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9 protocols using rap1a

1

Western Blotting Analysis of Rap1A Expression

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To analyze Rap1A expression in cells, we prepared cell lysates at 75% of confluence using 500 μL of radioimmunoprecipitation assay buffer (RIPA, 25 mmol/L Tris–HCl at pH 7.6, 150 mmol/L NaCl, 1% Nonidet P‐40, 1% sodium deoxycholate, and 0.1% sodium dodecyl sulfate). Protein concentrations of the lysates were determined with a Bio‐Rad protein assay kit (Hercules, CA). Immunoblotting analyses were performed as described previously. Antibodies against the following proteins were obtained from Santa Cruz Biotechnology: Rap1A, GAPDH. Antibodies against the following proteins were from Cell Signaling Technology (Danvers, MA): MEK1/2, ERK1/2, p38, pMEK1/2 (Ser217/221), pERK1/2 (Thr202/Tyr204), and pp38 (Thr180/Tyr182). The secondary antibodies were F(ab)2 fragment of donkey anti‐mouse immunoglobulin (product NA931) or of donkey anti‐rabbit immunoglobulin (product NA9340) linked to horseradish peroxidase from Amersham Biosciences (Little Chalfont, Buckinghamshire, UK). Immunoblotting reagents were from an electrochemiluminescence kit (Amersham Biosciences). Cells treated with U0126 (ERK inhibitor, Sigma) at indicated concentrations were also analyzed, using the above methods.
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2

Western Blot Analysis of Apoptotic Signaling

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Lysates were centrifuged, supernatants were collected, and protein concentration was determined using a DC Protein Assay (Bio-Rad Laboratories, Hercules, CA). Samples were electrophoresed using 4–15% gradient polyacrylamide gels (Bio-Rad) and then transferred to nitrocellulose membranes (Bio-Rad). Membranes were blocked, rinsed and incubated with primary antibodies against unprenylated Rap1A (Santa Cruz Biotechnology, Inc., Santa Cruz, CA), p-P38, total P38, p-Pak1, total Pak1 (Cell Signaling Technology, Inc., Danvers, MA), cleaved PARP-1 (Cell Signaling) and cleaved caspase-3 (eBioscience). After overnight incubation at 4°C, membranes were washed and incubated with their corresponding secondary antibody conjugated with horseradish peroxidase (HRP). Protein bands were detected with an enhanced chemiluminescence detection kit (GE Healthcare, Piscataway, NJ). β-Actin (Sigma Aldrich) and vinculin (Santa Cruz) were used as loading controls.
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3

Western Blot Analysis of Cell Signaling

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Cells were treated for 24 h at the indicated concentrations with the respective drugs. Total protein lysates were prepared, separated, and transferred onto a polyvinylidene difluoride membrane for Western blotting as described previously [75 (link)]. Following antibodies were used: Santa Cruz Biotechnology Inc (CA, USA): PDE4D (#sc-25100), 1:200; Rap1 (#sc-65) 1:1000; deprenylated Rap1 (C-17; Rap1A, #sc-65) 1:1000. Cell signaling Technology (MA, USA): phospho-PKA substrate (#9624), 1:1000; Creb (#9104), 1:1000; phospho-Creb (Ser133; #9198), 1:1000; Epac1 (#4155), 1:1000; Integrin α5 (#4705), 1:1000; Integrin αv (#4711), 1:1000; Integrin β1 (#9699), 1:1000; Integrin β5 (#3629), 1:1000; phospho-Erk (Thr202/Tyr204; #9101), 1:1000; Erk (#9102), 1:1000; phospho-S6 (Ser240/244; #2215), 1:1000; S6 (#2317), 1:1000; phospho-Src (Tyr416; #2101), 1:1000; Src (#2109), 1:1000; Rac (#2465), 1:1000; RhoA (67B9; #2117), 1:1000, and Vinculin (E1E9V, #13901). Sigma-Aldrich: β-actin (AC-15; #A1978), 1:1000. Secondary, horseradish peroxidase-labeled antibodies from Cell Signaling Technologies were used in working dilutions of 1:10 000.
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4

Real-Time PCR and Immunoblot Analysis

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Real-time PCR analysis was performed as previously described with probe sets from Applied Biosystems (Du et al., 2018 (link)). Immunoblot analysis was performed as described previously (Du et al., 2018 (link)) using the following antibodies: p-Foxo1 (Thr24)/Foxo3a (Thr32; 9464), p-Mob1 (Thr35; D2F10), p-Pak1 (Thr423)/2(Thr402; 2601), β-tubulin (9F3), and β-actin (8H10D10; all from Cell Signaling Technology), Pggt1b (5E4; Sigma), Tiam1 (AF-5038, R&D Systems), Rap1a (SC-1482; Santa Cruz Biotechnology), Gapdh (1E6D9; Proteintech), and Hdj-2 (KA2A5.6; Lab Vision).
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5

Western Blot Analysis of Extracellular Vesicle Proteins

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Proteins derived from cells and EVs were resolved using sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS–PAGE), transferred onto nitrocellulose membranes, bound with primary antibodies, and incubated with horseradish peroxidase (HRP)-conjugated secondary antibodies. Protein bands were visualized using enhanced chemiluminescence detection reagents (34580, Thermo Scientific, Waltham, MA, USA). Primary antibodies against the following proteins were used: Alix (ab56932, Abcam, Cambridge, UK), CD63 (ab68418, Abcam), TSG101 (ab56932, Abcam), Synthenin-1 (ab133267, Abcam), β-actin (112620, Cell Signaling Technology, Danvers, MA, USA), PD-L1 (13684, Cell Signaling Technology), Rab27a (ab55667, Abcam), Rab11 (ab18211, Abcam), Rab7 (ab50533, Abcam), pan Ras (sc-166691, Santa Cruz, Santa Cruz, CA, USA), Rap1A (sc-398755, Santa Cruz), p-B-Raf (2696S, Cell Signaling Technology), B-Raf (9433S, Cell Signaling Technology), p-MEK (9154S, Cell Signaling Technology), MEK (9126S, Cell Signaling Technology), p-ERK1/2 (4370S, Cell Signaling Technology), ERK1/2 (4695S, Cell Signaling Technology), p-AKT (4060S, Cell Signaling Technology), and AKT (9272S, Cell Signaling Technology).
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6

Western Blot Analysis of Rap1a Protein

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Tissue samples were placed in T-Per (Invitrogen, Waltham, MA, USA) supplemented with protease and phosphatase inhibitors and homogenized using a handheld tissue homogenizer. The BCA method was used to quantify protein concentration. Equal amounts of protein were run on SDSPAGE gels and transferred to PVDF membranes. Blots were incubated overnight at 4 °C in primary antibody (Rap1a, Santa Cruz sc-373968 and GAPDH, Cell Signaling Technology 5174S) and then for 2 hours at room temperature in secondary antibody. Protein was visualized using an electrochemiluminescence detection kit and a Bio-Rad Chemidoc imaging system. Uncropped western blot images are presented in supplemental figures 12 and 13.
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7

Immunophenotyping of Lung Tumor Samples

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Mouse lung tumor and syngeneic graft samples were fixed with 10% formalin, paraffin-embedded and sectioned for haematoxylin and eosin staining (H&E) and immunofluorescence staining. Elite ABC system (Vector labs) was applied where staining signal was weak. Immunoblotting analysis was performed according to standard protocols. For detecting Hdj2, RAP1A and Kras prenylation with mobility shift assay, proteins were separated with 15-cm 8% and 13% SDS-PAGE, respectively. Antibodies were purchased from Millipore (SPC, 1:2000), Cell Signaling (phos-ERK, total ERK, phos-AKT, total AKT, phos-MEK, phos-c-RAF, Cleaved Caspase-3, CHOP, BiP, phos-PERK, LC3I/II, phos-p70 S6K, phos-4E-BP1, all 1:1000), Abgent (p62, clone 2C11, 1:2000), Vector Labs (Ki-67, 1:500), and Santa Cruz Biotechnology (KRAS, HRAS, RAP1A, HDJ2, ACTIN, all 1:1000).
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8

Cerebellar Protein Expression Analysis

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The cerebellum was dissected from each mouse. Tissues were homogenized in cold radio-immunoprecipitation assay (RIPA) lysis buffer containing protease and phosphatase inhibitors (Thermo). Lysates were cleared by centrifugation (12,000 rpm for 20 min). The concentration of protein samples was determined using a standard BCA Protein Assay (Thermo). Loading protein samples were mixed with a loading buffer and boiled at 99 °C for 5 min. 30 μg total protein samples were resolved in a 10% or 12% SDS–PAGE for electrophoresis. Proteins in an electrophoresis gel were transferred to polyvinylidene fluoride membranes (Roche). The membrane was blocked with 5% non-fat milk (w/v) for 1 h and incubated with one of the following primary antibodies overnight at 4 °C: Ggpps (Santa Cruz, sc-271680), Pax6 (Biolegend, 901301), Rap1A (Santa Cruz, sc-65), Rap1 (Santa Cruz, sc-398755), RhoA (Santa Cruz, sc-418), p21 (CST, 64016S), Atp1a1 (Proteintech, 55187-1-AP), β-actin (ABclonal, AC026). After it was washed out for three times, the membrane was incubated with a horseradish peroxidase (HRP)-conjugated secondary antibody for 1 h at room temperature. The membrane was visualized using an enhanced chemiluminescence system (Tanon-4600, Tanon, China). ImageJ was used to quantify intensities for targeted protein bands.
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9

Western Blot Analysis of Rap1a Protein

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Tissues were homogenized in T-PER (Invitrogen) supplemented with proteinase inhibitors. Protein content was determined by the BCA method. Equal amounts of total protein were resolved by SDS-PAGE and then transferred to polyvinylidene difluoride membrane. Blots were incubated in primary and secondary antibodies and visualized using an ECL chemiluminescence detection kit and a Bio-Rad ChemiDoc MP imaging system. The following antibodies and antibody dilutions were used: Rap1a (Santa Cruz, cat# sc-1482, 1:250) and β-tubulin (Cell Signaling Technology, cat# 2146, 1:1000).
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