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48 protocols using xbp1s

1

Comprehensive Proteostasis Profiling Protocol

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BTZ (catalog S1013), CFZ (catalog S2853), MEL (catalog S8266), DEX (catalog S1322), and DOX (catalog S1208) were purchased from Selleck Chemicals. Recombinant human PSMB5 protein was custom-made by MedChemExpress. Recombinant human ISG20L2 protein was custom-made by Merry Bio Technology Co., Ltd.
Western blot antibodies against PSMB5 (catalog sc-393931), PSMD8 (catalog sc-514053), PSMD3 (catalog sc-393588), PSMC5 (catalog sc-390631), and eIF2a (catalog sc-133132) were purchased from Santa Cruz Biotechnology. Western blot antibodies against ISG20L2 (catalog 24639-1-AP) and GAPDH (catalog 60004-1-Ig) were purchased from Proteintech. Antibodies against ATF4 (catalog 11815), ATF6 (catalog 65880), cleaved caspase-3 (catalog 9661), p-p38MAPK (T180/Y182) (catalog 9211), p38MAPK (catalog 9212), p-eIF2α (S51) (catalog 3398), and XBP-1s (catalog 27901) were obtained from Cell Signaling Technology. Western blot antibodies against p-PERK (T982) (catalog WL05295), PERK (catalog WL03378), and CHOP (catalog WL00880) were obtained from Wanleibio.
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2

Probing the Unfolded Protein Response

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Antibodies against XBP-1s (Cell
Signaling Technology), IRE-1 (Cell Signaling Technology), ATF6 (Proteintech),
PERK (Cell Signaling Technology), p-eIF2α (Cell Signaling Technology),
eIF2α (Cell Signaling Technology), ATF4 (Cell Signaling Technology),
cleaved PARP (Cell Signaling Technology), and p97 (Fitzgerald) were
obtained commercially. Cysteine, methionine, glycine, GSH, and N-methylmaleimide (NMM) were procured from Sigma-Aldrich.
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3

ER stress response pathway analysis

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Foetal bovine serum (FBS) and Dulbecco's modified Eagle's medium (DMEM) were obtained from Thermo Fisher Scientific (Waltham, MA) and 4′,6-diamidino-2-phenylindole (DAPI) was from Sigma-Aldrich (Seelze, Germany). ER-tracker Red was obtained from Thermo Fisher Scientific (Waltham, MA). Mouse monoclonal antibodies (mAbs) against PERK, phosphorylated-eIF2a, CHOP, XBP-1s, cyclin A2 and Cdc25C were obtained from Cell Signaling Technology (Danvers, MA); and anti-β-actin and CDK1 were from Boster (Pleasanton, CA). Salubrinal was purchased from Calbiochem (San Diego, CA).
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4

Synthesis and Characterization of VLX1570

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VLX1570 was synthesized by OnTarget Chemistry AB (Uppsala, Sweden). BSO, Thapsigargin, Z-VAD-FMK were obtained from Sigma Aldrich (Darmstadt, Germany). Antibodies were from the following sources: ubiquitin Lys48 (Merck, Kenilworth, NJ, USA), active caspase-3, BIP, and XBP1S obtained from Cell Signaling Technology (Danvers, MA, USA). PARP and antiheme oxygenase-1 were obtained from BD Biosciences (San Jose, CA, USA). β-actin and HSP70B were obtained from Sigma-Aldrich (Darmstadt, Germany). USP14 was obtained from Bethyl Laboratories (Montgomery, TX, USA).
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5

Quantification of ER Stress-Related Proteins

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Cells were lysed in radioimmunoprecipitation assay buffer (50 mM Tris-HCl, pH 8, 150 mM NaCl, 1 % NP-40, 0.5 % sodium deoxycholate, and 0.1 % SDS, supplemented with protease inhibitor cocktail; Sigma-Aldrich) for 30 min at 4°C and the protein content was measured by DC Protein Assay (Bio-Rad). Protein samples (20 μg) were resuspended in Laemmli buffer and separated by SDS-PAGE. Next, samples were transferred to PVDF membranes (Immobilon-P, Millipore) and blocked with 5 % dry milk supplemented with 0.05% Tween 20 in PBS. The membranes were then immunoblotted by specific antibodies: FOXO1 (2880; Cell Signaling Technology), FOXO3 (D19A7; Cell Signaling Technology), FOXO4 (9472; Cell Signaling Technology), XBP-1s (83418; Cell Signaling Technology), IRE1α (3294; Cell Signaling Technology), IRE1α [pSer724] (NB100–2323SS; Novus Biologicals), eIF2α (9722; Cell Signaling Technology), ATF4 (11815; Cell Signaling), GAPDH (2118; Cell Signaling Technology) and β-actin (A5316; Sigma-Aldrich). For chemiluminescent detection, we used enhanced luminol-based chemiluminescent substrate (ECL) and ECL Hyperfilm (Amersham). Immunoblotting results were analyzed by densitometry (Image J).
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6

Cellular Protein Extraction and Analysis

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Cellular protein extraction, 4–15% gradient SDS-PAGE gel electrophoresis (Bio-Rad laboratories), transfer to PVDF membrane, and immunoblot development were performed as published recently.3 , 33 (link) The following rabbit anti-human antibodies were used (obtained from Cell Signaling): cleaved PARP-1 (5625), p-eIF2α (3398), total eIF2α (5324), SQSTM1 (8025), LAMP1 (9091), LC3-I/II (12741), cytochrome c (11940), ATF-4 (11815), and XBP-1s (40435). Equal protein loading was examined by β-actin detection using a mouse monoclonal antibody (Sigma Aldrich); secondary antibodies: HRP-conjugated goat anti-rabbit or goat anti-mouse (Jackson ImmunoResearch Laboratories). Densitometric image analysis was performed using Image Studio Lite quantification software (LI-COR Biosciences). For cytochrome c immunodetection, cell fractionation (mitochondrial versus cytosolic) was performed using the Mitochondria/Cytosol fractionation kit (ab65320, Abcam). Purity of fractions was confirmed according to kit instructions.
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7

Western Blot Analysis of Apoptosis Markers

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The cells were collected and lysed in lysis buffer (1 M Tris–HCl, 5 M NaCl, 1% Nonidet P-40 (v/v), 1% sodium deoxycholate, 0.05% SDS, 1 mM phenylmethylsulfonyl fluoride) for 20 min. After brief sonication, the lysates were centrifuged at 12,000 × g for 10 min at 4 °C, and the protein content in the supernatant was measured using a Bio-Rad Protein Assay kit. The protein lysates were denatured at 96°C for 5 min after mixing with SDS-loading buffer, applied on an SDS polyacrylamide gel (Daiichi Pure Chemicals Co., Ltd, Tokyo, Japan) for electrophoresis, and transferred to nitrocellulose membranes (Amersham Biosciences, Buckinghamshire, UK). Western blot analysis was performed using primary antibodies (1:1000) to CHOP (#5554), BiP (#3183), XBP-1s (#12782), cleaved caspase-8 (Asp391) (#9496), BID (#2002), Bcl-2 (#2876), Bax (#2772), caspase-3 (#9662), p38 (#9212), phospho-p38 (#4631) (Cell Signaling Technology, Danvers, MA, USA), and β-actin (Sigma-Aldrich). The secondary horseradish peroxidase (HRP)-conjugated antibodies (1:5000) were purchased from Cell Signaling Technology. The band signals were visualized using a luminescent image analyzer (LAS4000, Fujifilm Co., Tokyo, Japan) with the ECL chemiluminescence system (Amersham Biosciences) [17 (link)].
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8

Protein Extraction and Western Blot Analysis

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Proteins were extracted from the exosomes, liver tissue, and AML12 cells using a RIPA lysis buffer (Rockland Immunochemicals Inc., PA, United States) that included protease and phosphatase inhibitors (Thermo Fisher Scientific). First, the proteins were quantified using the Bradford protein assay (Bio-Rad Laboratories, Hercules, CA, United States), then 50–100 μg of protein were separated using 10% Mini-PROTEAN® TGX™ Precast Protein Gel (Bio-Rad Laboratories, Hercules, CA, United States) and electrotransferred onto polyvinylidene difluoride (PVDF) membranes (Bio-Rad Laboratories, Hercules, CA, United States). The membranes were blocked using EveryBlot blocking buffer (Bio-Rad Laboratories, Hercules, CA, United States) for 5 min at room temperature (RT) and were then incubated with primary antibodies against CD63, IRE1a (Invitrogen), p-IRE1a (LSBio, Seattle, WA, United States), PI3K p85, p-PI3K, Akt, p-Akt, β-actin, acetyl-CoA carboxylase (ACC), p-ACC, fatty acid synthesis (FAS), and XBP1s (Cell Signaling, MA, United States) for 12 h at 4°C. Subsequently, the membranes were incubated with a secondary antibody (Anti-Rabbit IgG-HRP, Bio-Rad Laboratories, Hercules, CA, United States) for 1 h at RT. Protein levels were determined using enhanced chemiluminescence (Bio-Rad Laboratories, Hercules, CA, United States) and ChemiDoc XRS + (Bio-Rad Laboratories, Hercules, CA, United States).
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9

Chondroprotective Effects of Salidroside

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The following reagents and antibodies were used in this study: salidroside (C14H20O7, CAS#:10338–51–9, Nanjing, China); recombinant human TNF-α, type II collagenase, and Safranin-O/Fast Green (Sigma-Aldrich, St. Louis, MO, USA).primary antibody against p65(Cat# 59674, RRID:AB_2799570), COX-2(Cat# 12282, RRID:AB_2571729), IκBα(Cat# 4812, RRID:AB_10694416), and XBP-1s (Cat# 12782, RRID:AB_2687943) were purchased from Cell Signaling Technology(Danvers, MA, USA); anti-iNOS (Cat# SAB4502012, RRID:AB_10744871) were bought from Sigma-Aldrich; antibodies against PCAF(Cat# ab110421, RRID:AB_11156343), H3K9ac(Cat# ab4441, RRID:AB_2118292), lamin-B1(Cat# ab22137, RRID:AB_446813), GAPDH(Cat# ab9485, RRID:AB_307275), cleaved caspase 3(Cat# ab2302, RRID:AB_302962), cleaved caspase 12(Cat# ab62484, RRID:AB_955729), cytochrome C(Cat# ab133504, RRID:AB_2802115), and cleaved PARP (Cat# ab32064, RRID:AB_777102) were obtained from Abcam (Cambridge, UK). Alexa Fluor 594- and Alexa Fluor 488-labelled anti-rabbit goat immunoglobulin G (H + L) inferior antibody were bought from Jackson Immuno Research (West Grove, PA, USA). Gibco (Carlsbad, CA, USA) provided cell-culture reagents.
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10

Integrated Akt-UPR Signaling Characterization

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All reagents used were of analytical grade. Tunicamycin, Dithiothreitol (DTT), Puromycin and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) were from Sigma. Thapsigargin was bought from Cayman Chemical Company. SC79, the small molecule activator of Akt, was purchased from Tocris Bioscience (catalog #4635). Antibodies against GIV (catalog #133371) and GRP78 (catalog #13968) were obtained from Santa Cruz Biotechnology. Antibodies against total Akt (tAkt; catalog #4691), phospho-Akt (pAkt-S473; catalog #4060), IRE1α (catalog #3294), XBP1s (catalog #12782), PERK (catalog #3192), eIF2α (catalog #5324), phospho-eIF2α (peIF2α; catalog #3398), ATF4 (catalog #11815), CHOP (catalog # 2895) and Glyceraldehyde 3-phosphate dehydrogenase (GAPDH; catalog #5174) were from Cell Signaling. Anti-ATF6 (catalog #ab122897) was from Abcam and anti-FLAG M2 antibody was from Sigma (catalog #F1804). Goat anti-rabbit and goat anti-mouse IRDye 680RD and IRDye 800CW secondary antibodies were obtained from LI-COR Biosciences.
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