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14 protocols using vectra polaris slide scanner

1

Postmortem Brain Tissue Analysis

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Postmortem brain tissue was fixed in periodate-lysine-paraformaldehyde (PLP) for at least 3 months at 4 °C. The neuropathological assessment was performed using procedures previously established [58 (link), 76 (link)]. Neuropathological evaluations were made by board-certified neuropathologists (ACM, TDS, BRH) according to published diagnostic criteria and were kept blinded to antemortem clinical information [58 (link)]. Cerebral arteriolosclerosis, atherosclerosis, and CAA were evaluated on a semiquantitative scale [12 (link), 73 (link)].
For immunohistochemical assessment, 20 µm slides from paraffin-embedded tissue blocks from the DLF were prepared and stained for AT8 as previously described [16 (link)]. Slides were scanned, digitized at 20× magnification, and analyzed for AT8 density (total area in the sulcus positive for AT8 staining divided by the total area of tissue analyzed) using Aperio Scanscope (Leica) as previously described [17 ]. The depth of the cortical sulcus was defined as the bottom third of two connecting gyri. Ki67 staining was completed using Leica’s Ready-to-Use Ki67 antibody reagent on the BOND staining system (Leica, Deer Park, IL) and imaged on the Vectra Polaris slide scanner (Akoya, Marlborough, MA).
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2

Immunohistochemical Staining of α-Dystroglycan

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Immunohistochemical (IHC) staining was carried out on 2 μm formalin-fixed, paraffin-embedded sections using standard procedures. In brief, antigen retrieval was achieved with target retrieval solution (S1699, Agilent Technologies) via microwave heating. Incubation with the primary antibody IIh6 (Santa Cruz) at a concentration of 4 μg/ml was done at room temperature for one hour. As a detection system, biotinylated anti-mouse IgM (BA2020, Vector Labs) and streptavidin-HRP (RE 7104, Novocastra, Newcastle, UK) was used. Samples were developed via exposure to 3,3`-diaminobenzidine (DAB+, K3468, Agilent) and counterstained with hematoxylin Gill’s Formula (H-3401, Vector Labs). For IHC staining against α-DG on mouse FFPE tissue, Crystal MausBlock (Fa. DCS, Hamburg, Germany, ML125R015) was used to avoid non-specific binding of the secondary antibody. Processed slides were scanned on a Vectra Polaris™ slide scanner using 40-fold scan resolution and snapshots taken via Phenochart 1.0.8 software (both AKOYA Biosciences, MA, USA).
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3

Immunohistochemical Detection of Gram-Negative Bacteria

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Immunohistochemistry staining was performed in 4-µm sections of FFPE tumor tissues according to the standard method, including a deparaffinization and rehydration step. Antigens were retrieved in slight boiling citrate buffer (10 mM of sodium citrate, 0.1% Tween 20, pH 6.0) for 10 min in the microwave at low-to-medium power. The slides were treated with an appropriate amount of Endogenous Peroxidase Blocker (PV-9002, ZSGB-BIO, Beijing, China) for 10 min. After being rinsed with phosphate-buffered saline (PBS), Gram-negative bacteria were stained with lipopolysaccharide (LPS) Core (1:1,000, HBT-HM6011-20UG, Hycult, Plymouth Meeting, PA, USA) overnight at 4°C in a humid chamber followed by 20-min incubation of secondary antibody (goat anti-mouse IgG) at 37°C in a humid chamber. Diaminobenzidine (DAB) (ZLI-9017, ZSGB-BIO) was used for chromogenic detection for 10 min. Reactions were terminated by washing with water. Samples were stained with hematoxylin for 2 min, washed under running water for 3 min, placed in 1% hydrochloric acid solution for 20 s, washed under running water for 3 min, then blued in saturated lithium carbonate, washed, dehydrated through alcohols, cleared in xylene, and sealed with neutral resin. All slides were scanned on a Vectra Polaris slide scanner (Akoya Biosciences).
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4

Histopathological Evaluation of FFPE Tissues

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Formalin-fixed, paraffin-embedded (FFPE) tissue blocks were processed and hematoxylin and eosin–stained after a standardized process in the hospital diagnostic pathology laboratory (18 (link)). Slides were reviewed by a group of specialist histopathologists who scored inflammation semiquantitatively (none = 0, mild = 1, moderate = 2, severe = 3). For immunophenotyping, multiplexed immunofluorescence on deparaffinized rehydrated FFPE slides was performed using combinations of primary antibodies against CD34, CD68, MRP8, CD4, CD8, and CD20, labeled with Tyramide Signal Amplification (TSA)-conjugated fluorophores, with antibody removal between steps. Images were captured using a Vectra Polaris slide scanner (Akoya Biosciences). Control tissue for immunophenotyping was obtained from lung cancer–resection specimens. Uninflamed lung tissue distinct from the site of carcinoma was used for immunofluorescence.
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5

Confocal Microscopy and Slide Scanning

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Immunofluorescence images were acquired using the SP8 X confocal microscope (Leica). H&E slides and immunohistochemistry slides were imaged with a conventional light microscope (Leica) or a Vectra Polaris slide scanner (Akoya Biosciences).
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6

Hematoxylin and Eosin Staining of FFPE Tissue

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Briefly, 4-µm-thick sections of formalin-fixed paraffin-embedded (FFPE) were cut. After deparaffinization and rehydration, the slides were stained in hematoxylin for 3–5 min and washed in running water for 5 min. After differentiation in 1% hydrochloric acid (70% ethanol with 1% hydrochloric acid) (30 s), the slides were stained in 1% eosin Y for 10 min. Then, these slides were dehydrated in increasing concentrations of alcohol (each for 2 min) and cleared in xylene for observation. These slides were observed on a Vectra Polaris slide scanner (Akoya Biosciences, Marlborough, MA, USA).
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7

Adipocyte Imaging and Analysis

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Adipocyte monolayers were imaged using a Nikon ECLIPSE Ti2 (Nikon, Tokyo, Japan). Sections were imaged with a Vectra Polaris slide scanner (Akoya, Marlborough, MA) and analyzed with QuPath (v0.2.2). Confocal images were taken with a Leica TCS SP8 (Leica Microsystems, Wetzlar, Germany) and analyzed using Imaris (v9.9.1; Oxford Instruments, Oxfordshire, UK).
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8

Multiplex Immunohistochemistry Staining Protocol

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The tissue sections were deparaffinized and rehydrated, followed by a 1-h EDTA pretreatment (pH 8.5) in the steamer. Blocking was done in Dako diluent for 20 min followed by the OLIG2 primary antibody application at 4 °C overnight. Secondary, biotinylated donkey anti-rabbit antibody was incubated for 1 h at room temperature, followed by a 1-h incubation with avidin-peroxidase at room temperature. Signal enhancement was done using biotinylated tyramide (CSA) for 20 min at room temperature. Sections were rinsed in PBS and steamed for 30 min in (EDTA pH 8.5), followed by primary antibody application (sheep-anti CAII and rabbit-anti GFAP) at 4 °C overnight. Secondary antibodies were subsequently incubated for 1 h at room temperature. Stained sections were scanned using a Vectra Polaris slide scanner (Akoya Biosciences).
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9

Quantifying Lung Lesions in M. avium Infection

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Lung accessory lobes were collected from infected mice 6 weeks after
M. avium 2-151 smt challenge and were perfused and stored
in 10% normal buffered formalin. Fixed lungs were embedded in paraffin at the
University of Washington Histology and Imaging (Seattle, WA, USA) as previously
described[29 (link)]. Paraffin embedded
lungs were sent to Dr. Brendan Podell, a boardcertified veterinary pathologist
at Colorado State University. Lungs were processed and sections were
H&E-stained and scanned at 20X magnification using a Vectra Polaris slide
scanner (Akoya Biosciences, Marlborough, MA). Visiopharm software (Horsholm,
Denmark) was used for image analysis as previously published[58 (link)]. For each tissue section, a region of interest
(ROI) was generated at a low magnification with a custom tissue detecting
algorithm using decision forest training and classification to differentiate
tissue versus background based on color and area. Lesions were identified within
tissue ROI’s at a high magnification with an additional custom-made
algorithm using decision forest training and classification based on staining
intensity, color normalization and deconvolution, area, and morphological
features. Percent lesion calculations were integrated into the same algorithm
and calculated from tissue area and lesion area as designated by the ROI and
lesions detected.
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10

Ki-67 Analysis of NCI-237-R PDX Tumors

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NCI-237-RPDX tumor fragments from vehicle- and NCGC00420737-treated animals were fixed in 10% neutral-buffered formalin and incubated at 4°C for 24 hours with gentle shaking. Fixed tumors were submitted to the UT Southwestern Histo Pathology Core for paraffin embedding and sectioning. Hematoxylin- and eosin-staining was performed by the UT Southwestern Histo Pathology Core. Ki-67 immunohistochemical staining was performed by the UT Southwestern Simmons Comprehensive Cancer Center Tissue Management Shared Resource using a BOND-RX Automated Stainer (Leica Biosystems) and human-specific anti-Ki-67 antibody (Cell Signaling Technology #9027, RRID: AB_2636984, 1:400 dilution). Whole-slide scans were captured at 40X magnification using a Vectra Polaris slide scanner (Akoya Biosciences) and images were generated using Phenochart 1.1.0 software (Akoya Biosciences).
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