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7 protocols using af 401 na

1

Macrophage Protein Extraction and Western Blot

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Protein extraction from macrophages was performed using TRIzol reagent (Thermo Fisher Scientific, 15596026) according to the manufacturer’s instructions. Briefly, after phase separation using chloroform, 100% ethanol was added to the interphase/phenolchloroform layer to precipitate genomic DNA. Subsequently, the phenol-ethanol supernatant was mixed with isopropanol to isolate proteins. The Bradford method was used to determine protein concentrations in the cell lysate. Equal amounts of protein were separated by SDS-PAGE and transferred to a polyvinylidene fluoride (PVDF) membrane. Membranes were incubated overnight with antibodies against GSDMD (Abcam, ab209845), CASP11 (abcam, ab180673), CASP1 (AdipoGen, AG-20B-0042-C100), murine IL-1b (R&D Systems, AF-401-NA), LC3A/B (Cell Signaling Technology, 12741) and GAPDH (Cell Signaling Technology, 2118). Corresponding secondary antibodies conjugated with horseradish peroxidase in combination with enhanced chemiluminescence reagent (Amersham, RPN2209,) were used to visualize protein bands. Densitometry analyses were performed by normalizing target protein bands to their respective loading control (GAPDH) using ImageJ software as previously described17 (link),19 (link).
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2

Western Blot Analysis of Inflammasome Activation

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Murine cell and tissue lysates were prepared with radioimmunoprecipitation assay (RIPA) buffer. Protein lysates were separated by sodium dodecyl-sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and transferred to nitrocellulose membranes (Bio-Rad, Hercules, CA). Membranes were probed with anti-CitH3 (Abcam #ab5103, 1:1000 dilution), anti-Caspase-1 (Abcam # ab179515, 1:1000 dilution), anti-IL-1 β (R&D system, # AF-401-NA, 1:1000 dilution) and anti- β -actin (Cell Signaling Technology, #3700, 1:1000 dilution) antibodies, followed by HRP-conjugated anti-rabbit secondary antibody (Invitrogen, #G-21234) or Dylight 800-conjugated anti-mouse secondary antibody (Cell Signaling Technology, #5257S). Images were visualized with ChemiDoc™ Touch Imaging System (Bio-Rad) and analyzed with Image Lab (Bio-Rad).
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3

Whole-Cell Lysate Protein Analysis

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Whole-cell lysates were generated using RIPA buffer (50 mM Tris, pH 8, 150 mM NaCl, 0.1% (w/v) SDS, 0.5% (w/v) sodium deoxycholate and 1% (v/v) NP-40, supplemented with protease inhibitor cocktail (cOmplete™ ULTRA Tablets, Roche, Basel, Switzerland)). The 10 μg protein samples (whole-cell lysate or cytoplasmic extracts) were run on 12% SDS-PAGE gels, transferred to nitrocellulose membrane and probed with primary antibodies against TLR2 (R&D system; AF2616-SP), caspase-11 (Sigma; C1354, clone 17D9), IL-1β (R&D system; AF-401-NA), NLRP3 (Cell signalling; 15101), HMGB1 (Cell signalling; 3935), Lamin B (Cell signalling, 12586) and actin (Sigma; A3854), followed by incubation with the appropriate HRP-secondary antibody. Immunoblots were developed with enhanced chemiluminescent (ECL) substrate (Millipore, Merck, Darmstadt, Germany) using the BioRad ChemiDoc TM MP Imaging System. Densitometric analysis was performed using Biorad Image Lab software.
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4

Inflammasome Activation by Bacterial Factors

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Flagellin purified from P. aeruginosa was purchased from InvivoGen. DOTAP liposomal transfection reagent was purchased from Sigma-Aldrich. Lipopolysaccharide (LPS), ATP, nigericin, pyocyanin, and proteinase K were purchased from Sigma-Aldrich. N-3-oxo-dodecanoyl-l-homoserine lactone (3-oxo-C12-HSL) and N-butyryl-l-homoserine lactone (C4-HSL) were obtained from Cayman. Antibodies were acquired to detect mouse caspase-1 (Adipogen, 20B-0042), mouse IL-1β (R&D, AF-401-NA), mouse IL-6 (Cell Signaling, 12912), mouse NLRP3 (Adipogen, 20B-0014), mouse ASC (Santa Cruz, SC-22514-R), and Flagellin (InvivoGen, mabg-flapa).
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5

Renal Tubular Epithelial Cell Characterization

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Human renal TECs and epithelial cell medium were obtained from ScienCell. Iohexol was obtained from GE Healthcare and Mannitol was obtained from Sigma. Mouse anti-rabbit IgG and Mouse anti-rat IgG antibodies were purchased from Cell Signaling Technology. We obtained antibodies targeting caspase-11 (Sigma, clone 17D9), caspase-4 (Abcam., ab40887), caspase-5 (Abcam, ab25898), IL-1β (R&D Systems, AF-401-NA), GAPDH (Cell Signaling Technology, #2118), Gsdmd (Novus Biologicals, NBP2-33422), and cytokeratin-18 (Abcam, ab668). Pan-caspase inhibitor Z-VAD-FMK was obtained from R&D Systems.
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6

NLRP3 Inflammasome Activation Pathway

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Ultrapure LPS and nigericin were purchased from Invivogen and Sigma-Aldrich, respectively. The following antibodies were purchased commercially: rabbit anti-NLRP3 (cryo-2; Adipogen, AG-20B-0014), rabbit anti-ASC (AL177; Adipogen, AG-25B-0006), mouse anti-caspase-1 (p20) (Casper-1; Adipogen, AG-20B0042), mouse anti-caspase-1 (p10) (Casper-2; Adipogen, AG-20B0044), goat anti-mouse IL-1β antibody (R&D, AF-401-NA), anti-gasdermin D (Cell Signaling, #93709), anti-actin (clone 4; Merck Millipore, #MAB1501), anti-F4/80 (Cell Signaling, #70076).
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7

Protein Extraction and Western Blot Analysis

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Protein extraction from macrophages was performed using TRIzol reagent according to the manufacturer's instructions. Briefly, after phase separation using chloroform, 100% ethanol was added to the interphase/phenol–chloroform layer to precipitate genomic DNA. Subsequently, the phenol–ethanol supernatant was mixed with isopropanol to isolate proteins. The Bradford method was used to determine protein concentrations in cell lysates. Equal amounts of protein or supernatants were separated by 13.5% SDS–PAGE and transferred to a polyvinylidene fluoride (PVDF) membrane. Membranes were incubated overnight with antibodies against CASP11 (Cell Signaling, 14340), murine CASP1 (Adipogen, AG‐20B‐0042‐C100), human cleaved CASP1 (Cell Signaling Technology, 4199), human CASP1 (Cell Signaling Technology, 2225), cleaved CASP7 (Cell Signaling Technology, 9491), human CASP4 (MBL, M0293), murine IL‐1β (R&D Systems, AF‐401‐NA), and GAPDH (Cell Signaling Technology, 2118). Corresponding secondary antibodies conjugated with horseradish peroxidase and in combination with enhanced chemiluminescence reagent were used to visualize protein bands. Densitometry analyses were performed by normalizing target protein bands to their respective loading control (GAPDH) using ImageJ software as previously described 8, 9.
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