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Detection and Validation of PRR Expression

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Receptor expression levels were detected in total protein extracts from THP-1 cells and control HEK-Blue-null1 and HEK-Blue-null2 cells by anti-NOD1 (Thermo Scientific, USA), anti-NOD2 (Santa Cruz Biotechnology, USA), anti-Dectin-1, and anti-Mincle (InvivoGen, USA) primary antibodies. Anti-GAPDH antibodies (Santa Cruz Biotechnology, USA) were used for sample normalization.
For verification of NF-κB activation after PRR stimulation, THP-1 cells were treated for 30 min with TDB (10 µg/mL) and L18-MDP (100 ng/mL) alone or in combination. Nuclear and cytoplasmic cellular extracts were prepared using an NE-PER kit (Thermo Fisher Scientific, USA) according to the manufacturer’s instructions and normalized using anti-lamin and anti-β-actin antibodies, respectively. The p65 subunit of NF-κB was detected using anti-p65 antibodies (all, Santa Cruz Biotechnology, USA). HRP-conjugated secondary anti-rabbit and anti-mouse antibodies were obtained from GE Healthcare (USA).
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Protein Complex Immunoprecipitation and Western Blot

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The cell lysates (0.5–1 mg of total protein) were immunoprecipitated with anti-HMGB1 (Abcam), or anti-NOD2 (Santa Cruz) at 4 °C overnight on protein A-Sepharose beads. The bead-bound complexes were pelleted, washed several times with lysis buffer, and boiled with a SDS sample buffer for 5 min prior to SDS-PAGE. For the Western blot analysis, the proteins were transferred to PVDF membranes after SDS-PAGE and blocked with 5% non-fat dry milk. The blots were incubated with specific primary antibodies, such as anti-HMGB1 (1:2000; ab190377, Abcam,), anti-NOD2 (1:1000; DF12125, Affinity Bioscience), or anti-ATG16 (1:2000; 8089, Cell Signaling Technology), overnight at 4 °C. The signals were detected, using a chemiluminescence kit (Merck Millipore).
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Protein Expression Analysis by Western Blotting

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Western blotting was performed as previously reported 23 (link). Primary antibodies anti-NOD2 (Santa Cruz Biotechnology, Inc. Dallas, TX, USA), anti-NADPH oxidase 2 (NOX2 , BD Transduction Laboratories, Lexington, KY, USA), anti-phospho-NF-κB p65, anti-IκBα, anti-JNK, anti-phospho-JNK, anti-p38, anti-phospho-p38 MAPK (Cell Signaling Technology, Beverly, MA, USA), anti-ERK1/2 and anti-phospho-ERK1/2 (Sigma-Aldrich, St. Louis, MO, USA) were used in this study. To document the loading controls, the membrane was reprobed with a primary antibody against the housekeeping proteins GAPDH or β-actin.
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4

Knockdown of Innate Immune Receptors

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Cytochalasin D (CytD), α-hemolysin, and calcein AM were purchased from Sigma-Aldrich (St. Louis, MO). siRNAs for NOD1 (NM_006092: 5′-GGCCAAAGUCUAUGAAGAUtt-3′), NOD2 (NM_022162: GGCUGAAAUUCAGAAUAUUtt-3′), TLR2 (NM_003264: 5′-GCCUUGACCUGUCCAACAAtt-3′), NLRC4 (NM_021209: 5′-GGUUCAAGCCAAAGUAUAAtt-3′) and RICK (NM_003821: 5′-GGAGAAGAAUUUGCCAAAGtt-3′) were purchased from Life Technologies (Grand Island, NY). Anti-Defb2, anti-NOD2, and anti-β-tubulin antibodies were purchased from Santa Cruz Biotechnology (Dallas, TX).
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