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11 protocols using anti pan cytokeratin

1

Optimized Immunohistochemical Profiling of IL33

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The conventional IHC staining (24 (link)) was performed on a DAKO Autostainer (DAKO) using DAKO LSAB+ and diaminobenzadine (DAB) as the chromogen. Serial sections of deparaffinized TMA sections were labeled with anti-human IL33 (Enzo; ALX-804-840-C100). Cores from several normal organ tissues were used as staining controls on each slide. The cores were analyzed for the expression of IL33 with an Aperio imaging system (Genetix). The specimens were digitalized with an automated platform (Aperio Technologies), ScanScope XT, and Spectrum Plus using TMA software version 9.1 scanning system. Multiplexed fluorescence staining was performed with Opal 4-plex staining system (PerkinElmer). Tissues were stained with anti-pan-cytokeratin (clone: AE1/AE3, DAKO), anti-CD31 (rabbit polyclonal, Abcam), anti-IL33 (clone: Nessy-1). The tissue slides were loaded into the Vectra slide scanner (PerkinElmer), imported, and analyzed with the relevant software (version 1.4; PerkinElmer). IL33 expression levels were assessed using H-score as we previously described (22 (link), 23 (link), 25 (link)). On the basis of the H-scores, we divided the samples into high (H-score > 15) and low (H-score ≤15) groups.
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2

Immunohistochemical Characterization of iehAM

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Explanted iehAM were fixed in 4% formaldehyde, embedded in paraffin, and stained with hematoxylin and eosin according to standard protocols. Additional sections were deparaffinized and pretreated with Ultra CC1 (Ventana Medical Systems, Tucson, AZ, USA) for antigen retrieval for anti-CD45, anti-CD20, anti-CD68, and anti-CD3 antibody staining and with target retrieval solution pH 9 (Dako, Heverlee, Belgium) for anti-pan-cytokeratin and anti-GFAP antibody staining. After endogenous peroxidase blocking, sections were incubated with 1:25 anti-CD45 (Dako, Heverlee, Belgium, clone 2B11 + PD7/26), 1:200 anti-CD20 (Dako, clone L-26), 1:1000 anti-CD68 (Merck, Darmstadt, Germany), 1:100 anti-pan-cytokeratin (Dako, clone 6F2), 1:200 anit-GFAP (Dako, clone AE1/AE3), and 1:20 anti-CD3 (Monosan, Uden, Netherlands, clone PS-1) antibodies. After incubation with peroxidase-labelled secondary antibodies, sections were visualized with a chromogen DAB (3,3′-diaminobenzidine) solution.
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3

Immunohistochemical Analysis of Tumor Samples

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FFPE tumour samples were sectioned and stained with haematoxylin and eosin (H&E), or the following antibodies: anti-pan-cytokeratin (mouse, AE1/AE3, Dako, North Sydney, NSW, Australia), anti-CD31 (mouse, JC70A, Dako), anti-CD34 (mouse, QBEnd10, Dako), anti-ERG (rabbit, EPR3864, Roche Diagnostics, North Ryde, NSW, Australia), anti-CAMTA1 (rabbit, polyclonal, Novus Biologicals, Noble Park North, VIC, Australia), and anti-TFE3 (rabbit, EPR11591, Abcam, Melbourne, VIC, Australia). H&E and IHC slides were scanned digitally at 20× magnification using the Pannoramic 1000 scanner (3DHISTECH Ltd., Budapest, Hungary). High-definition images were uploaded into CaseCenter (3DHISTECH Ltd.), and images were processed using FIJI image analysis software 2.14.0 [46 (link)].
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4

Comprehensive Immunohistochemistry Protocol

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Immunohistochemistry was performed using the IHC Staining Kit (Dako, Santa Clara, CA, USA). Tissue sections were deparaffinized in xylene (Thermo), hydrated in phosphate‐buffered saline (Welgene), and blocked with Background Reducing Solution (Dako). The sections were incubated with anti‐CASQ2 (#NBP1‐87304; NOVUS), anti‐aSMA (#BS70000; Bioworld Technology), anti‐FSP1 (#BS7671; Bioworld Technology), anti‐HIF1α (#NB100‐131; NOVUS), anti‐vimentin (#5741; Cell Signaling Technology), anti‐pan‐cytokeratin (#M3515; Dako), and anti‐ki67 (#9027; Cell Signal Technology) at 4 °C overnight, followed by incubation with horseradish peroxidase‐conjugated anti‐secondary antibody (Dako). The signal was developed using diaminobenzidine and hydrogen peroxide, resulting in a brown precipitate. The sections were counterstained with hematoxylin (Dako), dehydrated, and mounted. The DAB area was quantified using IHC Toolbox in ImageJ software (NIH) with 20 random histological fields from five slides of tumor tissues per group [22 (link)].
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5

Comprehensive Pancreatic Tissue Analysis

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Pancreatic tissue was fixed overnight in Zn-Formalin solution and embedded in paraffin, sectioned in 4µm slices, and stained with H&E. Immunohistochemistry was performed using the following antibodies: anti-insulin (Zymed); anti-β-galactosidase (Abcam); anti-BrdU (BD Pharmingen); anti-Glucagon (Zymed); anti-Pancreatic Polypeptide (Zymed); anti-Somatostatin (Zymed); anti-Amylase (Zymed); anti-Pan-Cytokeratin (Dako); anti-Ngn3 (generous gift from Michael German); anti-Nestin (Chemicon); anti-Pdx1 (Abcam); anti-GFAP and anti-SMAα (Dako); anti-Desmin (Thermo Scientific); anti-CD45 (BD Pharminigen).
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6

Antibody-Based Techniques for Cellular Analysis

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The following antibodies against human were used for Western blotting and immunoprecipitation technic: Anti-GAPDH (Sigma), anti-phospho-SRC Tyr416 and anti-SRC (Cell Signaling), anti-FGF-2 (Thermo Fisher Scientific Inc.), anti-FGFR1 and anti-β5 (Cell Signaling), all at 1/1000 dilution. Secondary antibodies used were: anti-rabbit-HRP and anti-mouse-HRP (Dako), both at 1/1000 dilution.
For FACS analysis, anti-αv-PE and anti-β5 (Biolegend), anti-β3-PE and anti-αvβ3-PE (BD Biosciences), anti-β6 (clone IC8C3, Dr. D. Sheppard, UCSF, San Francisco) were used at 1/100 dilution. Anti-αvβ5 (clone P5H9, R&D Systems) and anti-αvβ6 (clone 10D5, Merck Millipore) were used for FACS at 1/50 dilution, and for function blocking experiments at 10 μg/ml, as well as anti-FGF-2 (R&D Systems) and anti-β1 (clone Lia1/2, Beckman). Dead Cell Apoptosis Kit for PI-Annexin V staining was from Life technologies.
anti-phospho-SRC Tyr416 (Cell Signaling), anti-FGFR1 (Cell Signaling), anti-Phalloïdin-AlexaFluor 546 (Invitrogen), anti-FGF-2 (Thermo Fisher Scientific Inc.), as well as anti-αSMA (Sigma), anti-pan-Cytokeratin (Dako) and DAPI ProLong Gold mounting medium (Invitrogen) were used for immunofluorescent staining and immunohistochemistry.
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7

Immunofluorescence Analysis of Cell Markers

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Cells were seeded on glass coverslips, fixed with 4% PFA (Sigma-Aldrich) and incubated overnight at 4°C with the following primary antibodies: anti-PanCytokeratin (Mouse 1:200, Dako, Glostrup, Denmark), anti-Epcam (Mouse 1:1000, clone HEA-125, GeneTex, Irvine, CA, USA), anti-AQ-1 (Mouse 1:50, clone B-11, Santa Cruz Biotechnology, Heidelberg, Germany), anti-CD13-PE (Mouse 1:25, Biolegend, San Diego, CA, USA), anti-CD13-FITC (Mouse 1:25, Abcam, Cambridge, UK), anti-N-cadherin (Rabbit 1:50, Abcam, and Mouse 1:50, clone 32/N, Becton Dickinson, San Josè, CA, USA), anti-Calbindin (Mouse 1:100, clone CB-955, Sigma-Aldrich), anti-E-cadherin (Mouse 1:50, Becton Dickinson, and Rabbit 1:50, Cell Signalling Technology, Danvers, MA, USA) and anti-Paxillin (Mouse 1:50, Becton Dickinson). When necessary, the secondary antibodies Alexa 488 conjugated anti-mouse IgG and Alexa 594 conjugated anti-rabbit IgG (1:100, Molecular Probes, Carlsberg, CA, USA) were used. Stress fibers were labeled by Alexa-Fluor-594-phalloidin (1:100, Molecular Probes) and nuclei counterstained with Mounting DAPI (Molecular Probes). Immunofluorescence images were obtained with a Zeiss LSM810 confocal microscope, using a 63x objective, equipped with Zen2009 software (Zeiss, Oberkochen, Germany).
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8

Immunohistochemistry Analysis of FOXN1, IGF-1R, and Cytokeratins

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Formalin-fixed paraffin embedded samples and frozen samples were used for immunohistochemistry. Anti-Forkhead box protein N1 (FOXN1) antibody (Santa Cruz: sc-23566), anti-insulin growth factor 1 receptor (IGF-1R) antibody (Abcam: ab90657), anti-pan cytokeratin (Dako), and anti-cytokeratin 14 (CK14) antibody (Santa Cruz: sc-53253) were used for immunohistochemistry, which was performed as previously described (14 (link)). The number of FOXN1 positive cells in the thymus or thymic grafts was determined by counting the number of positive cells in at least five randomly chosen high power fields (x400).
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9

Immunostaining of Circulating Tumor Cells

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ScSCREENCELL CYTO kits were used for immunostaining of cancer cells isolated from the blood. For immunostaining, the protocol provided by SCREENCELL was followed. Briefly, cytofilters used for filtration were washed with 1× Tris-buffered saline (TBS) for 10 min. For antigen retrieval, samples were treated with Target Retrieval Solution (S1700; Dako) at 95°C for 20 min. The cytofilters were allowed to cool to room temperature before rinsing with 1× TBS, followed by a 5 min incubation in permeabilizing buffer (1× TBS, 0.2% Triton X-100). Next, the samples were incubated in 3% BSA at room temperature for 30 min. Cytofilters were subsequently incubated with the following primary antibodies in parallel in 3% BSA at 4°C overnight: anti-Pan Cytokeratin (MA5-17687; Dako) at 1:50 and anti-EpCAM (Ab71916; Abcam) at 1:100. After rinsing with Wash Buffer (1× TBS, 0.05% Tween 20), the samples were stained with the following secondary antibodies in parallel at 1:1,000 in 3% BSA for 1 hr at room temperature: goat anti-mouse Alexa 488 and goat anti-rat Alexa 594 (A11001, A11007; Life Technologies). Finally, cytofilters were rinsed with Wash Buffer and protected with ProLong Diamond Mountant containing DAPI nuclear stain (P36962; Life Technologies). Images were acquired using a Leica SP8 STED at the University of Iowa Central Microscopy Research Facility.
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10

Pulse-Chase Labeling of Proliferating Cells

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Six-week-old male mice (C57BL/6J, Harlan) were fed a CDE diet for two weeks or a DDC diet for three weeks. Following the aforementioned period, 1 mg/ml IdU (Sigma-Aldrich) was added to drinking water for 4 days. Following a washout period of 4 days, 1 mg/ml CldU (MP Biomedicals) was added to drinking water for 4 days. After another 2 days, mice were anesthetized, and one omental lobe was removed via laparotomy (Greene and Puder, 2003 (link)) for further analysis. For examining pulse-chase labeling after a “recovery period” (Figure S3F), mice were fed normal chow for another 4 weeks before sacrifice. For labeling experiments involving DDC treatment, DDC administration was performed as described earlier. Liver and small intestine tissue sections were triple stained with anti-bromodeoxyuridine antibodies as described elsewhere with minor modifications (Teta et al., 2007 (link)) and with anti-Pancytokeratin (DAKO). Every staining included mice that received only one of the thymidine analogs. Images were obtained with an inverted confocal microscope (Olympus). Cells were counted manually in a blinded fashion using ImageJ software (≥6 × 200 fields).
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