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14 protocols using amplification kit

1

Immunohistochemical Evaluation of ALK and ERBB2

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IHC was carried out using established methods. [11 (link)] In brief, sections were deparaffinized and incubated with the ALK work fluid (ALK IHC-5A4, Leica Biosystems) and ERBB2 work fluid (Her-2 IHC-UMAB36, ZSGB-BIO). A three-stage indirect immunoperoxidase technique was performed on a Benchmark Ventana staining module (Ventana, Tucson, AZ). Antigen retrieving was performed on the module using the cell conditioning buffer (CC1) pH 8.4 with Tris/Borate/EDTA (Ventana), for 1 h with the Amplification Kit (Ventana). The percentage of positive cells was evaluated, and staining scores were assessed as follows: 0, no staining; 1+, faint cytoplasmic staining; 2+, moderate cytoplasmic staining; and 3+, intense granular cytoplasmic staining.
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2

Immunohistochemical Detection of NICD1

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Standard 4-micron formalin-fixed, paraffin embedded tissue sections were stained using the Ventana Benchmark XT platform (Ventana Medical Systems) with extended heat-induced epitope retrieval (CC1 Buffer). Slides were incubated for 1 hr at room temperature with anti-NICD1 rabbit monoclonal antibody (clone D3B8, catalog #4147, Cell Signaling, final concentration, 8.5 μg/ml). Signals were then amplified (Ventana Amplification Kit) and visualized (Ventana Ultraview Universal DAB detection kit).
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3

PD-L1 Expression in Lung Carcinomas

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The PD-L1immunohistochemistry of 77 cases of non-small cell carcinomas of the lung diagnosed over a period of two years were reviewed and analyzed (2018-2020). All biopsies/ specimens were fixed in 10% neutral buffered formalin and processed by standard methods and stained with the Hematoxylin and Eosin stain. PD-L1 staining by immunohistochemistry was carried out on 4 μm sections, using the Ventana SP263 clone (10 (link)), OptiView Amplification Kit, and OptiView DAB IHC Detection Kit on Ventana Benchmark XT equipment. Hematoxylin was used as a counterstain. The tumor proportion score (TPS) of PD-L1 was calculated as the percentage of viable tumor cells with membrane positivity. Tumors with ≥50% TPS were considered to have high expression of PD-L1. Tumors with ≥ 1 to <50% TPS were considered to have low expression of PD-L1. Tumours with no or <1% TPS were considered negative.
All cases of non-small cell carcinomas of the lung primary/metastatic, received in the department of pathology of Apollo hospitals during the period 2018-2020 with PD-L1 immunohistochemistry were reviewed. Exclusion criteria included non-small cell carcinomas of the lung without PD-L1 immunohistochemistry or PD-L1immunohistochemistry in carcinomas of other sites.
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4

Automated Immunohistochemical Detection of HCMV

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All samples were subjected to H&E staining to detect signs of cytopathic damage (i.e., inclusion bodies). IHC staining for HCMV was performed on all formalin-fixed paraffin-embedded (FFPE) samples, sectioned at 4 μm on polarized slides. HCMV IHC was performed using a Benchmark ULTRA staining module (Ventana Medical Systems, Roche Diagnostics, MB, Italy) equipped with a fully automated protocol. Briefly, slides—previously baked overnight at 37 °C—were deparaffinized and rehydrated. Antigen retrieval was achieved using UltraCC1 (Ventana Medical Systems) for 36 min. The prediluted HCMV antibody (anti-HCMV blend cocktail 8B1.2, 1G5.2 & 2D4.2 mouse monoclonal primary antibody; catalogue No. 760-4703; Ventana Medical Systems) was incubated for 32 min at RT. Signal amplification was performed with the Amplification kit (Ventana Medical Systems), and detection was carried out with UltraView Universal DAB Detection kit (Ventana Medical Systems). To enhance visualization, counterstaining was performed with hematoxylin for 8 min, followed by 4-min incubation with Bluing Reagent (Ventana Medical Systems). Upon completion of the automated staining, the slides were subjected to dehydration and coverslipping through an HE600 platform (Ventana Medical Systems; Roche Diagnostics).
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5

Immunohistochemical Analysis of ROS1 Expression

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The formalin-fixed, paraffin-embedded (FFPE) tissue, with a thickness of 4 μm, was subjected to immunohistochemistry. A rabbit monoclonal ROS1 antibody (D4D6) provided by Cell Signaling Technology (Danvers, MA, USA) was used at a 1:75 dilution for a duration of 2 hours. The Benchmark ULTRA autostainer (Ventanaa, Tucson, AZ, USA) was used to perform staining, which was achieved through the OptiView DAB IHC detection kit (Roche) and an amplification kit (Ventana). To evaluate the staining intensity for each case, an assessment was conducted. An H-score, ranging from 0 to 300, was calculated for each case by multiplying the staining intensity (0 indicating no staining, 1 representing weak staining but more than the background staining, 2 indicating moderate staining, and 3 indicating strong staining) by the percentage of positive tumor cells. The positive controls included ROS1-rearranged lung adenocarcinoma tissue that tested FISH positive.
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6

Immunohistochemical Detection of IDH1 R132H

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4-micrometer-thick (4 micron) sections of formalin-fixed paraffin embedded tissues were placed on 3-aminopropyletxylene-covered slides. Subsequently, they were stained with rabbit polyclonal Dianova IDH1 R132H antibody (1/20 titer; H09 clone, mouse monoclonal antibody) following the manufacturer's protocol. Briefly, staining was performed on the Ventana Bench Mark Ultra (Ventana Medical Systems Inc.).
The staining protocol included cell conditioning 1 for 60 minutes, pre-peroxydase inhibition, and primary antibody incubation for 40 minutes at 37°C, applying the amplification kit (Ventana Medical Systems Inc.) for 4 minutes at 37°C to increase the signal intensity. UltraView Universal DAB Detection Kit (Ventana Medical Systems Inc.) was used to detect Isocytrate dehydrogenase 1 (IDH1) protein expression. Tissues were counterstained with hematoxylin for 16 minutes and bluing reagent for 4 minutes.
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7

Immunohistochemical Analysis of DLL3 and CD1A in Neuroendocrine Tumors

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FFPE tissue sections (3 µm thick) from 20 atypical and typical carcinoids were deparaffinized and stained with the Ventana DLL3 (SP347) assay, UltraView Universal DAB Detection Kit (Ventana Medical Systems and Amplification Kit (Ventana Medical Systems—Roche) on Ventana ULTRA autostainer (Ventana, Roche, Meylan, France), and with the CD1 rabbit monoclonal antibody (cl EP3622) (Ventana). The positivity of DLL3 was defined by the percentage of tumour cells exhibiting a cytoplasmic staining, whatever the intensity. The positivity of CD1A was defined by the percentage of the total surface of the tumour exhibiting a membrane staining with 1 corresponding to less than 1%, 2 to a percentage between 1 and 5%, and 3 to greater than 5%. Results are presented in Supplementary Data 9 and representative slides are shown in Fig. 4c.
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8

NLRP3 Expression in Human AML

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Immunohistochemistry (IHC) for NLRP3/NALP3 (Adipogen Life Sciences, AG-20-b-0014-C100, Liestal, Swiss) was performed on prepared cell blocks of the human cancer cell lines MOLM-13 and MOLM-13 ΔNLRP3 as well as on routinely archived formalin-fixed paraffin-embedded (FFPE) BM trephine samples of normal controls (n=10) and AML cases (n=13, primary diagnosis n=11) (AML-M5 NOS according to WHO classification). Sections were stained with primary NLRP3/NALP3 antibody using a Benchmark Ultra platform (Ventana, Tucson, USA) and an ultraView Universal DAB Detection Kit (Ventana) after application of the amplification kit (Ventana). The results were scored by assessing the extensity (% positive cells) and intensity of IHC staining (0-3) on three different representative microscope fields and expressed semi-quantitatively using the quickscore method by multiplication of the extensity and intensity (yielding values between 0-300) for each field. 15 Analysis of cytokine secretion in primary human AML samples was performed using the Cytokine/Chemokine/Growth Factor 45-Plex Human ProcartaPlex™ system (ThermoFisher).
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9

Lymphocyte Quantification in Graft Biopsies

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Month-6 formalin-fixed, paraffin-embedded graft biopsies were blindly analysed by two gastrointestinal pathologists (N.B., J.S), who described fibrosis and signs of graft rejection according to the Banff criteria [24] . Paraffin-embedded sections of liver biopsy specimens (4 mm thick) underwent immunostaining using an automated immunostainer (Ventana Medical Systems, Tucson, AZ) with antibodies directed against human CD3, CD4, CD8, CD20, CD138, CD68, CD1a and FoxP3. An amplification kit (Ventana Medical Systems) and a detection system including diaminobenzidine (Ventana Medical Systems) as a chromogen were used during the automated procedure. Archival lymph node sections were used as positive controls. For negative controls, the primary antibody was omitted. The mean number of positive cells in each patient calculated by counting these cells (original magnification, 400Â) in the three most cellular microscopic fields, also called hot spots.
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10

Immunohistochemical Analysis of Tumor Markers

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Immunohistochemistry was performed on cut sections from formalin fixed paraffin embedded (FFPE) tumour tissue. 4 μm tissue sections were cut and de-waxed through histolene, and graded alcohols then into water. Antigen retrieval was performed using Dako high pH Target Retrieval Solution (Dako) for 3 min at 125 °C for Glut-1, HIF-1 α and CA-9. Slides were then loaded onto a Dako autostainer (Dako) for the following incubations: primary antibody for Glut-1 (1:200, Dako), HIF-1α (1:50, Novus Biologicals) or CA-9 (1:4000, Novus Biologicals) for 60 min at room temperature; antibody detection with Envison+ (Dako) rabbit (Glut-1 and CA-9) or mouse (Hif-1α) antibody for 60 min at room temperature; colour reaction with 3,3′-Diaminobenzidine (DAB) for 10 min at room temperature. Staining for Ki-67 was performed on a Ventana BenchMark Ultra (Roche Diagnostics, USA). Antigen retrieval was performed in a high pH Ultra cell conditioning solution (CC1, Roche Diagnostics) for 52 min followed by incubation with the Ki-67 antibody (SP6, Cell Marque, diluted at 1/50), at 36 °C for 32 min. Amplification kit (amplifiers A and B, Roche Diagnostics) and UltraView Universal DAB detection kit (Roche Diagnostics) were used in accordance with the manufacturer’s instructions for on-board detection. Slides were then removed from the autostainer, counterstained with hematoxylin, mounted and coverslipped.
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