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13 protocols using msh2 clone g219 1129

1

Evaluating Mismatch Repair and ARID1A Deficiency

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Immunohistochemical staining was performed on TMAs with the Ventana Benchmark XT platform. The following panel of antibodies was used: anti-MLH1 (clone G168-728, Roche), -PMS2 (clone EPR3947, Roche), -MSH2 (clone G219-1129, Roche), -MSH6 (clone 44, Roche), and -ARID1A (clone D2A8U, Roche). According to the published criteria of abnormal expression of MMR and ARID1A [15 , 23 ], both markers were interpreted as loss of expression, whereas no tumor cells were stained.
We chose the recommended guidelines that the immunohistochemistry results be reported in a binary manner, either positive (indicating intact mismatch repair, showing intact nuclear expression in tumor cells) or negative (indicating deficient mismatch repair, showing nuclear expression completely lost in tumor cells) [24 , 25 ] Nuclei of lymphocytes and ovarian stromal cells served as positive internal controls. All staining results were reviewed by the above 2 pathologists. Because immunohistochemical examination was performed using a tissue microarray, when deficient mismatch repair (dMMR) was observed, the immunohistochemistry procedure was repeated on whole-slide sections to avoid heterogeneous expression, such as for MSH6 [26 ]. Ultimately, MMR protein restaining was performed in 51 instances involving 27 of 176 cases; ARID1A restaining was performed in 15 instances involving 3 cases of dMMR among 135 cases.
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2

Tissue Microarray Protocol for Immunohistochemistry

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Tissue microarray (TMA) techniques were used to make paraffin blocks for immunohistochemical slides using a TMA Master 3D Histech manual tissue arrayer. From each paraffin block containing invasive adenocarcinoma tissue, two cylindrical cores measuring 2 mm were taken from random tumor tissue sites. All cores were collected in a recipient TMA paraffin block. Each recipient block contained 20 samples from 10 cases. For immunohistochemistry, four µm-thick tissue sections were stained in a Ventana BenchMark ULTRA auto-stainer (Ventana Medical Systems, Tucson, Arizona). Monoclonal antibodies against SATB2 (CellMarque, EP281, 1:200), CK7 (clone OV-TL, BioSB, 1:500), PD-L1 (clone SP263, Roche, diagnostic kit), MutS homolog 2 (MSH2, clone G219-1129, Roche, ready to use), postmeiotic segregation 2 (PMS2, clone A16-4, Roche, ready to use), MutS homolog 6 (MSH6, clone 44, Roche, ready to use), and MutL homolog 1 (MLH1, clone M1, Roche, ready to use) were used. The positive reactions were visualized using the Ultraview Detection System (Ventana Medical Systems); slides were counterstained with hematoxylin. Stained slides were dehydrated and covered in a xylene-based mounting medium.
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3

Mismatch Repair Protein Immunohistochemistry

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Immunohistochemical staining was performed on TMAs with the Ventana Benchmark XT platform. The following panel of antibodies was used: anti-MLH1 (clone G168-728, Roche), -PMS2 (clone EPR3947, Roche), -MSH2 (clone G219-1129, Roche), -MSH6 (clone 44, Roche), and -ARID1A (clone D2A8U, Roche).
According to the published criteria of abnormal expression of MMR and ARID1A [15] [23], both markers were interpreted as loss of expression, whereas no tumor cells were stained.
We chose the recommended guidelines that the immunohistochemistry results be reported in a binary manner, either positive (indicating intact mismatch repair, showing intact nuclear expression in tumor cells) or negative (indicating de cient mismatch repair, showing nuclear expression completely lost in tumor cells) [ Nuclei of lymphocytes and ovarian stromal cells served as positive internal controls. All staining results were reviewed by the above 2 pathologists. Because immunohistochemical examination was performed using a tissue microarray, when de cient mismatch repair (dMMR) was observed, the immunohistochemistry procedure was repeated on whole-slide sections to avoid heterogeneous expression, such as for MSH6 [26] . Ultimately, MMR protein restaining was performed in 51 instances involving 27 of 176 cases; ARID1A restaining was performed in 15 instances involving 3 cases of dMMR among 135 cases.
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4

Immunohistochemistry for MMR and ARID1A

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Immunohistochemical staining was performed on TMAs with the Ventana Benchmark XT platform. The following panel of antibodies was used: anti-MLH1 (clone G168-728, Roche), -PMS2 (clone EPR3947, Roche), -MSH2 (clone G219-1129, Roche), -MSH6 (clone 44, Roche), and -ARID1A (clone D2A8U, Roche). As the published criteria of abnormal expression of MMR and ARID1A [15] [23], both markers were interpreted as loss of expression, whereas any tumor cells not staining.
Nuclei of lymphocytes and ovarian stromal cells served as positive internal controls. All staining results were reviewed by the above 2 pathologists. Because immunohistochemical examination was performed using a tissue microarray, when negative staining was observed, the immunohistochemistry procedure was repeated on whole-slide sections to avoid heterogeneous expression, such as for MSH6 [24] . Ultimately, MMR protein restaining was performed in 51 instances involving 27 of 176 cases; ARID1A restaining was performed in 15 instances involving 3 cases of dMMR among 135 cases.
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5

Immunohistochemical Mismatch Repair Screening

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MMR screening status was determined by immunohistochemical analyses of TMA slides of the protein products of genes involved in the DNA mismatch repair system, as described previously [16 (link)]. Antibodies (all from Ventana Medical Systems Inc., Tucson, Arizona, US) against the four key mismatch repair proteins (MLH1 (clone M1), MSH2 (clone G219-1129), PMS2 (clone A16-4) and MSH6 (clone SP93)) were used on an automated Ventana BenchMark ULTRA instrument. Tumors with loss of nuclear expression of one or more of these proteins were described as dMMR, while samples with positive staining for all four antibodies were denoted pMMR. Tumors where internal staining was lacking, such as positive lymphocytes, were considered uninformative.
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6

Immunohistochemical Analysis of DNA Mismatch Repair Proteins

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The formalin-fixed paraffin-embedded (FFPE) tumor samples were stained with MLH1, MSH2, MSH6, and PMS2 proteins. The loss of MMR proteins was defined as the absence of staining in the nuclei of tumor cells while the nuclei of lymphocytes and adjacent normal colonic epithelial cells were positive. MLH1 (clone M1, prediluted, Ventana, Roche, Basel, Switzerland), MSH2 (clone G219-1129, prediluted, Ventana), MSH6 (clone 44, prediluted, Ventana), and PMS2 (clone EPR3947, prediluted, Ventana) monoclonal primary antibodies were used.
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7

Comprehensive Biomarker Profiling in Extramammary Paget's Disease

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PD‐L1 expression was evaluated in the tumor (TC) and immune cells (IC) using SP142 antibody (Ventana). Any PD‐L1 expression was considered positive if either TC or IC exhibited staining. AR (clone 441, Leica Biosystems, Buffalo Grove, IL), ER (SP1 clone, Ventana, Tucson, AZ) and PR (1E2, Ventana, Tucson, AZ) were analyzed using a ≥10% threshold for nuclear positivity. HER2 (4B5 clone, Ventana) was considered positive if >10% cancer cells showed complete, circumferential (3+) expression or exhibited HER2 gene amplification (see below). Nine cases (five vulvar and four scrotal) of EMPD and four MPD were explored for the expression of the splice variant of AR (ARv7) using immunohistochemistry (EPR15656, Abcam). Three EMPD cases were tested for mismatch repair proteins: MLH1 (Clone M1, Ventana), MSH2 (Clone G219‐1129, Ventana), MSH6 (Clone 44, Cell Marque) and PMS2 (Clone EPR3947, Cell Marque). Topoisomerase 2α (Clone 3F6, Leica) expression was considered positive if cancer cells exhibited nuclear positivity in ≥10%.7
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8

Immunohistochemical Profiling of Liver Tumors

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All tumors with unstained slides were available. IHC staining was performed using Ventana automation with the corresponding detection system (Ventana Medical Systems, Tucson, AZ, USA) and antibodies against GPC3 (clone 1G12, prediluted; Maixin, Fuzhou, Fujian, People's
Republic of China), SALL4 (clone 6E3, 1:100; Biocare, Pacheco, CA, USA), Arg-1 (monoclonal, 1:6,000; Sigma-Aldrich, St. Louis, MO, USA), and Hepa-1 (clone OCH1E5, 1:100, Maixin).
Microsatellite instability was assessed using IHC staining for mismatch repair (MMR) proteins, including MLH1 (clone M1, prediluted; Ventana), PMS2 (clone A16-4, prediluted; Ventana), MSH2 (clone G2- 19–1129, prediluted; Ventana) and MSH6 (clone SP93, prediluted; Ventana). Loss of expression of any of the MMR proteins was considered when there was no corresponding IHC staining in the nuclei in tumor cells, whereas adjacent normal colonic mucosa and/or stromal cells had nuclear staining by contrast.
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9

IHC Analysis of PD-L1 and DNA Mismatch Repair in EUS-FNB Specimens

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EUS-FNB specimens obtained from treatment-naïve patients were archived respecting formalin fixation and paraffin embedding protocols and were subjected to IHC staining. Briefly, Ventana BenchMark Ultra automated slide-staining system was used in order to stain 4 μm thick tissue sections utilizing the following antibodies: anti-PD-L1 (clone SP263 Ventana), MLH1 (clone ES05 Leica), MSH2 (clone G219-1129, Ventana), MSH6 (clone SP93 Novus Biological), and PMS2 (clone A16-4, Ventana). Diaminobenzidine was used as a chromogen for UltraView detection in order to visualize antigen–antibodies reactions. A specimen was considered adequate for evaluation only if a minimum of 100 tumor viable cells were found on the slides. Membranous staining was the hallmark for positive PD-L1 expression (Figure 1C). The tumor proportion score (TPS) has been calculated as the percentage of viable tumor cells with complete or partial membrane staining at any intensity. PD-L1 expression was considered in specimens with TPS > 1% and high PD-L1 expression was considered in patients with TPS > 50%. In the case of absent nuclear staining of DNA mismatch repair protein (PMS2, MSH2, MSH6, or MLH1), the tumor was targeted as dMMR (Figure 2).
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10

Tumor Immunohistochemistry for MMR Status

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Tumor imaging was performed at baseline, every 8 weeks after randomization until the primary analysis, and every 12 weeks thereafter. AEs were graded according to the National Cancer Institute Common Terminology Criteria for Adverse Events version 4.0. AEs were monitored throughout the study until 30 days (120 days for serious AEs) after the last dose of study treatment.
Archived tumor tissue from the most recent biopsy or from a fresh biopsy (if no archival tumor tissue was available) was collected from all enrolled patients to assess MMR status. A sample collected following the latest systemic treatment was preferred. MMR proteins were chromogenically labeled for automated immunohistochemistry staining on the Ventana Benchmark Ultra using mouse and rabbit antibodies (Roche Diagnostics, Indianapolis, IN, USA). The MLH1 (clone M1, mouse monoclonal, Ventana Cat #790-5091), PMS2 (clone A16-4, mouse monoclonal, Ventana Cat# 790-5094), MSH2 (clone G219-1129, mouse monoclonal, Ventana Cat# 790-5093), and MSH6 (clone SP93, rabbit monoclonal, Ventana Cat# 790-5092) were used for immunohistochemical staining.
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