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5 protocols using mab3321

1

Immunofluorescence Protocol for Cellular Phenotyping

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To confirm the phenotype, zonula occludens-1 (ZO-1), cytokeratin-18 (CK18), and retinal pigment epithelium-specific 65 kDa protein (RPE65) immunofluorescence were used. The cells were fixed in 4% paraformaldehyde (PFA) (in phosphate buffer, PB) for 5 min at 4 °C. They were then transferred to 1% phosphate buffer saline (PBS) for washing purposes and incubated with a blocking buffer (1% bovine serum albumin, BSA, 0.5% Triton X-100, 0.2% sodium azide, and 1% FBS) for 1 h at 4 °C. The cells were incubated with an Alexa Fluor 594 mouse monoclonal antibody anti-ZO-1 (1:100, 339194, Invitrogen-Life Technologies, Gaithersburg, MD, USA), mouse monoclonal anti-CK18 (1:250, M7010, DAKO, Glostrup, Denmark), mouse monoclonal antibody to precursor and active MMP13 (1:250, MAB3321, Merck, Darmstadt, Germany), and rabbit polyclonal anti-RPE65 (1:250, NB100-355SS, Novus biologicals) at 4 °C overnight. After three 10 min washes, they were incubated with secondary fluorescent antibodies goat anti-mouse (1:250, A11029, Life technologies, Gaithersburg, MD, USA) and donkey anti-rabbit 594 (1:250, R37119, Invitrogen, Carlsbad, CA, USA) for 1 h in the dark. All antibody solutions were based on a blocking buffer. Nuclei were stained with 4′,6-diamidino-2-phenylindole (DAPI). Images were obtained using a laser scanning confocal microscope (LSM800, Zeiss, Oberkochen, Germany).
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2

Retinal Pigment Epithelium Imaging Protocol

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After euthanasia induction, the eyes of the mice were removed and fixed in a solution of 4% PFA diluted in BP at 4 °C for 1 h. The RPE–choroid–sclera complex was then isolated through microsurgery and bleached by incubating it with H2O2 (10% in PBS solution) at 55 °C for 1.5–2 h, which allowed for the removal of RPE and choroidal melanocyte pigmentation in whole mounts prior to antibody staining. The whole mounts were immersed in a blocking buffer (PBS, 3% Triton X-100, 0.5% Tween 20, 2% sodium azide, and 1% FBS) for 1 h at 4 °C. Afterwards, biotinylated isolectin (1:240, B-1205; Vector Labs, Burlingame, CA, USA) and mouse monoclonal antibody to precursor and active MMP13 (1:100, MAB3321, Merck, Darmstadt, Germany) were incubated with the flatmounts overnight at room temperature and subjected to PBS washing. Subsequently, the samples were incubated with goat anti-mouse 647 (1:250; 21235; Life Technologies, Carlsbad, CA, USA), streptavidin Alexa Fluor 488 (1:250; S32354; Thermo Fisher, Paisley, UK), and Hoechst 33342 (1:800, H1399, Thermo Fisher, Waltham, MA, USA). Finally, images were captured under a confocal microscope (LSM800; Zeiss, Oberkochen, Germany).
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3

Immunofluorescence Labeling of Extracellular Matrix

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The flatmounts were immersed in the blocking buffer for 5 h at 4 °C. They were then exposed for 3 days at RT to mouse monoclonal anti-MMP13 (for precursor and active forms; 1:100, MAB3321, Merck), biotinylated isolectin (1:240, B-1205; Vector Labs, Burlingame, CA, USA), and a goat collagen IV antibody (1:250, 1340-01, Southern Biotech, CA, USA). The samples were washed in PBS and subjected to a 3 h incubation in Alexa Fluor rabbit anti-mouse 647, Alexa Fluor donkey anti-goat 594 (1:250, Life Technologies, Carlsbad, CA, USA), streptavidin Alexa Fluor 488 (1:250; S32354; Thermo ThermoFisher, Paisley, UK), and DAPI (Sigma-Aldrich, St. Louis, MO, USA). Finally, mounting media consisting of PBS-glycerol (1:1) were applied, and a confocal microscope was used for visualization and images capture (LSM800, Zeiss, Oberkochen, Germany).
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4

Knockdown of BRD3OS and MMPs in cSCC

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cSCC cells were cultured to 50% confluence and transfected with commercially available siRNAs (75 nM) targeting BRD3OS (LINC00094), MMP-1, or MMP-13 (Qiagen, Hilden, Germany) by using siLentFect lipid reagent (Biorad, Hercules, CA, USA) (Supplementary Table S2). MMP levels in a serum-free medium of cSCC cell cultures were determined by Western blot analysis 72 h after siRNA transfection using antibodies specific for MMP-1 (1:1000, MAB3307, 41-1E5; Merck Millipore, Temecula, CA, USA) and MMP-13 (1:500, MAB3321; Merck Millipore). Expression of tissue inhibitor of matrix metalloproteinase 1, TIMP-1 (1:1000, MAB3300; Merck Millipore), was used as a control. Protein expression was quantitated using IRDye labeled secondary antibodies and the LI-COR Odyssey CLx fluorescent imaging system (LI-COR Biosciences, Lincoln, NE, USA). Quantitation was prepared by using Image Studio software (LI-COR Biosciences).
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5

Quantifying MMP13 Protein Expression

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Precursor and active MMP13 protein expressions were determined in ARPE-19 cell culture supernatants. A total of 60 µL was combined with Laemmli buffer (4× NuPage, Invitrogen, Carlsbad, CA, USA) and boiled for 5 min. The samples were subjected to a 10% sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and then transferred onto nitrocellulose membranes (GE Healthcare, Fairfield, CT, USA). Then, a blocking step consisting of 5% skimmed milk (w/v) and 0.1% Tween-20 (w/v) in Tris buffer saline (TBS) (1 h, RT) was carried out, and incubation was carried out overnight with a mouse monoclonal anti-MMP13 antibody (1:1000, MAB3321, Merck) at 4 °C. Then, the membranes were subjected to a horseradish peroxidase conjugated goat anti-rabbit antibody (7074S; 1:5000, Cell Signaling Technology Inc., Danvers; MA, USA). SuperSignalTM West Atto Ultimate Sensitivity Chemiluminescent Substrate (A38556, Thermo Fisher Scientific, Rockford, IL, USA) was used to detect the chemiluminescent signals, and Image Quant 400 software (GE Healthcare, Fairfield, CT, USA) was used to measure them. The relative intensities of the immunoreactive bands were determined with ImageQuant TL software (GE Healthcare, Fairfield, CT, USA). To confirm that protein loading was similar across samples, membranes were stained using a Ponceau S red solution (P7170-1L, Sigma, St. Louis, MI, USA) and imaged.
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