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3 protocols using ep1580y

1

Immunofluorescence Labeling Optimization for Colorectal Cancer

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CRC tissues were incubated with PBS/0.2% Triton X-100/10% dimethyl sulfoxide /6% donkey serum at 37 °C for 2 days to prevent nonspecific antigen-antibody binding and then washed with PBS/ 0.2% Tween-20, each containing 10 mg/mL heparin at 37 °C for 1 hour. Heparin was added to reduce background labeling.26 (link) Several primary antibodies, including antibodies against cytokeratin 19 (EP1580Y, rabbit monoclonal; 1:200, Abcam), desmin (goat polyclonal; 1:100, LifeSpan Biosciences), CD31 (JC/70A, mouse monoclonal; 1:100, Thermo Fisher Scientific), and E-cadherin (M168, mouse monoclonal; 1:150, Abcam) were used. Up to 3 primary antibodies were simultaneously applied. The antigen retrieval step was not included. After labeling with 2 or 3 primary antibodies, tissue samples were washed 5 times for 1 hour each with PBS/0.2% Tween-20 and 10 mg/mL heparin solution. The dense desmoplastic stroma in CRCs may represent a physical barrier to antibody penetration. Therefore, the following methods were used to increase antibody penetration: (1) gradual increase in antibody concentration, (2) application of centrifugal force, (3) application of smaller molecular pepsin-digested secondary antibody fragments, and (4) sonication. For example, for cytokeratin 19, the antibody concentration was gradually increased over 4 days from an initial dilution of 1:800 to a final dilution of 1:200.
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2

Western Blot Analysis of Cellular Proteins

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Cells were lysed on ice in RIPA buffer. Protein concentration was determined by using the Bradford dye method. Equal amounts of cell extracts were subjected to electrophoresis in 10% gradient SDS–PAGE gels and then transferred to 0.45 µm PVDF membranes (Millipore) for antibody blotting. The following antibodies were used: V5-tag, p21 Waf1/Cip1, Rb, Phospho-Rb (Ser780), Phospho-mTOR (Ser2448), Phospho-p70 S6 Kinase (Thr389), Phospho-p70 S6 Kinase (Ser371), and Phospho-4E-BP1 (Thr37/46) (Cell Signaling Technology 13202, 2947, 9309, 9307, 2971, 9205, 9208 and 2855, respectively), SOX1 (GeneTex EPR4766), KRT19 (Abcam EP1580Y), KRT13, mTOR, p70 S6 Kinase and 4E-BP1, (Epitomics 2713-1, 1612-1, 1494-1, and 1557-1, respectively), KRT5, CDK4, CDK6, c-Myc, PPARγ, and β-actin (Proteintech 66727-1-Ig, 11026-1-AP, 14052-1-AP, 10828-1-AP, 16643-1-AP, and 60008-1-Ig, respectively), UGT1A6 and UGT2B7 (Signalway Antibody 43176 and C32390, respectively). Horseradish peroxidase-conjugated goat anti-mouse or goat anti-rabbit IgG (Pierce) was used as a secondary antibody. Proteins were visualized with Immobilon Western Chemilum HRP Substrate (Millipore).
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3

Multiplex IHC for Immune Profiling

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Multiplex immunohistochemical staining was performed following the protocol of the Opal Polaris 7-Color Manual IHC Kit (Akoya Bioscience, NEL861001KT). Antibodies against mouse CD8α (1:800, D4W2Z), F4/80 (1:200, D2S9R) and GFP (1:400, D5.1) were purchased from Cell Signaling Technology. Antibodies against mouse PD-1 (1:100, EPR20665), and CK19 (1:1500, EP1580Y) were purchased from Abcam. Slides were imaged, whole slides were scanned using a Vectra Polaris Automated Quantitative Pathology Imaging System (Akoya Biosciences), and multispectral images were acquired using Phenochart software, version 1.0.12 (Akoya Biosciences), to unmix and remove autofluorescence. The distances between CD8+ cells andCK19+ cells were calculated by HALO software (Indica Labs).
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