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10 protocols using clone 8g7g3 1

1

NSCLC Specimen Collection and Analysis

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In accordance with the status as a multicenter study, the protocol for specimen collection was approved by The Single Joint Research Ethics Board of the Department of Health, Manila, Philippines (approval no. SJREB-2020-97). Blood and tissues samples were collected from recruited Filipino patients with NSCLC and were immediately processed for plasma testing, histopathological examination or cryopreservation at −80°C, as previously described (18 (link)). The specimens were tested for the presence of EGFR-sensitizing mutations using PCR, and assayed for PD-L1 and TTF-1 protein expression using IHC. EGFR mutations were assessed using the AmoyDx EGFR 29 Mutations Detection Kit (designed to detect mutations in EGFR exons 19–21; Amoy Diagnostics Co., Ltd.) as previously described (23 (link)). EGFR without driver mutations, with single and co-mutations were scored as 0, 1 and 2, respectively. Expression of PD-L1 and NKX2-1/TTF-1 in NSCLC were evaluated by IHC using the pharmDx 22C3 kit (cat no. SK006; Agilent Technologies, Inc.) (24 (link)) and clone 8G7G3/1 (cat no. M3575; Agilent Technologies, Inc.) (25 (link)), respectively. After pathology confirmation, expression was classified as negative (scored 0) if the TPS was <1%, or positive (scored as 1) if TPS was ≥1%. The representative histopathological data are shown in Fig. S1.
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2

SARS-CoV-2 Autopsy Lung Histopathology

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Human pathology studies were performed with the approval of the Institutional Review Board at Brigham and Women’s Hospital. Clinical autopsies with full anatomic dissection were performed on SARS-CoV-2 decedents by a board-certified anatomic pathologist (RFP) with appropriate infectious precautions. Lung samples were fixed in 10% neutral buffered formalin, embedded in paraffin, sectioned, and stained with hematoxylin and eosin using standard methods. Immunohistochemistry was performed on 4-µm-thick tissue sections following pressure cooker antigen retrieval (Target Retrieval Solution; pH 6.1; Agilent Dako) using a mouse monoclonal antibody directed against TTF-1 (clone 8G7G3/1; Agilent Dako) at 1:200 dilution. Control lung slides were obtained from the BWH Department of Pathology Autopsy Division archives. Glass slides were reviewed by a RFP using an Olympus BX41 microscope, and microscopic photographs were obtained with an Olympus DP27 camera and Olympus CellSens Entry software.
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3

Immunohistochemistry Profiling of Tissue Microarrays

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TMA blocks were cut into 4-µm sections. IHC reactions were performed using the Dako Autostainer Link48 (Dako, Glostrup, Denmark). Deparaffinisation, rehydration, and epitope retrieval (97°C, 20 min) were performed using a low pH Target Retrieval Solution (Dako/Agilent Technologies, Santa Clara, CA, USA) in a PT- Link (Dako). Subsequently, the sections were washed in Tris-buffered saline and incubated with primary antibodies at room temperature for 20 min. The following specific primary antibodies were used: polyclonal rabbit anti-Periostin (dilution 1:200; code no.NBP1-82472; Novus Biologicals, Littleton, CO, USA), monoclonal mouse anti-Ki-67 antibody (ready-to-use, Clone MIB-1, code IS626; Dako), anti-TTF-1 (ready-to-use, Clone 8G7G3/1, code IR056; Dako), anti-p63 (ready-to-use, Clone DAK-p63, code IR662; Dako), anti-Podoplanin (ready-to-use, clone D2-40 (PDPN), code ISO072; Dako), anti-Vimentin (ready-to-use, clone V9, code GA630; Dako), and anti-αSMA (ready-to-use, clone IS611, code 1A4; Dako). The sections were then visualized using an EnVision FLEX kit (Dako). All slides were counterstained with haematoxylin (Dako). Negative control sections were generated in the absence of the primary antibody.
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4

Immunohistochemistry Markers for Characterizing Unusual Cases

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We recently described the immunohistochemistry (IHC) setup at MGH (27 ). IHC markers that were employed in this study as needed to characterize morphologically unusual and genetically altered cases included TTF1 (performed in cases 1, 52, 53; clone 8G7G3/1; dilution 1:300; Dako, Carpinteria, CA), BRG1 (performed in case 9; clone EPR3912; dilution 1:50; Abcam, Cambridge, United Kingdom), GATA3 (performed in case 25; clone L50–823, dilution 1:200; Cell Marque, Rocklin, CA), mammaglobin (performed in case 25; clone 304–1A5; dilution 1:250; Dako, Carpinteria, CA), S100 protein (performed in case 25; polyclonal and prediluted; Ventana, Oro Valley, AZ), PAX8 (performed in cases 25, 52, 53; polyclonal, dilution 1:1000; Proteintech, Rosemont, IL), thyroglobulin (performed in cases 25, 52; dilution 1:800; Cell Marque, Rocklin, CA), E-cadherin (performed in case 46; clone 36B5; Leica Biosystems, Buffalo Grove, IL), p40 (performed in case 52; clone BC28, Biocare, Concord, MA) and BRAF V600E (performed in all cases; clone VE1; dilution 1:200; Abcam, Cambridge, United Kingdom).
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5

Cytological Evaluation of Papillary Thyroid Carcinoma

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A 30-year (1980-2013) retrospective review of the cytology slides from our cytology division of pathology department revealed a total of 750 PTCs. Out of these, 73 cases of CPTC, which were confirmed by histologic sections, were retrieved from the files: 55 females and 18 males, with an age range of 28-52 years. There was no pediatric case. The cyst sizes ranged between 2.8 cm and 3 cm. Aspiration was performed from the cysts tissue (42 cases under ultrasound guidance and the remaining without guidance). The cysts yielded 2-3 mL of the fluid that was hemorrhagic in 40 cases and clear yellow in color in the remaining cases. The smears were prepared from the sediment of cytocentrifuged specimens. The air-dried smears were stained with the Wright–Giemsa stain, and alcohol-fixed smears were stained with Papanicolaou stain. Some selected cases were subjected to immunocytochemistry for thyroid transcription factor-1 (TTF-1, Dako, clone 8G7G3/1, Denmark), cytokeratin 19 (CK 19) (Dako, Clone RCK108, Denmark), and cluster of differentiation 68 (CD68) (Dako, clone KP1, Denmark).
The FNA smears of other cystic thyroid lesions were retrieved from the files for the comparative study. These cases included 300 colloid goiters, 290 adenomatoid nodules, 11 follicular neoplasms, and 9 hurtle cell neoplasms.
Medical ethics committee of our university approved the study.
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6

Immunohistochemical Analysis of PD-L1, Ki-67, TTF-1, and p63

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Each TMA was sectioned at 4 μm and IHC reactions were performed using primary antibodies detecting the expression of the tested proteins. Deparaffinisation, hydration and thermal demasking of epitopes were performed using Dako PT Link (Dako, Glostrup, Denmark). The slides were incubated for 30 minutes at 97 °C (low pH Target retrieval solution; Agilent Technologies, Santa Clara, CA, USA). Monoclonal mouse anti-PD-L1 antibody (1:50 dilution; clone 22C3 (concentrate); code No. M3653; Dako) was used to detect the ligand using enhancer signal EnVision ™ FLEX + Mouse LINKER (Dako). Detection of other markers was performed using monoclonal mouse anti-Ki-67 antibody (ready to use, Clone MIB-1, code IS626; Dako), anti-TTF-1 (ready to use, Clone 8G7G3/1, code IR056, Dako) and anti-p63 (ready-to-use, Clone DAK-p63, code IR662, Dako). The immunohistochemical reactions were performed in an automatic system DAKO Autostainer Link48 (Dako). The EnVision FLEX kit (Dako) was used to visualize the antigens and the preparations were additionally stained with Mayer’s hematoxylin. To differentiate between AC and SCC, IHC with TTF-1 and p63 was performed.
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7

Immunohistochemical Characterization of Pulmonary Neuroendocrine Tumors

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For immunohistochemical characterization staining of whole tissue slides with antibodies directed against Pan-Cytokeratin (DAKO, Clone MNF116, Hamburg, Germany), CD56 (Zytomed, clone RCD56, Berlin, Germany), Chromogranin A (Novocastra, clone 5H7, Wetzlar, Germany) and TTF-1 (DAKO, Clone 8G7G3/1, Hamburg, Germany) was performed. The proliferation index was determined by staining with antibodies directed against the proliferation associated marker ki67 (Zytomed, clone K-2, Berlin, Germany) using a fully automated stainer (Dako AutostainerPlus). Apoptosis was determined by immunohistochemistry against cleaved caspase 3 (Cell Signalling, Beverly, MA, USA). The immunoexpression of ki67 was quantified by applying a four stage score (0= 0%, 1= <10%, 2=11 -50%, 3=> 50%), whereas cleaved caspase was scored by a different system (0 = 0%, 1= <5%, 2= 5-10%, 3= > 10%). Because PSMB4 was differentially expressed in any pulmonary NET subtype, the protein expression was assessed by immunohistochemistry (Sigma, polyclonal antibody, Taufkirchen, Germany).
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8

Immunohistochemistry Markers for Characterizing Unusual Cases

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We recently described the immunohistochemistry (IHC) setup at MGH (27 ). IHC markers that were employed in this study as needed to characterize morphologically unusual and genetically altered cases included TTF1 (performed in cases 1, 52, 53; clone 8G7G3/1; dilution 1:300; Dako, Carpinteria, CA), BRG1 (performed in case 9; clone EPR3912; dilution 1:50; Abcam, Cambridge, United Kingdom), GATA3 (performed in case 25; clone L50–823, dilution 1:200; Cell Marque, Rocklin, CA), mammaglobin (performed in case 25; clone 304–1A5; dilution 1:250; Dako, Carpinteria, CA), S100 protein (performed in case 25; polyclonal and prediluted; Ventana, Oro Valley, AZ), PAX8 (performed in cases 25, 52, 53; polyclonal, dilution 1:1000; Proteintech, Rosemont, IL), thyroglobulin (performed in cases 25, 52; dilution 1:800; Cell Marque, Rocklin, CA), E-cadherin (performed in case 46; clone 36B5; Leica Biosystems, Buffalo Grove, IL), p40 (performed in case 52; clone BC28, Biocare, Concord, MA) and BRAF V600E (performed in all cases; clone VE1; dilution 1:200; Abcam, Cambridge, United Kingdom).
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9

Immunohistochemical Analysis of Lung Tumors

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First, 4-µm slices were dyed with hematoxylin and eosin (HE), and the histological type was analyzed by selecting different markers using IHC. After dewaxing in xylene and rehydrating in gradient ethanol, the slides were prepared for antigen retrieval by boiling them in 10-mM sodium citrate buffer. Then, 3% hydrogen peroxide was used to block the endogenous peroxidase activity of the slides. Thereafter, the samples were incubated with the following primary antibodies at 4 °C overnight using thyroid transcription factor 1 (TTF-1) (clone 8G7G3/1, DAKO; dilution 1:200), napsin A (polyclone, Abcam; dilution 1:250), P40 (polyclone, Abcam; dilution 1:200), cluster of differentiation 56 (CD56, clone 123C3, DAKO; dilution 1:100), synaptophysin (Syn, clone DAK-SYNAP, DAKO; dilution 1:50), cytokeratin 5/6 (CK5/6, clone D5/16 B4, DAKO; dilution 1:100), and chromogranin A (CgA, clone DAK-A3; dilution 1:200). The slides were subsequently incubated with an anti-primary antibody and then stained with diaminobenzidine and hematoxylin. Finally, they were dehydrated in ethanol, washed in xylene, and then covered with coverslips for further microscopic observation.
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10

Rapid Immunohistochemistry for TTF-1

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The device (Histo-Tek R-IHC, Sakura Finetek Japan Co, Ltd) and its mechanism were previously described in detail [9] . Briefly, while under incubation with the primary antibody, tissue sections received a high-voltage, low-frequency AC electric field in order to markedly reduce the time required for antigen-antibody reaction. For each specimen, frozen sections were cut at 5-mm thickness and placed on slides, then air-dried for 30 seconds, fixed in acetone for 2 minutes at room temperature, air-dried for 15 seconds at room temperature, and subjected to the staining procedure.
Details of the R-IHC staining method are summarized in Table 1. Briefly, the sections were incubated with anti-TTF-1 (1:200 dilution, 5 mg/mL, clone 8G7G3/1; DAKO, Copenhagen, Denmark) for 5 minutes using the R-IHC system, followed by incubation with EnVisionTM þ System/HRP Mouse (DABþ) (DAKO) for 5 minutes. Thereafter, the slides were developed with 3,3' diaminobenzidine (DAB, Sigma-Aldrich Japan, Tokyo, Japan) substrate, counterstained with hematoxylin, dehydrated, and mounted on coverslips. Using this method, IHC analyses can be completed within almost 20 minutes and TTF-1-positive tumors were detected by the pathologists within about 30 minutes.
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