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18 protocols using lamin b1

1

Nuclear and Cytoplasmic Protein Extraction

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Protein extraction was performed using the Nuclear and Cytoplasmic Protein Extraction kit (Thermo Scientific, Pierce Biotechnology, IL, USA) according to the manufacturer’s instructions. The samples were separated using 10% sodium dodecyl sulfate-polyacrylamide gel electrophoresis and then transferred onto PVDF membranes (Bio-Rad, Hercules, CA, USA). Subsequently, the membrane was blocked in TBST (20 mM Tris base pH 7.6, 150 mM NaCl, 0.1% Tween-20) containing 5% non-fat milk for 4 h at room temperature. Then, the membrane was incubated with NF-kB (Invitrogen, Cat number MA5-15160) and Lamin B1 (Invitrogen, Cat number 33-2000) primary antibodies that were added to the blocking solution at 3 µg/mL, and the membrane was incubated at 4 °C overnight. After overnight incubation, the membrane was washed and then incubated with goat anti-rabbit immunoglobulin G HRP conjugated secondary antibodies (Invitrogen, Cat number G-21234) and goat anti-mouse immunoglobulin G HRP conjugated secondary antibodies (Invitrogen, Cat number PA1-86015) for an additional hour at room temperature. After washing three times with TBST (30 min each wash), proteins were detected by chemiluminescence and protein bands were analyzed by densitometry using ImageLab software (Bio-Rad 6.1, Hercules, CA, USA).
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2

Molecular Mechanisms of Cellular Stress

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FMK and BI-D1870 were purchased from Axon Medchem (Groningen, The Netherlands). PP2 was purchased from Cayman Chemical (Ann Arbor, MI, USA). PF-4708671 was purchased from Selleck Chemicals (Houston, TX, USA). 2′,7′-Dichlorodihydrofluorescein diacetate (H2DCFDA) and DAPI were purchased from Invitrogen (Carlsbad, CA, USA). TM, D-(+)-glucose and dimethyl sulfoxide (DMSO) were obtained from Sigma-Aldrich (St. Louis, MO, USA). Antibodies were purchased from the following vendors: TXNIP (MBL International, Woburn, MA, USA); ChREBP (Novus Biologicals, Centennial, CO, USA); KDEL (GRP94, GRP78) (Enzo Life Sciences, Lörrach, Germany); CREB-2 (ATF4), GADD153 (CHOP) and Src (Santa Cruz, Santa Cruz, CA, USA); Akt, p-Akt, PARP, cleaved Caspase-3, p-Src, p-S6, S6, ACC, and FAS (Cell Signaling Technology; Danvers, MA, USA); Lamin B1 (Invitrogen); α-tubulin (Sigma-Aldrich).
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3

Cdk1, Cdk5, and PCTAIRE1 Knockdown Protocol

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Pre-designed small interfering RNA (siRNA) directed against human Cdk1 (s464), Cdk5 (s2825), PCTAIRE1 (1472, 1566, 1656), p27 (s2837), and negative scramble control (#1, #2), were purchased from Life Technologies. Kinase inhibitors (SNS-032 and ABT-869) were purchased from Selleckchem. Antibodies against PCTAIRE1 (mouse: G6.1 Santa cruz, or rabbit: HPA001366 Sigma), pro-caspase 3 (#9662, Cell Signaling), cleaved caspase 3 (#9661, Cell Signaling), cleaved PARP (mouse, Cell Signaling), p27 (mouse G173-524: BD, or rabbit C-19: Santa Cruz), phospho-p27 Ser10 (sc-12939, Santa Cruz), phospho-p27 Thr187 (37-9700, Invitrogen), phospho-p27 Thr198 (AF3994, R and D), Lamin-B1 (Invitrogen), phospho-Histone H3 (D2C8, Cell Signaling), Eg5 (611186, BD), Cdk1 (610037, BD), Cdk2 (610145, BD), Cyclin B1 (#4138, Cell Signaling), phospho-cdc2 (Y15) (#9111, Cell Signaling), pericentrin (ab4448, Abcam), alpha-tubulin (T5168, Sigma), HA (3F10, Roche), Myc (Roche), beta-actin (Sigma), horseradish-peroxidase (HRP)-conjugated secondary antibodies (GE Health Care), and Alexa Fluor 488/594-conjugated secondary antibodies (Life Technologies) were purchased from the indicated sources.
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4

Western Blot Analysis of Cellular Proteins

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Total and cytosolic proteins were extracted and quantified as previously described [22 (link)], separated on SDS-PAGE gel, and transferred to nitrocellulose membranes. Proteins were detected using the following specific monoclonal antibodies (mAbs): FoxO3a (75D8, #2497), p-FoxO3a (Ser253; #13129), integrin α5 (#4705), pAkt (Ser 473, #4060), AKT (pan) (11E7, #4685), GAPDH (14C10 #2118) (all from Cell Signaling Technology, Danvers, MA, USA), β−Actin (AC-15) (Sigma-Aldrich, Merck, Milan, Italy), Lamin B1 (Invitrogen #702972) and IRDye secondary Abs (LI-COR Biosciences GmbH, Bad Homburg, Germany). Odyssey FC Imaging System was used for image acquisitions. Protein bands were quantified by means of Image Studio™ Lite v5.2 (LI-COR Biosciences GmbH, Bad Homburg, Germany). All “Original blots and densitometries” have been included in a separate file as Supplementary Information.
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5

Comprehensive Protein Expression Analysis

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Ea.Hy-926 cell pellets were directly lysed in 2× SDS sample buffer and then incubated at 95°C for 10 min to ensure complete lysis. Lysates were separated on 6.5–15% gradient cells and transferred to PVDF membranes. Membranes were blocked in 5% milk and incubated overnight with the respective primary antibodies. The following day, membranes were washed, incubated with secondary antibodies, washed again and developed using ECL.
Primary antibodies used were: GAPDH (polyclonal rabbit (pcRb), Santa Cruz Biotechnology), β-Aktin (monoclonal mouse (mcM), C4, Santa Cruz Biotechnology), TCF11/Nrf1 (mcRb, D5B10, Cell Signalling), DDI2 (pcRb, ab197081, Abcam), p97/VCP (pcRb, Lab Stock), PSMA7/α4 (pcRb, Lab Stock), PSMA1/α6 (mcM, MCP20, Enzo Life Sciences), Tubulin (mcM, Covance Antibody Products), Calnexin (mcM, BD Biosciences), Lamin B1 (mcM, Invitrogen), CAPNS1 (pcRb, GeneTex). Secondary antibodies used were anti-mouse HRP and anti-rabbit HRP (Calbiochem).
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6

Western Blot Protein Quantification

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Equal amounts of total, nuclear, or cytoplasmic protein from each sample were separated using SDS-PAGE and blotted onto polyvinylidene difluoride membranes. NE-PER Nuclear and Cytoplasmic Extraction Reagents (Thermo Fisher Scientific) were used for the extraction of separate nuclear and cytoplasmic protein fractions. Protein blots were hybridized with the indicated primary antibody of interest and followed by HRP-conjugated secondary antibody, followed by detection with Chemi-Lumi One L or Chemi-Lumi One Super (Nacalai Tesque) and the FUSION Chemiluminescence Imaging System (VILBER). Primary antibodies included antibodies against YAP (Cell Signaling Technology, #14074, 1:1,000), phospho-YAP (Ser127; Cell Signaling Technology, #4911, 1:1,000), phospho-Src family (Tyr416; Cell Signaling Technology, #2101, 1:1,000), Src (Cell Signaling Technology, #2110, 1:1,000), phospho-STAT3 (Tyr705; Cell Signaling Technology, #9145, 1:1,000), STAT3 (Cell Signaling Technology, #9132, 1:1,000), CTGF (Cell Signaling Technology, #10095, 1:1,000), CYR61 (Cell Signaling Technology, #39382, 1:1,000), phospho-YAP (Tyr357; Abcam, #ab62751, 1:3,000), a-tubulin (Sigma-Aldrich, #T9029, 1:1,000), Lamin B1 (Invitrogen, #33-2000, 1:1,000), and FLAG (DYKDDDDK; Wako Chemicals, #019-22394, 1:1,000).
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7

Mangiferin-Doxorubicin Synergistic Effects

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The reagent contained mangiferin, doxorubicin, dimethyl sulfoxide (DMSO), SDS, tris, glycine, BSA, 3-(4,5-dimethythiazol-2-yl)-2,5-diphenylTrazolium Bromide (MTT), and CelLytic (Sigma-Aldrich, St. Louis, MO, USA). Other ingredients included Dulbecco’s Modified Eagle Medium (DMEM), fetal bovine serum (FBS), antimycotic/antibiotic mixtures (Carlsbad, CA, USA), DCFH2-DA, and TUNEL staining kits (Roche, Mannheim, Germany), and antibodies were purchased from Invitrogen, Carlsbad, CA, USA. Antibodies to AKT, pPI3K, PI3K PERK1/2, ERK1/2, pP38, P38, BCL2 PARP, HO-1, NQO1, Keap-1, pNrf2, COX, TNF-α, pNFC-B, β-actin, and Lamin B1 were sourced from Invitrogen and Thermo Fisher, Waltham, MA, USA. The antibody against cleaved caspase-3 was purchased from Abcam (Branford, CT, USA).
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8

Antibody Validation and Characterization

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Primary antibodies used were: mouse monoclonal to vimentin (abcam, Cambridge, UK, Cat # ab 8069; 1:2000 dilution); rabbit polyclonal to GAPDH (abcam, Cambridge, UK, Cat # ab9485; 1:2000 dilution), lamin B2 (Thermofisher, Oxford, UK, Cat # PA5-29121, 1:500), CDH5 (abcam, Cambridge, UK, Cat # ab33168; 1:1000); rabbit monoclonal to laminA/C (Thermofisher, Oxford, UK, Cat # MA5-35284; 1:1000); lamin B1 (Thermofisher, Oxford, UK, Cat # 702972; 1:500). Secondary antibodies used were: goat anti-mouse IgG peroxidase conjugated (GE healthcare, Lisburn, UK, Cat # NA931V, 1:1000 dilution), donkey anti-Rabbit IgG peroxidase conjugated (GE healthcare, Lisburn, UK, Cat # NA934; 1:1000 dilution).
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9

Comprehensive Immunofluorescence and Immunoblotting Protocol

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Mouse monoclonal Lamin A/C ((636) Cat# sc7292, IF 1:200, WB 1:2000) from Santa-Cruz Biotechnology, rabbit polyclonal Lamin B1 (Cat# PA5-19468, WB: 1:1000) from ThermoFischer Scientific. Mouse monoclonal Actin ((AC-40) Cat# A3853, WB: 1:3000) from Sigma-Aldrich. Hoechst ((33342), Cat# H1399, IF 1:50), Rabbit polyclonal phospho-Paxillin (pY118, Cat# 44-722 G, IF 1:200), Phalloidin (Texas red 568, Cat# T7471, IF 1:400), secondary antibodies Chicken anti-mouse (AF488, Cat# A21200), Chicken anti-goat (AF488, Cat# A21467), Goat anti-Rabbit (AF633, Cat# A21070) were all diluted 1:200 for IF and obtained from ThermoFisher Scientific. Phalloidin (AF415, Cat# PK-PF415-7-01, IF 1:250) was from PromoKine. Emerin (clone CL0203, Cat# AMAb90562, IF 1:200) was from Atlas Antibodies. Fibronectin was from bovine plasma (Cat# F1141-2MG, Sigma-Aldrich) or human plasma (Cat# F0895-1MG, Sigma-Aldrich), final working concentration 20 µg/ml.
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10

Lamin B1 Immunostaining for Nuclei Segmentation

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E12.5 mouse lungs were fixated for 1 hr in 4% paraformaldehyde in PBS, and subsequently incubated with Lamin B1 (Thermo; Material No. 702972; 1:200) at 4°C for 3 days. As a structural component of the nuclear lamina, LaminB1 immunostaining makes crowded nuclei clearly distinguishable and easily segmentable. After washing in D-PBS, lungs were incubated with conjugated fluorescent secondary Alexa Fluor 555 donkey anti-mouse IgG (H+L) (Abcam; Material No. ab150106; 1:250) for 2 days at 4°C.
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