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53 protocols using integrin β1

1

Western Blot Analysis of Caspase-1 and IL-18 Cleavage

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of cell lysates or supernatants was used to monitor protein expression and the cleavage products of IL-18 and capase-1. Cells were lysed in RIPA buffer (150mM NaCl, 50mM Tris (pH 8), 0.5% sodium deoxycholate, 1% Nonidet P-40, 0.1% SDS) supplemented with protease inhibitor cocktail (RPI corp.) and 2 mM phenylmethanesulfonyl fluoride. Supernatant proteins were precipitated by the methanol-chloroform extraction method as described (36 (link)). Protein concentration in the cell lysate was determined using bicinchoninic acid (BCA) assay kit. Equal concentrations of protein were separated through 10–13.5% denaturing SDS-PAGE and transferred to polyvinylidene difluoride (PVDF) membranes. Membranes were incubated overnight at 4°C with primary antibodies diluted (1:1000) against: human activated caspase-1 p20, β1 integrin, FAK, and phospho-FAK all from Cell Signaling Technology. Other antibodies used were against human IL-18 from Santa Cruz Biotechnology; against Rac1 from Epitomics, a loading control antibody against Hsp70 from Santa Cruz Biotechnology. Blots were then washed as before and protein bands visualized by chemiluminescence. Relative caspase-1 protein levels were determined by densitometric analysis of Western blot bands using a Molecular Imager Gel Doc XR System (BioRad, Hercules, CA).
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2

Immunostaining of Tumor Tissue Sections

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Hematoxylin and eosin staining was performed with paraffin sections by Duke Pathology Laboratory (Durham, NC, USA). Immunostaining of OCT-embedded frozen subcutaneous tumor tissue sections were performed as previously described.44 (link) Five-micrometer-thick sections were fixed in 100% methanol for 15 min, blocked with 10% horse serum in PBS (Invitrogen) for 1 h and then incubated with antibodies against Ki-67 (SP6) (Thermo Fisher Scientific, Grand Island, NY, USA); cleaved caspase 3 (#9661), N-cadherin (#13116), E-cadherin (#3195) and β1-Integrin (#9699) (Cell signaling Technology) for 1 h at room temperature or 4 °C overnight. Sections were then washed five times in PBS with 0.05% Tween-20, followed by detection with Alex 555-conjugated secondary antibody (Thermo Fisher Scientific) and counterstaining with 1 μg/ml Hoechst 33258 for 1 min. For immunostaining, paraffin-embedded lung tissue sections were dewaxed in 100% xylene for 5 min followed by sequential 5-min treatments of 100, 90 and 70% ethanol, antigen unmasking by boiling in 10 mM citrate buffer for 10 min and then undergo immunostaining as described above with a primary antibody against Melan-A (HPA048662) (Sigma) and detection with a Dylight 549-conjugated secondary antibody. Fluorescent pictures were taken and processed using the Olympus BX41 microscopic imaging system (Olympus, Center Valley, PA, USA).
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3

Protein Extraction and Western Blot Analysis

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Cell monolayers were lysed in lysing buffer containing 1M Tris-HCl (pH 7.5), 3M NaCl, NP4O, distilled water, a protease inhibitor cocktail (Roche, Switzerland), PMSF and sodium orthovanadate. Cells were centrifuged at 13 000 RPM, 4°C. The amount of protein was measured using the Bradford assay [20 (link)] and stored at -80°C until used. Equal amounts of protein (20 μg) were run on Bolt® Bis-Tris Plus gels (Invitrogen, Thermo Fisher Scientific) and transferred to a nitrocellulose membrane using iBlot® Dry Blotting System (Invitrogen, Thermo Fisher Scientific). The membranes were blocked with 5% skim milk in a TBS buffer with 1% of Tween 20 for 1h and incubated with primary antibodies against vimentin (D21H3) (Cell Signaling Technology, MA, USA) and β1 integrin (Cell Signaling Technology, MA, USA) at 4°C overnight. Membranes were washed 3 times in TBS and incubated with suitable secondary antibodies and then washed 3 times in TBS. Signals were detected using LumiGLO® chemiluminescent substrate (Cell Signalling Technology, Danveers, MA).
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4

Antibody Sourcing for Cell Biology

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Antibodies were purchased as follows: β-actin (A5441, Sigma-Aldrich), β1 integrin (4706, Cell Signaling Technology, Frankfurt am Main, Germany), EGFR (2232, Cell Signaling Technology), αV integrin (4711, Cell Signaling Technology), α5 integrin (98,204, Cell Signaling Technology), α8 integrin (sc365798, Santa Cruz Biotechnology, Dallas, Texas), α9 integrin (NBP2-16,972, Novus Biologicals, Wiesbaden, Germany), Caspase-3 (9662, Cell Signaling Technology), HRP-conjugated sheep anti-mouse secondary antibodies (NXA931, GE Healthcare), and HRP-conjugated donkey anti-rabbit secondary antibodies (NA934V, GE Healthcare).
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5

Integrin Antibody Identification and Characterization

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Antibodies for Western blotting included α7 integrin (Invitrogen), α5 integrin, α6 integrin, αv integrin, β1 integrin, β3 integrin, β4 integrin, β5 integrin (Cell Signaling), α3 integrin (US Biologicals), β-actin (Millipore), and IRDye 800CW donkey anti-mouse and IRDye 680RD Donkey anti-rabbit antibodies (LI-COR). Antibodies for immunofluorescence staining included α3 integrin (US Biologicals), α5 integrin, β1 integrin, β4 integrin, αvβ3 integrin (Millipore), α6 integrin (Novus Biologicals), and Alexa594 anti-rabbit and Alexa488 anti-mouse antibodies (Invitrogen). Antibodies for immunoprecipitation included β1 integrin (clone AIIB2, Millipore), and rat immunoglobulin G (IgG; Santa Cruz Biotechnology). Antibodies for integrin inhibition included β1 integrin (clone AIIB2) and β4 integrin (clone ASC-8) from Millipore.
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6

PDAC Cell Line Protein Analysis

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Human PDAC cell lines Pt45.P1 (a kind gift of Prof. Holger Kalthoff), PaCa-44 (a kind gift of Prof. Stephan Haas), and HS766.T (ATCC) were cultured in DMEM supplemented with 10% fetal calf serum and antibiotics. Lysates were prepared with RIPA buffer (50 mM Tris HCl, pH 8.0; 150 mM NaCl, 0.5% w/v sodium deoxycholate; 0.1% SDS; 1% NP-40) containing 5mM EDTA along with Halt protease and phosphatase inhibitor cocktail (Thermo Fisher Scientific, Waltham, MA, USA, ref. 1861281) and loaded into 10% TGX gels (BioRad Hercules, CA, USA). Protein was transferred onto PVDF membranes and probed with antibodies specific for human α6 integrin (Cell Signaling Technology, Danvers, MA, USA, #3750, 1:1000), β1 integrin (Cell Signaling Technology, Danvers, MA, USA, #34971, 1:1000), flTF (clone TF9-10H10, Invitrogen/Thermo Fisher Scientific, Waltham, MA, USA, 1:500), asTF (custom rabbit polyclonal, ref. 14, 2 μg/mL), and beta-actin (Cell Signaling Technology, Danvers, MA, USA, #3700, 1:1000).
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7

Biotinylation and Affinity Purification of Integrins

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All procedures were performed on ice or at 4°C. Cells grown on 15-cm plates were incubated on ice for 20 min, washed three times with PBS, treated with 6 ml of 0.5 mg/ml NHS-SS-biotin (Fisher, cat. no. P121331) in PBS for 20 min, and quenched by 100 mM glycine/PBS for 10 min. After three washes with PBS, cells were lysed in RIPA buffer (20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate, 1 mM EDTA, 0.5% sodium orthovanadate, 0.1% sodium fluoride, and 1× protease inhibitor cocktail [Bimake, cat. no. B14001]). Cell lysates were adjusted to 5.86 mg/ml in lysis buffer, and 3-mg samples were incubated with 50 μl of streptavidin-agarose beads (GE Healthcare, cat. no.17-511-01) at 4°C overnight. After being washed, beads were boiled in SDS sample buffer with 100 mM DTT, and bound proteins were analyzed by SDS–PAGE, transferred to polyvinylidene difluoride (PVDF) membranes, and blotted with α5-integrin (Cell Signaling, cat. no. 4705), β1-integrin (Cell Signaling, cat. no. 4706), TfR (Invitrogen, cat. no. 13-6800), and β-actin (Proteintech, cat. no. 66009-1-Ig) antibodies.
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8

Isolation and Characterization of Extracellular Vesicles

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Isolated MVs were lysed in radio-immunoprecipitation assay buffer and supplemented with protease inhibitors (RIPA buffer, Thermo Scientific). MV samples were collected from the outlets of the microfluidic device and stored at −20 °C before analysis. Protein concentration was quantified using the bicinchoninic acid assay (BCA assay kit, Thermo Scientific). Protein lysates were loaded and resolved by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and transferred to PVDF membrane (Life Technologies). The PVDF membrane was then incubated overnight with antibodies against CD63 (Santa Cruz), Flotillin-1 (BD Biosciences), HSP90 (Cell Signaling), HSP70 (Cell Signaling) and β1-integrin (Cell Signaling). Following incubation with secondary antibody (Cell Signaling), enhanced chemiluminescence was used for detection.
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9

Antibodies for Signaling Pathway Analysis

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Antibodies against VEGFR2 (#2479), cyclin D1 (#2978S), cyclin B1 (#4135S), FAK (#3285, 1:1,000), phosphorylated (p)-FAK (Y397; #3283,), β1 integrin (#9699,), Akt (#9272,), p-Akt (S473; #9271, 1:1,000), caspase 3 (#9662S), cleaved PARP (#9541), p44/42 MAPK (ERK1/2; #9107), p-p44/42 MAPK (Thr 202/Tyr 204; #9101), vimentin (#3390), N-cadherin (#5296), β-catenin (#8480), GAPDH (#2118) and E-cadherin (#3195) were purchased from Cell Signaling Technology (Beverly, MA, USA). Antibodies against cyclin A (sc-271682) and FAK (sc-558) were purchased from Santa Cruz Biotechnology Inc. (Dallas, TX, USA). Cisplatin was purchased from Sigma (St. Louis, MO, USA).
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10

Immunoblotting Analysis of Melanoma Signaling

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Whole-cell protein lysates (20 μg each) of primary melanocytes and various melanoma cell lines were separated by electrophoresis on 12% sodium dodecyl sulfate polyacrylamide gel electrophoresis gel, transferred to nitrocellulose membrane and analyzed by immunoblotting with antibodies against MALT1 (#2494), pc-Jun(S73) (#9164), pIκBα(Ser32) (#28590), β1-Integrin (#9699) (Cell signaling Technology, Danvers, MA, USA); c-Jun (Ab-243) (GenScript); RelA/p65 (SC109), IκBα (SC847), MKK7 (SC13071) and Actin (SC16160) (Santa Cruz Biotechnology, Santa CruZ, CA, USA) followed by detection with Alexa IRDye-conjugated secondary antibodies (Invitrogen). Blots were scanned using the Odyssey CLX imaging system (LI-COR, Lincoln, NE, USA).
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