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Multiplex Immunofluorescence Staining Protocol

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Slides were incubated with SYNGR3 Invitrogen antibody at 1:300 for 1hr and was detected with ImmPress HRP anti-rabbit IgG and TSA Cy5 (SAT705A001EA; Perkin Elmer, Waltham, MA). After completion of SYNGR3 staining, a second round of denaturation (10 min, Bond-Epitope Retrieval solution 1) was followed by incubation in either anti- pan-Cytokeratin (30 min, 1:1500) or CD45 (30 min; ready to use) and detection with ImmPress HRP anti-rabbit IgG and TSA Cy3 (SAT704A001EA; Perkin Elmer). Following pan-Cytokeratin/CD45 staining, a third denaturation step was performed for 10 min in Bond-Epitope Retrieval solution 2 (pH 9.0; AR9640) followed by incubation with either anti-CD3 (1hr, 1:200) or p16 (1hr, 1:5) then detection with Bond Polymer (DS9455) and TSA Alexa-488 (B40953, Invitrogen).
Stained slides were dehydrated and coverslipped with either Cytoseal 60 (single DAB stains; 8310–4, Thermo Fisher) or Prolong gold (multiplex stains; P36930, Thermo Fisher). Positive and negative controls (no primary antibody) were included during staining runs. The slides were digitally scanned at 20x magnification using Aperio AT2 (Aperio Technologies, Vista, CA) and uploaded to the Aperio eSlideManager database (Leica Biosystems Inc) at the Pathology Services Core at UNC
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2

Multiplex IHC for Tumor Infiltrating Immune Cells

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Tissue sections were cut at 4 μm from FFPE blocks. All the sections were deparaffinized and subjected to heat-induced epitope retrieval in citrate buffer pH 9.0 (Biogenex). Six-plex panel IHC was performed for each tissue slide using the following antibodies: anti-FoxP3 (clone 236A/E7, dilution 1:100, Abcam), anti-PD-L1 (clone E1L3N, dilution 1:250, Cell Signaling Technology), anti-CD8 (clone SP16, dilution 1:50, Spring Bioscience), anti-CD3 (clone SP7, dilution 1:50, Spring Bioscience), anti-CD163 (clone MRQ26, Ventana), anti-Cytokeratin (clone AE1/AE3, dilution 1:100, DAKO). Antigen–antibody binding was visualized with TSA-Cy5 (PerkinElmer), TSA-Cy3 (PerkinElmer), TSA-FITC (PerkinElmer), TSA-Alexa594, TSA-Cy5.5 (PerkinElmer), and TSA-Coumarin (PerkinElmer), respectively.
Digital images were captured with PerkinElmer Vectra platform. Tumor areas with the highest immune cell (CD3+CD8+) infiltrates were scanned at 20X and selected for analysis in a blinded fashion. Three images of 0.36-mm2 each were analyzed per sample with InForm Software (PerkinElmer). Hematoxylin and eosin staining was performed on for each sample and reviewed by a pathologist to ensure a representative tissue sample.
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Multi-marker Immunofluorescence Analysis of GBM

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Double-immunofluorescence was performed on tissue microarray containing nine GBMs. The preparations as well as the first step in the stainings are as described above. After detection of JAM-A (1 + 200) using Catalyzed Signal Amplification II kit with FITC (CSA II, Dako), sections were incubated with antibodies against nestin (196,908, 1 + 200, R&D systems, USA), CD133 (W6B3C1, 1 + 40, Miltenyi Biotec, Germany), GFAP (Z0334, 1 + 8000, Dako), SOX-2 (245,610, 1 + 400, R&D systems), or IBA-1 (019-19741, 1 + 4000, Wako Pure Chemical Industries, Japan) followed by Tyramide Amplification Signal Cyanine-5 (TSA-Cy5, Perkin Elmer, USA). Nuclei were counterstained with 4.6-diamidino-2-phenylindole (DAPI) (VWR International, USA). Fluorescence images were taken with a Leica DM6000B microscope connected to an Olympus DP72 1.4 Mega Pixel CCD (Olympus, Japan) camera using DAPI (Omega XF06, Omega Optical, USA), FITC (Leica, Germany), and Cyanine-5 (Omega XF110-2) filters. Due to cross-reaction, a different JAM-A antibody-clone (EP1042Y, 1 + 400, Abcam, United Kingdom) was used for the double staining with CD133.
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4

Multiplexed Immunohistochemistry for PNS Biomarkers

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Formalin-fixed, paraffin-embedded (FFPE) samples were obtained from the VUMC pathology archives for patients with a
neurologic PNS, endocrinologic PNS, or no PNS under an IRB approved protocol (IRB# 160769). We performed multiplexed fluorescence
immunohistochemistry (FIHC) combined with automated quantitative analysis (AQUA® Technology; Navigate BioPharma Services,
Inc.) to assess CD3, CD4, CD8, PD-1, and PD-L1 expression as previously described17 (link). Two slides were used, one to assess CD3, CD4, and CD8, and one to assess PD-1 and PD-L1. Staining for CD3,
CD4, and CD8 was excluded for cytology specimens. The following primary antibodies were used: rabbit anti-CD3 (EP41, dilution
1:200, Biocare Medical), mouse anti-CD4 (4B12, dilution 1:50, DAKO), mouse anti-CD8 (C8/144B, 1:400, DAKO), 0.5 μg/mL mouse
anti-PD1 (NAT105, Biocare), 3.6 μg/mL rabbit anti-PD-L1 (E1L3N, Cell Signaling Technology), mouse anti-TTF1 (8G7G31, 1:500,
DAKO). The following secondary antibodies were used: anti-mouse Envision HRP (DAKO) and anti-rabbit Envision HRP (DAKO), plus
40,6-diamidino-2-phenylindole (DAPI). The following reagents were used to detect secondary antibodies: TSA-Cy3.5 (Perkin Elmer),
TSA-Cy5 (Perkin Elmer), Opal™520 (Perkin Elmer), and TSA-Cy3 (Perkin Elmer).
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