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6 protocols using ab270604

1

Western Blot Analysis of Protein Expression

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Proteins were obtained by RIPA lysis buffer containing fresh protease and phosphate inhibitor mixture and boiled for denaturation. Protein concentration was determined by BCA protein assay. Cell lysate was then prepared for western blotting using a 10% polyacrylamide gel and 30 μg of protein. After electrical transfer and blocking with 5% BSA, the membrane was incubated with primary antibodies at 4°C overnight. Antibodies against β-actin (A5441) were obtained from Sigma–Aldrich; antibodies against TFEB (ab270604), NLRP3 (ab263899), PINK1 (ab23707), and Parkin (ab77924) were purchased from Abcam; and antibodies against GAPDH (SC-365062), caspase-1 (SC-56036), and P62 (SC-48402) were obtained from Santa Cruz Biotechnology.
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2

Quantification of Autophagy-Related Proteins in Cells

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Total protein was collected from cells. Protein concentration was quantified using a BCA kit (Abcam, Shanghai). Afterwards, 30 µg of protein was separated by 12% SDS-PAGE at 120 V for 1 h. The separated protein was moved onto PVDF membranes (Millipore, Beijing), which was then sealed with nonfat milk. The membranes were incubated with primary antibodies including anti-TLR4 (ab13556, 1:500, Abcam, Shanghai), anti-TFEB (ab270604, 1:1000, Abcam, Shanghai), anti-LC3 I/II (ab128025, 1:1000, Abcam, Shanghai), anti-p62 (ab109012, 1:10000, Abcam, Shanghai), and anti-GAPDH (ab9485, 1:2500, Abcam, USA) at 4°C overnight and with secondary antibodies (ab205718, 1:10000, Abcam, Shanghai) at room temperature for 2 h. The bands were captured with an ECL kit (Abcam, Shanghai) and quantified using Scion Image v. 4.0.2 software (Scion Corporation).
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3

Western Blot Analysis of Autophagy and Inflammasome Proteins

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The cells were washed twice with cold PBS buffer and lysed on ice with RIPA (P0013B, Beyotime, China) lysis buffer for 30 min. The lysate was centrifuged at 4°C for 15 min at 14,000 g. The supernatant was collected, and protein was extracted by the Beyotime BCA kit (P0010, Beyotime, China) to determine the protein concentration. The protein was then denatured in loading buffer and denatured by boiling in a 95°C water bath for 5 min. The protein samples (20 μg of protein per gel lane) were loaded onto SDS–PAGE gels and then transferred to PVDF membranes. The membranes were blocked in 5% bovine serum albumin (BSA) for 2 h at room temperature and incubated overnight in the primary antibody at 4°C. The antibody information is as follows: LC3 (#3868 s, Cell Signaling Technology, USA), Lamp1 (ab24170, Abcam, UK), NLRP3 (bs-10021R, Bioss, China), Caspase-1 (#3866, Cell Signaling Technology, USA), Caspase-1 (bs-0169R, Bioss, China), IL-1β (bs-0812R, Bioss, China), TFEB (ab270604, Abcam, UK), and β-actin (AA128-1, Beyotime, China). The PVDF membrane was washed and incubated with horseradish peroxidase and secondary antibody for 1 h. An enhanced chemiluminescence kit (BL520B, Biosharp, China) and gel imaging system (Bio-Rad, USA) were utilized to collect protein development images. ImageJ software was used for the quantitative analysis of signals.
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4

Quantitative Analysis of Transcription Factors and Lipid-Modifying Enzymes

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Samples were collected from an equal number of intact cells in TRI Reagent® (#TR118; Molecular Research Center, Cincinnati, OH, USA). After reverse transcription on 500 ng of total RNA with GoScriptTM Reverse Transcription Mix, Oligo (dT) (#A2791, Promega, Madison, Wis, USA), quantitative PCR amplification was performed on the LightCycler 480 (Roche, Switzerland) using Eastep® qPCR Master Mix Kit (#LS2062, Promega, Madison, Wis, USA). Relative gene expression was calculated using the 2−ΔΔCt method, with GAPDH as the reference gene. Standard techniques were used for protein quantification, separation, transfer, and blotting in ECC-1 and KLE cells. Primary antibodies against the following targets were used: TFEB (1:1000; #ab270604, Abcam, London, UK), ERRα (1:500; #ab137489, Abcam, London, UK), LPCAT1 (1:1000; #66044-1-Ig, Proteintech, Wuhan, China), LPCAT3 (1:1000; #67882-1-Ig, Proteintech, Wuhan, China), MMP2 (1:1000; #AF1420, Beyotime Biotechnology, Shanghai, China), Cortactin (1:1000; #AF2134, Beyotime Biotechnology, Shanghai, China), E-cadherin (1:1000; #3195, Cell Signaling Technology, Shanghai, China), vimentin (1:1000; #5741, Cell Signaling Technology, Shanghai, China), and GAPDH (1:2000; #60004-1-Ig, Proteintech, Wuhan, China).
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5

TFEB ChIP-qPCR Protocol for ERRα

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Cells were harvested followed by cross-linking for 10 min with 1% (v/v) formaldehyde. Afterward, cells were lysed by sonication. The cell lysates were immunoprecipitated with anti-TFEB (1:100; ab270604, Abcam, London, UK) overnight at 4 °C. After washing and elution, the crosslinks were reversed for 4 h at 65 °C. The eluted DNA was purified and analyzed by qPCR using a Bio-Rad SYBR Green intercalating fluorophore system with the following ERRα primers: 5’-AGT TGT GAG GAG CCT TTG GAC-3’ (forward) and 5’-CGG TGG TAG CGA GCA GTT T-3’ (reverse). The Ct value of each sample was normalized to the corresponding input value.
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6

Evaluating ERRα and TFEB Expression in Tissue Microarrays

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All tissues were assembled into a tissue microarray. Immunostaining for ERRα and TFEB was performed according to standard procedures. Rabbit polyclonal anti-ERRα (1:100; #ab137489, Abcam, London, UK) and rabbit polyclonal anti-TFEB (1:100; #ab270604, Abcam, London, UK) antibodies were used. The percentage of positive cells was scored as 0 (cells < 5%), 1 (5% to 25%), 2 (26% to 50%), 3 (51% to 75%), and 4 (76% to 100%). The positive staining intensity was scored as 0 (no staining), 1 (weak staining), 2 (moderate staining), and 3 (strong staining). The expression levels of ERRα and TFEB were assessed to determine their immunoreactive scores (IRSs) using the algorithm IRS = Si × Pi (where Si and Pi represent the intensity and percentage of positively stained cells, respectively). Samples were divided into four groups based on their IRS: 0, negative (-); 1–4, weakly positive ( +); 5–8, positive (+ +); and 9–12, strongly positive (+ + +).
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