STAT3; anti-p53, anti-SOX2, anti-NANOG, anti-caspase-9, anti-RIP1 and anti-PARP-1 (Cell Signaling, Danvers, MA, USA); anti-FAS, and anti-DR5/TRAIL-R2 (Alexis, San Diego, CA, USA).The secondary antibodies were conjugated to horseradish peroxidase; signals were detected using the ECL system (Thermo Scientific, Rockford, IL, USA).
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5

Comprehensive Necroptosis Signaling Pathway

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Anti‐RIP1 (#3493), anti‐RIP2 (#4142), anti‐RIP3 (#13526), anti‐p‐RIP1 (#44590), anti‐MLKL (#14993), anti‐p‐MLKL (#91689), anti‐caspase‐8 (#4790), anti‐cleaved caspase‐8 (#9496), anti‐PARP (#9532), anti‐GSDMD (#96458), anti‐caspase‐8 (#9746), anti‐Myc 9B11 (#2276), anti‐GFP (#2956) (Cell Signaling Technology), anti‐actin (#MAB1501, MILLIPORE), anti‐IL18 (PM014, MBL), and anti‐FLAG antibodies (F7425, Sigma‐Aldrich) were obtained from the indicated suppliers. The following inhibitors, all obtained from Calbiochem, were used at the indicated final concentrations: z‐VAD‐FMK, 10 μM; RIP1 kinase inhibitor III, 5 μM; GSK872 (RIPK3 inhibitor), 5 μM; and caspase‐8 inhibitor II, 10 μM. Staurosporine was purchased from Sigma.
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6

Investigating Necroptosis Signaling Pathways

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Proteins were subjected by SDS/PAGE (12% or 10% gel), and the blots were incubated overnight with primary antibodies. The following primary antibodies were used: anti-RIP1 (Cell Signaling Technology, #3493), anti-RIP3 (Santa Cruz Biotechnology, sc-374639), anti-MLKL (phospho S345) (Abcam, ab196436), anti-MLKL (Cell Signaling Technology, #37705), anti-JNK1+JNK2+JNK3 (Abcam, ab208035), anti-JNK1+JNK2+JNK3 (phospho T183+T183+T221) (Abcam, ab124956), anti-c-Jun (Abcam, ab32137), anti-c-Jun (phospho S73) (Abcam, ab30620), anti-ERK1+ERK2 (Abcam, ab17942), anti-ERK1 (pT202/pY204)+ERK2 (pT185/pY187) (Abcam, ab50011), anti-p38 (Abcam, 170099), anti-p38 (phospho Y182) (Abcam, ab47363), anti-NF-κB (Abcam, ab16502), anti-NF-κB (phospho S536) (Abcam, ab86299), anti-IKBα (Abcam, ab32518), anti-IKBα (phospho S36) (Abcam, ab133462), and anti-GAPDH (Abcam, ab181603).
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7

Inflammatory Signaling Pathway Profiling

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TNFα (50435; Biomol Germany); IL-1β (211-11B; PeproTech); antibodies: anti-IκBα (sc-371, Santa Cruz, USA), anti-p-IκBα (9246; Cell Signaling), anti-NEMO (FL-419, Santa Cruz), anti-β Actin (sc-1616, Santa Cruz), anti-IKKβ (05–535; Millipore), anti-IKKα (14A231; Imgenex), anti-JNK1/2 (9252; Cell Signaling), anti-p-JNK1/2 (9251; Cell Signaling), anti-Rip1 (3493; Cell Signaling) anti-FLAG M2 (F3165, Sigma); anti-mCD3 (553057, BD Biosciences); anti-hCD28 (553294, BD Biosciences); anti-IgG (307-005-003, Dianova). Tris-d11 (CD4035P1, Cortecnet); DL-dithiothreitol-d10 (CD570P1, Cortecnet); D2O (151882, Aldrich); DMSO-d6 (156914, Aldrich); 15NH4Cl (CN80P100, Cortecnet); D-glucose 13C6 (CC860P20, Cortecnet); D-glucose 13C6-d7 (CCD860P20, Cortecnet).
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8

Hippocampal Protein Signaling Analysis

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Hippocampal tissues were homogenized with NP40 buffer containing 1% protease inhibitors and 1% phosphatase inhibitor (Sigma-Aldrich Co., MO, United States), followed by centrifugation at 12,000 g for 20 min at 4°C. The supernatant of the hippocampal homogenate was then collected. The protein concentration was determined using the bicinchoninic acid (BCA) protein assay kit (CWBio, China). Equal amounts of protein were subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis and subsequently transferred to the PVDF membrane (Bio-Rad, CA, United States). The membranes were blocked for 1 h with 5% non-fat milk, followed by incubation with the primary antibody of anti-RIP1 (1:200, Cell signalling technology, Danvers, United States) and either RIP3, MLKL, or anti-NF-κB antibody (1:1500, Abcam, MA, United States), respectively, followed by incubation for another hour with the IRDye®800CW goat anti-rabbit secondary antibody (1:8000, 926-32211, LI-COR®, United States). Immunoblotting bands were visualized under Odyssey CLx infrared imaging systems (LI-COR®, United States). Protein levels were quantified by densitometry using Image J software (National Institutes of Health, MD, United States) and were normalized to GAPDH, respectively.
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9

Labeling of Anti-MCMV Protein with FITC

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Anti-MCMV early antigen (EA) [38 (link)] was labeled with fluorescein isothiocyanate (FITC; Sigma-Aldrich, St. Louis, MO) as previously described [39 (link)]. Anti-RPE65 was kindly provided by Dr. Michael Redmond (National Eye Institute, National Institutes of Health, Bethesda, MD). Anti-caspase 1, antiphosphorylated NFκB (p-p65), anti-RIP1, anti-RIP3, goat anti-rabbit immunoglobulin G horseradish peroxidase (IgG-HRP), and goat anti-mouse IgG-HRP were purchased from Cell Signaling Technology, Inc. (Danvers, MA). Anti-β-actin was purchased from Sigma-Aldrich (St. Louis, MO). Texas Red–labeled anti-rabbit IgG was obtained from Vector Laboratories (Burlingame, CA).
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10

Immunoblotting Analysis of Inflammatory Pathways

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Anti-cleaved caspase-3 antibody, anti-caspase-3 antibody, anti-β-actin antibody, anti-RIP1 (receptor-interacting protein 1) antibody, anti-p-RIP1 (phospho-RIP1) antibody, cell lysis buffer (10×), and protease/phosphatase inhibitor cocktail were all from Cell Signaling Technology (Danvers, MA). Anti-caspase-11 antibody, anti-pro caspase-1+p10+p12 antibody, anti-GSDMD antibody, anti-GSDME antibody, and propidium iodide were from Abcam (Cambridge, UK). Anti-GFP antibody, Hoechst 33342, MitoTracker Deep Red FM, and LysoTracker Deep Red were from Invitrogen. Anti-F4/80 antibody was from BD Biosciences (Franklin Lakes, NJ). TMR red kit was from Roche (Basel, Switzerland). Lipofectamine 3000 Transfection Reagent was from Thermo Fisher Scientific.
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