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5 protocols using bond wash

1

PDL-1 Immunohistochemistry in Tumor Tissue

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Tumors were harvested and flash-frozen in liquid nitrogen. Frozen tissue sections were cut at 5 μm onto coated slides. Sections were air-dried overnight and then fixed in 10% neutral buffered formalin (NBF) for 5 min before being treated with 1% H2O2 in dH2O for 15 min at room temperature. Slides were then washed in dH2O to remove excess H2O2. Slides were rinsed in Bond Wash (Leica) and placed on the Leica Bond Automated stainer. The slides were stained with Rat primary PDL-1 (13-5982-52; EBio) 1:500 in Animal Free Diluent (SP-5035; Vector Labs). The BOND Polymer Refine Red Detection kit (Leica) was used according to the manufacturer’s protocol. The slides were then digitized according to a previously described protocol.57 (link)
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2

Multiplex Immunofluorescence for HNSCC

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Twenty-three formalin-fixed paraffin-embedded human HNSCC samples were stained using the Opal 7-Color Automation IHC Kit-50 Slide according to manufacturer’s instructions (Akoya Biosciences) using the following antibodies and antigen retrieval processes: with antibodies against PD-L1 (clone E1L3N, Cell Signaling Technologies cat. 13684S, Opal 620), CD11c (clone 5D11, Sigma Cell Marque cat. 111M-15, Opal 650), CD68 (clone KP1, Dako cat. M0814, Opal 690), and pan-CK (clone AE1/AE3, Dako cat. M351501-2, Opal 540) on a Bond RX autostainer (Leica Biosystems). Slides were dewaxed (Leica), heat treated in ER2 or ER1 antigen retrieval buffer depending on the antibody for 20 min at 93 °C (Leica), blocked in Antibody (Ab) Diluent (Akoya Biosciences), incubated for 30 min with the primary Ab, 10 min with horseradish peroxidase (HRP)-conjugated secondary polymer (anti-rabbit and anti-mouse, Akoya Biosciences), and 10 min with HRP-reactive OPAL fluorescent reagents (Akoya Biosciences). Slides were washed between staining steps with Bond Wash (Leica) and stripped between each round of staining with heat treatment in antigen retrieval buffer. After the final heat treatment in antigen retrieval buffer, the slides were stained with spectral DAPI (Akoya Biosciences), and coverslipped with Prolong Diamond mounting media (Thermo Fisher).
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3

Multiplex Immunohistochemistry for Synovial Complement

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After confirming the integrity and architecture of the synovial biopsies, simultaneous staining for the seven CS proteins as above was performed. To detect and quantitate levels of seven complement proteins and inhibitors using MIHC, Early RA synovial sections after dewaxing (Leica) were heat treated in epitope retrieval solution 2 (ER2, EDTA buffer pH 8.9–9.1) or epitope retrieval solution 1 (ER1, citrate buffer pH 5.9–6.1) depending on the antibody for 20 min at 93 °C (Leica), blocked in antibody (Ab) Diluent (Akoya Biosciences®, Marlborough, MA), incubated for 30 min with the primary Ab, 10 min with horseradish peroxidase (HRP)-conjugated secondary polymer (anti-rabbit and anti-mouse, Akoya Biosciences), and 10 min with HRP-reactive OPAL fluorescent reagents (Akoya Biosciences). Slides were washed between staining steps with Bond Wash (Leica) and stripped between each round of staining with heat treatment in antigen retrieval buffer. After the final heat treatment in antigen retrieval buffer, the slides were stained with spectral DAPI (Akoya Biosciences), and coverslipped with Prolong Diamond mounting media (Thermo Fisher). To detect cell nuclei in the synovium, 4′, 6-diamidino-2-phenylindole (DAPI) was used.
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Multiparameter Fluorescence Immunohistochemistry of Formalin-Fixed Paraffin-Embedded Tissue

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Tissue was fixed in formalin and paraffin-embedded for multiparameter fluorescence immunohistochemistry. Four mm sections mounted on glass slides were sequentially stained for Panel VHuP115: c-fos, TREM1, CA9, CAPS, VIPR2, CD14, Dapi (Akoya). Panel VHuP116: CD64, CD3, HLADR, TREM1, CD206, CD14, Dapi (Akoya) (Table S3). All antibodies were diluted in Biocare antibody dilutant, except the RTU antibodies. Slides were dewaxed (Leica), heat treated in ER2 or ER1 antigen retrieval buffer depending on the antibody for 20 min at 93°C (Leica), blocked in Antibody (Ab) Diluent (Akoya Biosciences), incubated for 30 min with the primary Ab, 10 min with horseradish peroxidase (HRP)-conjugated secondary polymer (anti-rabbit and anti-mouse, Akoya Biosciences), and 10 min with HRP-reactive OPAL fluorescent reagents (Akoya Biosciences). Slides were washed between staining steps with Bond Wash (Leica) and stripped between each round of staining with heat treatment in antigen retrieval buffer. After the final heat treatment in antigen retrieval buffer, the slides were stained with spectral DAPI (Akoya Biosciences), and cover slipped with Prolong Diamond mounting media (Thermo Fisher). Single stain controls, fluorescence-minus-one controls, and appropriate positive and negative control tissues were used throughout the staining process.
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5

Immunohistochemical Analysis of Tumor Immune Cells

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Resected tumor tissues and the spleen were fixed in 4% paraformaldehyde and embedded either in paraffin or in optimal cutting temperature (Sakura Finetek, Torrance, CA, USA) compound and frozen. Sections were deparaffinized, rehydrated, and boiled in a microwave for 20 min in 10 mM citrate buffer for antigen retrieval. Immunohistochemistry was performed using anti-human CD45 (ab40763; Abcam), anti-human CD8 (ab108343; Abcam), anti-human Granzyme B (ab208586; Abcam), anti-human PD-1 (ab234444; Abcam) and anti-human TNF-alpha (ab215188; Abcam). The secondary antibody included goat anti-rabbit IgG AF488 (ab150077, Abcam) and goat anti-mouse IgG AF647 (ab150115, Abcam). Sections were incubated overnight at 4°C before being incubated with the appropriate Alexa Fluor-conjugated secondary antibodies. Slides were washed between staining steps with Bond Wash (Leica) and stripped between each round of staining with heat treatment in antigen retrieval buffer. Nuclei were counterstained with DAPI (ab104139, Abcam). For acquisition, data were acquired by sequential acquisition, and tile-scan imaging was performed on an SP8 confocal microscope (Leica Microsystems, Wetzlar, Germany).
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