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5 protocols using pla probe anti rabbit minus

1

Proximity Ligation Assay for Protein Interactions

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HeLa cells were cultured on coverslips then washed with cold PBS and fixed with cold methanol for 20 min at −20 °C. Coverslips were washed again 4 times with cold PBS. All incubations were performed in a humidity chamber. Blocking was done with 0.1% tween-TBS with 1% BSA for 1 h at 37 °C. Incubations with primary antibodies were performed overnight at 4 °C. Cells were washed three times for 3 min with 0.1% tween-TBS with gentle agitation. Incubations with PLA Probe Anti-Mouse PLUS (Sigma-Aldrich, #DUO92001) and PLA Probe Anti-Rabbit MINUS (Sigma-Aldrich, #DUO92005) were performed for 2 h at 37 °C. Next, coverslips were washed three times for 3 min in T-PBS buffer under gentle shaking and then incubated with DNA ligase previously diluted in ligation buffer for 30 min at 37 °C according to manufacturer’s instructions. Coverslips were washed three times for 3 min in T-PBS buffer under gentle shaking and incubated with a DNA polymerase previously diluted in amplification buffer for 90 min at 37 °C. Finally, coverslips were rinsed for 10 min in the presence of DAPI under gentle shaking and then washed 2 min with 2X and then 0.02X SCC buffer (30 mM sodium citrate, 300 mM sodium chloride). Coverslips were mounted in Fluoromount Aqueous Mounting Medium (Sigma-Aldrich, #F4680) and analyzed using a Zeiss LSM confocal microscope.
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2

Proximity Ligation Assay for LSD1 and ACE2

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The Duolink proximity ligation assay was employed using PLA probe anti-mouse PLUS (DUO92001), PLA probe anti-rabbit MINUS (DUO92005), and Duolink In Situ Detection Reagent Red Kit (DUO92008) (Sigma Aldrich). Cells were fixed, permeabilized, and incubated with primary antibodies targeting LSD1 and ACE2. Cells were processed according to the manufacturer’s recommendations. Finally, coverslips were mounted onto slides and examined as above.
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3

Duolink Proximity Ligation Assay for PKC-θ and ZEB1

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Using our previously established protocols [34 (link),35 (link)], the Duolink proximity ligation assay was employed using PLA probe anti-mouse PLUS (DUO92001), PLA probe anti-rabbit MINUS (DUO92005), and Duolink In Situ Detection Reagent Red Kit (DUO92008) (Sigma-Aldrich). Cells were fixed, permeabilized, and incubated with primary antibodies targeting PKC-θ-Thr538p and ZEB1. Cells were processed according to the manufacturer’s recommendations. Finally, coverslips were mounted onto slides, which were examined as above.
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4

Quantifying Protein-Protein Interactions via Duolink PLA

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The Duolink proximity ligation assay was used with PLA probe anti-mouse PLUS (DUO92001), PLA probe anti-rabbit MINUS (DUO92005), and the Duolink In Situ Detection Reagent Red kit (DUO92008) (Sigma-Aldrich). Cells were fixed, permeabilized, and incubated with primary ACE2 antibodies targeting the NLS region and IMPα1 (staining conditions are shown in Supplementary Table 4). Cells were processed according to the manufacturer’s instructions. Finally, coverslips were mounted onto slides and examined as above. Image segmentation and analysis were carried out using QuPath open software (version 0.4.3) for bioimage analysis64 (link) with a custom script. An analysis workflow was developed with the following steps: (i) threshold-based cell detection using DAPI staining to create a mask for detected nuclei along with a 5 µm cell expansion setting to denote the cell cytoplasm boundary; and (ii) use of the QuPath subcellular detection module to detect the Duolink-positive spots in the Alexa Fluor 555 channel in each cell. The two functions were wrapped in a script to allow for batch analysis of images and data export. Total dots were counted per cell and then averaged for each cell and experimental group; approximately 100 cells were counted per group.
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5

Proximity Ligation Assay for GFP-VAP-A Interaction

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Cells were seeded on the cover glasses coated with collagen solution and processed as described in Section 4.7. permeabilization step. PLA was carried out using Duolink In situ Detection Reagents Red (DUO92008, Sigma-Aldrich) according to the manufacturer’s protocol. The cells were incubated with rat monoclonal anti-GFP antibody (#04404-26, Nacalai) and rabbit polyclonal anti-VAP-A antibody, followed by PLA probe anti-rat PLUS and PLA probe anti-rabbit MINUS (DUO92005, Sigma-Aldrich). The PLA probe anti-rat PLUS was prepared using Duolink In situ Probemaker PLUS (DUO92009, Sigma-Aldrich) against donkey anti-rat antibody (#712-005-150, Jackson ImmunoResearch) according to the manufacturer’s protocol. The cover glasses were mounted on a slide glass using Duolink In situ Mounting Medium with DAPI (DUO82040, Sigma-Aldrich), and the cells were analyzed by a BioZero digital microscope (Haze reduction function: condition 3) equipped with a Plan Apo V 60 × 1.40 oil immersion objective. The fluorescence and bright images were processed by Fiji/ImageJ software to measure the number of spots of PLA signals per cells.
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