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42 protocols using ab2105

1

Multiparameter Immunophenotyping of Cells

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CD4-VioGreen (130-106-655, Miltenyi Biotec), Anti-CCR10-PE (clone: REA326, 130-104-822, Miltenyi Biotec), CD183 (CXCR3)-PE-Vio770 (clone: REA326, 130-104-822, Miltenyi Biotec), CD194 (CCR4)-APC (clone: REA279, 130-103-813, Miltenyi Biotec), CD196 (CCR6)- PE-Vivo-615 (clone: REA190, 130-107-142, Miltenyi Biotec), Propidium iodide (130-093-233, Miltenyi Biotec), NESTIN rabbit-anti-mouse (ab7659, Abcam), SCA1 rat-anti-mouse (ab25195, Abcam), PDGFRα goat-anti-mouse (AF1062, R&D Systems), Alexa Flour 405 donkey-anti-Rabbit (ab175651, Abcam), Alexa Flour 488 donkey-anti-goat (A-11055, Thermo Fisher Scientific), Alexa Flour 594 donkey-anti-rat (A-21209, Thermo Fisher Scientific), PerCP-CyTM 5.5 CD45.2 conjugated mouse-anti-mouse (552950, BD Biosciences), ICAM1 rabbit-anti-human (ab53013, Abcam), VCAM1 rabbit-anti-human (ab134047, Abcam), IL-1β rabbit-anti-human (ab2105, Abcam), TNF-α rabbit-anti-human (ab9635, Abcam), actin rabbit-anti-human (A2066, Sigma-Aldrich), rabbit anti goat (81–1620, Invitrogen), goat anti rabbit (65–6120,Invitrogen), CD3 rabbit-anti mouse (AD452, Dako), and B220 rat-anti-mouse (MAB1217, R&D Systems).
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2

Protein Expression Analysis in Rat Tissues

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Briefly, rat liver, kidney, brain, and heart tissue samples were lysed in RIPA buffer supplemented with freshly added protease and phosphatase inhibitor cocktail 1:100 (Sigma), and protein concentration was determined by Bradford assay70 . The previously developed procedures with slight modifications were used to perform SDS-PAGE and western blot investigations71 (link),72 (link). For SDS-Page, equal amounts of proteins were loaded using BIO-RAD Mini protein TGX precast gels on the bio-rad Mini protein tetra system (10,025,025 REVA). After protein separation by gel electrophoresis, the proteins were transferred to PVD membranes using bio-rad trans blot Turbo transfer system. PVD membranes (bio-rad) were blocked for 2 h with either 5% BSA (Sigma) or 5% nonfat dry milk (Bio-Rad, Cat. #170–6404) then incubated with primary antibody overnight at 4 °C. The following antibodies were used: NFκB p65 (ThermoFisher Scientific Catalog # 2A12A7), STAT3 (Thermofisher Scientific Cat. # MA1-13,042), COX-2 (Invitrogen Cat. # PA1-9032), IL-1 (Abcam Cat. # ab2105), TNF-α (Abcam Cat. # EPR19147) and β-actin (Abcam Cat. # ab49900). The antibodies signals were detected by ECL western blotting substrate (bio-rad) and blots were visualized using the bio-rad Gel documentation system (ChemiDoc MP System).
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3

Quantifying RNA, miRNA, and Protein Levels

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RNA was extracted from cultured cells by using TRIzol. For serum samples, RNA was isolated by using TRIzol LS from 200 μl serum. Cel‐miR‐39 was added at 2 nM as a spike‐in control. Relative mRNA or miRNA expression was determined by using SYBR Green (Bio‐Rad) or TaqMan probe‐participated qPCRs, GAPDH and U6 served as internal controls for normalization of mRNA and miRNA expression, respectively. The sequences for qPCR primers are listed in Appendix Table S2. Proteins were isolated by using RIPA lysis buffer and separated by SDS–PAGE. After being transferred to PVDF membranes, membranes were incubated with various antibodies as indicated. Protein bands were detected by electrochemiluminescence with horseradish peroxidase‐labeled secondary antibodies. The used primary antibodies were as follows: TGF‐β (Abcam, ab92486, 1:1,000); TGFBR2 (Santa Cruz, sc‐17792, 1:500); β‐catenin (Abcam, ab32572, 1:1,000); CTGF (Santa Cruz, sc‐365970, 1:1,000); IL‐1β (Abcam, ab2105, 1:1,000); and ET‐1 (Abcam, ab2786, 1:1,000). Secondary antibodies used were as follows: anti‐mouse (Jackson, 515‐035‐003, 1:5,000) and anti‐rabbit (Jackson, 111‐035‐045, 1:5,000).
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4

Western Blot Analysis of Inflammatory and TGF-β Signaling

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The expression of NLRP3, ASC, caspase-1, IL-1β, Smad2, Smad3, p-Smad2, p-Smad3 and TGF-β in tissues and cells was detected by Western blotting. Total protein was extracted from BRL-3A cells and the left liver lobe tissues and quantified by the BCA protein analysis kit. The proteins were separated by SDS-PAGE and transferred to the PVDF membrane. The GAPDH gene acts as a reference gene. Subsequently, the membrane was sealed with 5% skim milk powder and incubated overnight with primary antibodies NLRP3 (ab214185, 1: 500, Abcam, UK), ASC (ab168811, 1: 2000, Abcam, UK), caspase-1 (ab62698, 1: 500, Abcam, UK), IL-1β (ab2105, 1: 1000, Abcam, UK), Smad2 (ab40855, 1: 2000, Abcam, UK), Smad3 (ab40854, 1: 1000, Abcam, UK), p-Smad2 (ab53100, 1: 500, Abcam, UK), p-Smad3 (ab63403, 1: 500, Abcam, UK) and TGF-β (ab92486, 0.5–4 µg/mL, Abcam, UK) at 4°C.The next day, after washing with TBST for 3 times, the membrane was incubated with horseradish peroxidase-labeled secondary antibody at room temperature for 1 h. Proteins were visualized using enhanced chemiluminescence kits and gel imaging systems. The results are analyzed by Image Tools.
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5

Investigating Inflammatory Signaling Pathways

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IL-1α antibody (SC-7929) was purchased from Santa Cruz Biotechnology. Antibodies directed against phospho-p38 MAPK (4511), p38 MAPK (8690), phospho-JNK (9251), JNK (9252), phospho-ERK (4370), ERK (4695), phosphor-AKT (9611) and AKT (4691) were purchased from Cell Signaling Technology. The antibody for human S100A7 (11141-RP02), soluble recombinant human S100A7 (11141-HNAE), IL17A (12047-HNAE), IL-22 (13059-HNAE), IL-33 (10368-HNAE), IL36γ (10124-HNAE) and TNFα (10602-HNAE) were purchased from Sino Biological Inc. The antibody against β-actin (ab8227), IL-1β (ab2105), RAGE (ab54741) and calpain-1 (ab28258) were purchased from Abcam. Antibody against mS100a7a15 (AP52284) was purchased from Abgent. The inhibitors including SB202190 (S7067), SP600125 (S5567), LY294002 (L9908) and caspase-8 inhibitor (C1230) were purchased from Sigma-Aldrich. PD151746 (S7424) was purchased from Selleck.
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6

Western Blot Analysis of Protein Expression

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Total proteins were lysed in RIPA lysis buffer (Beyotime Biotechnology, Shanghai, China), and the concentration of the protein samples was measured using a bicinchoninic acid (BCA) protein assay kit (Beyotime). Proteins were subjected to SDS-PAGE and then electrophoretically transferred onto PVDF membranes. Membranes were incubated with primary antibodies overnight at 4°C after blocking in 5% nonfat milk in TBST buffer, which was then coincubated with horseradish peroxidase (HRP)-conjugated anti-mouse/anti-rabbit IgG (Thermo Fisher Scientific). Proteins were visualized using a detection system of enhanced chemiluminescence (ECL), and the bands were analyzed using BandScan ImageJ software. The primary antibodies used in this study were as follows: anti-CHOP (diluted 1 : 1000, ab11419, Abcam), anti-caspase 12 (diluted 1 : 1,000, ab62484, Abcam), anti-GRP78 (diluted 1 : 100, ab21685, Abcam), anti-NLRP3 (diluted 1 : 500, ab214185, Abcam), anti-ASC (diluted 1 : 1000, ab155970, Abcam), anti-pro-IL-1β (diluted 1 : 500, ab2105, Abcam), anti-IL-1β (diluted 1 : 1500, ab9722, Abcam), anti-p-NF-κB (p-p65) (diluted 1 : 2000, ab86299, Abcam), anti-NF-kB p65 (diluted 1 : 300, ab19870, Abcam), anti-TLR4 (diluted 1 : 500, ab13556, Abcam), anti-MyD88 (diluted 1 : 1000, ab133739, Abcam), and anti-β-actin (diluted 1 : 1000, ab8226, Abcam). β-Actin was used as an internal control.
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7

Immunohistochemical Analysis of Pancreatic Tumor Markers

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Paraffin-embedded pancreatic tumor blocks were cut into 4 μm sections and placed on glass slides. The slides were placed in an oven at 60°C for 1 hr, cooled, deparaffinized, and rehydrated through xylenes and graded ethanol solutions to water. To block endogenous peroxidase, we treated all slides for 5 min with a 3% H2O2 solution in water. Using a Dako Autostainer, we stained the slides for 1 hr at room temperature with primary antibodies against NKp46 (1:1000, #bs-10027R), CD8 (1:500, #bs-0648R), IL-12 (1:200, #bs-0767R) from Bioss (Woburn, Massachusetts), antibodies against CD11b (1:40000, #ab133357), IL-1β (1:400, #ab2105), CD107a (1:500, #ab25245) from Abcam (Cambridge, MA), antibodies against sEH (1:2500, #sc-25797) from Santa Cruz Biotechnology (Dallas, TX), antibodies against Ki67 (1:500, #M7249) from Dako (Carpinteria, CA), or antibodies against cleaved caspase-3 (1:200, #9661) from Cell Signaling Technology (Danvers, MA). The stained slides were photographed at 20 × magnification, and the staining area was quantified, as previously described (18 (link)–20 ,30 ).
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8

Immunofluorescence Analysis of NLRP3 and IL-1β in Diabetic Retinopathy

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Samples from patients with PDR or donor eyecups were fixed with freshly prepared paraformaldehyde (4%) for 2 h at 4 °C, dehydrated using 30% sucrose solutions for 30 min and sent immediately to OCT compound (Sakura, PA, USA) for frozen sections. Frozen sections were cut at 10 μm thickness at −20 °C and stored at −80 °C until staining. Sections were stained by NLRP3 (1:500, Abcam, ab4207) or IL-1β (1:500, Abcam, ab2105) with CD31 (1:500, Abcam, ab24590). HRECs were fixed with freshly prepared paraformaldehyde (4%) for 30 min at 4°C. Then, cells and frozen tissue sections were washed 10 min with PBS (three times), and blocked with 1% FBS in PBS for 1 h at room temperature. After a 10-min washing with PBS three times, samples were incubated with NLRP3 or IL-1β overnight at 4 °C in a humidified chamber. After a 10-min washing with PBS three times, cells were incubated with corresponding secondary antibodies conjugated with Alexa Fluor 488 (1:500, Abcam) or Alexa 594 (1:500, Abcam) for 1 h at 37 °C in a darkened humidified chamber. Cell nuclei were stained with 4′,6-diamidino-2-phenylindole (DAPI, Sigma, St. Louis, MO, USA). Fluorescence was observed using a confocal microscope (Olympus 1X81, Olympus, Tokyo, Japan).
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9

Immunohistochemical Analysis of IL-1β and IL-1RA in Mitral Valve Tissue

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Mitral valve tissues were fixed in 4% PFA for 24 h. After fixation, the tissue was dehydrated to enable embedding in paraffin, which is water insoluble. The tissue was dehydrated gently by immersion in increasing concentrations of alcohol. The alcohol was then cleared by incubation in xylene prior to paraffin embedding. The paraffin was typically heated to 60 °C and allowed to harden overnight. Finally, the tissue was sectioned into 8-μm-thick paraffin sections using a microtome. Sections were deparaffinized and rehydrated. Endogenous peroxidase activity was blocked by incubation for 30 min in 3% H2O2 in methanol at room temperature. Antigen retrieval was performed using microwave treatment for 15 min in citrate buffer (pH 6.0). The sections were blocked with 10% goat serum at 37 °C for 1 h and incubated with rabbit polyclonal antibody against human IL-1β or rabbit monoclonal antibody against human IL1RA (both applied at 1:200, Abcam, USA) in a humidified chamber overnight at 4 °C. Next, the sections were incubated with HRP conjugated secondary antibody for 1 h at room temperature, developed with DAB chromogen for 10 min at room temperature, rinsed in running tap water for 5 min, and counterstained with haematoxylin-eosin staining. The antibodies used in the present study are as follows: anti-IL1β antibody (ab2105, Abcam, USA) and anti-IL1R1 antibody (ab106278, Abcam, USA).
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10

Soleus Muscle Western Blot Protocol

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Western blot was completed as previously described by us [5 (link),21 (link),22 (link)]. In brief, the soleus muscle was homogenized using radioimmunoprecipictation assay cell lysis buffer and the supernatant was used. Using the Bio-Rad protein assay (Bio-Rad, Hercules, CA, USA), protein concentration was estimated and 50 µg of protein was run onto a 10% or 15% SDS-PAGE gel (150 V for 1 h). Using a semi-dry transfer machine (Bio-Rad), gels were transblotted onto polyvinylidene difluoride membranes (Bio-Rad) and were subsequently blocked with 5% skim milk. Next, the membranes were incubates with primary antibodies overnight at 4 °C for inflammasome markers including TLR4 (1:1000, Cat# ab13556, 90 kDa; Abcam) and NLRP3 (1:1000, Cat# ab214185, 90 kDa; Abcam). Pyroptosis markers were detected using primary antibodies for IL-1β (1:1000, Cat# ab2105, 31 kDa; Abcam), and IL-18 (1:1000, Cat# ab7149, 22 kDa; Abcam). Inflammation was detected by primary antibody for TNF-α at a 1:500 dilution (Cat# ab6671, 17–22 kDa; Abcam). Finally, primary antibody for β-actin was used as a loading control at a 1:1000 dilution (Cat# ab16039, 45 kDa; Cell Signaling Technology, Danvers, MA, USA). Membranes were exposed to enhanced chemiluminescence substrate (ThermoFisher Scientific). Densitometric analysis was performed using NIH ImageJ software.
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